|
| Status |
Public on Dec 01, 2017 |
| Title |
upf3b-ASO-dose2-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
upf3b-ASO-dose2
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Upf3b-GalNAc-ASO
dose: 20 mg/kg weekly dosing
Sex: M
strain: hFIX-R29X
age: adult
tissue: liver
|
| Treatment protocol |
6 doses of ASOs were administrated subcutaneously at a volume of 10 µl/g, every 5 days
|
| Growth protocol |
mouse 8-14 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animal tissues were homogenized in guanidine isothiocyanate solution (Invitrogen) supplemented with 8% 2-mercaptoethanol (Sigma-Aldrich). Total RNA was prepared using the RNeasy mini Kit (Qiagen).
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 |
| |
|
| 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: comma-separated files containing gene symbol and TPM for genes
|
| |
|
| Submission date |
Jun 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sagar S Damle |
| E-mail(s) |
sdamle@ionisph.com
|
| Organization name |
Ionis Pharmaceuticals
|
| Street address |
2855 Gazelle Ct
|
| City |
Carlsbad |
| State/province |
CA |
| ZIP/Postal code |
92010 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE99619 |
Liver DGE analysis of hemophilia mice (hFIX9-R29X) treated with ASOs inhibiting NMD |
|
| Relations |
| BioSample |
SAMN07189771 |
| SRA |
SRX2880596 |
