|
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 |
SRX171661 |
BioSample |
SAMN01096086 |