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Sample GSM7780180 Query DataSets for GSM7780180
Status Public on Apr 15, 2024
Title TC-32 siFLI1, Input, rep 1
Sample type SRA
 
Source name TC-32
Organism Homo sapiens
Characteristics cell line: TC-32
cell type: Ewing sarcoma
chip antibody: none
sirna: siFLI1
Treatment protocol RNAi-based studies, cells were reverse transfected with 20 nM siRNA complexed with Lipofectamine RNAi-Max (Invitrogen). siNeg (SI03650318, Qiagen) and siFLI1 (s5266, Thermo Fisher Scientific)
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 ChIP assays were performed using SimpleChIP plus Enzymatic Chromatin IP kit (9005S; Cell Signaling Technology, Danvers, MA). Briefly, cells were crosslinked with final concentration of 1% formaldehyde for 10 miunites. After quenching, cell lysis and enyzmatically digested, chromatin was sonicated using Branson SFX250 Digital Sonifier (Branson Ultrasonics) to obtain a fragment size of 200 - 900 bp. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Thermo Fisher Scientific).
ChIP-seq libraries were using SMARTer ThruPlex TAKARA Library Prep kit following manufacturer's instructions. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplited using 8 cycles on the thermocycler.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 2000
 
Data processing ChIP-seq analysis were carried out using center for cancer research bioinfoirmatics resource (CCBR) pipeline (https://github.com/CCBR/Pipeliner/wiki/Pipeline-Documentation - chip-seq)
Sequence reads were triimmed for adaptor sequence using cutadapt v4.4
trimmed reads were aligned to GRCh38/hg38 human genes and Drosophila Melanogaster dm6 genes using BWA mem v.0.7.17
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: narrowPeak (except for Input sample)
 
Submission date Sep 13, 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)
GSE243171 EWSR1::FLI1 fusion oncoproteins’ regulation of ETS1 (ChIP-seq)
GSE243184 ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3
Relations
BioSample SAMN37387571
SRA SRX21773669

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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