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Sample GSM2049240 Query DataSets for GSM2049240
Status Public on Nov 23, 2016
Title p62f/f mice AlbCre positive - Specific deletion of p62 in hepatocytes 1
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics background strain: C57BL/6
tissue: Liver
genotype/variation: p62f/f mice AlbCre positive - Specific deletion of p62 in hepatocytes
Growth protocol p62F/F and Tsc1 F/F mice (Mori et al., 2009; Muller et al., 2013) were backcrossed to C57BL/6 mice for at least 7 generations, and then bred with Alb-Cre transgenic mice (also on C57BL/6 background) to generate p62F/F; Alb-Cre (p62Δhep) and Tsc1F/F; Alb-Cre (Tsc1Δhep)mice, respectively. p62Δhep mice were crossed to Tsc1Δhep and MUP-uPA mice to generate p62F/F; Tsc1F/F; Alb-Cre (Tsc1/p62Δhep) mice and p62Δhep/MUP-uPA transgenic mice, respectively. Genotyping was performed as described (Muller et al., 2013)
Extracted molecule total RNA
Extraction protocol Dissected liver sections were removed, flash frozen on dry ice, and RNA was harvested using Trizol RNA extraction.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 or paired-end sequenced on Illumina HiSeq 2000 using the High output V2 kit (Illumina Inc., San Diego CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description p62ffalbcre1
Data processing Fastq files containing passed-QC reads were uploaded to BaseSpace. Filtering, mapping and abundance measurements (FPKM) were performed with the app RNAexpress (Illumina) within BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files include FPKM raw counts from RNAexpress app.
 
Submission date Jan 28, 2016
Last update date Jul 07, 2022
Contact name Jorge Moscat
E-mail(s) jom4010@med.cornell.edu
Organization name WEILL CORNELL MEDICINE
Department Pathology and Laboratory Medicine
Lab Moscat and Diaz-Meco
Street address 1188 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL13112
Series (1)
GSE77323 p62, upregulated during preneoplasia, induces hepatocellular carcinogenesis by maintaining survival of stressed HCC-initiating cells
Relations
BioSample SAMN04446338
SRA SRX1550654

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

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