|
| Status |
Public on Feb 23, 2015 |
| Title |
NR2C2_ChIPseq_VA13 |
| Sample type |
SRA |
| |
|
| Source name |
WI-38 VA13 ALT (+) cells, NR2C2 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WI-38
alt status: +
chip antibody: anti-NR2C2 / Mouse monoclonal IgG (PPMX PP-H0107B-00)
|
| Growth protocol |
Cells were cultured in DMEM glutamax with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared by Fasteris SA (Switzerland) and were sequenced on HiSeq 2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
WI-38 VA-13_2RA is a SV40-transformed variant of the WI38 cell line (female embryonic lung fibrobasts).
|
| Data processing |
Base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.2)
50 nt-long sequenced reads were mapped onto the genome sequence of Homo sapiens (hg18 assembly) according to sequencing quality using Bowtie.
For genome-wide enrichment analysis, only reads perfectly matching the human genome were retrieved (one mismatch was nevertheless allowed on low-quality nucleotides using –e 20 option). Redundant reads as well as reads mapping to multiple genomic locations were also discarded.
Enrichment peaks were called using SISSRs v 1.4 (Jothi et al., 2008) with default parameters using input DNA as background. Peaks corresponding to repetitive regions were discarded using BEDTools (Quinlan & Hall, 2010) (satellites 2/3, alpha/beta satellites and ribosomal DNAs genomic positions were retrieved from the UCSC repeatmasker track (http://genome.ucsc.edu/)).
Annotation of the identified peaks as well as peak overlap and motif discovery were performed using HOMER tool suite (Heinz et al., 2010)
Genome_build: NCBI36
Supplementary_files_format_and_content: BigWig files were generated using HOMER tool suite (Heinz et al., 2010) and represent normalized fragment density profile (based on genome-unique unredundant perfectly mapping reads). BED files contain coordinates (chromosome, start and end) of called peaks.
|
| |
|
| Submission date |
Apr 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jérôme Déjardin |
| E-mail(s) |
jerome.dejardin@igh.cnrs.fr
|
| Organization name |
Institute of Human Genetics
|
| Lab |
Biology of Repetitive Sequences
|
| Street address |
141, rue de la Cardonille
|
| City |
MONTPELLIER CEDEX 5 |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46237 |
NR2C/F orphan receptors induce telomere-genome rearrangements in ALT |
|
| Relations |
| BioSample |
SAMN02053850 |
| SRA |
SRX268883 |
