|
| Status |
Public on Feb 13, 2019 |
| Title |
ASC + Ishikawa cells Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Ishikawa cancer cells_cultured_with_ASC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Ishikawa
cell type: Established endometrial cancer cell line
|
| Biomaterial provider |
Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AG17929&Product=CC
|
| 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:
ishi_gene_exp.txt
|
| 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 |
|
| Relations |
| BioSample |
SAMN07568607 |
| SRA |
SRX3141703 |
