|
| Status |
Public on Jun 24, 2022 |
| Title |
liver, 3e11 AAV8-scramble shRNA, chow diet, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: wild type
strain: C57BL6
treatment: chow diet, 3e11 AAV8-scramble shRNA
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected in Invitrogen TRIzol reagent and RNA was purified using standard protocols.
1 ug of RNA was used for cDNA library construction NEBNext® Ultra Directional RNA Library Prep Kit for Illumina® (#E7420S) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification and randomly fragmented by addition of fragmentation buffer. The first strand cDNA was synthesized using random hexamer primers, after which a second-strand synthesis buffer, dNTPs, RNase H, and DNA polymerase I were added to generate the second-strand. After terminal repair and sequencing adaptor ligation, the double-stranded cDNA library underwent size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PE150 (20M raw reads per library)
exp2_standardDiet_ExpMat.csv.gz
scramble_3554
|
| Data processing |
Raw reads were QC verified with FastQC v0.11.8
aligned to mm10 genome using Rsubread v2.4.3
reads quantified with Rsubread featureCounts
Assembly: mm10
Supplementary files format and content: gene-sample read counts matrix in csv.gz (compressed comma-delimited) format
|
| |
|
| Submission date |
Jun 24, 2022 |
| Last update date |
Jun 24, 2022 |
| Contact name |
Angelo Pelonero |
| E-mail(s) |
angelo.pelonero@gladstone.ucsf.edu
|
| Organization name |
Gladstone Institutes (UCSF)
|
| Department |
Cardiovascular Disease Institute
|
| Lab |
Srivastava Lab
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE206846 |
CSDE1 is a Post Transcriptional Regulator of the LDL Receptor |
|
| Relations |
| BioSample |
SAMN29328688 |
| SRA |
SRX15886747 |
