|
| Status |
Public on Jul 02, 2023 |
| Title |
HCT116_AFF4 MT_Ser5P+Serum |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: Human colon cancer cells
treatment: Serum induction
chip antibody: Abcam #ab5131
|
| 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 |
genomic DNA |
| Extraction protocol |
For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
The ChIP-seq libraries were prepared with VAHTS Universal DNA Library Prep Kit for Illumina V3
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Clean reads were aligned to the Human genome (UCSC genome, GRCh37/hg19) using Bowtie2 (v2.2.5) with default mode . Peak calling was performed with MACS2.
For AFF1 and AFF4 peaks, associated control samples were used to determine statistical enrichment at a p < 1e-8 and FDR < 0.05. For Pol II peaks, the enrichments were determined at p < 1e-8 and FDR < 0.05.
The ChIP-seq enrichment is displayed as reads per million (RPM). Gene annotations and transcript start site information were from Human genome (UCSC genome, GRCh37/hg19) by R package ChIPseeker.
Assembly: hg19
|
| |
|
| 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 |
GPL24676 |
| Series (2) |
| GSE207810 |
Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [ChIP-seq 2] |
| GSE207813 |
Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation |
|
| Relations |
| BioSample |
SAMN29621348 |
| SRA |
SRX16106046 |
