Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

ABSTRACT: Long intergenic noncoding RNAs (lincRNA) transcribed from intergenic regions of eukaryotic genomes play important roles in key biological processes; yet, plant lincRNAs remain poorly characterized. Here we profiled lincRNA expression in inflorescences, leaves and roots using ATH lincRNA v1 array. we found 92% lincRNAs could be detected in at least 2 ATH lincRNA v1 arrays and majority of the lincRNAs were expressed at levels higher than those of pri-miRNAs but lower than those of mRNAs.Using a cut-off of 2-fold change, we identified 149 lincRNAs preferentially expressed in inflorescences, 232 in leaves and 164 in roots. Nine arrays were hybridized with RNAs from inflorescences, leaves and roots with 3 biological replicates.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jun Liu

PROVIDER: E-GEOD-30394 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

Project description:Long intergenic noncoding RNAs (lincRNA) transcribed from intergenic regions of eukaryotic genomes play important roles in key biological processes; yet, plant lincRNAs remain poorly characterized. Here we profiled lincRNA expression in inflorescences, leaves and roots using ATH lincRNA v1 array. we found 92% lincRNAs could be detected in at least 2 ATH lincRNA v1 arrays and majority of the lincRNAs were expressed at levels higher than those of pri-miRNAs but lower than those of mRNAs.Using a cut-off of 2-fold change, we identified 149 lincRNAs preferentially expressed in inflorescences, 232 in leaves and 164 in roots.

2011-08-06 | GSE30394 | GEO

Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)

Project description:RNA-dependent RNA polymerase 2 (RDR2) is a crucial regulator of RNA-directed DNA methylation (RdDM). Recentily RDR2 was reported to regulate expression of long intergenic noncoding RNAs. Here we used ATH lincRNA v1 expression arrays to compare lincRNA expression in inflorescence tissues of rdr2-1 and WT. Among the 4,634 lincRNAs detected we found that more than 34% of them were differentially expressed, including 676 lincRNAs that were up-regulated and 890 down-regulated in rdr2-1. Inflorescences(Col-0) x Inflorescences(rdr2-1), 3 biological replicates.

2011-08-05 | E-GEOD-30395 | biostudies-arrayexpress

Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)

2011-08-06 | GSE30395 | GEO

Expression Profiling of Arabidopsis Long Noncoding RNAs Under Continuous Light Condition

Project description:Long intergenic noncoding RNAs (lincRNAs), Natural Antisense Transcripts (NATs), and microRNAs (miRNAs) play important roles in many biological processes. To profile circadian regulated long noncoding RNAs (lncRNAs), we grow Arabidopsis plants (Col-0) under short day SD (8h light/16h dark) condition and used the ATH lincRNA v1 array to profile lincRNA, NAT and miRNA gene expression under continuous light condition. Using JTK_CYCLE to search for cycling expression pattern of genes, we found ~900 genes encoding lincRNAs, NATs and miRNAs showed significant cycling expression patterns (Adjusted P-value < 0.05).

2017-08-11 | GSE80094 | GEO

Expression of Arabidopsis cis-NAT pairs in inflorescences, leaves and roots

Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To detect the expression levels of these NAT pairs, we designed an Agilent custom array, ATH NAT array, and analyzed RNA samples from Arabidopsis inflorescences, leaves and roots, with 3 biological replicates each. Expression levels of cis-NAT pairs were investigated in WT inflorescences, leaves and roots with 3 biological replicates.

2013-12-23 | E-GEOD-49381 | biostudies-arrayexpress

Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

Project description:Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions play important roles in key biological processes.Analysis of published transcriptom datasets suggested some lincRNAs may be regulated by SERRATE,CBP20 and CBP80 in Arabidopsis. To further investigate the regulation, we use Arabidopsis lincRNA arrays v1 to detect lincRNA expression in se-2 and cbp20/80 double mutants.We found the expression levels of 940 lincRNAs (20%) out of the 4,634 lincRNAs with probes in array were significantly alerted in all mutants (P-value of eBays ANOVA < 0.05 & fold change of signal intensity > 2). This group included 525 up-regulated and 415 down-regulated lincRNAs. Seedlings(Col-0), Seedlings(se-2), Seedlings(cbp20,80 double mutant) x 3 biological replicates

2012-09-29 | E-GEOD-35963 | biostudies-arrayexpress

Identification of long ncRNAs using RNA-seq in Arabidopsis

Project description:We profiled Arabidopsis transcriptom using RNA-seq. Each RNA library yielded 223-250 million 101-bp single-end reads (235M on average). Using Tophat and Cufflinks, 30,199~30,650 assembled transcripts were identified in each of 4 samples. Of them, 1340 ones were derived from intergenic regions including 278 long intergenic ncRNAs (LincRNAs). Comparing with the 6,480 lincRNAs we identified by analysis of 200 tiling array data sets, 2,708 lincRNAs were also detected by RNA-seq. Transcriptom profiling in roots, leaves, flowers and siliques.

2012-08-23 | E-GEOD-38612 | biostudies-arrayexpress

Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

2012-09-29 | GSE35963 | GEO

Expression of Arabidopsis cis-NAT pairs in inflorescences, leaves and roots

2013-12-23 | GSE49381 | GEO

Gene expression signatures for bladder cancer tissues and normal adjacent tissues

Project description:To identify aberrantly expressed long intergenic noncoding RNAs (lincRNAs) in bladder cancer tissues compared with normal adjacent tissues, we have employed microarray expression profiling as a discovery platform to identify lincRNAs that may play important roles in bladder cancer origin and progression. Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were obtained during surgical resection, and total RNA was extracted for microarray analysis. Expression of six mRNAs and lincRNAs (E2F1, CCNE2, CCNB1, lincRNA:chr1:205404014-205407007, lincRNA:chr7:130723313-130727663, lincRNA:chr4:15669186-15683175) from this signature was quantified in the same RNA samples by real-time PCR, confirming good quality of the microarray analysis. Data in the matrix are log2 transformed. Three pairs of fresh frozen bladder cancer tissues and corresponding normal adjacent tissues were used in the microarray analysis.

2013-03-15 | E-GEOD-45184 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data