|
| Status |
Public on Sep 27, 2023 |
| Title |
HBEC-ATACseq-biol_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
cell line: HBEC-3KT
cell type: Lung Epithelium
treatment: transposase
|
| Treatment protocol |
as previously described (Corces et al., 2018)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were purified using the Qiagen Mini elute PCR Purification kit
Libraries were PCR-amplified using the NEBNext High-Fidelity PCR Master Mix and amplified for 5 cycles using NEBNext 2x MasterMix and custom primers.Libraries were sufficiently amplified individually in addition to 5 cycles of PCR as computed from qPCR fluorescence curves. Libraries were purified using Zymo DNA Clean and Concentrator. The libraries were then size selected withwith a 1.5× AMPure XP Bead: DNA ratio. Final libraries were eluted and sequenced using Illumina Nextseq 550 System with NextSeq 500/550 mid Output Kit v2.5.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
ASJ01-19R_S11
|
| 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 ATAC-seq v1.2.1 pipeline .
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak
|
| |
|
| 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) |
| GSE228830 |
Enhancer somatic mutations with functional impact in lung cancers identified by leveraging the tissue-specific enhancer-target genes regulatory network [ATAC-seq] |
| GSE228832 |
Enhancer somatic mutations with functional impact in lung cancers identified by leveraging the tissue-specific enhancer-target genes regulatory network |
|
| Relations |
| BioSample |
SAMN34062752 |
| SRA |
SRX19859676 |
