|
| Status |
Public on Nov 14, 2024 |
| Title |
F1.AKPN.SIP.a2 |
| Sample type |
SRA |
| |
|
| Source name |
Small Intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Small Intestine
cell type: In Vitro organoids
genotype: AKPN
batch: 1
|
| Growth protocol |
Intestinal organoids were maintained in Advanced DMEM/F12 (ADF) media supplemented with penicillin (100ug/ml), 5ml 200 mM Glutamax, 5ml 10mM Hepes, B27 supplement (Invitrogen) and N2 supplement (Invitrogen). In addition to ADF we also use 50ng/ml recombinant Mouse EGF (Tebu-BIO), mouse Noggin-FC supernatant (~100ng/ml) and R-Spondin-FC supernatant(~ 500ng/ml). Cultures were maintained at 37 degrees celsius and checked monthly for mycoplasma contamination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Bioke Nucleospin RNA isolation kit (Bioke) according to the manufacturer’s protocol. DNA degradation was performed using Bioke RNase-Free DNase. We assessed the quality of our RNA samples using Agelent 2100 Bioanalyzer (Agilent Technologies) and only high quality RNA samples were selected based on RIN value.
The organoid RNAseq libraries were prepared using KAPA mRNA HyperPrep (Roche) following the manufacturer’s protocol. They were barcoded, quantified using the Qubit DNA HS kit from Thermofisher and Tapestation 4200 from Agilent, pooled and multiplex sequencing was performed on the Illumina Novaseq6000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
F1.AKPN.SIP.a2
RKW101BSIP
|
| Data processing |
The quality of raw data was assessed using FastQC (v.0.11.9) and MultiQC (v.1.9) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v1.18).
STAR (v.2.7.4.a) was applied to align sequences to the mouse genome (GRCm38) and to determine counts per gene.
After log2 transformation and quantile normalization, data were visualized using PCA plots to assess the quality of data after alignment and possible batch effects.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample
|
| |
|
| Submission date |
Jan 20, 2023 |
| Last update date |
Nov 14, 2024 |
| Contact name |
Arezo Torang |
| E-mail(s) |
a.torang@amsterdamumc.nl
|
| Organization name |
Amsterdam UMC
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE223323 |
Enterocyte like differentiation defines metabolic gene signatures of CMS3 colorectal cancers and provides therapeutic vulnerability |
|
| Relations |
| BioSample |
SAMN32809880 |
| SRA |
SRX19099119 |
