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Sample GSM6443229 Query DataSets for GSM6443229
Status Public on Jan 30, 2023
Title H2030, H3K4me1
Sample type SRA
 
Source name H2030
Organism Homo sapiens
Characteristics cell line: H2030
cell type: Human lung adenocarcinoma
chip antibody: H3K4me1 (Abcam, #ab8895)
Treatment protocol H2087-LCC cells were treated with TGF-β1 (100 nM, R&D Systems) for 4 days.
Growth protocol H2087-LCC and H2087-LCC-SO1 cells were cultured in RPMI 1640 media supplemented with 10% FBS, 2 mM glutamine, 100 IU/mL penicillin/streptomycin, 1 µg/mL amphotericin B, 0.5 mM sodium pyruvate, 10 mM HEPES, 50 nM hydrocortisone, 25 nM sodium selenite, 20 µg/mL insulin, 10 µg/mL transferrin, 0.5% bovine serum albumin (BSA), and 1 ng/mL recombinant human epidermal growth factor. H2030 cells were cultured in RPMI 1640 media supplemented with 10% FBS, 2 mM glutamine, 100 IU/mL penicillin/streptomycin, and 1 µg/mL amphotericin B. Cells were cultured at 37C at 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. ChIP was performed using the ChIP assay kit (Millipore Sigma, #17-295) according to the manufacturer’s instructions.
Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with an undetectable mass to 10 ng input DNA and 10 cycles of PCR.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing For mapping and visualization, paired-end (50/50 bp) FASTQ reads were mapped to human genome hg19 using Bowtie2 with default filtering criteria. Resulted SAM files were converted to BAM files though Samtools. BAM files were sorted and indexed with Samtools.
BAM files were normalized, converted to bigwig files using bamCoverage-deepTools and displayed with IGV browser.
Assembly: hg19
Supplementary files format and content: bigWig
 
Submission date Aug 10, 2022
Last update date Jan 30, 2023
Contact name Jing Hu
E-mail(s) huj2@mskcc.org
Phone 646-888-2063
Organization name Memorial Sloan Kettering Cancer Center
Street address 417 E 68th St
City New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL24676
Series (1)
GSE210946 STING suppresses the reactivation of dormant metastasis
Relations
BioSample SAMN30242777
SRA SRX17024217

Supplementary file Size Download File type/resource
GSM6443229_H2030_H3K4me1.bigwig 259.3 Mb (ftp)(http) BIGWIG
GSM6443229_H2030_H3K4me1_summits.bed.gz 1.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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