Jon Lim - Revision history

Jolim at 14:56, 23 March 2017

2017-03-23T14:56:17Z

2017-03-21T14:56:41Z

2017-02-16T12:05:05Z

2017-02-13T18:47:10Z

2017-02-07T15:56:58Z

2017-02-02T15:54:37Z

2017-01-31T15:56:51Z

2017-01-26T15:56:21Z

2017-01-26T15:54:06Z

Class, 01/26

2017-01-26T15:51:54Z

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 Ours is 001924, maintained by crossing 1924 females to F1 males, progeny of B6 and C3H. The male sterile phenotype is incompletely penetrant. Each CB# is an embryonic stem cell line, and the P# refers to the passage number. The maternal disomic lines are embryonic stem cells derived from embryos of the same 1924 carrier females, without the 17^16 chromosome. All of the paternal line are embryonic stem cells from embryos in a colony with rare fertile 1924 males. By nature, ES cell lines are XY, and the karyotypes of the cell lines have been monitored for chromosomal aberrations.<br>
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 Progress<br>
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 <br>
 GSEA from the Broad Institute<br>
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 <b>References</b><br>

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 [https://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser]<br>
 Human reference genome(s). Consider using a single version for the duration of the project.<br>
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 <b>References</b><br>

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 Ts65Dn genetic background<br>
 There are two Ts65Dn strains: 001924 (WT for Pde6b), and 005252 (mut for Pde6b). Pde6b is a protein-coding MMU5 gene, and mutations cause abnormal retinal physiology. Since 005252 is mutant for Pde6b, it is usually bred to C3Sn.BLiA-Pde6b+/DnJ)F1/J (003647) males to eliminate the mutant phenotype. The usual male strain for 001924, however, is B6EiC3SnF1/J (001875).<br>
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 NEXT TIME: Use MGI to look up gene names for easier comparison.<br>
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 <br>
 Ts65Dn genetic background<br>
-There are two Ts65Dn strains: 001924 (WT for Pde6b), and 005252 (mut for Pde6b). Pde6b is a protein-coding MMU5 gene, and mutations cause abnormal retinal physiology. Since 005252 is mutant for Pde6b, it is usually bred to C3Sn.BLiA-Pde6b+/DnJ)F1/J (003647) males to eliminate the mutant phenotype. The usual male strain for 001924, however, is B6EiC3SnF1/J (001875).
+There are two Ts65Dn strains: 001924 (WT for Pde6b), and 005252 (mut for Pde6b). Pde6b is a protein-coding MMU5 gene, and mutations cause abnormal retinal physiology. Since 005252 is mutant for Pde6b, it is usually bred to C3Sn.BLiA-Pde6b+/DnJ)F1/J (003647) males to eliminate the mutant phenotype. The usual male strain for 001924, however, is B6EiC3SnF1/J (001875).<br>
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 Vocabulary/Background for 'Trisomy 21 alters DNA Methylation in Parent-of-Origin-Dependent and Independent manners'<br>

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 <b>What is the critical region of HSA21?</b> See [www.ds-health.com/trisomy.htm], which states that Robertsonian Translocations between chr21 and chr14 help to narrow down the critical region. In fact, there is a list on that page listing genes with known input...mine references from that page.
+<br>
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 Vocabulary/Background for 'Trisomy 21 alters DNA Methylation in Parent-of-Origin-Dependent and Independent manners'<br>

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 Imprinting, the inheritance of maternal or paternal methylation, will be a huge part of our investigation. Note that paper 2_parent_of_origin reveals that sometimes imprinting doesn't affect transcription at all. This paper also gives great guidelines for searching for imprinting transcription effects. Note that there is a potential for one imprint to regulate transcription in an entire 'imprint-controlled region,' and the authors here used a 4-Mb region (pg 15). While this same paper points out <i>WRB</i> as an imprinted gene, we won't have epigenome data, only transcriptome data, so that finding isn't relevant.<br>
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 Jon Lim's scratchpad
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-<b>Our five genes of interest:</b><br>
+<br>
 HLCS<br>
 HMGN1<br>

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 [https://www.omim.org/ OMIM]<br>
 OMIM can be searched using gene names to find human information.<br>
 [http://www.genome.jp/kegg/disease/ KEGG Disease database]<br>
 Search this database with protein names from OMIM to find associated diseases. The 'Pathway' field of the disease entry brings up helpful pathway diagrams.<br>
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 <b>References</b><br>

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 Jon Lim's scratchpad
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-<u>Our five genes of interest:</u><br>
+<b>Our five genes of interest:</b><br>
 HLCS<br>
 HMGN1<br>
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 BRWD1<br>
 RUNX1<br>
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 Vocabulary/Background for 'Trisomy 21 alters DNA Methylation in Parent-of-Origin-Dependent and Independent manners'<br>
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 Fig. 6A-B Unlike at the WRB CGI-2 DMR, RUNX1 and TMEME131 methylation changes in Trisomy 21 probands were NOT PARENT-DEPENDENT.<br>
 Pgs 14-16: no evidence that the WRB DMR imprinting effects changes in gene expression (evidenced by biallelic mRNA reads for all neighboring SNPs that had available data.<br>