|
| Status |
Public on Apr 20, 2018 |
| Title |
Cells grown in standard medium for 24 h, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
cultured yeast cells
|
| Organism |
Cryptococcus neoformans var. grubii H99 |
| Characteristics |
growth condition: standard medium
time: 24 h
|
| Treatment protocol |
none
|
| Growth protocol |
Cells were grown in titan-like cell medium (TCM) inoculated with C. neoformans at low density (10^4 cell/mL, that induces titan-like cells) and high density(10^6 cells/mL, that produces cells of regular size). Cells were incubated at 37oC with 5% CO2, and RNA was extracted after 7 and 18 h of incubation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using Trizol (TRI Reagent, Sigma Aldrich) with some modifications. Cells of regular size were broken during 5 minutes with FastPrepR -24 (MP), alternating 20 seconds beating with 1 minute on ice. Titan-like cells were disrupted for 10 minutes following the same procedure. The RNAs concentration and quality was determined with a Nanodrop 8000 Spectrophotometer (Thermo Scientific). Then RNA samples were purified using RNeasy® Mini Kit (Qiagen) and RiboZero kit (EpiCentre, Illumina).
The total RNA samples (0.5-1 µg) were treated to remove rRNA using Ribo-Zero Magnetic Kit (Epicentre, Illumina, San Diego, CA) according to the manufacturer´s instructions. Then, mRNA was processed for Library preparation using the strand-specific ScriptSeq™ v2 RNA-Seq Library Preparation KIT (Epicentre, Illumina, San Diego, CA). Libraries were quantified using the QuantiFluor® RNA System (Promega) and the quality and average size was determined using an Agilent 2100 Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Control_Small_Cells_24h_rep3
Annotated Probe Report All 24h
Annotated Probe Report DESeq2 24h_p005
OZ-020_S20
|
| Data processing |
Reads were filtered for length>= 50 nt and average quality Q>= 30). For each sample, two fastq files were combined and subjected to the alignment step
Alignment was made with Bowtie2 2-1.0 (sensitive, local mode) and SAM files generated
SAM files were loaded into Seqmonk v1.39.0 (Brabaham Institute) and two replicate sets were created ("Small" [3 samples] and "Titan-like" [2 samples]). The RNA-Seq pipeline was used (CDS probes, same strand specific, merge transcript isoforms, raw counts) yielding 6974 probes. Both sets were analyzed for differential expression using the Bioconductor DESeq2 algorithm (p<0.05). Reads for selected probes were then quantitated as reads per million.
Genome_build: CNA3 (Gene Bank assembly accession: GCA_000149245.3)
Supplementary_files_format_and_content: Four .txt files. Two of them contain reads for all probes at 7 or 24 h and the other two include only probes that are differentially expressed according to DESeq2 (p <0.05)
|
| |
|
| Submission date |
Mar 05, 2018 |
| Last update date |
Apr 20, 2018 |
| Contact name |
JOAQUIN ARINO |
| E-mail(s) |
joaquin.arino@uab.es
|
| Organization name |
UNIVERSITAT AUTONOMA BARCELONA
|
| Department |
Biochemistry & Mol. Biol.
|
| Lab |
Yeast Molecular Biology
|
| Street address |
ED. IBB
|
| City |
CERDANYOLA DEL VALLES |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24689 |
| Series (1) |
| GSE111400 |
Transcriptomic profiling of the Cryptococcus neoformans transition to titan-like cells |
|
| Relations |
| BioSample |
SAMN08635012 |
| SRA |
SRX3764003 |
