|
| Status |
Public on Mar 11, 2014 |
| Title |
Bc_myc |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Botrytis cinerea |
| Characteristics |
age: 10 days
strain: B05.10
sample type: mycelium
|
| Treatment protocol |
B. cinerea mycelium and conidiospores were separated using miracloth as filter
|
| Growth protocol |
B. cinerea was grown on malt agar for 10 days at 23 degree celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using hot phenol method. Small RNAs were size-separated on a 15% PAGE for library cloning
Small RNA libaries were generated using miRCAT cloning kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads of Bc_total were trimmed for adaptor sequence using fastx_clipper v0.0.13.2 with parameters -Q 33 -l 18 -a CTGTAGGCACCATCAATC. Sequenced readsof Bc_myc and Bc_spore were trimmed for adaptor sequence using fastx_clipper v0.0.13.2 with parameters -Q 33 -l 18 -a CACTCGGGCACCAAGGAC.
Sequenced reads were masked low-quality sequence using fastq_quality_filter v0.0.13.2 with parameters -Q 33 -q 30 -p 70 and masked low-complexity sequence using fastx_artifacts_filter v0.0.13.2 with default parameters.
Sequenced reads were mereged using fastx_collapser v0.0.13.2 with default parameters.
Supplementary_files_format_and_content: Each row of tab-delimited text are sequence and small RNA count.
|
| |
|
| Submission date |
Mar 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hailing Jin |
| E-mail(s) |
hailingj@ucr.edu
|
| Phone |
951-827-7995
|
| Organization name |
University of California, Riverside
|
| Department |
Department of Plant Pathology and Microbiology
|
| Street address |
3447 Boyce Hall
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL16844 |
| Series (1) |
| GSE45320 |
Genome-wide high-throughput small RNA sequence analysis of B. cinerea |
|
| Relations |
| SRA |
SRX252394 |
| BioSample |
SAMN01984767 |
