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Sample GSM5832456 Query DataSets for GSM5832456
Status Public on Jan 21, 2025
Title 16HBE14o- cl42 -20.9 kb
Sample type SRA
 
Source name Human airway epithelium
Organism Homo sapiens
Characteristics cell line: 16HBE14o-
genotype: Wild type
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 SAMN25227217
SRA SRX13883759

Supplementary file Size Download File type/resource
GSM5832456_16HBE14o-_cl42_-209_AH1345.fastq.bw 5.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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