|
| Status |
Public on Jun 01, 2020 |
| Title |
HCT116 KMT2C KI1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human colorectal cancer cell line
cell line: HCT116, ATCC CCL-247
genotype/variation: KMT2C knock-in
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were trypsinized and pelleted and total RNA was isolated using the Qiagen RNeasy mini kit with on-column DNAse digestion. The RNA integrity and concentration was determined on a Bioanalyzer 2100 instrument (Agilent) using an RNA 6000 Nano kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
KMT2C KI H-1-1-E11
|
| Data processing |
The reads were aligned to the human genome hg19 assembly (https://genome.ucsc.edu) using Tophat2 software (version 2.0.4)
The FPKM summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each Sample.
|
| |
|
| Submission date |
May 20, 2019 |
| Last update date |
Jun 01, 2020 |
| Contact name |
L. H. |
| Organization name |
Uppsala University
|
| Street address |
Dag Hammarskjölds Väg 20
|
| City |
Uppsala |
| ZIP/Postal code |
751 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE131507 |
Gene regulation by restoration of KMT2C in human colorectal cancer cells HCT116 and RKO |
|
| Relations |
| BioSample |
SAMN11786209 |
| SRA |
SRX5869429 |
