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| Status |
Public on Mar 04, 2024 |
| Title |
CRL-3038, rep B, NEUROD1 (CUT&RUN) |
| Sample type |
SRA |
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| Source name |
CRL-3038
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| Organism |
Homo sapiens |
| Characteristics |
cell line: CRL-3038
cell type: Atypical Teratoid Rhabdoid Tumor cells
antibody: NEUROD1 (#PA5-47381, Invitrogen)
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| Growth protocol |
Cells were grown according to ATCC protocol for each cell line
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested by removing the media with cells from flasks and centrifuging the media 175G for 7 minutes. Supernatant was removed and cells washed once with PBS followed by centrifugation in 175G for 7 minutes. Cells were counted and 100,000 cells were collected for each reaction.
CUT&RUN was performed using Cell Signaling Technology CUT&RUN assay kit #86652.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
D1_b_3038
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| Data processing |
*library strategy: CUT&RUN
TrimGalore! version 0.6.7 was used to trim adapter reads, discarding reads with a length of less than 25 bp.
Reads were aligned to hg38 using bowtie2 version 2.4.5 and the –dovetail flag.
Duplicated reads were removed using Picard MarkDuplicates version 2.27.1
Regions overlapping with the regions described by Nordin et al. (Nordin et al, 2023) were removed using bedtools intersect version 2.29.1.
Afterwards, the reads were divided in reads with a length shorter or equal to 120 bp and reads longer than 120 bp with samtools view (version 1.8).
MACS3 version 3.0.0.bl was used to call the peaks for both fragment lengths.
Peaks located outside of the canonical chromosomes as well as on chrX or chrY were filtered out.
Peaks that overlapped with peaks in the negative control samples (input DNA) were removed using bedtools intersect version 2.29.1. Positive and negative controls were only filtered for canonical chromosomes.
Assembly: hg38
Supplementary files format and content: narrowPeak files, peaks filtered as described above
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| Submission date |
Feb 06, 2024 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Kirsi Rautajoki |
| E-mail(s) |
kirsi.rautajoki@tuni.fi
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| Organization name |
Tampere university
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| Street address |
Arvo Ylpön katu 34
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| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE197569 |
Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM8065053_D1_b_3038_less_than_120_filtered.narrowPeak.gz |
8.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM8065053_D1_b_3038_more_than_120_filtered.narrowPeak.gz |
10.2 Kb |
(ftp)(http) |
NARROWPEAK |
| Raw data are available in SRA |
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