|
| Status |
Public on Aug 31, 2013 |
| Title |
mycelia_incubated_50C_24h |
| Sample type |
SRA |
| |
|
| Source name |
mycelia_50C
|
| Organism |
Rhizomucor miehei |
| Characteristics |
strain: CAU432
tissue: mycelia
development stage: mycelia
|
| Growth protocol |
R. miehei CAU432 after incubation at 30C and 50C for 1 day
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from mycelia of R. miehei CAU432 after incubation at 30C and 50C for 1 day according to the previous report (Cloonan et al. 2008), and poly(A) mRNA was purified on oligo d(T) conjugated magnetic beads using FastTrack MAG mRNA Isolation Kits (Invitrogen, USA) according to the manufacturer's protocol. The purified mRNA was fragmented, ligated with SOLiD adaptor mix and reversely transcribed by using SOLiD Total RNA-Seq Kit according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System |
| |
|
| Description |
polyA RNA from mycelia of R. miehei CAU432 after incubation at 50C
|
| Data processing |
High quality SOLiD reads with median QV (quality value) over 13 were, using Corona_Lite_Plus_4.2.1 (Applied Biosystems), mapped to the R. miehei genome and splice junction database on the base of the predicted gene models. The splice junction database were constructed with the 45 bp length sequences extracted from the termini of each exon. The 50 bp length RNA-seq reads were mapped to R. miehei assembled genome at 5 mismatch, the unmapped reads were mapped to artificial splice junction database. Iteratively, the first 45 bp (at 4 mismatches), 40 bp (at 4 mismatches), 35 bp (at 3 mismatches) and 30 bp (at 3 mismatches) sequences extracted from unmapped reads were mapped to genome and splice junction database in the order.
|
| |
|
| Submission date |
Aug 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiang Zhengqiang |
| E-mail(s) |
Z. Q. zhqjiang@cau.edu.cn
|
| Organization name |
College of Food Science and Nutritional Engineering, China Agricultural University
|
| Department |
Department of Biotechnology
|
| Street address |
Qinghua East Road, Haidian Distric
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL14182 |
| Series (1) |
| GSE31580 |
Genome and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei |
|
| Relations |
| SRA |
SRX096390 |
| BioSample |
SAMN00716171 |
