GcatWiki - User contributions [en]

Vocabulary

2017-01-24T15:16:42Z

Grharper:

'''5mCpG''': A methylated CpG site (CpG is short for 5’—C—phosphate—G—3’)

'''Androgenic hydatidiform mole''': An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.

'''Bisulfite conversion''': A method providing single nucleotide resolution information about DNA methylation status. Treating DNA with bisulfite converts cytosine to uracil, but will not convert methylcytosine. Bisulfite treated DNA is then sequenced and compared to the original sequence to assess methylation status.

'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites''': ''CpG sites'' are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). ''CpG Islands'' are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.

'''DMR''': (differentially methylated region) stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR''': (Germline differentially methylated region) These differentially methylated regions are present immediately after fertilization and are contributed by the gametes.

'''hESC''': (human embryonic stem cells) generated by growing cells from a preimplantation-stage embryo in a culture medium; pluripotent

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR''': (imprinting control region) imprinting is an epigenetic process which the methylation of a parental gene is inherited and replicated by the offspring. ICRs are non-coding RNAs and DMRs that control the imprinting of one or more genes

'''MSRE-PCR''': (methylation sensitive restriction enzyme polymerase chain reaction) It can determine methylation status at a given CpG island

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''': "normal" nuclear family trio without Down syndrome

'''NCBI GEO''': a genomics data repository supporting array- and sequence-based data. da Silva et al. queried GEO to obtain RNAseq data for SNPs neighboring the WRB locus.

'''Nondisjunction''': is the failure of homologous chromosomes or sister chromatids to separate properly during cell division.
There are three forms of nondisjunction:
(1) failure of a pair of homologous chromosomes to separate in meiosis I
(2) failure of sister chromatids to separate during meiosis II, and
(3) failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).
this is the non-lethal form of nondisjunction that can result in Down's syndrome.

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': (Reference SNP) - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': (single nucleotide polymorphisms) difference in a single nucleotide at a specific position; the most common type of genetic variation among people

'''SNuPE''': (single-nucleotide primer extension) A molecular biology technique in which an oligo flanking a target site is extended and terminated by a ddNTP complementary to the following base.

'''SRA''': (sequence read archive) large database online which stores high-throughput sequencing data for researchers to compare and contrast

'''STR''': (Short tandem repeats) A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

'''TSS''': (Transcription Start Site) location where transcription starts in the genome. These occur on the 5' end a number of base pairs away from the promoter

'''WRB''': (Tryptophan Rich Basic Protein coding gene) This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T15:12:35Z

Grharper:

'''5mCpG''': A methylated CpG site (CpG is short for 5’—C—phosphate—G—3’)

'''Androgenic hydatidiform mole''': An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.

'''Bisulfite conversion''': A method providing single nucleotide resolution information about DNA methylation status. Treating DNA with bisulfite converts cytosine to uracil, but will not convert methylcytosine. Bisulfite treated DNA is then sequenced and compared to the original sequence to assess methylation status.

'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites''': ''CpG sites'' are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). ''CpG Islands'' are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.

'''DMR''': (differentially methylated region) stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR''': (Germline differentially methylated region) These differentially methylated regions are present immediately after fertilization and are contributed by the gametes.

'''hESC''': (human embryonic stem cells) generated by growing cells from a preimplantation-stage embryo in a culture medium; pluripotent

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR''': (imprinting control region) imprinting is an epigenetic process which the methylation of a parental gene is inherited and replicated by the offspring. ICRs are non-coding RNAs and DMRs that control the imprinting of one or more genes

'''MSRE-PCR''': (methylation sensitive restriction enzyme polymerase chain reaction) It can determine methylation status at a given CpG island

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''': "normal" nuclear family trio without Down syndrome

'''NCBI GEO''': a genomics data repository supporting array- and sequence-based data. da Silva et al. queried GEO to obtain RNAseq data for SNPs neighboring the WRB locus.

'''Nondisjunction''': is the failure of homologous chromosomes or sister chromatids to separate properly during cell division.
There are three forms of nondisjunction:
(1) failure of a pair of homologous chromosomes to separate in meiosis I
(2) failure of sister chromatids to separate during meiosis II, and
(3) failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).
this is the non-lethal form of nondisjunction that can result in Down's syndrome.

