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Sample GSM7780321 Query DataSets for GSM7780321
Status Public on Apr 15, 2024
Title TC-32 siNEG, rep 1
Sample type SRA
 
Source name TC-32
Organism Homo sapiens
Characteristics cell line: TC-32
cell type: Ewing sarcoma
sirna: siNeg
Treatment protocol RNAi-based studies, cells were reverse transfected with 20 nM siRNA complexed with Lipofectamine RNAi-Max (Invitrogen). siNeg (SI03650318, Qiagen), siFLI1 (s5266, Thermo Fisher Scientific) and siERG (s4812, Thermo Fisher Scientific)
Growth protocol Cells were cultured in RPM1 1640 (TC-32, TC71, ES-5838) or DMEM media (A673) (Thermo Fisher Scientific, Waltham, MA) 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 total RNA
Extraction protocol Total RNA was extracted using Maxwell 16 LEV simply RNA kits (Promega)
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep Ligation kit following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description siNeg_1
Data processing RNA-seq analysis were carried out using center for cancer research bioinfoirmatics resource (CCBR) pipeline (https://github.com/CCBR/Pipeliner/wiki/Pipeline-Documentation - rna-seq)
Sequence reads were triimmed for adaptor sequence using cutadapt v4.4
Trimmed reads were mapped to the GRCh38/hg38 human genome using STAR v.2.7.3 with standard parameters.
FeatureCounts in the Subread v.2.0.3 package (Liao et al., 2013) was used to summarize gene level reads by counting reads that overlapped the GRCh38/hg38 annotated gene exons.
Gene counts were normalized and used to quantify differential gene expression between control and experimental conditions using limma v.3.38.3.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each samples
 
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)
GSE243183 EWSR1::FLI1 fusion oncoproteins’ regulation of ETS1 (RNA-seq)
GSE243184 ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3
Relations
BioSample SAMN37390499
SRA SRX21775230

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

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