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| Status |
Public on Jun 30, 2023 |
| Title |
ATAC-Seq BSC, Ctrl, rep3 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
cell type: Basal stem cell
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
BSCs were cryopreserved in 50% FBS/40% SAGM/10%DMSO solution prior to ATAC-seq by Active Motif (Carlsbad, CA, USA). Cells were thawed in a 37℃ water bath, pelleted, and tagmented using Nextera Library Prep Kit (Illuminutesa, Cat# FC-130-1064). Tagmented DNA was purified using the MinutesElute PCR purification kit (Qiagen, Cat# 13323).
The DNA was then amplified with 10 cycles of PCR, purified using Agencourt AMPure SPRI beads (Beckman Coulter).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
BSC, Ctrl, rep3
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| Data processing |
The paired-end 42 bp sequencing reads are mapped to the human hg38 reference genome using the BWA v0.7.12 algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads are removed.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option.
Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: hg38
Supplementary files format and content: bigWig
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| Submission date |
Aug 22, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Xingbin Ai |
| E-mail(s) |
xai@mgh.harvard.edu
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| Organization name |
MASSACHUSETTS GENERAL HOSPITAL
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| Department |
Pediatrics
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| Street address |
55 Fruit St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE211788 |
A tracheal aspirate-derived airway basal cell model reveals a proinflammatory epithelial defect in congenital diaphragmatic hernia (ATAC-Seq) |
| GSE211790 |
A tracheal aspirate-derived airway basal cell model reveals a proinflammatory epithelial defect in congenital diaphragmatic hernia |
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| Relations |
| BioSample |
SAMN30439288 |
| SRA |
SRX17237027 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6502201_5_09A6_01BJMGH_TermT-3_ATAC_hg38_i221_uniqnorm_signal.bw |
111.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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