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Sample GSM6718843 Query DataSets for GSM6718843
Status Public on May 31, 2023
Title KO2
Sample type SRA
 
Source name Pancreatic beta cells
Organism Mus musculus
Characteristics tissue: Pancreatic beta cells
cell type: beta cell
genotype: Chd4KO
Extracted molecule genomic DNA
Extraction protocol A total of 27,000-80,000 Tomato+ mature β-cells were collected for ATAC-Sequencing. Cells were first lysed to collect nuclei by incubating with 100 μL lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 0.10% Nonidet P40 Substitute, 0.01% Digitonin, 1% BSA, 1 mM DTT, 40 U/uL RNase Inhibitor) for 3 minutes, centrifuging at 300 rcf for 5 minutes at 4°C, and discarding the supernatant. The resulting nuclei were then washed with 1 mL wash buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 1% BSA, 1 mM DTT, 40 U/μl RNase Inhibitor) and centrifuged at 200 rcf for 5 minutes at 4°C for 2-3 times. The final nuclei, ranging from 14,000-45,000 in number, were used for tagmentation and library preparation
Nuclei were immediately suspended in 50 μL tagmentation reaction using 2xTD buffer (Illumina, FC-121-1030) and Nextera Tn5 Transposase enzyme (Illumina, FC-121-1030). Fragments greater than 600 bp were excluded in library preparation. Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing The pooled libraries were then denatured and neutralized before loading to NovaSeq 6000 sequencer at 300 pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 100 x 106 reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).
Assembly: mm10
Supplementary files format and content: peaks.narrowPeak
 
Submission date Nov 07, 2022
Last update date May 31, 2023
Contact name Jason Spaeth
E-mail(s) jspaeth@iu.edu
Phone 3172748986
Organization name Indiana University
Department Pediatrics
Lab MS2021
Street address 635 Barnhill Dr.
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
 
Platform ID GPL24247
Series (2)
GSE217444 The Chd4 helicase regulates chromatin accessibility and gene expression critical for β-cell function in vivo [ATAC-seq]
GSE217446 The Chd4 helicase regulates chromatin accessibility and gene expression critical for β-cell function in vivo.
Relations
BioSample SAMN31643045
SRA SRX18193249

Supplementary file Size Download File type/resource
GSM6718843_KO2_macs2_cuttingSite_shited_peaks.narrowPeak.gz 2.9 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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