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Series GSE87563 Query DataSets for GSE87563
Status Public on Nov 02, 2017
Title RNAseq of normal associate fibroblasts after treatment with large oncosomes from prostate cancer cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary In order to detect the alteration in the transcriptomic profile of fibroblasts exposed to the large oncosomes and detemine the transcription factor responsible for those alteration we performed whole RNA sequncing with and without treatment with large oncosomes. Deep sequencing data were generated in duplicate using a NextSeq 500 platform (Illumina) using 75 single-end sequencing obtaining about 20 million reads per sample. Raw reads obtained from RNA-Seq were aligned to the custom human GRCh38 transcriptome reference ( using Bowtie (version 1.1.1) and RSEM (version 1.2.20) with default parameters. of 207 differentially expressed genes were identified between control and large oncosomes treated fibroblasts and master regulator analysis performed using TF-target interaction information collected from public databases revealed MYC and SPI1 as main transcription factors responsible for these alterations.
Overall design mRNA profile in 2 different treatment conditions fibroblasts ctrl and fibroblasts treated with large oncosomes
Contributor(s) Minciacchi VR, You S, Di Vizio D
Citation(s) 28202510
Submission date Oct 03, 2016
Last update date May 15, 2019
Contact name Sungyong You
Organization name Cedars-Sinai Medical Center
Street address 8700 Beverly Blvd
City Los Angeles
ZIP/Postal code 90048
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (4)
GSM2333829 NAF control-1
GSM2333830 NAF control-2
GSM2333831 NAF+LO(22RV1)-1
BioProject PRJNA345199
SRA SRP090756

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Supplementary file Size Download File type/resource
GSE87563_RAW.tar 1.7 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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