|
| Status |
Public on Sep 27, 2023 |
| Title |
NCIH460-INPUT |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
cell line: NCI-H460
cell type: large-cell lung carcinoma
treatment: Input
|
| Treatment protocol |
Immunoprecipitation (IP) was performed with H3K27ac antibody (Catalogue No. AB4729) or control IgG (AB37415).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
phenol/chloroform extraction
The Input and IP samples were ligated with illumina barcodes and amplified using the Kapa library amplification kit, followed by size-selection with AMPure XP Beads. ASPRI cleanup with a 1.5× AMPure XP Bead: DNA ratio was performed and final libraries were eluted and sequenced using Illumina Nextseq 550 System with NextSeq 500/550 High Output Kit v2.5. For each sample (IP and Input) approximately 90 million paired-end reads were obtained.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Paired-end raw reads were filtered based on the quality value obtained from FastQC v0.11.9 (-q 10 and -p 30) using the Trim Galore! software v0.6.4_dev. The filtered reads were aligned to the hg19 reference genome using BWA v0.7.17-r1188 to produce the alignment file (BAM). The PCR duplicates were removed from the aligned BAM files using PICARD tools v2.23.1. The BAM files were sorted and indexed for peak calling using SAMtools. The BedGraph files were generated by comparing BAM files of IP and input (IP read coverage/input read coverage) resulting in a ratio for every base across the whole genome using bamCompare from deepTools v3.4.3. To call the peaks MACS2 v2.2.7.1 was used. This framework was implemented using nfcore ChIP-seq v1.2.1.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Francesco Ferrari |
| E-mail(s) |
francesco.ferrari@ifom.eu
|
| Organization name |
IFOM ETS, the AIRC Institute of Molecular Oncology
|
| Street address |
Via Adamello 16
|
| City |
Milan |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE228831 |
Enhancer somatic mutations with functional impact in lung cancers identified by leveraging the tissue-specific enhancer-target genes regulatory network [ChIP-seq] |
| GSE228832 |
Enhancer somatic mutations with functional impact in lung cancers identified by leveraging the tissue-specific enhancer-target genes regulatory network |
|
| Relations |
| BioSample |
SAMN34052179 |
| SRA |
SRX19850834 |
