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| Status |
Public on Mar 09, 2022 |
| Title |
Vv1 |
| Sample type |
SRA |
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| Source name |
Botrytis cinerea Vv1
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| Organism |
Botrytis cinerea |
| Characteristics |
strain: Vv1
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| Growth protocol |
Botrytis cinerea strains were cultivated 48 hours on solid media made from grape juice or tomato juice supplemented with agar and covered with a sheet of cellophane.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted with the TRIzol reagent (InvitroGen) and submitted to a DNAse treatment (DNA-free kit, Ambion).
Libraries were performed from at least 1µg of extracted total RNA with a RIN greater than 7. Before starting, total RNAs were purified with miRNeasy kit (Qiagen) which allows the selection of the small RNA fraction less than 100 bases. From these samples enriched in small RNAs, libraries were performed according to the protocol published by Vigneault et al. (2012) with adjustments to improve the ligation.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Adapters were removed with Cutadapt (Martin, 2011) .
Processed reads shorter than 16 bases were discarded.
Then, the reads were preprocessed using fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), i.e. low-quality sequences were masked with fastq_quality_filter -q 30 -p 70, low-complexity sequences were masked with fastx_artifacts_filter.
Finally, identical sequences were collapsed into a single sequence (while maintaining reads counts) with fastx_collapser.
Only single sequences (called unireads) of length 20-24nt and with at least five reads per million in at least one library were kept, i.e., 146395 unireads.
Supplementary_files_format_and_content: Raw counts for the 146395 unireads in the 16 libraries (txt).
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| Submission date |
Aug 06, 2021 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Adeline SIMON |
| Organization name |
INRAE
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| Lab |
BIOGER
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| Street address |
22 place de l'agronomie
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| City |
Palaiseau |
| ZIP/Postal code |
91120 |
| Country |
France |
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| Platform ID |
GPL25020 |
| Series (1) |
| GSE181592 |
Repertoires of small RNAs in Botrytis cinerea strains isolated from tomato or grapevine. |
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| Relations |
| BioSample |
SAMN20602280 |
| SRA |
SRX11663875 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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