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Sample GSM6319674 Query DataSets for GSM6319674
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
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
BioSample SAMN29621348
SRA SRX16106046

Supplementary file Size Download File type/resource 68.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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