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RL-SAGE analysis of Zea mays leaf transcriptome

ABSTRACT: Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library.

ORGANISM(S): Zea mays

PROVIDER: GSE25994 | GEO | 2010/12/10

SECONDARY ACCESSION(S): PRJNA135425

REPOSITORIES: GEO

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RL-SAGE analysis of Zea mays leaf transcriptome

Project description:Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-10 | E-GEOD-25994 | biostudies-arrayexpress

Application of Serial Analysis of Gene Expression to the study of the gene expression profile of Leishmania infantum chagasi promastigote

Project description:This study describes the application of the LongSAGE methodology to study the gene expression profile in Leishmania infantum chagasi. A tag library was created using the LongSAGE method and consisted of 14,208 tags of 17 bases. Of these, 8,427 (59.3%) were distinct. BLAST research of the 1,645 most abundant tags showed that 12.8% of them identified the coding sequences of genes, while 82% (1,349/1,645) identified one or more genomic sequences that did not correspond with open reading frames. Only 5.2% (84/1,645) of the tags were not aligned to any position in the L. infantum genome. The UTR size of Leishmania and the lack of CATG sites in some transcripts were decisive for the generation of tags in these regions. LongSAGE revealed the gene expression profile in promastigotes of L. i. chagasi. Additional analysis will allow a better understanding of the expression profile and discovering the key genes in this life cycle.

2011-08-10 | GSE29369 | GEO

LongSAGE analysis significantly improves genome annotation

Project description:Owing to its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS: A fraction of LongSAGE tags could not be unambiguously assigned to its gene, due to the presence of widely conserved sequences downstream of particular CATG anchor sites. The presence of alternative forms of transcripts was confirmed in 45% of all detected genes. Surprisingly, a large fraction of LongSAGE tags with hits to the genome (66%) could not be assigned to any gene annotated in EnsEMBL. Among such cases, 2098 LongSAGE tags fell into a region containing a putative gene predicted by GenScan, providing experimental evidence for the presence of real genes, while 9112 genes were found out to be left out or wrongly annotated by the EnsEMBL pipeline. CONCLUSIONS: LongSAGE transcriptome data can significantly improve the genome annotation by identifying novel genes and alternative transcripts, even in the case of thus far best-characterized organisms like the mouse. Keywords: other

2005-07-20 | GSE2967 | GEO

LongSAGE analysis significantly improves genome annotation

2005-07-20 | E-GEOD-2967 | biostudies-arrayexpress

Maize leaf development, bundle sheath

Project description:Band9 maize B73 leaf, Bundle sheath strand section1(0-1.5cm) biological replica1 SDS-PAGE trypsin Orbitrap

2011-04-15 | PRD000190 | Pride

Genetic factors that respond to N in maize leaf tissue

Project description:Genotype and nitrogen-dosage effect on maize leaves collected at V8 leaf stage B73 is a model maize genotype while Illinois high protein line (IHP) is a metabolic extreme selected for higher grain protein concentration. It is a well known fact that the leaves serve as source and earshoot as a sink. Microarray analysis of V8 leaf collected from B73 and IHP genotypes grown at vairable nitrogen applications. Keywords: Genotype and N-treatment response

2009-12-11 | GSE18011 | GEO

Ralstonia sp. RL isolate:RL

Project description:Ralstonia sp. RL isolate:RL Genome sequencing and assembly

| PRJNA316535 | ENA

Deinococcus sp. RL strain:RL

Project description:Deinococcus sp. RL strain:RL Genome sequencing and assembly

| PRJNA244453 | ENA

Pseudomonas sp. RL strain:RL

Project description:Pseudomonas sp. RL strain:RL Genome sequencing and assembly

| PRJNA236066 | ENA

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem

Project description:Background: Maize plants developed typical gray leaf spot disease (GLS) symptoms initiating at the lower leaves and progressing to upper leaves through the season. Leaf material was collected at 77 days after planting, at which stage there were a large number of GLS disease necrotic lesions on lower leaves (8% surface area on average determined by digital image analysis), but very few lesions and only at chlorotic stage on leaves above the ear (average of 0.2% lesion surface area). Method:To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each. Result: A systems genetics strategy revealed regions on the maize genome underlying co-expression of genes in susceptible and resistance responses, including a set of 100 genes common to the susceptible response of sub-tropical and temperate maize.

2016-10-15 | GSE81344 | GEO

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