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| Status |
Public on Jun 25, 2024 |
| Title |
WS234 H3K4me3 Rep 1 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Skeletal muscle
cell line: WS234
cell type: muscle progenitor
genotype: Wildtype
treatment: proliferative conditions
antibody: Rabbit anti-Histone H3 (tri methyl K4) abcam ab8580
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| Treatment protocol |
CUT&Tag experiements were performed on 75,000 cells
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| Growth protocol |
WS234 cells were cultured on 0.1% gelatin-coated plates in LHNC media (4:1 DMEM:Medium 199, 15% BGS (v/v), 0.03 ug/ml Zinc Sulfate, 1.4 ug/ml vitamin B12, 0.055 ug/ml dexamethasone, 2.5 ng/ml HGF, 10 ng/ml FGF, 0.6X penicillin/streptomycin, 20 mM HEPES (pH 7.4)). Cells were collected under proliferating conditions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tn5-PA tagmented DNA was treated with proteinase K, extracted with phenol chloroform, and precipitated with ethanol.
Extracted DNA was amplified with barcoded i5 and i7 compatible primers
CUT&Tag libraries were sequenced on the Illumina NextSeq 6000 instrument
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Nextera adapters were trimmed from sequenced reads with Cutadapt 4.4 (Python 3.9.6).
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.4.4 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Duplicates, non-uniquely aligned reads were marked with Picard (3.1.1) and filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads with greater than 10 Q-score.
Genome coverage was calculated using bamCoverage v3.5.3 (deepTools v3.5.3) with the following parameters: --effectiveGenomeSize 2467481108 --binSize 1 --normalizeUsing 'RPKM' --ignoreForNormalization 'chrM' --extendReads.
Peaks were called using MACS (3.0.0) with parameters: -f BAMPE -g 2805636331 -q 1e-5.
Assembly: GRCh38_hg38
Supplementary files format and content: bigWig, bigBed
Library strategy: CUT&Tag
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| Submission date |
May 13, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Jeffrey Dilworth |
| E-mail(s) |
fdilworth@wisc.edu
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| Phone |
6082653758
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| Organization name |
University of Wisconsin
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| Street address |
1111 Highland Ave
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| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE267354 |
Enrichment of various epigenetic histone marks in human myoblasts |
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| Relations |
| BioSample |
SAMN41385122 |
| SRA |
SRX24539709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8264437_JD-SH-WISC-H3K4me3-1_RPKM.bw |
97.7 Mb |
(ftp)(http) |
BW |
| GSM8264437_JD-SH-WISC-H3K4me3-1_peaks.narrowPeak.bed_MACS.bb |
337.0 Kb |
(ftp)(http) |
BB |
SRA Run Selector |
| Raw data are available in SRA |
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