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Sample GSM2757341 Query DataSets for GSM2757341
Status Public on Feb 13, 2019
Title Control -Ishikawa cells Rep1
Sample type SRA
Source name Ishikawa cancer cells_control
Organism Homo sapiens
Characteristics cell line: Ishikawa
cell type: Established endometrial cancer cell line
Treatment protocol Adipose stromal cells (ASCs) with catalog number AG17929 were obtained from the Coriell Institute (Camden, NJ) . The cells were obtained from fat tissue during subject's abdomen and waist ante-mortem elective cosmetic tumescent liposuction. ASCs were seeded on a matrigel-layered insert of a Boyden chamber. In the bottom well, endometrial cells were seeded for co-culture experiment. Control wells contained the matrigel-layered insert without ASCs. Co-cultures were carried out for three weeks, followed by lysis of endometrial cells for RNA isolation.
Growth protocol Routine cell media for endometrial epithelial cells and adipose stromal cells used, respectively. ASCs were seeded on a matrigel-layered insert of a Boyden chamber during co-culture.
Extracted molecule total RNA
Extraction protocol RNA extracted using Rneasy Plus kit (Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description processed data file:
Data processing Raw fastq is mapped to human genome by TopHat using default parameters
Cufflinks produces assembled transfrags for each replicate
Cuffmerge merges the assembly files
CuffDiff is used to detect differentially expressed genes between each two of cell population
R package CummeRbund is used to to generate the expression plots
Genome_build: HG19
Supplementary_files_format_and_content: em_gene_exp.txt is the list of all differentially expressed genes of ASC + endometrial cells vs Control - endometrial cells. ishi_gene_exp.txt is the list of all differentially expressed genes of ASC+Ishikawa cells vs Control-Ishikawa cells.
Submission date Aug 28, 2017
Last update date May 15, 2019
Contact name Yufan Zhou
Organization name UT health Science Center at San Antonio
Street address 7703 Floyd Curl Dr
City San Antonio
State/province TX
ZIP/Postal code 78229
Country USA
Platform ID GPL11154
Series (1)
GSE103203 Endometrial epithelial cell transcriptome response to co-culture with adipose stromal cells
BioSample SAMN07568605
SRA SRX3141701

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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