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': (Reference SNP) - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': (single nucleotide polymorphisms) difference in a single nucleotide at a specific position; the most common type of genetic variation among people

'''SNuPE''': (single-nucleotide primer extension) A molecular biology technique in which an oligo flanking a target site is extended and terminated by a ddNTP complementary to the following base.

'''SRA''': (sequence read archive) large database online which stores high-throughput sequencing data for researchers to compare and contrast

'''STR''': (Short tandem repeats) A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

'''TSS''': (Transcription Start Site) location where transcription starts in the genome. These occur on the 5' end a number of base pairs away from the promoter

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T15:11:27Z

Grharper:

'''5mCpG''': A methylated CpG site (CpG is short for 5’—C—phosphate—G—3’)

'''Androgenic hydatidiform mole''': An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.

'''Bisulfite conversion''': A method providing single nucleotide resolution information about DNA methylation status. Treating DNA with bisulfite converts cytosine to uracil, but will not convert methylcytosine. Bisulfite treated DNA is then sequenced and compared to the original sequence to assess methylation status.

'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites''': [[CpG sites]] are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). [[CpG Islands]] are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.

'''DMR''': (differentially methylated region) stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR''': (Germline differentially methylated region) These differentially methylated regions are present immediately after fertilization and are contributed by the gametes.

'''hESC''': (human embryonic stem cells) generated by growing cells from a preimplantation-stage embryo in a culture medium; pluripotent

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR''': (imprinting control region) imprinting is an epigenetic process which the methylation of a parental gene is inherited and replicated by the offspring. ICRs are non-coding RNAs and DMRs that control the imprinting of one or more genes

'''MSRE-PCR''': (methylation sensitive restriction enzyme polymerase chain reaction) It can determine methylation status at a given CpG island

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''': "normal" nuclear family trio without Down syndrome

'''NCBI GEO''': a genomics data repository supporting array- and sequence-based data. da Silva et al. queried GEO to obtain RNAseq data for SNPs neighboring the WRB locus.

'''Nondisjunction''': is the failure of homologous chromosomes or sister chromatids to separate properly during cell division.
There are three forms of nondisjunction:
(1) failure of a pair of homologous chromosomes to separate in meiosis I
(2) failure of sister chromatids to separate during meiosis II, and
(3) failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).
this is the non-lethal form of nondisjunction that can result in Down's syndrome.

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': (Reference SNP) - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': (single nucleotide polymorphisms) difference in a single nucleotide at a specific position; the most common type of genetic variation among people

'''SNuPE''': (single-nucleotide primer extension) A molecular biology technique in which an oligo flanking a target site is extended and terminated by a ddNTP complementary to the following base.

'''SRA''': (sequence read archive) large database online which stores high-throughput sequencing data for researchers to compare and contrast

'''STR''': (Short tandem repeats) A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

'''TSS''': (Transcription Start Site) location where transcription starts in the genome. These occur on the 5' end a number of base pairs away from the promoter

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T15:08:54Z

Grharper:

'''5mCpG''': A methylated CpG site (CpG is short for 5’—C—phosphate—G—3’)

'''Androgenic hydatidiform mole''': An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.

'''Bisulfite conversion''': A method providing single nucleotide resolution information about DNA methylation status. Treating DNA with bisulfite converts cytosine to uracil, but will not convert methylcytosine. Bisulfite treated DNA is then sequenced and compared to the original sequence to assess methylation status.
'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites''': [[CpG sites]] are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). [[CpG Islands]] are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.

'''DMR''':differentially methylated region; stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR''': Germline differentially methylated region. These differentially methylated regions are present immediately after fertilization and are contributed by the gametes.

