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| Status |
Public on Jun 07, 2023 |
| Title |
16HBE14o- CFTRhigh #4 rep2 [ATAC-seq] |
| Sample type |
SRA |
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| Source name |
16HBE14o-
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 16HBE14o-
cell type: human bronchial epithelial cells
genotype: CFTRhigh
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| Treatment protocol |
50,000 cells were isolated prior to lysing/transpostion
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| Growth protocol |
Cells were grown in DMEM + 10% FBS using standard protocols
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| 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
16HBE_CFTR_high_IDR.bw
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| 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
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| Submission date |
Dec 13, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Ann Harris |
| E-mail(s) |
axh575@case.edu
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| Organization name |
Case Western Reserve University
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| Department |
Genetics and Genome Sciences
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| Street address |
2109 Adelbert Rd
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| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
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| 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. |
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| Relations |
| BioSample |
SAMN32192575 |
| SRA |
SRX18671786 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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