|
| Status |
Public on Jun 28, 2021 |
| Title |
#9-control-2 |
| Sample type |
SRA |
| |
|
| Source name |
CRC sphere cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Control medium
cell line: #9
|
| Treatment protocol |
Colorectal cancer cells were starved from EGF and b-FGF for 24 hours and then treated with with conditioned medium from subcutaneous (S-ASCs) or visceral (V-ASCs) adipose stromal cells, or control medium, for 48 hours. RNA was then collected using Trizol.
|
| Growth protocol |
Cells were grown in serum-free stem cell medium (SCM) supplemented with EGF and b-FGF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the samples
mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation were measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's protocols. A concentration of 1.6 pM of DNA was used. NextSeq control software 2.0.2 was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17
Raw sequencing reads were aligned to Ensembl release 84 (GRCh38 assembly) using the HISAT2 2.1.0 pipeline
Counts were summarized per gene using the summarizeOverlaps function in the GenomicsAlignment R package
Gene counts were normalized to reads per million and log2 transformed
Genome_build: GRCH38
Supplementary_files_format_and_content: count text files
|
| |
|
| Submission date |
Dec 02, 2020 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Sander Roeland van Hooff |
| Organization name |
AUMC
|
| Department |
Center for Experimental and Molecular Medicine (CEMM),
|
| Lab |
Laboratory for Experimental Oncology and Radiobiology (LEXOR)
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE162561 |
Adipose stromal cell niche reprograms the colorectal cancer stem cell metastatic machinery |
|
| Relations |
| BioSample |
SAMN16983193 |
| SRA |
SRX9621349 |
