|
| Status |
Public on Dec 13, 2016 |
| Title |
ph_13f_alone-1 |
| Sample type |
SRA |
| |
|
| Source name |
vegetative mycelium
|
| Organism |
Rhizopus microsporus |
| Characteristics |
isolate: host (ATCC 52813) isolate
growth protocol: alone
growth stage: 67h post inoculation
cell type: vegetative mycelium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Ambion ToTALLY Total RNA Isolation Kit (Life Technologies, Grand Island, NY) and rRNA was removed with RiboZero Magnetic Gold Kit (Epicentre, Madison, WI)
RNA sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina®
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
edgeR_count.txt_13_ph_fungal
13f_edgeR_counts_by_Rhimi_id.txt.ph_13f_alone_vs_ph_13f_wb.edgeR.DE_results
|
| Data processing |
Reads were quality controlled using FASTQ and trimmed with Trimmomatic to eliminate low quality reads and Illumina adapters
reads were aligned to the fungal genomes of R. microsporus ATCC 52813 (GenBank accession JOSV00000000) and R. microsporus ATCC 52814 (GenBank MCOJ00000000) using TopHat with following parameters tophat -p 11 -o outputdirectory -G genome.gff3 --transcriptome-index xxx --no-novel-juncs genomefile xxx_R1_paired.fq xxx_R2_paired.fq
Transcript abundances were quantified with CuffDiff and the counts file used for differential expression analysis with EdgeR
Genome_build: R. microsporus ATCC 52813 NCBI accession number: JOSV00000000
Genome_build: R. microsporus ATCC 11559 NCBI accession number: MCOJ00000000
Supplementary_files_format_and_content: tab-delimted text file with read counts generated by CuffDiff which was then used for differential expression analysis with EdgeR. EdgeR-generated tab-delimited text file with fold change, p- and and false discovery rate-values for all the genes.
|
| |
|
| Submission date |
Oct 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Olga Lastovetsky |
| E-mail(s) |
ol57@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
334 Plant Science Building, 236 Tower Rd, Cornell University
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL22615 |
| Series (1) |
| GSE89305 |
Transcriptional responses of Rhizopus microsporus host and non-host isolates to physical interaction with Burkholderia endobacteria of the host |
|
| Relations |
| BioSample |
SAMN05952673 |
| SRA |
SRX2288671 |
