|
| Status |
Public on Feb 11, 2019 |
| Title |
APC_hiWNT-1 |
| Sample type |
SRA |
| |
|
| Source name |
colon organoids
|
| Organism |
Homo sapiens |
| Characteristics |
mutation status: APC 2 20AAR
wnt in medium: high
donor: 3
|
| Treatment protocol |
WT and APC KO organoids were seeded in their regular growing medium containing 50%Wnt (high Wnt), 10% Wnt (low Wnt) or 0% Wnt (no Wnt) in the presence of constant concentration (20%) of Rspo for 6 days.
|
| Growth protocol |
Human colon organoids were cultured as described previously (Sato et al., 2011, Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett’s Epithelium. Gastroenterology 141, 1762–1772.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Macherey-Nagel NucleoSpin RNA kit.
The Illumina TruSeq Stranded RNA 50 cycle kit was used for library preparation.
Illumina TruSeq RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
20190114_Stim_Wnt.csv
|
| Data processing |
FastQC Analysis
quality score filtering, poly-A trimming, artifact removal, removal of ‘N’ containing reads and clearing of rRNA contamination using a pipeline provided by the HUSAR platform, DKFZ.
Genomic mapping to Human genome 38 was performed using TopHat2 (version 2.0.14)
The number of reads per gene was determined using HTSeq count and the gencode annotations (release 24)
Unpaired differential analysis was performed using ‘DESeq2’ (version 1.12.4 for samples 1-12 and 1.18.1 for samples 13-42)
Genome_build: Human genome 38
Supplementary_files_format_and_content: .csv
Supplementary_files_format_and_content: processed data files contain readcounts as well as DESeq analysis results
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Henner F. Farin |
| E-mail(s) |
[email protected]
|
| Phone |
+49-69-63395-520
|
| Organization name |
DKTK/Georg-Speyer-Haus
|
| Department |
Institute for Tumor Biology and Experimental Therapy
|
| Lab |
Farin
|
| Street address |
Paul-Ehrlich-Str. 42-44
|
| City |
Frankfurt |
| ZIP/Postal code |
60596 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE125578 |
Human colon organoids reveal distinct physiologic and oncogenic Wnt responses II |
|
| Relations |
| BioSample |
SAMN10805316 |
| SRA |
SRX5286908 |
