Notes - Revision history

Nibalanda at 19:28, 4 February 2016

2016-02-04T19:28:35Z

2016-02-02T18:52:52Z

2016-02-02T18:48:41Z

2016-01-19T19:54:52Z

2016-01-14T19:21:10Z

2016-01-14T19:15:40Z

2016-01-14T19:10:41Z

2016-01-12T19:55:07Z

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2016-01-12T19:37:57Z

Created page with "Jan 12"

New page

[[Jan 12]]

@@ Line 25: / Line 25: @@
 antiporter - ion travels opposite desired substance
 --------------------
@@ Line 37: / Line 46: @@
 -normalizing RNA read data
 - > total read-count normalization (TC) divide transcript read count by total number of reads, rescale by factor of counts per million
--> DESeq *** what we are using***
+-> DESeq *** what we are using*** have to normalize both # of reads and length of genes - b/c longer genes (because randomly fragmented) will be overexposed compared to shorter genes

← Older revision		Revision as of 18:48, 2 February 2016
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	antiporter - ion travels opposite desired substance		antiporter - ion travels opposite desired substance
		+
		+
		+	--------------------
		+	2/2/16
		+
		+	Reports on individual tasks:
		+
		+	- intestines -> only one notable over-expressed genes "PREDICTED: Python bivittatus solute carrier family 15 (oligopeptide transporter), member 1 (SLC15A1), mRNA" snake 2
		+
		+	-someone found genes linked to gene ontology terms in excel file, will use to annotate genome
		+
		+	-normalizing RNA read data
		+	- > total read-count normalization (TC) divide transcript read count by total number of reads, rescale by factor of counts per million
		+	-> DESeq * what we are using*

	simporter - ion travels across membrane with desired substance		simporter - ion travels across membrane with desired substance

← Older revision		Revision as of 19:54, 19 January 2016
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	antiporter - ion travels opposite desired substance		antiporter - ion travels opposite desired substance
		+
	simporter - ion travels across membrane with desired substance		simporter - ion travels across membrane with desired substance
		+
		+
		+
		+	--------------------
		+	1/19/16
		+
		+	antibodies - react based on shape and charge, thus can with substances other than target

@@ Line 20: / Line 20: @@
 looking for papers that identify enzymes involved in uptake -- involved in transport proteins across membrane:
 - SGLT1 --- glucose transporter
 antiporter - ion travels opposite desired substance
 simporter - ion travels across membrane with desired substance

← Older revision		Revision as of 19:10, 14 January 2016
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	-use reverse transcriptase (RT)- enzyme in HIV/retroviruses- to form cDNA from mRNA + nucleotides		-use reverse transcriptase (RT)- enzyme in HIV/retroviruses- to form cDNA from mRNA + nucleotides
	-primers made of every possible 6 letter bp combination --> allows us to amplify every primer fragment		-primers made of every possible 6 letter bp combination --> allows us to amplify every primer fragment
		+
		+	-------------------
		+	1/14/16
		+	looking for papers that identify enzymes involved in uptake -- involved in transport proteins across membrane
		+
		+	antiporter - ion travels opposite desired substance
		+	simporter - ion travels across membrane with desired substance

← Older revision		Revision as of 19:55, 12 January 2016
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−	~~[[Jan~~ 12]]	+	Snakes 1,2,3 not fed
		+	Snakes 4,5,6 fed
		+	--info in excel file
		+	RNA seq in multiplex --12 different samples, amplified with unique barcode (3 letter code) - simplified in excel file as individual letters.
		+
		+	'''How to seq RNA:'''
		+	-snakes fed and decapitated upon mouse tail disappearing
		+	-organs removed and flash frozen to preserve RNA
		+	-tissue from organ shaved off to ~.1g to begin RNA isolation kit (2 organs, 6 snakes, 12 total samples)
		+	----may not have sampled right part of organ, may have sampled connective tissue rather than proper organ
		+	-use mRNA to make cDNA copy, cDNA more stable
		+	---used magnetic beads with TTTTTT (poly T) end that binds to AAAAA (poly A), use magnet to attract beads, attached are mRNA
		+	---High throughput sequencing gives only short reads (~75 base pairs from each end)
		+	-fragment mRNA into smaller strands so that with short reads ^^ each bp can be read
		+	-use reverse transcriptase (RT)- enzyme in HIV/retroviruses- to form cDNA from mRNA + nucleotides
		+	-primers made of every possible 6 letter bp combination --> allows us to amplify every primer fragment