|
| 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 |
| E-mail(s) |
jeromeeroger@gmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN02390186 |
| SRA |
SRX372139 |
