|
| Status |
Public on May 03, 2017 |
| Title |
RNA-IPS-Fibr_F_Y-fMG02 |
| Sample type |
SRA |
| |
|
| Source name |
fibroblast-derived iPSCs fMG02
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: fibroblast-derived derived iPSCs fMG02
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from freshly isolated retinas using RNeasy Plus Mini kit (Qiagen #74134). Technologies #Q33120)
Libraries were prepared from ~ 500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 2500 sequencers according to the manufacturer’s directions (Illumina.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
gene_iPSC_CPM.txt
|
| Data processing |
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the mouse genome mm9 (MGSCv37) using in-house software StrongArm.
We required > 30% of exon have > 30x depth. And then classic FPKM have been calculated by cufflink package( version 2.1.1 along with default parameters and “--frag-bias-correct --multi-read-correct“) based on GENCODE annotation vM7.
For Differential Expression analysis between f-iPSC and r-iPSC, we counted reads by HTSEQ(version 0.6.1p1) and used Voom packge(R 3.23, edgeR 3.12.1, limma 3.26.9) for statical tests. CPM(counts per million) have been provided for iPSC RNA-seq
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tab-delimited text files include FPKM or CPM values for each Sample
|
| |
|
| Submission date |
Sep 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
|
| Organization name |
St Jude Children's Research Hosipital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE87043 |
The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [RNA-Seq_Mm] |
| GSE87064 |
The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis |
|
| Relations |
| BioSample |
SAMN05785458 |
| SRA |
SRX2173069 |
