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| Status |
Public on Oct 20, 2018 |
| Title |
S Lycopersicum w TAP, IL, rep2 |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Solanum lycopersicum |
| Characteristics |
adapter: standard
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| Treatment protocol |
the RNA was TAP treated prior to library construction
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| Growth protocol |
the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light
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| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using standard Illumina adapters
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v 3.2
Supplementary_files_format_and_content: csv, raw abundances
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| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Dalmay |
| E-mail(s) |
T.dalmay@uea.ac.uk
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| Phone |
+44 1603593221
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| Organization name |
University of East Anglia
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| Department |
School of Biological Sciences
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| Street address |
Earlham Road
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| City |
Norwich |
| ZIP/Postal code |
NR4 7TJ |
| Country |
United Kingdom |
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| Platform ID |
GPL19694 |
| Series (1) |
| GSE102581 |
Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum with TAP treatment |
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| Relations |
| BioSample |
SAMN07500989 |
| SRA |
SRX3089981 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2741435_S4_Sly_TapPlus_IL2.csv.gz |
30.9 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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