|
| Status |
Public on Apr 28, 2024 |
| Title |
HCT8_1 |
| Sample type |
SRA |
| |
|
| Source name |
colorectal cancer chemo-sensitive cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT8
molecule subtype: non-coding RNAs and mRNAs
phenotype: chemo-sensitive
|
| Growth protocol |
chemo-sensitive and chemo-resistant cells were maintained in RPMI1640 medium supplemented with 10% FBS. All the cells were incubated in a 37 humifidified CO2 chamber equipped with 5%CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including non-coding RNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HCT8_1
|
| Data processing |
Raw reads sequence data (.fastq files) was acquired and filtered.
HISAT2 was used to perform reads alignment.
Ballgown and R were used to analyze differential gene expression and visulation.
DEseq2 was used to produce plots and differential expression tables.
Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Apr 29, 2021 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Qingming Wu |
| Organization name |
wuhan university of science and technology
|
| Street address |
huangjiahu east
|
| City |
wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430065 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE173606 |
Non-coding RNA and mRNA expression profile in multi-drug resistance of colorectal cancer |
|
| Relations |
| BioSample |
SAMN18926665 |
| SRA |
SRX10715482 |
