|
| Status |
Public on Feb 12, 2014 |
| Title |
Hela S3 WT RNA-seq Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Hela S3 WT RNA-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa S3
cell type: Cervical cancer
genotype/variation: wild type
|
| Growth protocol |
HeLa S3 overexpressing eCenH3 or the parental cell line (WT) are grown in spinner flask to a concentration of 1.106 cells/ml with a viability of at least 97%.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5x10^6 cells were used in each case. Total RNA was extracted using the Qiagen Rneasy Mini-kit.
Libraries were prepared using the Epicenter ScriptSeq Strand-specific Library preparation kit with Ribo-Zero and then sequenced on an Illumina Hi-Seq2000 machine.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Strand specific RNA-seq
|
| Data processing |
Reads were mapped onto the human reference genome (hg19) using STAR mapper v2.1 (https://code.google.com/p/rna-star/) with default settings.
SAM files were converted to BAM files, sorted and indexed using Samtools
Read counts for each gene were calculated using htseq-count from the HTSeq package using gene annotation from Gencode v12 (http://www.gencodegenes.org/)
Differential expression analysis was carried out using the R package DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts for each gene across all cell lines and replicates (merged output from HTSeq)
|
| |
|
| Submission date |
Jun 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Genevieve Almouzni |
| E-mail(s) |
genevieve.almouzni@curie.fr, adam.woolfe@curie.fr
|
| Phone |
+33156246701
|
| Organization name |
Institut Curie
|
| Department |
Nuclear Dynamics and Genome Plasticity
|
| Lab |
Chromatin dynamics
|
| Street address |
26 Rue D'Ulm
|
| City |
Paris |
| State/province |
Ille De France |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE42951 |
Genome-wide maps of WT and over-expressing CenH3/CENP-A in Human HeLa S3 cells |
|
| Relations |
| BioSample |
SAMN02192683 |
| SRA |
SRX297972 |
