|
| Status |
Public on Aug 30, 2017 |
| Title |
RNA-seq CC rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HCA-7 derived CC subline
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human colorectal cancer cell line
culture type: 3D culture
cetuximab sensitivity: sensitive
|
| Growth protocol |
3D collagen cultures were set up using 3 layers of type I collagen. 14-day old colonies from CC and CC-CR embedded in collagen were isolated for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells embedded in collagen were first isolated by TRIzol (Invitrogen) and then purified using miRNeasy Mini Kit (Qiagen).
RNA and small RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: RNAseq_counts.txt
|
| Data processing |
RNA-seq reads were aligned to the hg19 genome assembly using TopHat2
HTSeq was used to count reads in features
Count data was given to edgeR to test for differential expression
small RNA-seq reads were trimmed for adapter sequence of by Cutadpt, then the sequences shorter than 15 bp were excluded from the downstream analysis
Reads were aligned to the human genome hg19 using Bowtie (version 0.12.7)
Mapped reads were annotated and miRNA expressions were quantified using ncPRO-seq (version v1.5.1) based on miRbase v19
Differentially expressed miRNAs were detected by edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Jun 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing Wang |
| Organization name |
Vanderbilt University Medical Center
|
| Street address |
2220 Pierce Avenue
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE82236 |
Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture |
|
| Relations |
| BioSample |
SAMN05202138 |
| SRA |
SRX1818988 |
