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Sample GSM4955597 Query DataSets for GSM4955597
Status Public on Jan 08, 2021
Title HEK293flpGR3KR_RNAseq_DMSO-EtOH_rep1
Sample type SRA
 
Source name Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, RNA
Organism Homo sapiens
Characteristics cell line: HEK293
cell type: human embryonal kidney cell line
stably expressing: SUMOylation-defective GR (GR3KR)
treatment: DMSO + EtOH
concentration: 0.01% + 0.01%
time: 24 h + 6 h
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 wither with vehicle (EtOH) or 100 nM of dexamethasone for 1 h prior ChIP or ATAC. For RNA-seq 6 h hormone treatment was used. SAE inhibitor treatment was 1 uM for 24 h prior extraction. HEK293flpPIAS1 cells were treated with 100 ng/ml of tetracycline for 24 h prior 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 polyA RNA
Extraction protocol For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using Qiagen RNeasy Mini kit.
For ChIP-seq, NEBNext Ultra II DNA Library Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
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
Peaks were called using HOMER program version 4.9. with default parameters in findPeaks. Rabbit IgG sample from HEK293flpFRT cells or mouse IgG sample from HEK293flpGR cells was used as control.
Alignment of RNA-seq data to human reference genome version hg19 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.
 
Submission date Dec 03, 2020
Last update date Jan 10, 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 GPL18573
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 SAMN16989145
SRA SRX9628187

Supplementary file Size Download File type/resource
GSM4955597_HEK293flpGR3KR_RNAseq_DMSO-EtOH_rep1.ucsc.bedGraph.gz 125.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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