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Sample GSM6822486 Query DataSets for GSM6822486
Status Public on Jun 07, 2023
Title 16HBE14o- CFTRhigh #7 rep1 [ATAC-seq]
Sample type SRA
 
Source name 16HBE14o-
Organism Homo sapiens
Characteristics cell line: 16HBE14o-
cell type: human bronchial epithelial cells
genotype: CFTRhigh
Treatment protocol 50,000 cells were isolated prior to lysing/transpostion
Growth protocol Cells were grown in DMEM + 10% FBS using standard protocols
Extracted molecule genomic DNA
Extraction protocol Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were constructed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Description 16HBE_CFTR_high_IDR.bw
Data processing Raw files were trimmed using Sickle (Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33)
Trimmed reads aligned to the hg19 genome using the BWA aligner (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60).
Aligned reads were marked for duplicates using Picard and coverage tracks were generated using deepTools bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016))
Assembly: hg19 genome
Supplementary files format and content: hg19 aligned IDR ATAC-seq of CFTRhigh or CFTRlow cells (n=4) in bigWig format
Supplementary files format and content: hg19 aligned IDR ATAC-seq of each clonal line (2 passages) in bigWig format
 
Submission date Dec 13, 2022
Last update date Jun 07, 2023
Contact name Ann Harris
E-mail(s) axh575@case.edu
Organization name Case Western Reserve University
Department Genetics and Genome Sciences
Street address 2109 Adelbert Rd
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL21697
Series (2)
GSE220853 Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts [ATAC-seq]
GSE220855 Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts.
Relations
BioSample SAMN32192574
SRA SRX18671787

Supplementary file Size Download File type/resource
GSM6822486_16HBE_SC_7high_IDR.bw 584.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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