 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 14, 2024 |
| Title |
20240402_KS232_ChIP_NCIH526_BRG1_ab_CKX |
| Sample type |
SRA |
| |
|
| Source name |
NCIH526
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCIH526
chip antibody: BRG1 (abcam, ab110641, GR3255117-11)
treatment: DMSO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq: Cells were fixed with 2mM disuccinimidyl glutarate 40min room temperature then 1.0% paraformaldehyde 10min room temperature, quenced with 375mM Tris HCL and then sonicated using Covaris E220 ultra-focused sonicator. 1-10ng of immunoprecipitated DNA was used for library prep. For ATAC-Seq: 100K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 8 cycles of amplification For RNA-Seq: All RNA was collected using the TRIzol extraction (Invitrogen) method and treated with DNAse using the DNA-free DNA Removal Kit (Invitrogen). 1ug of DNAse-treated RNA was used for the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for standard Illumina sequencing.
ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters. ATAC-seq samples were sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters. RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation. For ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively. For ChIP Data, reads were aligned, then duplicates removed and read quality filtered using using Bowtie2 v2.29, Sambamba v0.7.1, and SAMtools v0.1.19.
For ChIP and ATACseq data, tracks were generated using deepTools bamCoverage (--normalizeUsing CPM -bs 40), ATACseq data was first filtered insert sizes between 38 and 100 bp. For RNAseq data, tracks were generated using deepTools bamCoverage (--normalizeUsingRPKM).
Assembly: hg19
Supplementary files format and content: Cut&Run and ATACseq bigWig files give the normalized coverage of DNA fragments across the genome in RPM, and gene count tables give raw RNA read counts mapped to exons of given genes. RNAseq bigWig files give the give the normalized coverage of DNA fragments across the genome in RPKM.
|
| |
|
| Submission date |
Apr 16, 2024 |
| Last update date |
Jun 14, 2024 |
| Contact name |
Cigall Kadoch |
| E-mail(s) |
Cigall_Kadoch@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Kadoch Lab
|
| Street address |
440 Brookline Ave
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE249362 |
Non-Canonical BAF and mSWI/SNF Regulates POU2F3 and are Selective Targetable Dependencies for POU2F3-Positive Small Cell Lung Cancer |
|
| Relations |
| BioSample |
SAMN40981581 |
| SRA |
SRX24271884 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8209581_20240402_KS232_ChIP_NCIH526_BRG1_ab_CKX.bed.gz |
393.7 Kb |
(ftp)(http) |
BED |
| GSM8209581_20240402_KS232_ChIP_NCIH526_BRG1_ab_CKX.bw |
139.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
