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Sample GSM6319680 Query DataSets for GSM6319680
Status Public on Jul 02, 2023
Title AFF4 MT-1 +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: AFF4 MT
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
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
BioSample SAMN29621366
SRA SRX16106028

Supplementary file Size Download File type/resource 12.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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