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Sample GSM7782759 Query DataSets for GSM7782759
Status Public on Apr 15, 2024
Title TC-32 WT, B, FLI1, rep 2
Sample type SRA
 
Source name Cell line
Organism Homo sapiens
Characteristics tissue: Cell line
cell line: TC-32
cell type: Ewing sarcoma
chip antibody: FLI1 (Abcam, #ab15289)
treatment: none
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)
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
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
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)
 
Submission date Sep 14, 2023
Last update date Apr 15, 2024
Contact name Natasha J Caplen
Organization name National Institutes of Health
Department National Cancer Institute
Lab Functional Genetics
Street address 37 Convent Drive, Bldg. 37, Rm 6128
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
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)
Relations
BioSample SAMN37403535
SRA SRX21783253

Supplementary file Size Download File type/resource
GSM7782759_B_TC32_WT_FLI1_2_vs_TC32_WT_IgG_2.dedup.narrow.peaks.bed.gz 655.0 Kb (ftp)(http) BED
GSM7782759_TC32_WT_FLI1_B_2.dedup.bigwig 64.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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