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Sample GSM5150319 Query DataSets for GSM5150319
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.
 
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

Supplementary file Size Download File type/resource
GSM5150319_Ribo-CPC3-1wt_1.txt.gz 218.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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