|
| Status |
Public on Aug 20, 2013 |
| Title |
A replicate 5 |
| Sample type |
SRA |
| |
|
| Source name |
Strategene Universal Human Reference RNA (UHRR) from 10 human cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
sample composition: 10 human cell lines (B lymphocyte, brain, breast, cervix, liposarcoma, liver, macrophage, skin, testis, and T lymphocyte)
ercc: 2% by volume of ERCC mix #1
replicate number: 5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard Illumina RNA-seq protocol and reagents
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Strategene Universal Human Reference RNA
|
| Data processing |
Basecalls and demux was performed using CASAVA version 1.8.0
All sequenced libraries were mapped to the human genome (hg19) using TopHat(v.2.0.3) (Trapnell et al., 2013) with the following parameters: '-r 70 --mate-std-dec 90'. A custom GTF file that includes both RefSeq information (from UCSC genome browser) and the ERCC transcript information was used (--GTF \$SEQCLB/hg19\_150\_ERCC.gtf) along with the transcriptome index option (--transcriptome-index \$SEQCLIB/hg19\_150\_ERCC). Genes shorter than 150 bp were excluded from this GTF file.
HTSeq (v.0.5.3p3) was used to generate the count matrix with the following parameters: 'htseq-count -m intersection-strict -s no' with the same GTF file used for the alignment step ($SEQCLIB/hg19\_150\_ERCC.gtf)
FPKM values were generated by Cufflinks
genome build: hg19
processed data files format and content: tab delimited text files of gene read counts or FPKM values
|
| |
|
| Submission date |
Aug 09, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Doron Betel |
| Organization name |
Weill Cornell Medical College
|
| Department |
Medicine
|
| Street address |
1305 York Avenue (Box 140)
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE47792 |
SEQC Project |
| GSE49712 |
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data |
|
| Relations |
| BioSample |
SAMN02315086 |
| SRA |
SRX333355 |
