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Sample GSM3633019 Query DataSets for GSM3633019
Status Public on Feb 27, 2019
Title MDA-MB-231-SET-KO-Clone1-R2
Sample type SRA
 
Source name MDA-MB-231
Organism Homo sapiens
Characteristics cell type: breast cancer cell
passages: Low passages (6-10)
strain: MDA-MB-231-SETKO-Clone1
Growth protocol Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10% serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C
Extracted molecule total RNA
Extraction protocol RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Cells treated with SET1B-SETKO gRNA
Data processing Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9. Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
 
Submission date Feb 27, 2019
Last update date Feb 28, 2019
Contact name Ali Shilatifard
E-mail(s) ash@northwestern.edu
Organization name Northwestern University Feinberg School of Medicine
Department Department of Biochemistry and Molecular Genetics
Lab Shilatifard Lab
Street address 320 E Superior St
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platform ID GPL18573
Series (1)
GSE86855 A cytoplasmic COMPASS is necessary for cell survival and triple-negative breast cancer pathogenesis by regulating metabolism
Relations
BioSample SAMN11026807
SRA SRX5439067

Supplementary file Size Download File type/resource
GSM3633019_MDA-MB-231-SET-KO-Clone1-R2.minus.bw 44.5 Mb (ftp)(http) BW
GSM3633019_MDA-MB-231-SET-KO-Clone1-R2.plus.bw 46.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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