|
| Status |
Public on Nov 12, 2019 |
| Title |
SW480-SCR-3 |
| Sample type |
SRA |
| |
|
| Source name |
SW480
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colorectal cancer cell line
cell line: SW480
transfection: SCR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent and isolated according to the manufacturer's instructions.
Illumina TruSeq RNA Exome Sample Prep Kit (Cat#FC-122-1001) was used with 1μg of total RNA for the construction of sequencing libraries. More specifically, total RNA libraries were prepared with TruSeq RNA Library Prep for Enrichment kit (Cat. No. 20020189) and transcriptome enrichment was performed with TruSeq RNA Enrichment kit (Cat. No. 20020490),
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina Nextseq 550 reas quality was checked for each sample using FastQC v0.11.5.
Pseudoalignment and transcript quantification are done with kallisto 0.44.0.
Normalization of read counts for each gene and RNA abundance analysis were done in R (DESeq2_1.24.0).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 normalized counts for each sample .
|
| |
|
| Submission date |
Nov 11, 2019 |
| Last update date |
Nov 13, 2019 |
| Contact name |
Samantha Perakis |
| E-mail(s) |
[email protected]
|
| Organization name |
Diagnostic & Research Institute of Human Genetics; MedUniGraz
|
| Street address |
Neue Stiftingtalstraße 6
|
| City |
Graz |
| ZIP/Postal code |
8010 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE140198 |
RNA-seq analysis of colorectal cancer cell lines HT29-POLR1D-silenced and SW480-POLR1D-silenced |
|
| Relations |
| BioSample |
SAMN13256461 |
| SRA |
SRX7124430 |
