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Series GSE135807 Query DataSets for GSE135807
Status Public on Aug 04, 2022
Title ChIP-seq assay in human cancer cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ChIP-seq assay was performed for the quantitative detection of the binding of TFs and histones upon acute stimulations.
Overall design MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). LNCAP cells were maintained at 37°C and 5% CO2 in Advanced RPMI 1640 medium (GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).
For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNF⍺ (R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples. For knock-down of Top1 genes, the siTop1_1 (SASI_Hs01_00047440, Sigma, CACAAAGAGAGGAAUGCUA[dT][dT], UAGCAAUCCUCUCUUUGUG[dT][dT]) and siTop1_3 (SASI_Hs02_00335354, Sigma, GACAAGAUCCGGAACCAGU[dT][dT], ACUGGUUCCGGAUCUUGUC[dT][dT]) were employed. For knock-down of Cbx3 genes, the siCbx3_1 (SASI_Hs01_00170890, Sigma, CCAAGAGGAUUUGCCAGAG[dT][dT], CUCUGGCAAAAUCCUCUUGG[dT][dT]) and siCbx3_2 (SASI_Hs01_00196532, Sigma, CCAAGAGGAUUUGCCAGAG[dT][dT], CUCUGGCAAAAUCCUCUUGG[dT][dT]) were employed. For ChIP-seq and PRO-seq experiments, cells were transfected in 10-cm plates in regular DMEM without antibiotics. 20 μl of 20 μM small interfering RNA (siRNAs) and Lipofectamine® 2000 reagent (Invitrogen Cat# 11668-019) were diluted in Opti-MEM I Reduced Serum Medium (Invitrogen Cat# 11058-021), and incubated for 6 h, and then changed to phenol red-free medium.
Contributor(s) Tan Y
Citation(s) 36747093
Submission date Aug 14, 2019
Last update date Jun 01, 2023
Contact name Yuliang Tan
Organization name University of California, San Diego
Department School of Medicine
Street address Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648
City La Jolla
State/province California
ZIP/Postal code 92037-0648
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (104)
GSM4030486 ChIP-seq_AP2y_E2_MCF7
GSM4030487 ChIP-seq_AP2y_Veh_MCF7
GSM4030488 ChIP-seq_BRD4_E2_exp1_MCF7
This SubSeries is part of SuperSeries:
GSE135808 Topoisomerase 1 Nicking-dependent HP1gamma Engagement Mediates Acute Activation of Phase-separated Enhancers
BioProject PRJNA560179
SRA SRP218314

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE135807_RAW.tar 22.9 Gb (http)(custom) TAR (of BED, BEDGRAPH, BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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