|
| Status |
Public on Aug 10, 2021 |
| Title |
Ribo-WT-3opt_2 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
host strain: WT
reporter expressed in host strain: 3хOPT-EDP
tissue: mycelia
molecule: ribosome protected fragments
|
| Treatment protocol |
For both of ribosome profiling and the accompanying mRNA-seq, CHX (final concentration of 0.1 mg/ml) was only added into the cell lysis buffer.
|
| Growth protocol |
For both of ribosome profiling and the accompanying mRNA-seq, fresh conidia (one week post inoculation on slants) of Δcpc-3 and wild-type strains were cultured in plates with 50 ml growth medium (1 × Vogel’s, 2% glucose) at room temperate for two days. The cultures were cut into small discs with a diameter of 1 cm and then were transferred into flasks with the same medium and grown with orbital shaking (200 rpm) under constant light for 12 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For both of ribosome profiling and the accompanying mRNA-seq, the ribosome protected fragments (RPFs) and total RNAs were extracted according to ARTseq Ribosome Profiling Kit(Catalog Number: RPYSC12116).
For both of ribosome profiling and the accompanying mRNA-seq, libraries were prepared for sequencing according to ARTseq Ribosome Profiling Kit(Catalog Number: RPYSC12116).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence by our in-house scripts.
Clean reads were then mapped to reference sequences using bowtie2 and RPKM values were calculated by cufflinks with parameters --min-intron-length 4 --max-intron-length 5000 --library-type fr-firststrand --multi-read-correct --upper-quartile-norm
Genome_build: All of the ribosome profiling and accompanying mRNA-seq clean reads were mapped to coding sequence (CDS) regions of N. crassa genes.
Supplementary_files_format_and_content: For both of ribosome profiling and accompanying mRNA-seq, tab-delimited text files including RPKM values were generated by cufflinks for each sample.
|
| |
|
| Submission date |
Mar 09, 2021 |
| Last update date |
Aug 10, 2021 |
| Contact name |
xueliang lyu |
| E-mail(s) |
lvxueliang0715@aliyun.com
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Physiology
|
| Lab |
Yi Liu
|
| Street address |
6001 Forest Park Road
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75235 |
| Country |
USA |
| |
|
| Platform ID |
GPL29831 |
| Series (1) |
| GSE168595 |
Codon usage and protein length-dependent feedback from translation elongation to translation initiation and kinetics |
|
| Relations |
| BioSample |
SAMN18234674 |
| SRA |
SRX10299140 |
