|
| Status |
Public on Aug 30, 2016 |
| Title |
HCT116_PBS 2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human colon carcinoma cell line
treatment: PBS
|
| Growth protocol |
HCT116 were maintained in McCoy’s 5A medium and cultured according to standard mammalian tissue culture protocols and sterile technique.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Zymo Direct-Zol RNA mini prep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using KAPA Stranded RNA-Seq Kit with RiboErase (HMR) according to manufacturer's protocol and pooled according to strandard Illumina protocols
Total RNA sequencing with ribosomal RNA depleted
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
alignment using TopHat2
assemble transcriptome using Cufflink
compute FPKM and differential gene expression using Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: tsv containing FPKM and differential gene expression as output by cuffdiff
|
| |
|
| Submission date |
Jan 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter A Jones |
| E-mail(s) |
Peter.Jones@vai.org
|
| Organization name |
Van Andel Research Institute
|
| Department |
Center for Epigenetics
|
| Lab |
Jones Lab
|
| Street address |
333 Bostwick Ave
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE77034 |
Total RNA sequencing of HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells II |
|
| Relations |
| BioSample |
SAMN04430475 |
| SRA |
SRX1538739 |
