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TranscriptomicssmallRNA-seq of Solanum lycopersicum bearing the sulfurea epiallele in nrpe1 versus WT
Plants bearing a sulfurea epiallele (TAB2sulf) were crossed with nrpe1 (largest polV subunit) mutants in Solanum Lycopersicum. 7 plants of a F3 progeny expected to be 100% TAB2sulf and segregating for the nrpe1 mutation were sequenced. 4 plants bear the nrpe1 mutation and 3 plants have NRPE1 WT all...
ORGANISM(S): Solanum lycopersicum 
2021-07-02 | E-MTAB-10565 | biostudies-arrayexpress
TranscriptomicssmallRNA-seq of Solanum lycopersicum segregating for the sulfurea epiallele in cmt3 versus WT
Plants bearing a sulfurea epiallele (TAB2sulf) were crossed with cmt3 mutants in Solanum Lycopersicum. 6 plants of a F2 progeny segregating both for TAB2sulf and cmt3 mutation were sequenced. 4 plants bear the cmt3 mutation and 2 plants have CMT3 WT alleles. the aim of the experiment was to compare ...
ORGANISM(S): Solanum lycopersicum 
2021-06-21 | E-MTAB-10557 | biostudies-arrayexpress
TranscriptomicssmallRNA-seq of Solanum lycopersicum cv M82 WT versus Solanum lycopersicum cv Lukullus bearing the sulfurea epiallele
3 sRNA-seq bioreps of WT and sulfurea samples. The aim of this experiment was to compare sRNA abundance at between the two genotypes with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background.
ORGANISM(S): Solanum lycopersicum 
2021-06-21 | E-MTAB-10556 | biostudies-arrayexpress
TranscriptomicsBisulfite-seq of the Solanum lycopersicum sulfurea paramutation in the cmt3 mutant background and upon reintroduction of WT CMT3
Whole genome bisulfite sequencing was done in F3 plants resulting from a cross between Solanum lycopersicum plants bearing the sulfurea epiallele and cmt3 mutants. 6 F3 plants were sequenced: 3 WT and 3 cmt3. The F3 WT plants had methylation levels (quantified with McrBC-qPCR) consistent with the TA...
ORGANISM(S): Solanum lycopersicum 
2021-06-24 | E-MTAB-10568 | biostudies-arrayexpress
TranscriptomicsHi-C data of Solanum lycopersicum plants bearing the sulfurea epiallele versus plants bearing WT epiallele
The aim of this experiment was to detect possible chromatin organisation differences between sulfurea and WT plants.
ORGANISM(S): Solanum lycopersicum 
2021-06-27 | E-MTAB-10574 | biostudies-arrayexpress
TranscriptomicsHigh-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and polIV mutants
Comparison of the endogenous small RNA content of Arabidopsis flower bud tissue: wild type vs. mutants in polIV pathways Keywords: High throughput 454 small RNA sequencing. Size fractionated small RNA from total RNA extracts was ligated to adapters, purified again and reverse transcribed. After PCR ...
ORGANISM(S): Arabidopsis thaliana 
2008-02-25 | E-GEOD-10180 | biostudies-arrayexpress
TranscriptomicsMaternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds.
Seed size is important to crop domestication and natural selection and is affected by the balance of maternal and paternal genomes in endosperm. Endosperm, like placenta in mammals, provides reserves to the developing embryo. Interploidy crosses disrupt the genome balance in endosperm and alter seed...
ORGANISM(S): Arabidopsis thaliana 
2011-11-11 | E-GEOD-25280 | biostudies-arrayexpress
TranscriptomicsSmall RNAs in Arabidopsis hybrid siliques
Five days post-fertilization siliques were collected for RNA extraction. After purification, small RNA libraries were generated for high throughput sequencing. Resulting sequences were analyzed to determine the contribution of the paternal genome to the small RNA transcriptome. Keywords: Epigenetic...
ORGANISM(S): Arabidopsis thaliana 
2009-03-24 | E-GEOD-15348 | biostudies-arrayexpress
TranscriptomicsCollection of various small RNA sequencing libraries of C. Reinhardtii.
Collection of various small RNA libraries of C. Reinhardtii sequenced using Illumina sRNA sequencing. Libraries are derived from various C. Reinhardtii genotypes (CC1883, CC4350, CC125, J), ecotypes, life cycles (Vegatative, Zygote) treatments and mutants. Preparation was done over a period of sev...
ORGANISM(S): Chlamydomonas reinhardtii 
2020-06-16 | E-MTAB-8526 | biostudies-arrayexpress
TranscriptomicsExamples of ribosome profiling in chlamydomonas and mouse
Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here, we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and...
ORGANISM(S): Chlamydomonas reinhardtii 
2015-10-16 | E-MTAB-2934 | biostudies-arrayexpress
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