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Sample GSM5903228 Query DataSets for GSM5903228
Status Public on Sep 15, 2022
Title H1963_BAP1
Sample type SRA
Source name NCI-H1963
Organism Homo sapiens
Characteristics cell type: small cell lung cancer
passages: Low passages (6-10)
cell line: H1963_BAP1
chip antibody: anti-BAP1 (home made)
genotype: normal cells
Treatment protocol no treatment
Growth protocol Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium containing 10% FBS (Sigma)
Extracted molecule genomic DNA
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 ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
Description normal cells
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 for single-end or bwa version 0.7.12 for paired-end. 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 or Star version 2.5.2. 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 16, 2022
Last update date Sep 15, 2022
Contact name Lu Wang
Organization name Northwestern University
Department Biochemistry and Molecular Genetics
Lab Lu Wang
Street address 303 E. Superior Street Simpson Querrey 7-414
City Chicago
State/province Illinois
ZIP/Postal code 60611
Country USA
Platform ID GPL24676
Series (1)
GSE196860 MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer
BioSample SAMN25996055
SRA SRX14203241

Supplementary file Size Download File type/resource 85.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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