|
| Status |
Public on Jul 28, 2017 |
| Title |
NC, 3 |
| Sample type |
SRA |
| |
|
| Source name |
HT-29 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human colorectal cancer cells
agent: none
|
| Treatment protocol |
The cultured F.nucleatum was used to treat the HT29 colorectal cancer cells, while the blank culture medium-teated HT29 CRC cells was used as negative controls.
|
| Growth protocol |
The human colorectal cancer cells HT-29 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA of HT-29 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Reads were mapped to the human genome (hg19) using TopHat v2.0.11 (http://tophat.cbcb.umd.edu) with the following default options with a TopHat transcript index built from Ensembl_GRCh37. Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file.
Genome_build: Ensembl_GRCh37(hg19)
Supplementary_files_format_and_content: count
|
| |
|
| Submission date |
Dec 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Haoyan Chen |
| Organization name |
Renji Hospital
|
| Street address |
145 Shandong Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE90944 |
RNA-seq in HT-29 colorectal cancer cells after F. nucleatum treatment |
|
| Relations |
| BioSample |
SAMN06113534 |
| SRA |
SRX2399060 |
