JaDenCyli
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75886 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR13158722.fastq.gz | Fastqsanger.gz | |||
| ERR13158723.fastq.gz | Fastqsanger.gz | |||
| ERR13148288_1.fastq.gz | Fastqsanger.gz | |||
| ERR13148288_2.fastq.gz | Fastqsanger.gz |
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Project description:To understand the basic biological properties of supporting cells of the mammalian inner ear, we examined the transcriptome of adult pillar and Deiters’ cells. Morphologically distinct pillar and Deiters’ cells were isolated from the organ of Corti from adult CBA/J mice. One thousand pillar and Deiters’ cells were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of three biological replicates, each with two technical repeats, was performed. The resulting sequenced reads were mapped. Comparisons between pillar cells and Deiters’ cells allow identification of enriched genes, as well as differentially expressed genes that result in cellular specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult mouse pillar and Deiters’ cells.
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Project description:Prunus persica (peach) trees carrying the ‘Pillar’ or ‘Broomy’ trait (br) have vertically oriented branches caused by loss of function mutations in a gene called TILLER ANGLE CONTROL 1 (TAC1). TAC1 encodes a protein in the IGT gene family that includes LAZY1 and DEEPER ROOTING 1 (DRO1), which regulat lateral branch and root orientations, respectively. Here, we found that some of the native TAC1 alleles in the hexaploid plum species Prunus domestica, which has a naturally more upright stature, contained a variable length trinucleotide repeat within the same exon 3 region previously found to be disrupted in pillar peach trees. RNAi silencing of TAC1 in plum resulted in trees with severely vertical branch orientations similar to those in pillar peaches but with an even narrower profile. In contrast, PpeTAC1 over-expression in plum led to trees with wider branch angles and more horizontal branch orientations. Pillar peach trees and transgenic plum lines exhibited pleiotropic phenotypes including differences in trunk and branch diameter, stem growth, and twisting branch phenotypes. Expression profiling of pillar peach trees revealed differential expression of numerous genes associated with biotic and abiotic stress, hormone responses, plastids, reactive oxygen, and secondary and cell wall metabolism. Collectively, the data provide important clues for understanding TAC1 function and show that alteration of TAC1 expression may have broad applicability to agricultural and ornamental tree industries.
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Project description:The surprising observation that virtually the entire human genome is transcribed means we know very little about the function of many emerging classes of RNAs, except their astounding diversity. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their ability to classify classes of non-coding RNAs (ncRNAs). To address this, we developed CoRAL, a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length, cleavage specificity, and antisense transcription to distinguish between different ncRNA classes. We evaluated CoRAL using genome-wide small RNA sequencing (smRNA-seq) datasets from two human tissue types (brain and skin [GSE31037]), and were able to classify six different types of RNA transcripts with 79~80% accuracy in cross-validation experiments, and with 71~73% accuracy when CoRAL uses one tissue type for training and the other as validation. Analysis by CoRAL revealed that long intergenic ncRNAs, small cytoplasmic RNAs, and small nuclear RNAs show more tissue specificity, while microRNAs, small nucleolar, and transposon-derived RNAs are highly discernible and consistent across the two tissue types. The ability to consistently annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using smRNA-seq data in less characterized organisms.
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