Sample 5
Protocols: The samples were collected by RNA isolation (Qiagen) from macro-dissected CRC lesions from lung lubes (lobe 1) and corresponding re-isolation of tumor organoids from lung lobe 2 of the same animal. The quantity and quality of the RNA samples were assessed using the following methods. Sample purity and preliminary quantitation were measured using Bioanalyzer 5400 (Agilent Technologies, USA) and it was also used to check the RNA integrity and final quantitation.  For library preparation, the mRNA present in the total RNA sample was isolated with magnetic beads of oligos d(T)25. This method is known as polyA-tailed mRNA enrichment. The library preparation kit used was “Novogene NGS Stranded RNA Library Prep Set (PT044)*” (based on NEBNext® Ultra™ Directional RNA Library Prep Kit). Briefly, mRNA was randomly fragmented and cDNA synthesis proceeds through the use of random hexamers and the reverse transcriptase enzyme. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The resulting products go through purification, end-repair, A-tailing and adapter ligation. The second strand of DNA is degraded via USER enzyme digestion. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 5400 for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount.
ENA first public
2026-07-31
INSDC center name
Division of Molecular and Experimental Surgery, Dept of Surgery, University Medical Center Erlangen and Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg
INSDC status
public
Submitter Id
E-MTAB-15585:Sample 5
age
12-18
broker name
ArrayExpress
cell type
Macrodissected CRC lesion from lung
collection date
not collected
common name
house mouse
developmental stage
adult
genotype
knockout genotype
geographic location (country and/or sea)
not collected
individual
KO_3551
isolate
not applicable
organism part
lung
phenotype
SPARCL1/Sc1 KO
sample name
E-MTAB-15585:Sample 5
scientific_name
Mus musculus
sex
male
strain
C57BL/6NJ