2025-07-18
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114412605
External Id
1Department of Surgery, UT Southwestern Medical Center, Dallas, Texas 75390, USA
INSDC center name
2023-09-22T14:27:35Z
INSDC last update
public
INSDC status
ERS16401269
SRA accession
E-MTAB-13371:Sample 11
Submitter Id
8
week
age
ArrayExpress
broker name
not collected
collection date
house mouse
common name
Protocols: we used high-throughput next-generation sequencing technology to compare transcriptomics between each samples that were harvested from the mouse xenografts Total RNA was extracted and purified from cultured cells using the RNeasy Plus Mini Kit (QIAGEN, 74136) according to the manufacturer’s instructions. An Agilent 2100 Bioanalyzer system and RNA Nano chip kit (5067-1511) were used for RNA quality measurement. An Illumina TruSeq Stranded mRNA Library prep kit (20020594) was used to generate the RNA libraries. The first step in the workflow involved purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers. Second-strand cDNA synthesis followed, using DNA polymerase I and RNase H. The cDNA fragments then went through an end repair process, the addition of a single “A” base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final cDNA library. AMPure XP beads (Beckman Coulter, A63881) purifications were performed two times before the assessment took place. The library quantity was measured using a picogreen method. A Quant-iT PicoGreen dsDNA Assay kit (Invitrogen, P7589) and PerkinElmer plate reader (PerkinElmer Victor X3, 2030 Multilabel Reader) were used in the assessment. The library quality was verified on an Agilent 2100 Bioanalyzer instrument using an Agilent DNA 1000 kit (5067-1504). All libraries must have met the QC requirements before we moved forward with sequencing.
description
wild type genotype
genotype
not collected
geographic location (country and/or sea)
KPC cells injected subcutaneously to generate tumors
growth condition
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
xenograft-derived tumor
organism part
Mus musculus
scientific_name
female
sex
C56B6
strain
Sample 11
title
KPCP1 xenograft
xenograft