|
| Status |
Public on Nov 16, 2024 |
| Title |
NH4Cl plus TGF-β treatment, replicate 1, RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colon cancer cell line
tissue: colon
treatment: NH4Cl + TGF-β
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, RNA was extracted from HCT116 cells under different conditions using the RNeasy Plus Mini kit. RNA quality and concentration were assessed using the Thermo Scientific Nanodrop spectrophotometer before RNA sequencing.
About 1 μg of RNA was used to generate barcoded sequencing libraries. Novogene Corporation performed library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
NT1
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: hg38 for human samples
Supplementary files format and content: tab-delimited text files include fpkm values for each sample from the treated HCT116 cells
|
| |
|
| Submission date |
Nov 11, 2024 |
| Last update date |
Nov 16, 2024 |
| Contact name |
Lopa Mishra |
| E-mail(s) |
[email protected]
|
| Organization name |
The Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory
|
| Street address |
350 Community Drive
|
| City |
Manhasset |
| State/province |
NY |
| ZIP/Postal code |
11030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE281613 |
Microbial metabolite ammonia disrupts CEACAM1-TGF-β signaling to promote colon cancer |
|
| Relations |
| BioSample |
SAMN44676168 |
| SRA |
SRX26686075 |
