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TranscriptomicsSequencing random oligonucleotides using standard GA II protocol
Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol. Four replicates for N21 (21 random nucleotides), one replicate for N9 (9 random nucleotides), using either standard Illumina...
ORGANISM(S): synthetic construct 
2012-07-23 | E-GEOD-36540 | biostudies-arrayexpress
TranscriptomicsMicroarray analysis of gene expression from different developmental stages of the tomato fruit
The goal of this research was to measure the gene expression levels thoughout 10 stages of tomato fruit development. Whole buds, flowers or fruits were collected at various developmental timepoints. Total RNA was extracted from 10 stages of flower and fruit development. A single technical and biolog...
ORGANISM(S): Solanum lycopersicum 
2012-08-29 | E-GEOD-22300 | biostudies-arrayexpress
TranscriptomicsSmall RNA profile in Moso Bamboo root and leaf
The small RNA libraries from Moso bamboo (Phyllostachy heterocycla) roots and leaves were constructed by using high definition adapters . The small RNA profiles were analyzed. A collection of micro RNAs with similarity to the micro RNA entries in mirbase were discovered. The putative genomic loci o...
ORGANISM(S): Phyllostachys edulis 
2014-08-01 | E-GEOD-55305 | biostudies-arrayexpress
TranscriptomicsEndogenous short RNAs in Mucor circinelloides sequenced on the Illumina platform (Solexa)
We sequenced Endogenous short RNAs in Mucor circinelloides fungus grown in standard liquid culture. Short RNAs were profiled in wild type, Dicer-like 1 mutant (dcl1-), Dicer-like 2 mutant (dcl2-) and double Dicer mutant (dcl1-/dcl2-) strains. We identified many loci that produced less short RNAs in ...
ORGANISM(S): Mucor circinelloides 
2010-04-28 | E-GEOD-18958 | biostudies-arrayexpress
TranscriptomicsNovel players in myogenesis identified by target validation for muscle specific microRNAs in C2C12 myoblasts
Search of novel miR-206 target genes in C2C12 cells, based on differential expression of transcripts containing putative miR-206 binding sites. miR-206 candidate target genes were hpothesized to be upregulated in AM206 vs Day2 sample and downregulated in siRNA vs Day 1 sample. total RNA extracted fr...
ORGANISM(S): Mus musculus 
2012-07-22 | E-GEOD-34069 | biostudies-arrayexpress
TranscriptomicsHigh-throughput sequencing of small RNAs in chicken somite embryos
High-throughput sequencing of small RNAs in chicken somite embryos Dissected tissue white leghorn chicken embryos was disaggregated and RNA extracted using the miRVana kit (Ambion). Small RNA fraction between 19 and 24 nt was isolated from 15% denaturing polyacrylamide gel and 15 micro gram was liga...
ORGANISM(S): Gallus gallus 
2009-04-27 | E-GEOD-15513 | biostudies-arrayexpress
TranscriptomicsHigh-throughput sequencing of small RNAs in Medicago truncatula
Medicago truncatula endogenous small RNAs The dataset contains Medicago truncatula Gaertn. cv. Jemalong endogenous small RNA sequences in the range 18-28 nucleotides. High-throughput Solexa/Illumina sequencing was carried out at the Sainsbury Laboratory, Norwich, UK. Please see www.illumina.com for...
ORGANISM(S): Medicago truncatula 
2009-11-09 | E-GEOD-13761 | biostudies-arrayexpress
TranscriptomicsHigh-throughput sequencing of small RNAs from different developmental stages of tomato fruits
Comparison of endogenous small RNA profiles from different developmental stages of tomato fruits Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput py...
ORGANISM(S): Solanum lycopersicum 
2011-06-02 | E-GEOD-18110 | biostudies-arrayexpress
TranscriptomicsHigh-throughput sequencing of small RNAs in Vitis vinifera
Vitis vinifera endogenous small RNAs Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves, inflorescences, tendrils and small berries were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high thr...
ORGANISM(S): Vitis vinifera 
2010-04-29 | E-GEOD-18405 | biostudies-arrayexpress
TranscriptomicsmicroRNA-target RNA pairs revealed by Parallel analysis of RNA ends in Vitis vinifera
Vitis vinifera RNA degradome Isolated polyadenylated RNA from total RNA extracts of Vitis vinifera leaves, were ligated to 5'-adapter that include san MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel ...
ORGANISM(S): Vitis vinifera 
2010-04-29 | E-GEOD-18406 | biostudies-arrayexpress
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