GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1257274 Query DataSets for GSM1257274
Status Public on Jan 13, 2014
Title P21_WT_rep1
Sample type SRA
Source name wild type mouse retina at age postnatal day 21
Organism Mus musculus
Characteristics genotype: wild type
strain: C57BL/6J
tissue: Retina
age: post natal day 21
Extracted molecule total RNA
Extraction protocol Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for directional next-generation sequencing using a modified TruSeq RNA Sample Preparation Kit protocol as described (Brooks et al. 2012). The protocol utilizes the labeling of the second strand of cDNA with uracil, which allows the degradation of this strand prior to sequencing
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing Single read sequence-by-synthesis of 76 base length using TruSeq SBS v5 reagents was carried out on Genetic Analyzer IIx running SCS2.9 software (Illumina).
RNA-seq reads passing chastity filter were analyzed using Genomatix Software Suite (Genomatix Software GmbH, Munich Germany).
Sequences were aligned to NCBI mouse reference genome Build 37 on Genomatix Mining Station with Genomatix Mapper 3.5.1.
Alignments were annotated on Genomatix Genome Analyzer using ElDorado 08-2011 database, and differential expression analysis was performed using DEseq
Genome_build: NCBI build 37 Eldorado version 08-2011
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, fold change, adjusted p-value
Submission date Nov 01, 2013
Last update date May 15, 2019
Contact name Jerome Eric Roger
Phone +33169156835
Organization name CNRS-Universite Paris Sud
Department CERTO
Lab Neuro-PSI
Street address 151 Route de la Rotonde, Campus CEA Saclay - Bat 151
City Saclay
State/province Please select
ZIP/Postal code 91400
Country France
Platform ID GPL11002
Series (1)
GSE52006 OTX2 loss causes rod differentiation defect in CRX-associated congenital blindness
BioSample SAMN02390186
SRA SRX372139

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap