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| Status |
Public on Nov 23, 2016 |
| Title |
p62f/f mice Cre negative - WT 1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: Liver
genotype/variation: p62f/f mice Cre negative - WT
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| 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)
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
p62ff1
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| 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.
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| Submission date |
Jan 28, 2016 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Jorge Moscat |
| E-mail(s) |
jom4010@med.cornell.edu
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| Organization name |
WEILL CORNELL MEDICINE
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| Department |
Pathology and Laboratory Medicine
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| Lab |
Moscat and Diaz-Meco
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| Street address |
1188 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE77323 |
p62, upregulated during preneoplasia, induces hepatocellular carcinogenesis by maintaining survival of stressed HCC-initiating cells |
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| Relations |
| BioSample |
SAMN04446335 |
| SRA |
SRX1550651 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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