'''hESC''': (human embryonic stem cells) generated by growing cells from a preimplantation-stage embryo in a culture medium; pluripotent

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR''': (imprinting control region) imprinting is an epigenetic process which the methylation of a parental gene is inherited and replicated by the offspring. ICRs are non-coding RNAs and DMRs that control the imprinting of one or more genes

'''MSRE-PCR''': methylation sensitive restriction enzyme polymerase chain reaction. It can determine methylation status at a given CpG island

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''':"normal" nuclear family trio without Down syndrome

'''NCBI GEO''': a genomics data repository supporting array- and sequence-based data. da Silva et al. queried GEO to obtain RNAseq data for SNPs neighboring the WRB locus.

'''Nondisjunction''': is the failure of homologous chromosomes or sister chromatids to separate properly during cell division.
There are three forms of nondisjunction:
-failure of a pair of homologous chromosomes to separate in meiosis I,
-failure of sister chromatids to separate during meiosis II, and
-failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).
this is the non-lethal form of nondisjunction that can result in Down's syndrome

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': (Reference SNP) - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': (single nucleotide polymorphisms) difference in a single nucleotide at a specific position; the most common type of genetic variation among people

'''SNuPE''': (single-nucleotide primer extension) A molecular biology technique in which an oligo flanking a target site is extended and terminated by a ddNTP complementary to the following base.

'''SRA''': (sequence read archive) large database online which stores high-throughput sequencing data for researchers to compare and contrast

'''STR''': (Short tandem repeats) A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

'''TSS''': (Transcription Start Site) location where transcription starts in the genome. These occur on the 5' end a number of base pairs away from the promoter

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T15:07:47Z

Grharper:

'''5mCpG''': A methylated CpG site (CpG is short for 5’—C—phosphate—G—3’)

'''Androgenic hydatidiform mole''': An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.

'''Bisulfite conversion'''

'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites''': [[CpG sites]] are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). [[CpG Islands]] are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.

'''DMR''':differentially methylated region; stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR'''

'''hESC''': (human embryonic stem cells) generated by growing cells from a preimplantation-stage embryo in a culture medium; pluripotent

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR''': (imprinting control region) imprinting is an epigenetic process which the methylation of a parental gene is inherited and replicated by the offspring. ICRs are non-coding RNAs and DMRs that control the imprinting of one or more genes

'''MSRE-PCR''': methylation sensitive restriction enzyme polymerase chain reaction. It can determine methylation status at a given CpG island

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''':"normal" nuclear family trio without Down syndrome

'''NCBI GEO''': a genomics data repository supporting array- and sequence-based data. da Silva et al. queried GEO to obtain RNAseq data for SNPs neighboring the WRB locus.

'''Nondisjunction''': is the failure of homologous chromosomes or sister chromatids to separate properly during cell division.
There are three forms of nondisjunction:
-failure of a pair of homologous chromosomes to separate in meiosis I,
-failure of sister chromatids to separate during meiosis II, and
-failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).
this is the non-lethal form of nondisjunction that can result in Down's syndrome

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': (Reference SNP) - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': (single nucleotide polymorphisms) difference in a single nucleotide at a specific position; the most common type of genetic variation among people

'''SNuPE''': (single-nucleotide primer extension) A molecular biology technique in which an oligo flanking a CpG site is extended and terminated by a ddCTP (dideoxycytosine nucleotide) if the site is methylated, or a ddTTP (dideoxythymine nucleotide) if the site is unmethylated.

'''SRA''': (sequence read archive) large database online which stores high-throughput sequencing data for researchers to compare and contrast

'''STR''': (Short tandem repeats) A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

'''TSS''': (Transcription Start Site) location where transcription starts in the genome. These occur on the 5' end a number of base pairs away from the promoter

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T15:05:16Z

Grharper:

'''5mCpG'''

'''Androgenic hydatidiform mole''': An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.

'''Bisulfite conversion'''

'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites''': [[CpG sites]] are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). [[CpG Islands]] are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.

