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| Status |
Public on Jan 30, 2023 |
| Title |
H2030, H3K4me1 |
| Sample type |
SRA |
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| Source name |
H2030
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H2030
cell type: Human lung adenocarcinoma
chip antibody: H3K4me1 (Abcam, #ab8895)
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| Treatment protocol |
H2087-LCC cells were treated with TGF-β1 (100 nM, R&D Systems) for 4 days.
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Aug 10, 2022 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Jing Hu |
| E-mail(s) |
huj2@mskcc.org
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| Phone |
646-888-2063
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Street address |
417 E 68th St
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| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE210946 |
STING suppresses the reactivation of dormant metastasis |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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