|
| Status |
Public on Oct 11, 2023 |
| Title |
reverse_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon
cell line: HCT116
cell type: Colorectal cancer
genotype: reverse
treatment: +dox
|
| Treatment protocol |
Cells were stimulated with 1ug/ul Doxycycline 48 prior to RNA extraction
|
| Growth protocol |
HCT116 cells were cultured under standard conditions in DMEM media with 10% FCS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using QIAGEN RNeasy mini spin columns
Libraries were constructed using the TruSeq RNA stranded polyA kit according to manufacturers instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Read QC (FastQC)
Sequence trimming (TrimGalore)
rRNA removal (SortMeRNA)
Mapping and read-group annotation (STAR)
Alignment-QC (RSeQC, Preseq)
PCR duplicate detection (Sambamba MarkDup)
Gene-expression/biotype quantification ( featureCounts)
Gene-expression normalization ( edgeR, DESeq2)
Transcript quantification (Salmon)
Variant calling (GATK4)
QC report (MultiQC, CustomQC)
Assembly: Human - GRCh38
Supplementary files format and content: Tab delimited matrix with DeSeq2 feature counts
|
| |
|
| Submission date |
Jul 17, 2022 |
| Last update date |
Oct 11, 2023 |
| Contact name |
Jurian Schuijers |
| E-mail(s) |
j.schuijers@umcutrecht.nl
|
| Organization name |
University Medical Center Utrecht
|
| Department |
Center for Molecular Medicine
|
| Street address |
Universiteitsweg 100
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE208345 |
Effect of condensate perturbing CR3 peptide on HCT116 gene expression |
|
| Relations |
| BioSample |
SAMN29786904 |
| SRA |
SRX16311362 |
