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GEO help: Mouse over screen elements for information. |
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Status |
Public on May 31, 2023 |
Title |
CN1 |
Sample type |
SRA |
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Source name |
Pancreatic beta cells
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Organism |
Mus musculus |
Characteristics |
tissue: Pancreatic beta cells cell type: beta cell genotype: Control
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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
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Nov 07, 2022 |
Last update date |
May 31, 2023 |
Contact name |
Jason Spaeth |
E-mail(s) |
jspaeth@iu.edu
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Phone |
3172748986
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Organization name |
Indiana University
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Department |
Pediatrics
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Lab |
MS2021
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Street address |
635 Barnhill Dr.
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City |
Indianapolis |
State/province |
IN |
ZIP/Postal code |
46202 |
Country |
USA |
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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. |
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Relations |
BioSample |
SAMN31643049 |
SRA |
SRX18193245 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6718839_CN1_macs2_cuttingSite_shited_peaks.narrowPeak.gz |
2.3 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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