|
| Status |
Public on Nov 08, 2011 |
| Title |
FB2 RNA_seq |
| Sample type |
SRA |
| |
|
| Source name |
Middle-term fruiting-bodies
|
| Organism |
Cordyceps militaris |
| Characteristics |
strain: Cm 01
growth medium: silkmoth pupae
growth duration: 29 days
developmental stage: middle-term fruiting bodies
|
| Growth protocol |
The conidia of Cordyceps militaris were injected into Chinese Tussah silkmoth (Antheraea pernyi) pupae and incubated at 22 °C, 12:12 hr light:dark control for up to 29 days. The samples were harvested for RNA extraction and RNA-seq analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen's RNeasy kit. Messenger RNA was purified from 6 ug of the total RNA from each sample using Oligo (dT) magnetic beads and reversely transcribed into cDNA. The generation of 5' CATG ends of tags was conducted using the endonuclease NlaIII and the Illumina adapter 1 was added to the 5' ends. The combination of the Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts the cDNA at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, the Illumina adapter 2 was introduced at the 3' ends of each tag to generate the tag libraries. After 15 cycles of linear PCR amplification, 85 base strips were purified by 6% TBE PAGE Gel electrophoresis and the single-chain molecules fixed onto the Solexa Sequencing Chip (flowcell) for sequencing with the method of sequencing by synthesis (SBS). Each tunnel generated millions of raw reads with sequencing length of 35bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Cordyceps militaris growth on silkmoth pupae for 29 days.
|
| Data processing |
After base calling by transforming the raw image data into sequence data, the 3' adaptor was cleaned and the tags with "N" or the tags with only one copy were removed to generate clean tags. All clean tags were mapped onto the Cordyceps militaris genome (AEVU00000000.1) by allowing no more than 1nt mismatch. Clean tags mapping to the reference genome in multiple places were filtered. The remaining clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).
|
| |
|
| Submission date |
Mar 16, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Chengshu Wang |
| E-mail(s) |
cswang@sibs.ac.cn
|
| Organization name |
Shanghai Institutes for Biological Sciences, CAS
|
| Department |
Institute of Plant Physiology and Ecology
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL13293 |
| Series (1) |
| GSE28001 |
Developmental transcriptomics of the model caterpillar fungus Cordyceps militaris |
|
| Relations |
| SRA |
SRX048041 |
| BioSample |
SAMN00222127 |
