|
Status |
Public on Feb 23, 2015 |
Title |
TRF2_ChIPseq_HeLa1.2.11 |
Sample type |
SRA |
|
|
Source name |
HeLa 1.2.11 ALT (-) cells, TRF2 ChIP
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa alt status: - chip antibody: anti-TRF2 / Rabbit polyclonal IgG (Santa Cruz sc-9143)
|
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 |
Telomerase-positive HeLa cervical carcinoma cell line
|
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 |
SAMN02053852 |
SRA |
SRX268885 |