|
| Status |
Public on Jan 11, 2017 |
| Title |
Infected splenic macrophage Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Splenic macrophage
|
| Organism |
Mesocricetus auratus |
| Characteristics |
strain: Outbred
tissue / cells: Splenic macrophage
infectious agent: Leishmania donovani (MHOM/SD/001S-2D)
gender: female
age: 10-12 weeks
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from fresh (unfrozen) samples using RNAqueus kit (Ambion-Life Technologies, CA) following the manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Spleen harvested at 28 days post-infection and splenic macrophages isolated from the collagenase-treated, mechanically disrupted spleen by adherence to a plastic culture flask for 4 hrs at 37C. RNA isolated from adherent macrohages immediately after removal of non-adherent cells by washing.
Sample_9
|
| Data processing |
assemble de novo transcripts using the software Trinity (r2012-06-08) and BRANCH (v1.8.1)
blast (v 2.2.28+) each transcripts from BRANCH against Rattus norvegicus (Rnor_5.0.73) and Mus musculus (GRCm38.73) genomes to identified genes for assembled transcripts
align non-Leishmania-like raw sequencing reads to assembled transcripts using bowtie2 (v2.1.0)
measure expression abundance using the software eXpress (v1.1.1)
ran differential expression analysis using edgeR (v3.4.0)
Supplementary_files_format_and_content: raw counts, edgeR output
|
| |
|
| Submission date |
Dec 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter C Melby |
| Organization name |
University of Texas Medical Branch
|
| Department |
Department of Microbiology and Immunology
|
| Street address |
Marvin Graves Bldg, Rm. 4.210, Route 0435
|
| City |
Galveston |
| State/province |
TX |
| ZIP/Postal code |
77550 |
| Country |
USA |
| |
|
| Platform ID |
GPL22776 |
| Series (1) |
| GSE91187 |
Transcriptional profiling by next generation sequencing of the spleen and splenic macrophages in the hamster model of visceral leishmaniasis |
|
| Relations |
| BioSample |
SAMN06128122 |
| SRA |
SRX2409162 |
