|
| Status |
Public on Dec 01, 2012 |
| Title |
cmc_candida_donor_5 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
group: cmc
treatment: candida
individual: donor_5
|
| Treatment protocol |
Freshly isolated cells were incubated for 4 hours with heat-killed Candida albicans (1x10^6/mL) or left untreated. After 4 hours, supernatants were removed and trizol was added to cells. Samples were stored at -80C until RNA extraction
|
| Growth protocol |
Cells were isolated and resuspended in RPMI 1640 culture medium Dutch modifications (Sigma-Aldrich) supplemented with 1% gentamicin, 1% L-glutamine and 1% pyruvate (Life Technologies)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted in 800 μl of TRIzol reagent (Invitrogen), according to the protocol of the manufacturer
Libraries were prepared using the instructions for the whole transcriptome library preparation: low input of the SOLiD® Total RNA-Seq kit (part no 4445374) Poly(A) RNA was selected by the ambion® MircoPoly(A) purist kit (part no AM1919).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
Human_peripheral blood mononuclear cells_cmc_candida_donor_5
|
| Data processing |
XSQ conversion to csfasta and qual using xsqconvert version 1.4
Reads alignment using tophat v1.4.1, insert size set 110 bp
Abundances were calculated using cufflinks v2.0.0
Log2 transformation (with an offset of 1.0) of FPKM expression values using Partek 6.6
A multifactoral ANOVA was performed with factors; GROUP, TREATMENT and INDIVIDUAL using Partek 6.6.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample as created by cufflinks 2.0.0
|
| |
|
| Submission date |
Nov 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eugene Thomas Pieter Verwiel |
| E-mail(s) |
e.verwiel@gen.umcn.nl
|
| Organization name |
Radboud University Medical Centre
|
| Department |
Human Genetics
|
| Street address |
Geert Grooteplein zuid 10
|
| City |
Nijmegen |
| State/province |
Gelderland |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE42630 |
Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans |
|
| Relations |
| SRA |
SRX207531 |
| BioSample |
SAMN01821248 |
