|
| Status |
Public on Mar 30, 2014 |
| Title |
5h-HUVEC.control-Candida.SC5314.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mock infected
|
| Organism |
Candida albicans |
| Characteristics |
candida strain: SC5314
infected human culture: none (C. albicans cells alone in tissue culture media)
time point: 5 hours
|
| Growth protocol |
C. albicans cells were used to infect HUVEC cells or OKF6-TERT2 cells in tissue culture media for the indicated amount of time at 37 degrees celcius. The negative control samples were the host or C. albicans cells alone in tissue culture media for the indicated amount of time.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extractions were performed using RiboPure RNA Purification Kit, yeast (Life Technologies, AM1926) following manufacturer's protocols
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 |
SRX123784
31_5h_c
|
| Data processing |
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh38 whole genome reference and/or C. albicans SC5314 or WO1 reference using TopHat v1.4.0
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: H. sapiens (GRCh38), C. albicans (sc5314; GCF_000182965.2), C. albicans (wo1; GCA_000149445.2)
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 |
GPL15645 |
| Series (2) |
| GSE56091 |
Characterization of transcriptome dynamics in response to contact with host cells [Phase I In Vitro] |
| GSE56093 |
Characterization of transcriptome dynamics in response to contact with host cells |
|
| Relations |
| BioSample |
SAMN02693660 |
| SRA |
SRX123784 |