'''DMR''':differentially methylated region; stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR'''

'''hESC'''

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR''': (imprinting control region) imprinting is an epigenetic process which the methylation of a parental gene is inherited and replicated by the offspring. ICRs are non-coding RNAs and DMRs that control the imprinting of one or more genes

'''MSRE-PCR''': methylation sensitive restriction enzyme polymerase chain reaction. It can determine methylation status at a given CpG island

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''':"normal" nuclear family trio without Down syndrome

'''NCBI GEO''':

'''Nondisjunction''': is the failure of homologous chromosomes or sister chromatids to separate properly during cell division.
There are three forms of nondisjunction:
-failure of a pair of homologous chromosomes to separate in meiosis I,
-failure of sister chromatids to separate during meiosis II, and
-failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).
this is the non-lethal form of nondisjunction that can result in Down's syndrome

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': “Reference SNP” - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': single nucleotide polymorphisms; difference in a single nucleotide at a specific position; the most common type of genetic variation among people

'''SNuPE'''

'''SRA''': (sequence read archive) large database online which stores high-throughput sequencing data for researchers to compare and contrast

'''STR''': (Short tandem repeats) A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

'''TSS''': (Transcription Start Site) location where transcription starts in the genome. These occur on the 5' end a number of base pairs away from the promoter

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T15:03:18Z

Grharper:

'''5mCpG'''

'''Androgenic hydatidiform mole''': An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.

'''Bisulfite conversion'''

'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites''': [[CpG sites]] are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). [[CpG Islands]] are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.

'''DMR''':differentially methylated region; stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR'''

'''hESC'''

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR'''

'''MSRE-PCR''': methylation sensitive restriction enzyme polymerase chain reaction. It can determine methylation status at a given CpG island

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''':"normal" nuclear family trio without Down syndrome

'''NCBI GEO''':

'''Nondisjunction''': is the failure of homologous chromosomes or sister chromatids to separate properly during cell division.
There are three forms of nondisjunction:
-failure of a pair of homologous chromosomes to separate in meiosis I,
-failure of sister chromatids to separate during meiosis II, and
-failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy).
this is the non-lethal form of nondisjunction that can result in Down's syndrome

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': “Reference SNP” - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': single nucleotide polymorphisms; difference in a single nucleotide at a specific position; the most common type of genetic variation among people

'''SNuPE'''

'''SRA'''

'''STR''': Short tandem repeats. A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

'''TSS'''

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T14:59:32Z

Grharper:

'''5mCpG'''

'''Androgenic hydatidiform mole'''

'''Bisulfite conversion'''

'''Capillary electrophoresis''': a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility

'''CpG Islands/Sites'''

'''DMR''':differentially methylated region; stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

'''gDMR'''

'''hESC'''

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

'''ICR'''

'''MSRE-PCR'''

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''':"normal" nuclear family trio without Down syndrome

NCBI GEO
Nondisjunction

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

'''rs#''': “Reference SNP” - way to reference specific SNPs (Single Nucleotide Polymorphisms)

'''SNP''': single nucleotide polymorphisms; difference in a single nucleotide at a specific position; the most common type of genetic variation among people

SNuPE
SRA

'''STR''': Short tandem repeats. A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

TSS

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T14:56:46Z

Grharper:

5mCpG

Androgenic hydatidiform mole

Bisulfite conversion

Capillary electrophoresis

CpG Islands/Sites

'''DMR''':differentially methylated region; stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples

gDMR

hESC

'''HhaI''': a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.

ICR

MSRE-PCR

'''MT21''': nuclear family trio with Down syndrome of maternal origin

'''N21''':"normal" nuclear family trio without Down syndrome

NCBI GEO
Nondisjunction

'''Oogenesis''': The development of a mature egg cell (ovum) from the primary oocyte.

'''Proband''': A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.

'''PT21''': nuclear family trio with Down syndrome of paternal origin

rs#

'''SNP''': single nucleotide polymorphisms; difference in a single nucleotide at a specific position; the most common type of genetic variation among people

SNuPE
SRA

'''STR''': Short tandem repeats. A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage

TSS

'''WRB''': Tryptophan Rich Basic Protein coding gene. This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.

Vocabulary

2017-01-24T14:50:52Z

Grharper: Created page with "DMR CpG Islands/Sites SNP 5mCpG Nondisjunction Oogenesis Proband WRB SNuPE hESC STR HhaI MSRE-PCR MT21 PT21 N21 rs# Capillary electrophoresis SRA NCBI GEO..."

