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Series GSE134375 Query DataSets for GSE134375
Status Public on Jul 17, 2019
Title Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Inhibiting STAT3 signaling reduces tumor progression, metastases and chemoresistance, however the precise molecular mechanism has not been fully delineated in ovarian cancer. Methods: In this study, we generated STAT3 knockout (KO) ovarian cancer cell lines. Effect of STAT3 KO on cell proliferation, migration and spheroid formation was assessed in vitro and effect on in vivo tumor growth was tested using several tumor xenograft models. We used multi-omic genome-wide profiling to identify multi-level (Bru-Seq, RNA-Seq, and MS Proteomic) expression signatures of STAT3 KO ovarian cancer cells.
Overall design Cells were lysed with TRIzol® Reagent (ThermoFisher Scientific) at room temperature. RNA was further purified with DirectZol kit (Zymo Research, Irvine, CA). RNA quality was assessed using the TapeStation (Agilent Technologies, Santa Clara, CA). Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared with TruSeq Stranded mRNA Library Prep (Illumina) per the supplier’s protocol with 1g of RNA and 12 cycles of PCR amplification. Libraries were checked for size on the TapeStation and quantified using the Kapa Biosystems library quantification kit (Illumina). The libraries were barcoded, pooled and sequenced on the HiSeq 4000 at the University of Michigan DNA Sequencing Core using 50bp single-end 50bp (OVCAR3 and OVCAR8) and paired-end 50bp (SKOV3) sequencing. Reads were mapped to GRCh38 using STAR v2.5.2 [69] and gene quantifications were calculated using Cufflinks v2.2.1 [70] to quantify refGene annotations. Gene read counts calculated using featureCounts [71] v1.6.1 were used to evaluate differential expression using DESeq2 v1.18.1 [72]. For OVCAR3 and OVCAR8, genes were considered significantly differentially expressed with a mean FPKM > 0.5 and absolute fold change > 1.5 and FDR adjusted p-value < 0.05. For SKOV3, genes were considered significantly differentially expressed with mean FPKM > 0.5 and absolute log2 fold change > 1.5 and FDR adjusted p-value < 0.05. All gene readouts where required to be mappable to both an HGNC and Entrez identifier to be considered for gene set enrichment analyses.
Please note: Majority of paper figures are based on OVCAR3=OV3,OVCAR8=OV8, and SKOV3 with CAS9 control.
Contributor(s) Neamati N, Lu T, Bankhead A
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Submission date Jul 16, 2019
Last update date Jul 19, 2019
Contact name Armand Bankhead
Organization name University of Michigan
Department Biostatistics
Street address 1415 Washington Heights
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (24)
GSM3944441 SKOV3-WT-1
GSM3944442 SKOV3-WT-2
GSM3944443 SKOV3-WT-3
BioProject PRJNA554895
SRA SRP214924

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE134375_RAW.tar 10.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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