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| Status |
Public on Nov 24, 2023 |
| Title |
human adipocyte, ATAC-seq, control replicate 2 |
| Sample type |
SRA |
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| Source name |
adipocyte
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| Organism |
Homo sapiens |
| Characteristics |
cell type: adipocyte
treatment: siRNA with nontargeting sequences
genotype: control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear isolation by hypotonic buffer and mechanical lysis followed by centrifugation in 0.3M sucrose buffer
PCR amplification, qPCR to determine additional cycles, and library purification were performed using reagents indicated in the Omni-ATAC protocol (Corces et al., https://doi.org/10.1038/nmeth.4396)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
To process the raw Bcl files obtained from Illumina sequencing, we used the bcl2fastq program to perform conversion and demultiplexing, resulting in fastq files
We used STAR to index to the human reference genome (hg38/GRCh38), which was obtained from UCSC, and then aligned the fastq files
Assembly: hg38
Supplementary files format and content: bedGraph
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| Submission date |
Nov 15, 2023 |
| Last update date |
Nov 24, 2023 |
| Contact name |
Niklas Mejhert |
| E-mail(s) |
niklas.mejhert@ki.se
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| Organization name |
Karolinska Institute
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| Street address |
Blickagången 16
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| City |
Huddinge |
| ZIP/Postal code |
141 52 |
| Country |
Sweden |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE247815 |
Transcriptional determinants of lipid mobilization in human adipocytes [ATAC-seq] |
| GSE247818 |
Transcriptional determinants of lipid mobilization in human adipocytes |
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| Relations |
| BioSample |
SAMN38265325 |
| SRA |
SRX22533384 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7901093_C2_tbp1r1lngNrm100.bedGraph.gz |
62.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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