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| Status |
Public on Nov 24, 2023 |
| Title |
Human adipocyte, IgG ChIP |
| Sample type |
SRA |
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| Source name |
adipocyte
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| Organism |
Homo sapiens |
| Characteristics |
cell type: adipocyte
chip antibody: normal rabbit IgG polyclonal antibody - Millipore Sigma, 12-370
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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. Isolated nuclei were crosslinked in 1% formaldehyde for 10 minutes, quenched with 137mM glycine for 5 minutes, lysed in denaturing buffer (50 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 150 mM NaCl and Protease Inhibitor Cocktail) and sonicated by 30x30 second cycles in the Bioruptor Pico (Diagenode B01060010).
NEBNext® UltraTM Library Prep Kit for Illumina with 12 cycles using dual index oligos for Illumina (New England Biolabs, E6440S)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
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| Data processing |
The nf-core/chipseq pipeline (https://zenodo.org/record/7139814#.ZC3eMXtByUk (58)) was used to perform the Quality control, mapping and peak calling of the ChIP-seq analysis in conjunction with Docker
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
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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) |
| GSE247814 |
Transcriptional determinants of lipid mobilization in human adipocytes [ChIP-seq] |
| GSE247818 |
Transcriptional determinants of lipid mobilization in human adipocytes |
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| Relations |
| BioSample |
SAMN38264838 |
| SRA |
SRX22532979 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7901089_IgG_R1.bigWig |
246.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM7901089_IgG_R1_peaks.narrowPeak.gz |
19.9 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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