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| Status |
Public on Nov 05, 2013 |
| Title |
wt_dex_SUMO_2_3_rep2 |
| Sample type |
SRA |
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| Source name |
Isogenic HEK293 Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Human Embryonal Kidney Cells
chip antibody: SUMO-2/3 (MBL International, M114-3, lot # 23)
stably expressing: wild-type GR
treatment: dexamethasone
concentration: 100 nM
time: 1 h
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| Treatment protocol |
Isogenic HEK293 cells were seeded at 70 % confluence in 175 cm2 bottles and allowed to grow in steroid-depleted medium (2.5 % charcoal stripped FBS in DMEM) 72 h and the cells were subsequently treated with 100 nM of dexamethasone for 1 h prior ChIP
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| Growth protocol |
Isogenic HEK293 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
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and GR-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols, as utilized at the Gene Core in EMBL, Heidelberg, Germany
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
isogenic HEK293 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 the raw reads to 40 bp 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 MACS program version 1.4.2. with the following setting: bandwidth (100 for GR; 200 for SUMO_2_3), mfold (10,30 for GR; 10,15 for SUMO_2_3), p-value cut-off (0.0001), Input as control for GR and IgG for SUMO_2_3
statistically significant peaks had tags (> 50), fold enrichment (> 8), false discovery rate (< 0.1) and peak had to be present in two biological replicates
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks from each immunoprecipitated sample: chr, start, end, length, summit, tags, -log10(p-value), fold enrichment, FDR(%)
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| Submission date |
Jun 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ville Paakinaho |
| E-mail(s) |
villepaakinaho@gmail.com
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| Organization name |
University of Eastern Finland
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| Department |
School of Medicine
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| Lab |
Biomedicine
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| Street address |
Yliopistonranta 8
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| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE48374 |
SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor (ChIP-seq) |
| GSE48379 |
SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor |
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| Relations |
| BioSample |
SAMN02215310 |
| SRA |
SRX316367 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1176705_wt_dex_SUMO_2_3_rep2_peaks.bed.gz |
261.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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