Sequences tags expressed in ovules of Arabidopsis thaliana using Massively Parallel Signature Sequencing (MPSS)
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Alma Armenta
PROVIDER: E-GEOD-50020 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We report the use of MPSS data to compare transcripts expressed in wild-type and sporocyteless mutant ovules
2013-08-21 | GSE50020 | GEO
Project description:This series represents a very deep survey of all transcripts expressed in a wide range of human tissues and cells by Massively Parallel Signature Sequencing (MPSS). These datasets have been generated and donated to the scientific community by Lynx Therapeutics, Inc in Hayward, CA. The data contained in this submission is described in the following publication: 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004 Abstract of the publication: 'We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of over 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences between cell and tissue types are largely determined by the expression of a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little over half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the notion that most human genes have been mapped, if not functionally characterised. This dataset should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance.' Keywords: other
2005-11-29 | GSE1747 | GEO
Project description:A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent. Keywords: MPSS, Affymetrix, Agilent For the comparison, 11 different samples were used: Callus, Inforescence, Leaf, Root, Silique, Afamous Inflorescence, Ap1-10 Inflorescence, Ap3-6 Inflorescence, Sup/Ap1 Inflorescence, Leaves SA 4 hr and Leaves SA 52 hr. For details about samples, see Meyers Lab (http://mpss.udel.edu/at). All RNA samples were created in Meyers Lab. MPSS experiments were performed in Meyers Lab. Affymetrix experiments were performed in St. Clair Lab (http://stclairlab.ucdavis.edu/). Agilent experiments were performed by Sean J Coughlan from Agilent (http://www.agilent.com/). Two replicates for each samples were used in Affymetrix platform except Silique sample. Two replicates for each samples were used in Agilent platform.
2007-09-14 | E-GEOD-8994 | biostudies-arrayexpress
Project description:MPSS mouse transcriptome analysis project. See http://www.ncbi.nlm.nih.gov/geo/info/mouse-trans.html for more details. Keywords: other
2004-10-26 | GSE1581 | GEO
Project description:We used the MPSS technology to uncover gene expression profiling in a greater depth in the early embryonic gonads and primordial germ cells (PGCs) in the chicken. Total numbers of sequenced signatures were 1,012,533 and 995,676 for the PGCs and gonad. Using a false discovery rate cut-off of 0.05, we found 3.05 % of all signatures in the PCGs and 1.89 % of all signatures in the gonad signatures were significantly up-regulated compared to each sample. The MPSS result was very consistent with our previous result using EST data(http://chickgce.snu.ac.kr/). Keywords: cell type comparison Experimental animals provided for this experiment were maintained at the University Animal Farm, Seoul National University, and all experimental procedures were performed at the affiliated laboratories of the university. Gonadal cells were retrieved from the gonads of 6.5-day-old (stage 29) White Leghorn (WL) embryos by our standard procedure [26]. Embryos were freed from the yolk by rinsing with calcium- and magnesium-free PBS and the gonads were retrieved by dissection of embryo abdomen with sharp tweezers under a stereomicroscope. Embryonic gonads were collected from total 1,947 embryos by 10 highly-skilled persons through 8 separated experimental batches. Gonadal tissues were dissociated by gentle pipetting in 0.05% (v:v) trypsin solution supplemented with 0.53 mM EDTA. After centrifuged at 200xg for 5 min, total gonadal cells were loaded into MACS (Miltenyi Biotech, Germany), and the separated primordial germ cells (PGCs) were immediately stored in liquid nitrogen (-190ºC) until processed further. The numbers of PGCs in cell population before and after loading were counted. MACS treatment for chicken PGCs and counting PGC number Chicken gonadal cells were incubated with PGC-specific primary antibody, anti-stage specific embryo antigen (anti-SSEA)-1 antibody for chicken PGCs (mouse IgM isotype), for 20 min at the room temperature of 20-25?C. Anti-SSEA-1 antibody developed by [27] was obtained from the Developmental Studies Hybridoma Bank developed under the auspices of the NICHD and maintained by the University of Iowa, Development of Biological Science. After washing with 1mL buffer (PBS supplement with 0.5% BSA and 2mM EDTA), the supernatant was completely removed. The pellet was mixed with 100 ? buffer containing 20? of rat anti-mouse IgM microbeads for 15 min at 4?C. Treated cells were carefully washed by the addition of 500 ? buffer and subsequently loaded with MACS.[28] For counting cell number, chicken PGCs before or after MACS treatment were fixed with 1% (v:v) glutaraldehyde for 5 min and rinsed with 1x PBS twice. The anti-SSEA-1 ascites fluid diluted 1:1,000 in PBS was added and subsequent steps were carried out using DAKO universal LSAB® kit, Peroxidase (DAKO, USA) according to the manufacturer’s instruction. After 8 batches of cell preparation, total cell number of PGC-enriched fraction and gonadal stromal cells was 5.26X106 and 1.76X108, respectively. These cell populations were further used for total RNA isolation and massively parallel signature sequencing (MPSS) analysis.
2007-02-28 | E-GEOD-5909 | biostudies-arrayexpress
Project description:A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent. Keywords: MPSS, Affymetrix, Agilent
2007-09-14 | GSE8994 | GEO
Project description:SAGE and MPSS libraries were produced from the same RNA sample extracted from an activated CD4+ T cell clone in order to compare the ability of these techniques to indentify the full range of genes expressed in a single cell type. Keywords: Technical comparison of tag-based technologies SAGE and MPSS
2007-08-02 | GSE8612 | GEO
Project description:We used the MPSS technology to uncover gene expression profiling in a greater depth in the early embryonic gonads and primordial germ cells (PGCs) in the chicken. Total numbers of sequenced signatures were 1,012,533 and 995,676 for the PGCs and gonad. Using a false discovery rate cut-off of 0.05, we found 3.05 % of all signatures in the PCGs and 1.89 % of all signatures in the gonad signatures were significantly up-regulated compared to each sample. The MPSS result was very consistent with our previous result using EST data(http://chickgce.snu.ac.kr/). Keywords: cell type comparison
2007-03-01 | GSE5909 | GEO
Project description:MPSS analysis of mouse BLK CL.4 cells and liver cells. Total RNA, nuclear RNA and post-nuclear RNA examined. Keywords: other
2004-10-26 | GSE1067 | GEO
Project description:Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abundant of the non-redundant set of more than 75,000 sequences, whereas more than half represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly-regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs. Keywords: small RNA identification , modified MPSS
2005-09-02 | GSE3008 | GEO