DMR

CpG Islands/Sites

SNP

5mCpG

Nondisjunction

Oogenesis

Proband

WRB

SNuPE

hESC

STR

HhaI

MSRE-PCR

MT21

PT21

N21

rs#

Capillary electrophoresis

SRA

NCBI GEO

TSS

Androgenic hydatidiform mole

ICR

gDMR

Bisulfite conversion

Mouse Down Syndrome ES RNAseq Project

2017-01-24T14:45:17Z

Grharper:

==Lab Methods in Genomics, Spring 2017 ==

We will be looking at the transcriptome of mouse embryonic stem cells (ES) that have an extra copy of the human orthologous chromosome #21 which causes [http://www.ndss.org/Down-Syndrome/Preferred-Language-Guide/ Down Syndrome]. In particualr, we will be looking at two different populations of cells. One population will have the father's extra copy of "chromosome #21". The other popuation wil have the mother's extra chromosome. This class has three components that contribute to its research foundation. 

# We will search for any differences in the transcriptomes of these two different sources of ES.
# We will be collaborating with a class from Colby College in Maine; [http://www.colby.edu/directory/profile/artilden/ Dr. Andrea Tilden] will be offering a parallel course for her students. We will benefit from collaborating with her students as we conduct our research because both classes will exchange information that could be of interest to everyone. This collaboration mirrors modern research in the post-genomics era.
# We are also collaborating with Drs. [https://www.jax.org/education-and-learning/course-and-conferences/staff Charlie Wray] and [https://www.jax.org/research-and-faculty/research-labs/the-reinholdt-lab# Laura Reinholdt] at Jackson Laboratory in Bar Harbor, ME. We are part of an educational pilot experiment to see if it is feasible to offer research experiences to a national network of undergraduates using RNAseq data to answer legitmate research questions.

[[Vocabulary]]

'''Papers about Embryonic Stem Cells''' 

'''Papers/Resources about Down Syndrome''' 

[https://ghr.nlm.nih.gov/condition/down-syndrome# Down Syndrome Overview]

 
'''Davidson Research Teams''' 
* [[Andy + Ben]]
* [[Camille + Daniel]]
* [[Grace H + Drew + Jon]]
* [[Grace L + Jack]]
* [[Paul + Eric]]

File:Dog.jpg

2017-01-19T14:58:29Z

Grharper:

Grace Harper

2017-01-19T14:56:26Z

Grharper:

Hello Me

[[File:dog.jpg]]
<center>
[[File:JAX.png|300px|]]
</center>

Grace Harper

2017-01-19T14:55:22Z

Grharper:

Hello Me

[[File:dog.png|300px]]

<center>
[[File:JAX.png|300px|]]
</center>

Grace Harper

2017-01-19T14:54:58Z

Grharper:

Hello Me

[[File:dog.png|300px]]
<center>
[[File:JAX.png|300px|]]
</center>

Grace Harper

2017-01-19T14:54:33Z

Grharper:

Hello Me

[[File:dog.png|300px|]]
<center>
[[File:JAX.png|300px|]]
</center>

Grace Harper

2017-01-19T14:53:01Z

Grharper:

Hello Me

<center>
[[File:dog.png|300px|]]
</center>

Grace Harper

2017-01-19T14:51:45Z

Grharper:

Hello Me

[[File:dog.png]]
<center>
[[File:JAX.png|300px|]]
</center>

not centered

File:Dog.png

2017-01-19T14:50:22Z

Grharper:

Grace Harper

2017-01-19T14:49:51Z

Grharper: Created page with "Hello Me File:dog.png <center> 300px| </center> not centered"

Hello Me
[[File:dog.png]]
<center>
[[File:JAX.png|300px|]]
</center>

not centered

Grace H + Drew + Jon

2017-01-19T14:45:47Z

Grharper: Created page with "Grace Harper Drew Krueger Jon Lim"

[[Grace Harper]]
[[Drew Krueger]]
[[Jon Lim]]

File:Transcriptome Analysis of Mouse Stem Cells and Early Embryos.pdf

2017-01-17T15:44:23Z

Grharper: Abstract: Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with so...

Abstract:
Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.