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Status |
Public on Jan 08, 2021 |
Title |
HEK293flpGR_PIAS1+2_dex_rep1 |
Sample type |
SRA |
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Source name |
Isogenic HEK293 cells, wild-type GR, dex, PIAS1+2 ChIP
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Organism |
Homo sapiens |
Characteristics |
cell line: HEK293 cell type: human embryonal kidney cell line stably expressing: wild-type GR treatment: dexamethasone concentration: 100 nM time: 1 h chip antibody: PIAS1+PIAS2 (Abcam, ab77231, lot # YI122105C)
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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.
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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.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Description |
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).
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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.
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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 |
SAMN03269297 |
SRA |
SRX818636 |