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Sample GSM6502199 Query DataSets for GSM6502199
Status Public on Jun 30, 2023
Title ATAC-Seq BSC, Ctrl, rep1
Sample type SRA
 
Source name Lung
Organism Homo sapiens
Characteristics tissue: Lung
cell type: Basal stem cell
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).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description BSC, Ctrl, rep1
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
 
Submission date Aug 22, 2022
Last update date Jun 30, 2023
Contact name Xingbin Ai
E-mail(s) xai@mgh.harvard.edu
Organization name MASSACHUSETTS GENERAL HOSPITAL
Department Pediatrics
Street address 55 Fruit St
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
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
Relations
BioSample SAMN30439290
SRA SRX17237029

Supplementary file Size Download File type/resource
GSM6502199_3_09A4_01BJMGH_TermT-1_ATAC_hg38_i219_uniqnorm_signal.bw 79.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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