|
| Status |
Public on Nov 23, 2016 |
| Title |
TSC1f/f / p62f/f mice AlbCre positive - Specific deletion of TSC1 and p62 in hepatocytes 1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: Liver
genotype/variation: TSC1f/f / p62f/f mice AlbCre positive - Specific deletion of TSC1 and 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 NextSeq 500 |
| |
|
| Description |
TSC1/p62Dhep-1
|
| 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 |
GPL19057 |
| Series (1) |
| GSE77323 |
p62, upregulated during preneoplasia, induces hepatocellular carcinogenesis by maintaining survival of stressed HCC-initiating cells |
|
| Relations |
| BioSample |
SAMN04446344 |
| SRA |
SRX1550660 |
