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| Status |
Public on Apr 15, 2024 |
| Title |
TC-32 WT, B, H3K9me3, rep 2 |
| Sample type |
SRA |
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| Source name |
Cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Cell line
cell line: TC-32
cell type: Ewing sarcoma
chip antibody: H3K9me3 (Abcam, #ab8898)
treatment: none
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| Growth protocol |
Cells were cultured in RPM1 1640 supplemented with 10% FBS and Plasmocin Prophylactic (Invivogen, San Diego, CA), and grown at 37°C, 5% CO2. We confirmed the identity of cell lines using short tandem repeat (STR) analysis (ATCC) at intervals throughout experimentation, and we monitored for mycoplasma contamination using the MycoAlert Plus system (Lonza, Walkersville, MD)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN (14-1048, EpiCypher) was carried following manufacture's instructions with slight modifications. In brief, 5 x 105 cell/condition were harvested, washed, and bound to activated Concanavalin A (ConA) conjugated paramagnetic beads. The ConA beads–cell complex was resuspended in antibody buffer, and incubated with the appropriate antibody overnight at 4°C. Following incubation, pAG-MNase was added to each CUT&RUN reaction to allow binding to the antibody-labelled chromatin. Targeted chromatin was digested and released by addition of CaCl2 (supplemented with S. cerevisiae spike-in, 29987L; Cell Signal Technology). Fragmented chromatin was purified using CUTANA Purification kit. Purified DNAs were quantified using Qubit fluorometer.
The CUTANA CUT&RUN Library Prep kit (14-1001, EpiCypher) was used for library preparation following manufacturer’s instructions
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
CUT&RUN analysis were carried out using center for cancer research bioinfoirmatics resource (CCBR) pipeline (https://github.com/CCBR/CARLISLE)
Sequence reads were triimmed for adaptor sequence using cutadapt v4.4
trimmed reads were aligned to GRCh38/hg38 human genes and S. cerevisiae genes using Bowtie2
PCR duplicates were removed with the Picard v.2.17.11 SamToFasq (for blacklist read removal) and MarkDuplicates (to remove PCR duplicates)
Peak calling was performed against input control using model-based MACS2 v2.1.1, with the cut-off q-value < 0.02.
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak.bed (except for Input sample)
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| Submission date |
Sep 14, 2023 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Natasha J Caplen |
| Organization name |
National Institutes of Health
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| Department |
National Cancer Institute
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| Lab |
Functional Genetics
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| Street address |
37 Convent Drive, Bldg. 37, Rm 6128
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE243184 |
ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3 |
| GSE243277 |
EWSR1::FLI1 fusion oncoproteins’ regulation of ETS1 (CUT&RUN) |
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| Relations |
| BioSample |
SAMN37403533 |
| SRA |
SRX21783255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7782761_B_TC32_WT_H3K9me3_2_vs_TC32_WT_IgG_2.dedup.broad.peaks.bed.gz |
537.2 Kb |
(ftp)(http) |
BED |
| GSM7782761_TC32_WT_H3K9me3_B_2.dedup.bigwig |
90.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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