|
| Status |
Public on Sep 13, 2023 |
| Title |
CRC organoid, asparaginase |
| Sample type |
SRA |
| |
|
| Source name |
organoid
|
| Organism |
Mus musculus |
| Characteristics |
tissue: organoid
cell line: Rspo3 fusion positive CRC organoids
cell type: colorectal cancer cells
treatment: vehicle
|
| Treatment protocol |
On day 1, 100 U/L asparaginase or vehicle (PBS) were added to organoids, which were cultured in basal medium without growth factor supplementation.
Subsequently, organoids were split every 48h and treatment pressure was maintained by continuously adding asparaginase or vehicle to achieve outgrowth of resistant organoids.
On day 13, RNA was isolated for sequencing.
|
| Growth protocol |
Organoids were resuspended in Matrigel composed of 25% advanced DMEM/F12 (Gibco) and 75% Matrigel (Corning)
After the Matrigel polymerized, organoids were cultured in complete small-intestinal organoid growth medium consisting of organoid basal medium supplemented with murine Noggin (50 ng/mL), murine EGF (R&D Systems, 50 ng/mL), and human RSPO1 (R&D Systems).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated at indicated time points using the RNeasy kit (Qiagen) according to the manufacturer’s protocols.
Library preparation was performed by eurofins genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Initial quality control of transcriptomics data was performed using FastQC version 0.11.9
“filter by tile” function of BBMap was used to discard low-quality reads
trimming with trimmomatic version 0.39 using specifications: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True HEADCROP:14 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
preprocessed reads were mapped using kallisto version 0.46.1 with a transcriptome index of Mus musculus GRCm38.p6
Assembly: Mus musculus NCBI:GCA_000001635.8
Supplementary files format and content: table in tab-separated values formating including kallisto estcount and TPM, as well as log2FC for the samples
|
| |
|
| Submission date |
Jun 13, 2023 |
| Last update date |
Sep 25, 2023 |
| Contact name |
Laura Hinze |
| E-mail(s) |
hinze.laura@mh-hannover.de
|
| Organization name |
Hannover Medical School
|
| Street address |
Carl-Neuberg-Straße 1
|
| City |
Hannover |
| State/province |
Niedersachsen |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE234801 |
Effect of asparagine depletion on Rspo3 fusion positive colorectal cancer cell organoid transcriptomes |
| GSE234803 |
Amino acid availability is a crucial factor for survivability of cancer cells |
|
| Relations |
| BioSample |
SAMN35724828 |
| SRA |
SRX20670037 |
