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| Status |
Public on Apr 05, 2013 |
| Title |
AC MG |
| Sample type |
SRA |
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| Source name |
whole fruit
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| Organism |
Solanum lycopersicum |
| Characteristics |
variety: Ailsa Craig
developmental stage: mature green
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| Treatment protocol |
Fruits kept at -80C untill further use, and ground in liquied nitrogen before RNA extraction
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| Growth protocol |
Tomato plants were grown in a greenhouse on rockwool with liquied nutrient solution
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an InviTrap Spin Plant RNA mini kit (Stratec, Berlin); PolyA RNA was purified using oligo-dT Dynabeads
cDNA was synthesized according to the PARE protocol described by German et al. (Nature protocols 4(3),2009). Libraries were prepared with a SOLEXA GEX1 adapter on the 5' end and the Illumina 3' TruSeq adapter with barcode was ligated on the 3' end after MmeI digestion. Products were amplified and sequenced on a HiSeq 2000. Samples were pooled with 4 other bar-coded samples, and each pool was sequenced in two lanes.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Image analysis, base-calling, and quality check was performed with the Illumina data analysis pipeline RTA v1.12.4.2 and/or OLB v1.9, and CASAVA v1.8.0
5' and 3' adapter sequences were removed and filtered for quality, oligo-A reads up to 15A's, tomato chloroplast DNA and for small non-coding RNAs as present in the Rfam 10.1 database. This was performed using parts of the FASTX Toolkit v.0.0.13 and Vmatch v2.0
Remaining reads were mapped on the sense strand strand of the ITAG release 3 predicted cDNAs (SL2.4) using SHRiMP v2.0 allowing 1 mismatch and retaining only the best scoring hit or hits in the event of of equally scoring his
Mapped reads were matched to potential miRNA target sites in tomato cDNAs, identified using the TargetFinder v1.6 script (Allen et al., 2005; Fahlgren et al., 2007), using an updated version of the CleaveLand pipeline (Addo-Quaye et al., 2009), Cleaveland v3.0.1 (kindly provided by Dr. M. Axtell), according to the instructions of the author. In order to allow for inaccurate target cleavage or variations in miRNA 5’ ends, the pipeline was modified to recognize targets cleaved at the 9th or 11th position of the miRNA, as well as the at the 10th position.
Tag numbers for any position were normalized for library size by using the formula TP10M (tags per 10 million)=(raw abundance/total filtered tags-cDNA matches)*10,000,000.
Genome_build: SL2.40
Supplementary_files_format_and_content: cDNAp9.txt; cDNAp10.txt, cDNAp11.txt are tab-delimited table files reporting miRNA, iTAG2.3 cDNA number, cDNA annotation, target finder penalty, peak category, total read number, peak read number, p-value and q-value for each of the four libraries at miRNA position 9, 10, and 11, respectively.
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| Submission date |
Nov 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruud A de Maagd |
| E-mail(s) |
ruud.demaagd@wur.nl
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| Organization name |
Plant Resarch International
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| Street address |
PO Box 619
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| City |
Wageningen |
| ZIP/Postal code |
NL-6700AP |
| Country |
Netherlands |
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| Platform ID |
GPL16345 |
| Series (2) |
| GSE42661 |
Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis |
| GSE42784 |
Comparison of tomato fruit gene expression data obtained by microarray analysis and by treatment of degradome sequencing data as an RNAseq experiment |
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| Relations |
| SRA |
SRX207914 |
| BioSample |
SAMN01821789 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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