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| Status |
Public on May 22, 2020 |
| Title |
mRNA-seq-WT-replicate_1 |
| Sample type |
SRA |
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| Source name |
mycelia
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| Organism |
Neurospora crassa |
| Characteristics |
strain: 87-3
tissue: mycelia
genotype/variation: wild type
molecule: mRNA
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| Treatment protocol |
For the ribosome profiling and accompanying mRNA-seq, CHX (final concentration of 50 g/ml) was added 10 min before collecting the samples. For the mRNA-seq, no special treatment was performed.
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| Growth protocol |
For the ribosome profiling and accompanying mRNA-seq, fresh conidia (one week post inoculation on slants) of adat2-silenced mutant and wild-type strain were cultured in plates with 50 ml growth medium (1 × Vogel’s, 0.1% glucose, 10-2 M QA) at room temperate for three 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 one day. For the independent mRNA-seq, the culture condition was identical to that described above, except that CHX was not added.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For the ribosome profiling and accompanying mRNA-seq, the ribosome protected fragments (RPFs) and total RNAs were extracted according to ARTseq™ Ribosome Profiling Kit(Catalog Number: RPYSC12116). For the independent mRNA-seq, total RNA was extracted using Trizol reagents (Invitrogen) and treated with DNase (Turbo DNase, Ambion) accoding to standard RNA extraction protocal.
For the ribosomal profiling and the accompanying mRNA-seq, libraries were prepared for sequencing according to ARTseq™ Ribosome Profiling Kit(Catalog Number: RPYSC12116). For the independent mRNA-seq, libraries were constucted using Illumina TruSeq reagents. All RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence by our in-house scripts.
Clean reads were then mapped to reference sequences using tophat2 with parameters --library-type fr-firststrand --min-intron-length 20 --max-intron-length 50000 --read-mismatches 4.
Fragments Per Kilobase Million (FPKM) were calculated using cufflinks with parameters --library-type fr-firststrand --multi-read-correct --min-intron-length 20 --max-intron-length 50000 --frag-bias-correct
Genome_build: For the ribosome profiling, the reference sequences are all mRNAs with uptream and dowmstream 100 bp respectively; for the mRNA-seq, the reference sequence is whole genome sequence with gtf annotation file from NCBI database.
Supplementary_files_format_and_content: For the mRNA-seq, tab-delimited text files include FPKM values for each sample; for the ribosome profiling, tab-delimited text file includes absolute codon occupancy values.
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| Submission date |
Apr 22, 2019 |
| Last update date |
May 22, 2020 |
| Contact name |
xueliang lyu |
| E-mail(s) |
lvxueliang0715@aliyun.com
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| Organization name |
UT Southwestern Medical Center
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| Department |
Physiology
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| Lab |
Yi Liu
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| Street address |
6001 Forest Park Road
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| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75235 |
| Country |
USA |
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| Platform ID |
GPL26551 |
| Series (1) |
| GSE130155 |
Effect of adat2 silencing in Neurospora crassa on translation kinetics and transcriptome |
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| Relations |
| BioSample |
SAMN11477781 |
| SRA |
SRX5723322 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3732955_mRNA-seq-WT-replicate_1.txt.gz |
483.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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