|
Status |
Public on Jul 28, 2017 |
Title |
NC, 1 |
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 |
SAMN06113536 |
SRA |
SRX2399057 |