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Status |
Public on Apr 15, 2024 |
Title |
TC-32 siNEG, rep 1 |
Sample type |
SRA |
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Source name |
TC-32
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Organism |
Homo sapiens |
Characteristics |
cell line: TC-32 cell type: Ewing sarcoma sirna: siNeg
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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)
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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)
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
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Description |
siNeg_1
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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
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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) |
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 |
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Relations |
BioSample |
SAMN37390499 |
SRA |
SRX21775230 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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