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| Status |
Public on Nov 23, 2022 |
| Title |
H446 ND1-KO, BRD2, CST |
| Sample type |
SRA |
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| Source name |
H446
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H446
cell type: small cell lung cancer SCLC-N subtype
genotype: NEUROD1 knockout
chip antibody: BRD2 (CST, #5848)
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| Growth protocol |
RPMI, 10% heat-inactivated FBS, 1x penicillin/streptomycin. Cells were cultured at 37 ⁰C at 5% CO2 in a humidified atmosphere.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Sonic Dismembrator (Fisher brand Model 705).
Libraries were constructed using entire ChIPed DNA or 300 ng of the input DNA using a NEBNext Ultra II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter). Estimation of library quality and quantity was performed using a Bioanalyzer and Qubit assays.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
H446_ND1-KO_BRD2
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| Data processing |
Fastq files were processed using PartekFlow.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, discarding reads left with < 25 bp.
ChIP-seq reads were aligned to the UCSC hg19 genome using BWA-backtrack version 0.7.12 with the parameters '-n 0.04 -o 1 -e -1 -d 10 -i 5 -k 2 -E 4 -R 30 -t 32'.
Duplicated reads were discarded. Peaks were called using MACS v2.1.1 with the significance cut-off q-value <=0.05.
Assembly: hg19
Supplementary files format and content: narrowPeak (NEUROD1) and BroadPeak (H3K27Ac, RPII, BRD2, BRD3, BRD4) files.
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| Submission date |
Jul 29, 2022 |
| Last update date |
Nov 23, 2022 |
| Contact name |
Haobin Chen |
| E-mail(s) |
[email protected]
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| Phone |
(845) 300-2498
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| Organization name |
National Institutes of Health
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| Department |
Thoracic Surgery Branch
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| Street address |
10 Center Drive, Room 3-5888
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE210113 |
BET Inhibitors Target the SCLC-N subtype of Small Cell Lung Cancer by Blocking NEUROD1 Transactivation |
| GSE210114 |
BET Inhibitors Target the SCLC-N subtype of Small Cell Lung Cancer by Blocking NEUROD1 Transactivation |
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| Relations |
| BioSample |
SAMN30058150 |
| SRA |
SRX16739014 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6421559_BRD2_ND1-KO_peaks.broadPeak.gz |
1.0 Mb |
(ftp)(http) |
BROADPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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