|
| Status |
Public on Aug 01, 2013 |
| Title |
input DNA basal SF-1 expression |
| Sample type |
SRA |
| |
|
| Source name |
H295R/TR SF-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H295R adrenocortical tumor cell line
sf-1 dosage: basal SF-1
sample type: input DNA
|
| 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 |
FAIRE-seq was performed according to the method described in Giresi PG, Lieb JD (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48: 233-239.
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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Reads were aligned to the hg19 genome assembly using ELAND version 2.0
Pëaks were called from each FAIRE-seq sample compared to input DNA in SF-1 basal and overexpression conditions, 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 |
Feb 11, 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) |
| GSE44221 |
Identification of chromatin regulatory sites in conditions of basal and increased SF-1 dosage in the H295R adrenocortical tumor cell line |
| GSE44224 |
Mechanisms of dosage-dependent regulation of gene expression by transcription factor SF-1 |
|
| Relations |
| SRA |
SRX235051 |
| BioSample |
SAMN01919584 |
