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Sample GSM2319629 Query DataSets for GSM2319629
Status Public on May 03, 2017
Title RNA-Adult-Rod_T_N-MDMX replicate 2
Sample type SRA
 
Source name retina
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: p107-/-MDMXTg
age: adult
Extracted molecule total RNA
Extraction protocol RNA was extracted from freshly isolated retinas using RNeasy Plus Mini kit (Qiagen #74134). Technologies #Q33120)
Libraries were prepared from ~ 500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 2500 sequencers according to the manufacturer’s directions (Illumina.)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description gene_exp.all.mdmx.txt
Data processing Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the mouse genome mm9 (MGSCv37) using in-house software StrongArm.
We required > 30% of exon have > 30x depth. And then classic FPKM have been calculated by cufflink package( version 2.1.1 along with default parameters and “--frag-bias-correct --multi-read-correct“) based on GENCODE annotation vM7.
For Differential Expression analysis between f-iPSC and r-iPSC, we counted reads by HTSEQ(version 0.6.1p1) and used Voom packge(R 3.23, edgeR 3.12.1, limma 3.26.9) for statical tests. CPM(counts per million) have been provided for iPSC RNA-seq
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tab-delimited text files include FPKM or CPM values for each Sample
 
Submission date Sep 16, 2016
Last update date May 15, 2019
Contact name Beisi Xu
E-mail(s) beisi.xu@stjude.org
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL13112
Series (2)
GSE87043 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [RNA-Seq_Mm]
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
Relations
BioSample SAMN05785461
SRA SRX2173066

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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