VBPNR_2_2
Mus musculus
Protocols: Organoids were grown in cell culture dish in BME gel and growth medium. Organoids with BME gel and growth medium were taken from the culture dish and centrifuged. Supernatant was aspirated and organoids were transfered to a separate tube for nucleic acid extraction.  RNA was extracted from tumor and organoid samples using the RNeasy Mini Kit following the manufacturer's protocol (Qiagen, #74106). RNA quantity and integrity were evaluated on an Agilent Bioanalyzer using the Agilent RNA Kit (#5067-1513). Whole-transcriptome sequencing libraries were prepared using a modified SMART-seq2-based workflow. Reverse transcription was carried out using 1 µM template-switching oligo (IDT), 1 mM dithiothreitol (Takara Bio Clontech, #707265ML), 1 U/µl RNase inhibitor (Promega, #N2615), Maxima H Minus Reverse Transcriptase (Thermo Fisher/Life Technologies, #EP0753), and 1× Maxima H Minus Reverse Transcriptase buffer. The resulting cDNA was tagmented and further processed for sequencing library generation using the Nextera XT DNA Library Preparation Kit (Illumina, #FC-121-1030).
ENA first public
2026-06-26
INSDC center name
German Cancer Research Center, Heidelberg, Germany
INSDC status
public
Submitter Id
E-MTAB-17082:VBPNR_2_2
age
minimum 8
broker name
ArrayExpress
collection date
not collected
common name
house mouse
developmental stage
adult
genotype
VBPNR
geographic location (country and/or sea)
not collected
individual
VBPN_mouse
isolate
not applicable
organism part
colon
sample name
E-MTAB-17082:VBPNR_2_2
scientific_name
Mus musculus
sex
unknown