|
Status |
Public on Aug 01, 2013 |
Title |
input DNA (replicate 2) |
Sample type |
SRA |
|
|
Source name |
input DNA
|
Organism |
Homo sapiens |
Characteristics |
chip antibody: None cell type: adrenocortical tumor cell line: H295R/TR SF-1 cells
|
Treatment protocol |
To induce SF-1 overexpression, doxycycline (1 mg/mL) was addred in some samples to the culture medium for 3 days before formaldehyde fixation and harvesting of the cells.
|
Growth protocol |
H295R/TR SF-1 cells were cultured in DMEM-F12 (Invitrogen) supplemented with 2% NuSerum (BD), 1% ITS+ (BD) and penicillin-streptomycin (Invitrogen).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and SF-1 - DNA complexes were isolated with antibody, as described in Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nature Protoc 1(2):729-748. Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane. The quality of starting DNA was assessed prior to library construction at Fasteris SA using an Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA).
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Basecalls performed using CASAVA version 1.6 ChIP-seq reads were aligned to the hg19 genome assembly using ELAND version 2.0 PĂ«aks were called using the the CisGenome v2 SeqPeak algorithm using default parameters. Genome_build: hg19 Supplementary_files_format_and_content: bed files were generated using the cod to bed CisGenome utility
|
|
|
Submission date |
Jul 18, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Enzo LALLI |
E-mail(s) |
ninino@ipmc.cnrs.fr
|
Phone |
+33 (0)4 93 95 77 55
|
Organization name |
IPMC
|
Department |
CNRS UMR 7275
|
Lab |
402
|
Street address |
660 route des Lucioles
|
City |
Valbonne |
ZIP/Postal code |
06560 |
Country |
France |
|
|
Platform ID |
GPL11154 |
Series (2) |
GSE44224 |
Mechanisms of dosage-dependent regulation of gene expression by transcription factor SF-1 |
GSE49014 |
Identification of NRSF/REST genomic binding sites in conditions of basal and increased SF-1 dosage in the H295R adrenocortical tumor cell line |
|
Relations |
BioSample |
SAMN02260373 |
SRA |
SRX326491 |