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Sample GSM1568309 Query DataSets for GSM1568309
Status Public on Jan 08, 2021
Title HEK293flpPIAS1_PIAS1+2_tet_rep2
Sample type SRA
 
Source name Isogenic HEK293 cells, 3x-FLAG-PIAS1, tet, PIAS1+2 ChIP
Organism Homo sapiens
Characteristics cell line: HEK293
cell type: human embryonal kidney cell line
stably expressing: 3x-FLAG-PIAS1
treatment: tetracycline
concentration: 100 ng/ml
time: 24 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 HEK293flpPIAS1 cells were created by using the Flp-In T-REx 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
E-mail(s) villepaakinaho@gmail.com
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
Relations
BioSample SAMN03269302
SRA SRX818644

Supplementary file Size Download File type/resource
GSM1568309_Sample_13_HEK293flpPIAS1_PIAS1_tet_rep2.bedgraph.gz 1.3 Gb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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