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| Status |
Public on Oct 10, 2023 |
| Title |
SLC16A11_C2 [ATAC-Seq] |
| Sample type |
SRA |
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| Source name |
MEL1 (INSGFP/W)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MEL1 (INSGFP/W)
cell type: human embryonic stem cell
genotype: SLC16A11 knockout
treatment: beta-cell differentiation
time: Day 24
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 hESC-beta cells were washed them with 1000 μl of ice-cold PBS, and resuspended the pellets in 25 μl of ice cold 1X ATAC Buffer [20mM Tris-HCl (pH 7.4), 20mM NaCl and 6mM MgCl2]. We incubated the samples for 5 minutes on ice, thoroughly mixed in 25 μl of ice cold ATAC-Detergent-buffer [20mM Tris-HCl (pH 7.4), 20 mM NaCl and 6 mM MgCl2, 0.2% Igepal CA-630, 0.2% Tween 20 and 0.02% Digitonin, and continued incubating the samples on ice for another 3 minutes. After incubation, we centrifuged the samples and collected the pellets.
ATAC libraries for ATAC-seq were prepared according to Weill Cornell Medicine Epigenetics Core facility protocol <https://epicore.med.cornell.edu/services.php?option=atacseqdescription#seq> protocols.
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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 |
We trimmed adaptor sequences using CTA (v0.1.2; https://github.com/ParkerLab/cta).
We aligned the trimmed reads to the GRCh38 genome assembly using BWA-MEM v0.7.17-r1194 with the -M option (Li & Durbin 2009).
We called peaks using MACS2 v2.2.7.1 (Zhang et al. 2008) with options “--nomodel --shift -100 --extsize 200 -B --keep-dup all”.
We merged peaks across libraries, and then generated a master peak across libraries.
We quantified read counts per master peak per library and generated the raw read count matrix.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include read counts per genomic peak region per sample
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| Submission date |
Mar 31, 2023 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Shuibing Chen |
| E-mail(s) |
shuibing.chen@gmail.com
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| Phone |
2127465431
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| Organization name |
Weill Cornell Medical College
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| Department |
Surgery
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| Street address |
A 827B, 1300 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE228663 |
Functional interrogation of twenty Type 2 Diabetes-associated genes using isogenic hESC-derived β-like cells [ATAC-Seq] |
| GSE228665 |
Functional interrogation of twenty Type 2 Diabetes-associated genes using isogenic hESC-derived β-like cells |
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| Relations |
| BioSample |
SAMN34031371 |
| SRA |
SRX19839598 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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