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SRP110167
Arabidopsis thaliana
36 Downloadable Samples
Illumina HiSeq 2500
Description
The NGS-associated mRNA-seq analysis was conducted to survey transcriptome changes responding to three UPR inducers (tunicamycin, DTT, & Azetidine-2-cytosine) by four double mutant of three UPR-associated transcription factors (bZIP17, bZIP28, & bZIP60) and two activators (S1P & S2P). Overall design: Four double mutant lines (bz17/28, bz28/60, bz17/60, and s1p/s2p) were subjected to the analysis.
Publication Title
ER-Anchored Transcription Factors bZIP17 and bZIP28 Regulate Root Elongation.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Microarray experiments were performed using Arabidopsis wild type plants (Col-0) and srk2cf double knockout mutants to investigate functions of two osmotic stress-activated protein kinases, SRK2C and SRK2F. Transcription profiles of wild type and mutants were compared under abscisic acid (ABA) treatment for 0, 1 and 4 h.
Publication Title
Two closely related subclass II SnRK2 protein kinases cooperatively regulate drought-inducible gene expression.
Sample Metadata Fields
Age, Time
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Microarray experiments were performed using Arabidopsis wild type plants (Col-0) and srk2cf double knockout mutants to investigate functions of two osmotic stress-activated protein kinases, SRK2C and SRK2F. Transcription profiles of wild type and mutants were compared under drought stress for 0, 1 and 4 h.
Publication Title
Two closely related subclass II SnRK2 protein kinases cooperatively regulate drought-inducible gene expression.
Sample Metadata Fields
Age, Time
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The transition from vegetative growth to flower formation is critical for the survival of flowering plants. The plant-specific transcription factor LEAFY (LFY) has central, evolutionarily conserved roles in this process, both in the formation of the first flower and later in floral patterning. We performed genome-wide binding and expression studies to elucidate the molecular mechanisms by which LFY executes these roles. Our study reveals that LFY directs an intricate regulatory network in control of floral homeotic gene expression and, unexpectedly, controls the expression of genes regulating the response to external stimuli in Arabidopsis. We further show that LFY dampens responses to a bacterial MAMP (microbe-associated molecular pattern) and to pathogen challenge. Our findings suggest a molecular mechanism for the coordination of reproductive stage development and disease response programs in plants. Regulation of these distinct survival programs by a single transcription factor may ensure optimal allocation of plant resources for reproductive fitness.
Publication Title
LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- IonTorrentProton
Description
Paf1 and Ski8 were selected as representative subunits of the Paf1 complex (PAF1C), and RNA-seq analysis was performed in triplicate to compare the genes affected by Paf1, Ski8, and Rtf1 knockdown in HeLa cells. Overall design: Total RNA was harvested from control HeLa and Ski8 knockdown cells at day 4 and from Rtf1 or Paf1 knockdown cells at day 7 and was subjected to RNA-seq in triplicates.
Publication Title
Correction for Cao et al., Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
To identify the transcripts fractionated into microsome fraction in ribosome-independent manner, we isolate rough microsome fraction by sucrose density gradient ultracengrifugation, then the rough microsome fraction is centrifugated following treatment with puromycine and EDTA in high-salt buffer to remove ribosomes. The pellet and surpernatant are named naked microsome fraction (NM) and stripped ribosome fraction (SR), respectively. By calculating the ratio of the level of each mRNA in NM and SR, we identify the enriched transcripts in NM. Overall design: Transcript profiles of subcellular fractions from S2-DRSC Drosophila cultured cell
Publication Title
Control of tissue size and development by a regulatory element in the <i>yorkie</i> 3'UTR.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 11 Downloadable Samples
Description
Purpose: Characterize the role of the coactivator subunit TAF9b during differentiation of embryonic stem cells into motor neurons as well in mouse newborn spinal column tissues. Overall design: RNA-seq comparing WT and TAF9B KO mouse ES cells differentiated into motor neurons. RNA-seq comparing WT and TAF9B KO mouse newborn spinal column tissues. ChIP-seq mapping TAF9b and RNA Pol II binding sites in in vitro differentiated motor neurons.
Publication Title
Core promoter factor TAF9B regulates neuronal gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The purpose of this study was to isolate NCSCs from oral mucosa using the neurosphere technique.
Publication Title
Sphere-Derived Multipotent Progenitor Cells Obtained From Human Oral Mucosa Are Enriched in Neural Crest Cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To recruit phagocytes, apoptotic cells characteristically release ATP, which functions as a danger signal. Here, we found that the culture supernatant of apoptotic cells activated the macrophages to express anti-inflammatory genes such as NR4A and Thbs1. A high level of AMP accumulated in the apoptotic cell supernatant in a Pannexin1-dependent manner. A nucleotidase inhibitor and A2a adenosine receptor antagonist inhibited the apoptotic supernatant-induced gene expression, suggesting AMP was metabolized to adenosine by an ecto-5-nucleotidase expressed on macrophages, to activate the macrophage A2a adenosine receptor. Intraperitoneal injection of zymosan into AdoR A2a- or Panx1-deficient mice produced high, sustained levels of inflammatory mediators in the peritoneal lavage. These results indicated that AMP from apoptotic cells suppresses inflammation as a calm down signal.
Publication Title
Immunosuppression via adenosine receptor activation by adenosine monophosphate released from apoptotic cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples