|
| Status |
Public on Oct 10, 2017 |
| Title |
RNAseq ESC (5D0) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
cell type: Pluripotent Stem Cells
|
| Growth protocol |
Mouse embryonic EomesEGFP reporter stem cells were cultured on mouse embryonic fibroblast feeders in standard ES cell medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy isolation kit (Qiagen).
Sequencing libraries were prepared according to Illumina RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq 2500 (2x100bp) using 2 lanes/sample with a multiplex level of 1 (approximately 5x10e8 reads per sample).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
5D0
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz
|
| Data processing |
Base calling was with Illumina GAP Pipeline Software v1.90.
Sequences were aligned to mm10 reference genome using STAR 2.0.4.
Novel transcripts were predicted with Cufflinks 2.2.1.
Novel transcripts predictions were merged with mm10 reference genome using Cuffmerge 2.2.1 with option -G with mm10 reference GTF.
Counts were generated using htseq-count v0.6.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw_counts.txt.gz, normalized_counts_CPM.txt.gz: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package edgeR calcNormFactors and cpm function. Count data are provided in tab-delimited text format.
|
| |
|
| Submission date |
Aug 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Frederic Burdet |
| E-mail(s) |
frederic.burdet@sib.swiss
|
| Organization name |
Swiss Institute of Bioinformatics
|
| Street address |
Quartier Sorge - Batiment Amphipole
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE103261 |
RNAseq and ChIPseq on Mouse Embryonic Stem Cells and Sorted Mesendoderm Progenitor Cells [RNA-seq] |
| GSE103263 |
RNAseq and ChIPseq on Mouse Embryonic Stem Cells and Sorted Mesendoderm Progenitor Cells |
|
| Relations |
| BioSample |
SAMN07572267 |
| SRA |
SRX3145137 |
