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GSE30166
Arabidopsis thaliana
78 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 25 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under standard pH (pH 5.7) or roots that had been transfered to low pH (pH 4.6) media for 24 hours.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the effect of low pH on developmental stages in the root, we dissected the root into four developmental zones after exposure to low pH and expression profiled each zone.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Age
View Samples- Arabidopsis thaliana
- 14 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were used. FACS cell populations were isolated from roots grown under sulfur deficient conditions for 3 hours.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We preformed at time-course of the expression of whole Arabidopsis roots for 3H, 12H, 24H, 48H and 72H after transfer to media lacking sulfur. We combined these data with 13 other datasests and performed a meta-analysis to ask whether a universal stress response exists in Arabidopsis roots.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the effect of sulfur deficiency on developmental stages in the root, we dissected the root into four developmental zones after exposure to sulfur deficiency and expression profiled each zone.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 3 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To estimate the effect of protoplasting and sorting on low pH-regulated gene expression, we generated expression profiles for whole roots treated with low pH for 24 hours and whole roots that had been protoplasted and FACS sorted after 24 hours of exposure to low pH.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 58 Downloadable Samples
IlluminaGenomeAnalyzerII, IlluminaGenomeAnalyzer
Description
Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer–associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1–repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes. Overall design: 21 prostate cell lines sequenced on the Illumina Genome Analyzer and GAII. Variable number of replicates per sample. RNA-Seq data from prostate cancer tissues used in this study will be made available on dbGAP.
Publication Title
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 10 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 34 Downloadable Samples
- Illumina HiScanSQ
Description
RNA sequencing was performed on proliferating and differentiating wildtype and emerin-null myogenic progenitors to identify molecular pathways implicated in Emery-Dreifuss Muscular Dystrophy. Overall design: Total RNA was isolated from 2 million wildtype or emerin-null H2Ks during proliferation and at each day of differentiation using the miRNeasy Mini Kit (Qiagen, product #217004) and processed according to manufacturer's protocol. RNA was isolated from three independent cell culture plates for each sample.
Publication Title
Expression Profiling of Differentiating Emerin-Null Myogenic Progenitor Identifies Molecular Pathways Implicated in Their Impaired Differentiation.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples