|
| Status |
Public on Jan 01, 2018 |
| Title |
Sm_PZQ_39_2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: Swiss Webster (CFW)
tissue: liver
days post infection: 39 days
treatment: Praziquantel (250 mg/kg)
|
| Treatment protocol |
Mice were gavaged at 32-35 days post infection with either Vehicle (Cremophor EL(250 mg/kg)) or Praziquantel (250 mg/kg).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, placed in RNA at 4°, and RNA was harvested using RNA Maxi Kit (Qiagen #75162). RNA was tested on nanodrop and Bioanalzer. Illumina TruSeq RNA Library Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
TRUSEQ RNA Library Preparation on the Sciclone NGS Liquid Handler
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw read data was demultiplexed (segregated by library index) using Illumina CASAVA version 1.8.2.
Thereafter, NCGR's custom contaminant filtering pipeline removed anomalous sequences. These aberrant sequences include Illumina Phix control, library adapters, primer dimers and library indexes not part of the experiment. NCGR's contaminant filtering pipeline ensures only the highest quality data goes into downstream analyses.
Sequenced reads were mapped to Ensembl Mouse release 75 (GRCm38) whole genome using Tophat2 v.2.0.12 using default settings.
Genome_build: Ensembl Mouse release 75 (GRCm38)
Supplementary_files_format_and_content: A matrix of the samples in a tab-delimited text file with the FPKM values.
Supplementary_files_format_and_content: A matrix of the samples in a tab-delimited text file with the raw count of the sequence reads.
|
| |
|
| Submission date |
Jan 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Cunningham |
| E-mail(s) |
ccunnin@unm.edu
|
| Organization name |
University of New Mexico
|
| Department |
Biology
|
| Street address |
1 University of New Mexico
|
| City |
Albuquerque |
| State/province |
New Mexico |
| ZIP/Postal code |
87131-0001 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE94132 |
Effect of Praziquantel on the Differential Expression of Mouse Hepatic Genes and Parasite ATP Binding Cassette Transporter Gene Family Members During Schistosoma mansoni Infection |
|
| Relations |
| BioSample |
SAMN06275961 |
| SRA |
SRX2522365 |
