|
| Status |
Public on Oct 24, 2018 |
| Title |
RNA-seq_iPS_shUbc9_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblast cells E13.5
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iPS derived from MEF
passages: -
genotype: shUbc9
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-Seq: trizol extraction and clean-up using RNeasy kit (QIAGEN). Experiments were done in triplicates.
Libraries prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit (# RS-122-2301, Illumina) following manufacturer's protocol. Surplus primers were removed using AMPure XP beads (Agencourt Biosciences Corporation).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
For RNA-seq paired-end reads were mapped applying the 2-pass mapping mode of STAR v2.5.0a; best unique matches of concordant pairs were kept.
Mapped pairs were deduplicated with the Picar toolkit v1.94 and reads summarized over annotations with the featureCounts function of the Rsubread R package v1.26.0.
genome build: mm9
Supplementary_files_format_and_content: tdf files were generated with igvtools v2.3.25. ChIP-seq, ATAC-seq and RNA-seq libraries were merged by pooling the biological replicates. Prior to pooling, quality assurance clustering and principal component analysis were performed to identify and discard outlying replicates. The read coverage of the merged libraries was calculated over non-overlapping windows of 50 bp genome wide and library size normalization was applied to allow comparisons of the read coverage between samples: quantile normalization for the ChIP-seq and ATAC-seq datasets and DESeq2 size normalization for the RNA-seq datasets.
Supplementary_files_format_and_content: bed files with selected peaks were generated by MACS2 and then filtered according to the IDR protocol; tab delimited format: chromosome start end MACS_peak_ID -log10(p-value)*10 . foldChange -log10(p-value) -log10(q-value) relativeSummitPosition
Supplementary_files_format_and_content: RNA-seq_MEF-D4-D7-iPS-ES_shCtr-shUbc9_counts.txt: File with summarized counts (not normalized) for all the RNA-seq samples
|
| |
|
| Submission date |
May 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Claudia Chica |
| Organization name |
Institut Pasteur
|
| Lab |
Biostatistics and Bioinformatics Hub
|
| Street address |
25-28 Rue du Dr Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE99009 |
SUMO safeguards somatic and pluripotent cell identities by enforcing distinct chromatin states |
|
| Relations |
| BioSample |
SAMN07137718 |
| SRA |
SRX2831388 |
