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Sample GSM4100939 Query DataSets for GSM4100939
Status Public on Jan 14, 2021
Title 15143X8 SC1956-4-OH-Tam
Sample type SRA
Source name pancreas
Organism Mus musculus
Characteristics strain: mixed 129/B6
hnf4a status: Negative
agent: 4-OH-Tamoxifen treated culture
Growth protocol Organoids were cultured in 50% L-WRN conditioned media and treated for 72hs with 4-OH-Tamoxifen or vehicle to delete Hnf4a
Extracted molecule total RNA
Extraction protocol TRIzol extraction followed by PureLink RNA Mini Kit purification
TruSeq Stranded RNA kit with Ribo-Zero Gold (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 3D cultures derived from murine pancreas. 4-OH-Tamoxifen treated culture
Data processing 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).
Submission date Sep 30, 2019
Last update date May 16, 2022
Contact name Eric Snyder
Organization name University of Utah, Huntsman Cancer Institute
Department Pathology
Street address 2000 Circle of Hope Drive
City Salt Lake City
State/province UT
ZIP/Postal code 84103
Country USA
Platform ID GPL24247
Series (2)
GSE138142 Hnf4a regulated transcriptome in organoid cultures derived from murine pancreas where HNnf4a is deleted after tumor initiation. [organoid]
GSE138145 Hnf4a regulated transcriptome
BioSample SAMN12871795
SRA SRX6922451

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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