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| Status |
Public on Nov 24, 2023 |
| Title |
human adipocyte, H3K9me3 CUT&Tag, ZNF189 depletion replicate 1 |
| Sample type |
SRA |
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| Source name |
adipocyte
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| Organism |
Homo sapiens |
| Characteristics |
cell type: adipocyte
genotype: ZNF189 depletion
antibody: H3K9me3
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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. CUT&Tag was then performed following the protocol from Kaya-Okur et al. (https://doi.org/10.1038/s41596-020-0373-x).
IDT primers (Illumina, 20027213) and PCR enzyme mix (NEB, M0541S) were used for library preparation, and AMPure beads (Beckman Coulter, A63881) were used for PCR cleanup
CUT&Tag with DNA-sequencing
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Sequencing files (FASTQ) were aligned to the GRCh38/hg38 version of the human reference genome, using Bowtie2 on the Galaxy platform
Peak calling was done using MACS2
Assembly: hg38
Supplementary files format and content: bedGraph, bed
Library strategy: CUT&Tag
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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) |
| GSE247817 |
Transcriptional determinants of lipid mobilization in human adipocytes [CUT&Tag] |
| GSE247818 |
Transcriptional determinants of lipid mobilization in human adipocytes |
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| Relations |
| BioSample |
SAMN38266072 |
| SRA |
SRX22533963 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7901228_ZNFKD_H3K9me3_rp1.bed.gz |
1021.6 Kb |
(ftp)(http) |
BED |
| GSM7901228_ZNFKD_H3K9me3_rp1_CUTtag.UCSC.bedGraph.gz |
67.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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