|
| Status |
Public on Jul 02, 2023 |
| Title |
WT-2 +Serum RNA-SEQ |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: Human colon cancer cells
treatment: Serum induction
genotype: WT
|
| Treatment protocol |
For serum induction, the complete medium of 60%-70% confluent HCT116 cells was replaced with fresh medium without FBS after washed by PBS for three times. The starved cells were incubated for 40 hours. The incomplete medium was changed with pre-heated complete medium and the cells were incubated for 30 minutes before fixation for ChIP-seq.
|
| Growth protocol |
DMEM (HyClone) supplemented with 10% FBS (Ex-Cell Bio) and 1% Penicillin-Streptomycin (HyClone), at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using the RNeasy kit (Qiagen) according to the instructions of the manufacturer. RNA was treated with DNase I (NEB) and re-purified on the column.
To generate RNA-seq library, total RNA was polyadenylated, fragmented and reversed. Then reversed cDNA was ligated to adapters for sequencing (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
The clean reads were subjected to TopHat and Cufflinks pipeline based on Human genome (UCSC genome, GRCh37/hg19) . The Cuffdiff program within Cufflinks was used to test statistically significant differences of genes expressions between control and AFF4 mutant cells.
Assembly: hg19
Supplementary files format and content: bw
|
| |
|
| Submission date |
Jul 09, 2022 |
| Last update date |
Jul 02, 2023 |
| Contact name |
Xiaoxu Liu |
| E-mail(s) |
liuxiaoxu1010@126.com
|
| Organization name |
Southeast University
|
| Department |
Institute of Life Sciences
|
| Lab |
the Key Laboratory of Developmental Genes and Human Disease
|
| Street address |
2 Sipailou
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210018 |
| Country |
China |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE207812 |
Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [RNA-seq] |
| GSE207813 |
Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation |
|
| Relations |
| BioSample |
SAMN29621367 |
| SRA |
SRX16106027 |
