|
| Status |
Public on Dec 21, 2012 |
| Title |
H9 XIST- |
| Sample type |
SRA |
| |
|
| Source name |
hESC
|
| Organism |
Homo sapiens |
| Characteristics |
passage: p27
xist expression: XIST-
cell line: H9
cell type: embryonic stem cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 10µg of total RNA was depleted of rRNA using the Ribo-Zero rRNA removal kit (EpiCentre). Sequencing libraries with fragment size 200-400bp were prepared using a strand-specific ScriptSeq kit (EpiCentre) according to manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2000 using paired-end protocols (Illumina) with 100 bp read lengths for all samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using CASAVA version 1.7
RNA-Seq reads were aligned to the current version of the human genome (hg19) using Bowtie-0.12.7 with the following parameters: -v 2 -k 10 -m 10 -y --best
Reads per millions of mapped reads (RPM) was used to estimate expression
SAM tools Mpileup was used to analyze allelic expression of X-linked transcripts using published H9 SNP data (GEO:GSM377524)
Genome_build: hg19
|
| |
|
| Submission date |
Jul 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Céline Vallot |
| E-mail(s) |
celine.vallot@univ-paris-diderot.fr
|
| Organization name |
CNRS/UMR7216
|
| Street address |
35 rue Hélène Brion
|
| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE39757 |
Transcriptomic analysis of XIST+ and XIST- hES cells |
|
| Relations |
| SRA |
SRX171662 |
| BioSample |
SAMN01096087 |
