|
| Status |
Public on Oct 15, 2020 |
| Title |
donor1_control_xeno_invivo-3 |
| Sample type |
SRA |
| |
|
| Source name |
human xenograft
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
condition: control
cell type: bulk tumor
status: in vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Macherey-Nagel NucleoSpin RNA kit.
2 ug of RNA was used for library synthesis using HiSeq SBS Kit v5 50 cycle kit. For Sample 13-18, 25 ng of RNA was used for library synthesis using SMART-seq v4 ultra low input kit. All samples were sequenced by HiSeq 2000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
donor#1 control human organoids injected subcutaneously in rag1 mice
For sample 25-30, human primary crc tumor organoids were established as reported before (Sato 2011) Control organoids or organoids express mouse Sfrp1 were injected subcutaneously in Rag1 mice for about 8 weeks. Whole tumors were then digsted and RNA of the whole tumor was extracted and subjected to RNAseq.
20200715_humanXeno_stroma_only_Sfrp1.txt
Sample 27
|
| Data processing |
FastQC Analysis
For human xenografts (samples 25-30), "Xenome" software (version 1.0.0) was used to deconvolute human and mouse reads from xenograft bulk RNA sequencing data and only host reads "mouse" were used for subsequent steps.
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 mm10 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)
differential analysis was performed using ‘DESeq2’ (version 1.12.4) for samples 25-30, "Limma" package (version: 3.9) was used for performing differntial analysis.
Genome_build: mm10
Supplementary_files_format_and_content: .txt. processed data files contain readcounts as well as DESeq analysis results
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Oct 15, 2020 |
| Contact name |
Mohammed Hossameldin Mosa |
| Organization name |
Frankfurt Cancer Institute/Georg-Speyer-Haus
|
| Lab |
Human Organoids Biobank
|
| Street address |
Paul-Ehrlich Str. 42-44
|
| City |
Frankfurt am Main |
| State/province |
Hessen |
| ZIP/Postal code |
60596 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16512 |
| Series (1) |
| GSE155364 |
A Wnt-induced phenotypic switch in cancer-associated fibroblasts inhibits EMT in colorectal cancer |
|
| Relations |
| BioSample |
SAMN15667664 |
| SRA |
SRX8844224 |
