|
| Status |
Public on Oct 21, 2016 |
| Title |
UCLA4_XIST_Neg_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonic stem cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
none provided by the submitter
none provided by the submitter
stranded RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
UCLA4 5iLAF XIST Negative Replicate2
|
| Data processing |
RNA-seq library reads were mapped to the hg19 reference genome using TopHat v2.1.0 (Trapnell et al., 2009) with parameters set to '--b2-sensitive --no-novel-juncs --library-type fr-unstranded --no-mixed --no-discordant --prefilter-multihits --transcriptome-max-hits 1 --max-multihits 15'
The annotation of aligned reads with genomic features was prefomed using HTSeq 0.6.1p1 (Anders et al., 2014) with parameters set to '--type=exon --mode=union --minaqual=0 --stranded=no'
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Raw read counts for each samples
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
Nov 19, 2020 |
| Contact name |
Kathrin Plath |
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
BSRB 390B
|
| Street address |
615 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1737 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE87231 |
Human naïve pluripotent stem cells exhibit X chromosome dampening and X-inactivation (RNA-Seq) |
| GSE87239 |
Human naive pluripotent stem cells exhibit X chromosome dampening and X-inactivation |
|
| Relations |
| BioSample |
SAMN05805781 |
| SRA |
SRX2185477 |
