|
Status |
Public on Aug 10, 2021 |
Title |
Ribo-CPC3-1wt_1 |
Sample type |
SRA |
|
|
Source name |
mycelia
|
Organism |
Neurospora crassa |
Characteristics |
host strain: Δcpc-3 reporter expressed in host strain: 1хWT-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.
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|
|
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 |
SAMN18234695 |
SRA |
SRX10299142 |