|
Status |
Public on Jan 21, 2025 |
Title |
16HBE14o- KLF5null cl4 CFTR promoter |
Sample type |
SRA |
|
|
Source name |
Human airway epithelium
|
Organism |
Homo sapiens |
Characteristics |
cell line: 16HBE14o- genotype: CRISPR/Cas9 mediated KLF5-null growth media: DMEM + 10% FBS
|
Treatment protocol |
KLF5 depletion and CRISPR KLF5-null cell generation was performed as per Paranjapye, A et al, 2021, (PMID: 34217701).
|
Growth protocol |
Cells were grown in indicated media using standard methods
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclei from 1e7 cells grown to confluency were made as per Krijger, P et al, 2020, Methods (PMID: 31351925) with corresponding samples as listed in the treatment protocol section. All libraries were constructed as per PMID: 31351925 with the samples corresponding to the Methods papers as listed in the treatment protocol section. 4C-seq Barcoded libraries with Illumina sequencing adapters were made as per PMID: 31351925 for corresponding samples as listed in the treatment protocol section.
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 550 |
|
|
Description |
4C-seq library with the CFTR -20.9 kb region as the viewpoint
|
Data processing |
Libraries were sequenced on the Nextseq550 machine and demultiplexed using the primer sequences. 4C-seq was quantified and mapped using the pipe4C v1.1 (https://github.com/deLaatLab/pipe4C) processing pipeline using default parameters, aligned to the hg19 genome. Genome_build: hg19 Supplementary_files_format_and_content: Aligned 4C-seq of each clone and viewpoint in bigWig format
|
|
|
Submission date |
Jan 24, 2022 |
Last update date |
Jan 21, 2025 |
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 Building
|
City |
Cleveland |
State/province |
Ohio |
ZIP/Postal code |
44106 |
Country |
USA |
|
|
Platform ID |
GPL21697 |
Series (1) |
GSE194288 |
Krüppel-Like Factor 5 regulates CFTR expression through repression by maintaining chromatin architecture coupled with direct enhancer activation |
|
Relations |
BioSample |
SAMN25227215 |
SRA |
SRX13883761 |