|
| Status |
Public on Mar 30, 2014 |
| Title |
kidney_infected_Candida_6h.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organisms |
Candida albicans; Mus musculus |
| Characteristics |
mouse strain: BALB/c
candida strain background: SC5314
strain genotype/variation: wild type
tissue: Kidney
timepoint: 6 Hours
|
| Growth protocol |
C. albicans cells were either injected into the tail vein of a mouse or swabbed onto the tongue of a anesthetized mouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit (Cat#74104)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SRX336609
|
| Data processing |
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse (GRCm38.70 + NT_096355 + NT_095534) whole genome reference using TopHat v1.4.0 and/or C. albicans SC5314 using Bowtie v0.12.9
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: M.musculus (GRCm38.70 + NT_096355 + NT_095534), C. albicans (sc5314)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Mar 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Amol Carl Shetty |
| E-mail(s) |
ashetty@som.umaryland.edu
|
| Organization name |
University of Maryland Baltimore
|
| Department |
Institute for Genome Sciences
|
| Street address |
670 W. Baltimore Street, Floor 3
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL18449 |
| Series (2) |
| GSE56092 |
Characterization of transcriptome dynamics in response to contact with host cells [Phase II In Vivo] |
| GSE56093 |
Characterization of transcriptome dynamics in response to contact with host cells |
|
| Relations |
| BioSample |
SAMN02693715 |
| SRA |
SRX336609 |
