|
| Status |
Public on Aug 27, 2015 |
| Title |
WT_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
mouse optic cups_WT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: optic cups
Stage: 10.5E Embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was purified from 200 optic cups of 10.5 days mouse embryos
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
wildtype
|
| Data processing |
libraries sequenced usign Illumina GAIIx single end 75nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated using CASAVAv1.7
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using TMM from edgeR package
Processed_data_file_format_and_content: tab separated file. Contains normalized counts. Samples in columns, Genes in rows
Genome_build: mm10
|
| |
|
| Submission date |
Oct 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Carlos Torroja |
| E-mail(s) |
ctorroja@cnic.es
|
| Phone |
(+34) 91 4531200
|
| Organization name |
Centro Nacional de Investigaciones Cardiovasculares (CNIC)
|
| Department |
Bioinformatics Unit
|
| Street address |
Melchor Fernandez Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE62786 |
Meis1 coordinates a network of genes implicated in eye development and microphthalmia |
|
| Relations |
| BioSample |
SAMN03145630 |
| SRA |
SRX745812 |
