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Series GSE130155 Query DataSets for GSE130155
Status Public on May 22, 2020
Title Effect of adat2 silencing in Neurospora crassa on translation kinetics and transcriptome
Organism Neurospora crassa
Experiment type Expression profiling by high throughput sequencing
Summary The silencing of tRNA-specific adenosine deaminase adat2 in Neurospora crassa abolished most of the I34 modification, resulting in major tRNA profile changes. The adat2 silencing caused genome-wide codon usage-biased ribosome pausing on mRNAs corresponding to changes in the tRNA profile, which reprograms translation elongation kinetics on ADAT-related codons. The ribosome profiling in this study was used to measure the effect of defective I34 modification of the eight tRNAs on translation kinetics during elongation stage. The accompanying mRNA-seq was used to normalize the ribosome profiling data using the same library construction protocol (reference to ARTseqâ„¢ Ribosome Profiling Kit (Catalog Number: RPYSC12116)) under the same growth condition. The independent mRNA-seq was used to measure the effect of I34 abolishment on transcriptome change using standard Illumina protocols. Meanwhile, to isolate the role of codon usage in translation elongation and protein level changes when adat2 is silenced, the independent mRNA-seq was also used to exclude the effect of mRNA level changes.
Overall design The transcription profile and ribosome protected fragment (RPF) profiles of wild-type strain and adat2-silenced mutant of Neurospora crassa were generated by deep sequencing using Illumina sequencing platform.
Contributor(s) Lyu X, Liu Y
Citation(s) 32479508
Submission date Apr 22, 2019
Last update date Jun 17, 2020
Contact name xueliang lyu
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
Platforms (2)
GPL16164 Illumina HiSeq 2000 (Neurospora crassa)
GPL26551 Illumina NovaSeq 6000 (Neurospora crassa)
Samples (12)
GSM3732951 Ribosome-profiling-WT
GSM3732952 Ribosome-profiling-Siadat2
GSM3732953 mRNA-seq-for-normalization-WT
BioProject PRJNA534111
SRA SRP193378

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE130155_RAW.tar 2.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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