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Sample GSM1568300 Query DataSets for GSM1568300
Status Public on Jan 08, 2021
Title HEK293flpGR_PIAS1+2_EtOH_rep2
Sample type SRA
Source name Isogenic HEK293 cells, wild-type GR, vehicle, PIAS1+2 ChIP
Organism Homo sapiens
Characteristics cell line: HEK293
cell type: human embryonal kidney cell line
stably expressing: wild-type GR
treatment: EtOH vehicle
concentration: 0.01%
time: 1 h
chip antibody: PIAS1+PIAS2 (Abcam, ab77231, lot # YI122105C)
Treatment protocol HEK293flpGR cells were seeded at 70% confluence in 10-cm plates and allowed to grow in steroid-depleted medium (2.5% charcoal stripped FBS in DMEM) 72 h, and the cells were subsequently treated with vehicle (EtOH) or 100 nM of dexamethasone for 1 h prior to ChIP. HEK293flpPIAS1 cells were treated with 100 ng/ml of tetracycline for 24 h prior to ChIP.
Growth protocol HEK293flpGR cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. HEK293flpPIAS1 cells were also supplemented with 15 µg/ml of blasticidin.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description HEK293flpGR cells were created by using the Flp-In System (Invitrogen).
Data processing Basecalls performed using CASAVA.
FASTX-toolkit was used to trim low-quality reads and sequence duplicates were collapsed.
The reads were aligned to human reference genome version hg19 by using Bowtie software version 0.12.9 with the command line: -e 70 -l 50 -n 1 -k 1 -m1 \ -t -p 12 -q -S --best
Peaks were called using HOMER program version 4.6 with default parameters in findPeaks. Rabbit IgG immunoprecipitated sample from HEK293flpFRT cells was used as control.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: HOMER program generated bedGraph (makeUCSCfile-command) from alignment file.
Submission date Dec 17, 2014
Last update date Jan 08, 2021
Contact name Ville Paakinaho
Organization name University of Eastern Finland
Department School of Medicine
Lab Biomedicine
Street address Yliopistonranta 8
City Kuopio
ZIP/Postal code 70210
Country Finland
Platform ID GPL11154
Series (2)
GSE64301 SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites [sequencing]
GSE64373 SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites
BioSample SAMN03269304
SRA SRX818635

Supplementary file Size Download File type/resource
GSM1568300_Sample_4_HEK293flpGR_PIAS1_EtOH_rep2.bedgraph.gz 61.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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