|Public on Jan 14, 2021
|strain: mixed 129/B6
hnf4a status: Positive
agent: Control condition
|Organoids were cultured in 50% L-WRN conditioned media and treated for 72hs with 4-OH-Tamoxifen or vehicle to delete Hnf4a
|TRIzol extraction followed by PureLink RNA Mini Kit purification
TruSeq Stranded RNA kit with Ribo-Zero Gold (Illumina)
|Illumina NovaSeq 6000
|3D cultures derived from murine pancreas. Control condition
|The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).
|Sep 30, 2019
|Last update date
|May 16, 2022
|University of Utah, Huntsman Cancer Institute
|2000 Circle of Hope Drive
|Salt Lake City
|Hnf4a regulated transcriptome in organoid cultures derived from murine pancreas where HNnf4a is deleted after tumor initiation. [organoid]
|Hnf4a regulated transcriptome