 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 11, 2023 |
| Title |
LSD1_HCT116_WT_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal cancer cell line
genotype: wild-type
|
| Growth protocol |
Human colorectal carcinoma HCT116 cell line was cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin (Procell, Wuhan, China, CM-0096). Human colonic epithelial cell line NCM460 was cultured in DMEM medium (Gibco, NY, USA, C11965500BT) supplemented with 10% FBS (Lonsera, S712-012S) and 100 U/mL penicillin/streptomycin (Gibco, USA, 15140122).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were used to extract the total RNA using the Total RNA Extraction Kit (Omega).
In brief, a total of 1ug RNA per sample was used as input material, and then sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. All libraries were constructed using the TruSeq SBS v3-HS kit before sequencing to investigate the global transcriptome of the control group using Illumina HiSeq 2500 (Illumina, Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Filter sequencing adapters and low-quality reads using Trimmomatic (v0.39).
The clean reads were mapping to the GENCODE reference trancriptome (GRCh38 v36 release) and quantifying with Salmon (v1.4.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Jan 10, 2023 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Cao Qiang |
| E-mail(s) |
csqasds@gmail.com
|
| Organization name |
Sun Yat-sen University
|
| Department |
School of Medicine
|
| Street address |
No. 66 Gongchang Road, Guangming District, Shenzhen
|
| City |
Shenzhen |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE222521 |
Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications[RNA-seq] |
| GSE222612 |
Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications |
|
| Relations |
| BioSample |
SAMN32658387 |
| SRA |
SRX18988327 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
