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| Status |
Public on Jun 08, 2023 |
| Title |
U2OS ASH1L knockout cells, no UV, biol rep1 |
| Sample type |
SRA |
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| Source name |
U2OS
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| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
genotype: ASH1L knockout
treatment: no UV
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| Treatment protocol |
Cells grown to 80-90% confluency were left untreated (non-UV) or were UV-C irradiated at 20 J/m2 and left to recover for 3h. Cells were treated with DNAse to digest dead or damaged cells, and counted.
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| Growth protocol |
Low glucose DMEM, 10% fetal calf serum. Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA to be tagmented was processed according to the Omni-ATAC-seq protocol by Corces et al. 2017 (doi: 10.1038/nmeth.4396). 50k cells were pelleted, incubated in ATAC-seq lysis buffer, washed, and re-pelleted; nuclei were exposed to the transposition reaction using Tn5 pre-loaded with Illumina adapters.
Purified transposition reactions were PCR-amplified with custom ATAC-seq primers using the minimum number of PCR cycles determined from qPCR. The resulting libraries were purified and size selected with AMPure beads, analyzed on a TapeSttation to verify desired fragment size range, pooled at equimolar concentration, and submitted to the Functional Genomics Center Zurich to be sequenced as 50 bp paired-end reads on a NovaSeq 6000.
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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 |
Raw reads (FASTQ files) were processed based on the ENCODE ATAC-seq pipeline for paired-end reads. Adapters were trimmed (cutadapt v.1.9.1) and trimmed reads aligned (bowtie2 v.2.4.5) to the human reference genome build GCA hg38 excluding chromosome Y but including non-canonical contigs.
Alignments underwent further filtering steps (samtools v.1.7, bedtools v.2.29.2, Picard MarkDuplicates v.2.23.8) to exclude reads that were PCR or optical duplicates, were unmapped or non-primary alignments, failed platform and/or vendor quality checks, had mapping quality scores below 30, or that mapped to ENCODE blacklisted regions, non-canonical chromosomes or mitochondrial DNA.
Filtered alignments were used to generate signal tracks and to call peaks (macs2 v.2.2.7.1 with default parameters), which were used to verify replicability across biological replicates (idr v.2.0.4.2).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak BED files
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| Submission date |
Mar 09, 2023 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Michelle Yancoskie |
| Organization name |
Institute of Veterinary Pharmacology and Toxicology, University of Zurich
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| Department |
Vetsuisse Faculty
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| Lab |
Naegeli Lab
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| Street address |
Winterthurerstr. 260
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| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE227007 |
ASH1L methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair [ATAC-Seq] |
| GSE227009 |
ASH1L-MRG15 methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair |
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| Relations |
| BioSample |
SAMN33699059 |
| SRA |
SRX19611514 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7089929_ATACseq_ALKO_noUV_Rep1.bw |
1.5 Gb |
(ftp)(http) |
BW |
| GSM7089929_ATACseq_ALKO_noUV_Rep1.narrowPeak.gz |
5.0 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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