|
| Status |
Public on Oct 16, 2018 |
| Title |
G1_PBS_PBS_0_Liver_G3 |
| Sample type |
SRA |
| |
|
| Source name |
G1 Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Apol1 G1 transgenic
tissue: Liver
aso: PBS
concentration: 0 mg/kg
stimulation: PBS
|
| Treatment protocol |
APOL1 G0 and G1 transgenic mice were dosed with PBS (vehicle), 50 mg/kg control ASO (non-targeting ASO of the same chemistry as targeting ASO) or 50 mg/kg APOL1 ASO once/week for 4 weeks. One day after the last ASO dose, cohorts were divided and half were challenged with PBS and half were challenged with IFNgamma. Kidney and Liver tissues were harvested 48 hours after challenge for analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogenized in Guanidine Isothiocyanate solution (Life Technologies) containing 8% β-mercaptoethanol (Sigma Aldrich) and total RNA was isolated using RNeasy 96 Kits (Qiagen) according to the manufacturer’s recommendations.
Digital gene expression (DGE) was performed by sequencing fragment libraries from purified total RNA as described previously (Patro et al., Nat Methods, 2017) using the QuantSeq 3' mRNA-Seq Library Prep Kit from Lexogen.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
12849
|
| Data processing |
Demultiplexing and base-calling was performed by Illumina bcl2fastq2 software (version 2.17.1.14).
Reads were associated to transcripts using a quasi-mapping based mode of Salmon (version 0.7.2).
Gene-level TPM was computed by normalizing number of reads mapped per transcript by number of mapped reads, using gene models from mouse Ensembl build 81.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: *txt: Comma-separated files containing gene symbol and TPM for genes.
|
| |
|
| Submission date |
Oct 15, 2018 |
| Last update date |
Jan 03, 2019 |
| Contact name |
Sagar S Damle |
| E-mail(s) |
sdamle@ionisph.com
|
| Organization name |
Ionis Pharmaceuticals
|
| Department |
Functional Genomics
|
| Street address |
2855 Gazelle Ct
|
| City |
Carlsbad |
| State/province |
CA |
| ZIP/Postal code |
92010 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE121286 |
Evaluation of APOL1 ASO in a novel model of APOL1-associated renal disease |
|
| Relations |
| BioSample |
SAMN10245287 |
| SRA |
SRX4890591 |
