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Rice Transcriptome - Slide A; Slide B

ABSTRACT: [Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. Rice 30K Operon Version 1.0 -70 mer oligos. The array is in 48 pin conformation. It has 25 columns and 25 rows in each of 4 x 12 subarrays. This is the slideA of the two slide sets. Platform_catalog_number: XDEN-A Platform_coating: poly L lysine Platform_manufacture_protocol: Omnigrid 100 contact printer; TeleChem Stealth SMP3 split pins; See http://keck.med.yale.edu/dnaarrays/printing Platform_manufacturer: Keck Biotechnology Resource Lab at Yale Platform_support: glass slide Platform_technology: spotted oligonucleotide ] Series_sample_order: Sample 1-15 Slide A; Sample 16-30 Slide B Keywords: other

ORGANISM(S): Oryza sativa Oryza sativa Indica Group

PROVIDER: GSE2691 | GEO | 2005/05/24

SECONDARY ACCESSION(S): PRJNA92201

REPOSITORIES: GEO

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Rice Transcriptome - Slide A; Slide B

Project description:[Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. Rice 30K Operon Version 1.0 -70 mer oligos. The array is in 48 pin conformation. It has 25 columns and 25 rows in each of 4 x 12 subarrays. This is the slideA of the two slide sets. Platform_catalog_number: XDEN-A Platform_coating: poly L lysine Platform_manufacture_protocol: Omnigrid 100 contact printer; TeleChem Stealth SMP3 split pins; See http://keck.med.yale.edu/dnaarrays/printing Platform_manufacturer: Keck Biotechnology Resource Lab at Yale Platform_support: glass slide Platform_technology: spotted oligonucleotide ] Series_sample_order: Sample 1-15 Slide A; Sample 16-30 Slide B

2010-06-10 | E-GEOD-2691 | biostudies-arrayexpress

Validation of gene expression from rice locus (dye-swap experiment)

Project description:Transcription from 23K TIGR-loci were confirmed by full-length cDNA mapping, but other 33K TIGR-loci were not confirmed. However, it was not natural to think that full-length cDNA libraries was included almost rice genes, because the transcription of 3K CDS-ANE were confirmed by other transcriptome resources in TIGR OSA1. So, for detection of gene expression from FL-locus and TIGR-locus, we designed about 82K 60mer oligo probes based on TIGR Pseudomolecules release 2. However, TIGR-locus was revised according to revised Pseudomolecules and other additional transcriptome resources. Therefore designed 82K probes were re-mapped on TIGR4 ,and 63455 probes were mapped on 43090 locus Keywords: tissue type comparison

2007-11-28 | GSE7374 | GEO

Validation of gene expression from rice locus (self-hybridization)

Project description:Transcription from 23K TIGR–loci were confirmed by full–length cDNA mapping, but other 33K TIGR–loci were not confirmed. However, it was not natural to think that full–length cDNA libraries was included almost rice genes, because the transcription of 3K CDS–ANE were confirmed by other transcriptome resources in TIGR OSA1. So, for detection of gene expression from FL–locus and TIGR–locus, we designed about 82K 60mer oligo probes based on TIGR Pseudomolecules release 2. However, TIGR–locus was revised according to revised Pseudomolecules and other additional transcriptome resources. Therefore designed 82K probes were re-mapped on TIGR4 ,and 63455 probes were mapped on 43090 locus Keywords: tissue type comparison

2007-11-28 | GSE7366 | GEO

Oryza sativa Indica Group

Project description:Rice Transcriptome - Slide A; Slide B

| PRJNA92201 | ENA

Preliminary exploration of Oryza sativa small RNAs - Run 1 and 2

Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.

2009-06-08 | GSE16248 | GEO

miRNA post transcriptional control of umbilical cord mesenchymal stem cell osteogenic differentiation.

Project description:Umbilical cord mesenchymal stem cells were stimulated to osteogenesis by 24h, 48h and 7 days. Undifferentiated and treated cells have their total RNA extracted and 25 ug were used to extract micro RNAs by Flash PAGE Fractionator (Ambion). These miRNA were labeled and used to hybridize to 662 oligo arrays corresponding to miRNA sequences from human, rat and mouse. The hybridized slides were scanned in the Amersham Automatic Slide Processor, quantified by TIGR Spotfinder software and submitted to stathiscal treatment in TIGR MEV software.

2011-07-31 | E-MEXP-3080 | biostudies-arrayexpress

Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

Project description:Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed. Missing from these measurements, however, is the ability to routinely and easily spatially localise these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are ‘tagged’ with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as input into a wide variety of single-nucleus profiling assays. We used Slide-tags to profile two different stages of development in the mouse brain.

2023-10-03 | GSE244355 | GEO

Gene expression profiles of various tissues under different physiological conditions

Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues

2008-04-01 | GSE7530 | GEO

Spatial transcriptome analysis (Slide-seq2) of mouse main olfactory bulb

Project description:Spatial transcriptome analysis (Slide-seq2) of mouse main olfactory bulb

| PRJNA714910 | ENA

Spatial transcriptome analysis (Slide-seq2) of mouse main olfactory bulb

Project description:The goal of spatial transcriptome analysis is to profile the glomeruli position representing different olfactory receptors. 20 OB sections were obtained with equal spacing (130 μm) along the anterior-posterior axis. In total, two sets of 20 slides were obtained from different animals. All of the Slide-seqV2 procedures were performed as previously described

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