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Sample GSM2409939 Query DataSets for GSM2409939
Status Public on Sep 30, 2017
Title WT Hb9 Rep1
Sample type SRA
 
Source name Mus musculus retina, P6
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: retina
genotype/variation: WT Hb9
development age: postnatal day 6
Extracted molecule total RNA
Extraction protocol Dissociated retinal cells were FACS sorted directly into lysis buffer from PicoPure RNA isolation kit (Invitrogen). RNA was extracted and purified with PicoPure RNA isolation kit (Invitrogen) and RNA Clean & Concentratorâ„¢- 5 Kit (Zymo). cDNA was synthesized and amplified with the Ovation RNA-Seq kit (Nugen)
RNA libraries were prepared for sequencing using ultralow system V2 kit (Nugen)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description single end RNA-seq data
Data processing Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using cufflinks (inferred counts and tpm values)
FPKM was transformed into log10(TPM)
mm10
Genome_build: tab-delimited text files include lgTPM values for each Sample
 
Submission date Nov 29, 2016
Last update date May 15, 2019
Contact name Yi-Rong Peng
E-mail(s) yirongpeng@gmail.com
Organization name University of California, Los Angeles
Department Department of Ophthalmology
Lab Yi-Rong Peng
Street address 100 Stein Plaza Driveway, B-133
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL19057
Series (2)
GSE90652 The transcriptome comparison between wildtype Hb9-GFP and Satb1-/-Hb9-GFP retinal ganglion cells (RGCs).
GSE90673 Expression profiles of retinal neuronal cells
Relations
BioSample SAMN06067979
SRA SRX2381206

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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