|
| Status |
Public on Sep 17, 2013 |
| Title |
HT29 at 0 μM of 5-Aza, biological rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HT29 treated with 0 μM of 5-Aza
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT29
cell type: colon cancer
treatment: control
|
| Treatment protocol |
Triplicate cultures of HT-29 cells were treated in the following three experimental groups: 1.) Vehicle (DMSO) alone or 0 µM 5-Aza-deoxycytidine (5-Aza); 2.) 5 µM 5-Aza; 3.) 10 µM 5-Aza
|
| Growth protocol |
HT-29 colon cancer cells were cultured as monolayers in 150 mm dishes in DMEM with 10% fetal bovine serum, 1% kanamycin, streptomycin-penicillin at 37 CO2 5% .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.
Paired end 100 bp RNA-Seq 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 |
RNA samples from human colon cancer HT29 cell line
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4
mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0)
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Oct 15, 2012 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Xiao Xu |
| E-mail(s) |
slowsmile820@gmail.com
|
| Organization name |
Stony Brook University BME
|
| Street address |
Stony Brook University
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE41586 |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq] |
| GSE41588 |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine |
|
| Relations |
| SRA |
SRX195293 |
| BioSample |
SAMN01765636 |
