|
| Status |
Public on Dec 05, 2017 |
| Title |
LD2_4 Chemotherapeutic Model Day 2 Post Infection |
| Sample type |
SRA |
| |
|
| Source name |
whole mouse lungs
|
| Organisms |
Mus musculus; Aspergillus fumigatus |
| Characteristics |
mouse strain: CD1
a. fumigatus strain: CEA10
model: Chemotherapeutic
time point: day 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole mouse lung tissue was lyophilized and processed through triazol extraction followed by Qiagen clean-up
Library preparation was performed using the TruSeq RNA preparation kit (Illumina, FC-122-1001/1002) from purified RNA (100 ng-1 mg of total RNA with RIN ≥ 8.0).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adaptor sequences were trimmed and filtered based on phred score (>33) and length (> 36) using Trimmomatic-0.35. Non-paired reads were also filtered out.
A master GTF was created using the GRCm38 mouse genome build and the Af1163 genome scaffolds
Filtered pair-ended RNA-Seq reads were mapped to the merged reference genome using the splice-aware short read mapping tool TopHat 2.1.0 with Bowtie2 2.2.7118
Abundance estimation and differential expression analysis for the reference genes and transcripts were performed using Cufflinks 2.2.1 and visualized in part via CummRbund120
Abundance estimation and differential expression analysis for fungal genes and transcripts were performed using HTSeq-DeSeq2 1.12.4
Genome_build: GRCm38, EnsembleFungi: Aspergillus fumigatus A1163
Supplementary_files_format_and_content: tab-delimited text containing standard Cufflinks and DeSeq2 output for abundance measurement and differential expression
|
| |
|
| Submission date |
Sep 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shiv D. Kale |
| E-mail(s) |
sdkale@vt.edu
|
| Phone |
540-231-3784
|
| Organization name |
Virginia Tech
|
| Department |
Biocomplexity Institute
|
| Street address |
1015 Steger Hall, Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL24049 |
| Series (1) |
| GSE104290 |
Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis |
|
| Relations |
| BioSample |
SAMN07703393 |
| SRA |
SRX3218154 |
