|
| Status |
Public on Jan 08, 2021 |
| Title |
HEK293flpGR_H3K4me2_dex_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Isogenic HEK293 cells, wild-type GR, dex, H3K4me2 ChIP
|
| 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: H3K4me2 (Abcam, ab7766, lot # GR203810-1)
|
| 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 |
| E-mail(s) |
[email protected]
|
| 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 |
SAMN03269306 |
| SRA |
SRX818638 |
