|
| Status |
Public on Aug 20, 2019 |
| Title |
UBC.CreER_VHL2B.lox-lox_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
UBC.CreER_VHL2B.lox-lox, retina
|
| Organism |
Mus musculus |
| Characteristics |
experimental group: UBC.CreER_VHL2B.lox-lox
tissue: retina
genotype: VHL-/VHL2B
|
| Treatment protocol |
Pups were intraperitoneally (i.p.) injected each day with 1 mg/ml of tamoxifen (Fisher) from postnatal day 1 (P1) to 3. Retinal harvest occurred on P7. Cre-recombination activity following tamoxifen exposure was verified using a Cre reporter mouse line.
|
| Growth protocol |
Mice expressing Cre-recombinase ubiquitously [Tg(UBC-cre/ERT2), denoted in the current study as UBCCreER/+ with CreER negative animals denoted as UBC+/+] were bred with Vhlfl/fl mice. Vhl2B/+ mice were also crossed with Vhlfl/fl mice to yield Vhlfl/2B offspring. Breeding UBCCreER/+; Vhlfl/fl males with Vhlfl/2B females produced experimental litters with genotypes: (1 and 2) non-mutant littermate control -- UBC+/+; Vhlfl/fl, (littermate control with 1 WT Vhl allele and 1 2B mutant Vhl allele -- UBC+/+; Vhlfl/2B , (3) conditional Vhl null -- UBCCreER/+; Vhlfl/fl, (4) conditional Vhl type 2B mutant -- UBCCreER/+; Vhlfl/2B. Where possible, animals were distributed across sex to avoid the introduction of sex biasing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Following induction of the genetic mutations as described above, retinas were collected from P7 mice and immediately digested in TRIzol to extract mRNA transcripts (n=2 for each genotype). RNA was further isolated with 1-Bromo-3-chloropropane (Sigma) and ethanol and purified with an RNeasy Plus Kit (Qiagen). Using an Agilent Bioanlayzer, the Virginia Tech Biocomplexity Institute ensured the isolated mRNA was of a sufficiently high quality for RNA sequencing.
Eight samples (4 genotypes x 2 replicates per genotype) were sent to GeneWiz (South Plainfield, NJ) for additional quality assessment, library generation, and sequencing on an Illumina HiSeq with a 2x150 configuration.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Sample.12-1_S8
|
| Data processing |
Sequencing reads were aligned against the Mouse GENCODE genome, Version M14 (January 2017 freeze, GRCm38, Ensembl 89) using the Spliced Transcripts Alignment to a Reference (STAR) software (PMID: 26187010 and 23104886).
Reads were preprocessed and index using SAMtools (PMID: 19505943).
Mapped reads were assigned to gene features and quantified using featureCounts (PMID: 24227677).
Genome_build: Mouse GENCODE genome, Version M14 (January 2017 freeze, GRCm38, Ensembl 89)
Supplementary_files_format_and_content: Raw Counts
|
| |
|
| Submission date |
Jan 11, 2018 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Aguirre A de Cubas |
| E-mail(s) |
a.decubas@vumc.org
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Hematology and Oncology
|
| Lab |
Rathmell Lab
|
| Street address |
2220 Pierce Ave
|
| City |
NASHVILLE |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE109102 |
Von Hippel-Lindau (VHL) mutations disrupt vascular patterning and maturation via Notch |
|
| Relations |
| BioSample |
SAMN08354823 |
| SRA |
SRX3554398 |
