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Caenorhabditis elegans
25 Downloadable Samples
Illumina Genome Analyzer II, Illumina Genome Analyzer IIx
Description
In C. elegans, the bilateral Q neuroblasts and their neuronal descendants undergo long-range migrations. QR (on the right) polarizes and migrates anteriorly, whereas QL (on the left) polarizes and migrates posteriorly. The Hox transcription factor MAB-5 is a determinant of this posterior migration of QL, and likely regulates target genes that determine posterior versus anterior migration. We sought to identify these downstream networks of genes via RNA-seq, and identify transcripts that are differentially expressed between wildtype and mab-5 mutant genotypes. We sequenced RNA extracted from early L1 staged animals from four C. elegans genotypes: wildtype worms, mab-5(e1239) and mab-5(gk670) loss-of-function mutants, and the mab-5(e1751) gain-of-function mutant. Tests revealed a number of differentially expressed genes, many of which were validated by subsequent RNAi.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Disease, Cell line
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal is to identify changes in gene expression with aging in the heads of mated female D. melanogaster. We measured lifespan in mated females from several hundred RILs (Recombinant Inbred Lines) derived from the "B" panel of the DSPR (Drosophila Synthetic Population Resource), additionally sampling young (Day 3) and old (day on which at least 50% of the animals were dead) animals. Subsequently we harvested RNA, specifically from heads (5-10 per strain per sample), from six RILs, for each RIL generating 2 RNA samples (from young and from old females). Each of the 12 total RNA samples was used to construct an Illumina TruSeq RNAseq library, and all 12 libraries were mixed, and run over two PE50 "Rapid Run" HiSeq2500 lanes.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
We carried out genetic mapping in the Drosophila Synthetic Population Resource (FlyRILs.org, Genome Research 22:1558-66) to identify QTL (quantitative trait loci) contributing to variation in the nicotine resistance of first-instar larva. To follow up this work, and look for candidate genes exhibiting differential gene expression, we carried out RNAseq on pools of first-instar larvae from two of the inbred strains that founded the DSPR: Lines A3 (derived from Bloomington Stock 3844) and A4 (derived from Bloomington Stock 3852). In addition we exposed groups of larvae from each genotype to nicotine for a short period of time, resulting in four samples: A3-control, A3-nicotine, A4-control, and A4-nicotine. Analysis revealed a number of genes that changed in expression between genotypes and/or treatments.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal is to identify changes in gene expression with aging in the bodies (thorax plus abdomen) of mated female D. melanogaster. We measured lifespan in mated females from several hundred RILs (Recombinant Inbred Lines) derived from the "B" panel of the DSPR (Drosophila Synthetic Population Resource), additionally sampling young (Day 3) and old (day on which at least 50% of the animals were dead) animals. Subsequently we harvested RNA from subsets of the samples, generating 4 pools of RNA from (a) young animals from short-lived lines, (b) old animals from short-lived lines, (c) young animals from long-lived lines, and (d) old animals from long-lived lines. Each pool was used to construct an Illumina TruSeq RNAseq library, all 4 libraries were mixed, and run over a single SR100 HiSeq2500 lane.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 5 Downloadable Samples
- Illumina Genome Analyzer
Description
Next Generation Sequencing Analysis of Wild Type and Mist1-/- Pancreatic Transcriptomes
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Glycine max
- 12 Downloadable Samples
Affymetrix Soybean Genome Array (soybean)
Description
Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation. Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions. To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature. After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChip Soybean Genome Arrays. A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. The microarray data was supported by quantitative real-time PCR data.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples
SRP011480- Zea mays
- 92 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer IIx
Description
Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the "Zeanome", a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 83 Downloadable Samples
- Illumina HiSeq 2000
Description
No description.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 74 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq transcriptome profiles of genetically fate-mapped serotonin neurons, manually sorted from multiple anatomic domains, at both population and single cell resolution.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Zea mays
- 64 Downloadable Samples
- Illumina HiSeq 2000
Description
Heterosis which is the improved vigor of F1-hybrids compared to their parents is widely exploited in maize (Zea mays L.) breeding to produce elite hybrids of superior yield. The transcriptomes of the maize inbred lines B73 and Mo17 and their reciprocal hybrid offspring were surveyed in the meristematic zone, the elongation zone, cortex and stele tissues of primary roots, prior to the developmental manifestation of heterosis. Single parent expression (SPE) is consistent with the dominance model for heterosis in that it denotes genes that are expressed in only one parent but in both reciprocal hybrids. In primary root tissues, between 1,027 (elongation zone) and 1,206 (stele) SPE patterns were observed. As a consequence, hybrids displayed in each tissue >400 active genes more than either parent. Analysis of tissue-specific SPE dynamics revealed that 1,233 of 2,233 SPE genes displayed SPE in all tissues in which they were expressed while 1,000 SPE genes displayed in at least one tissue a non-SPE pattern. In addition, 64% (17,351/ 27,164) of all expressed genes were assigned to the two subgenomes which are the result of an ancient genome duplication. By contrast, only between 18 and 25% of the SPE genes were assigned to a subgenome suggesting that a disproportionate number of SPE genes are evolutionary young and emerged after genome duplication. We hypothesize that this phenomenon is associated with human selection of favorable maize genotypes which might primarily affect younger genes rather than genes whose functions have been conserved for millions of years.
Publication Title
Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples