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Items: 1 to 20 of 2025

1.

RNA-Seq analysis of wild-type and mutant D. discoideum amebae

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL26668 GPL26000
83 Samples
Download data
Series
Accession:
GSE156813
ID:
200156813
2.

RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae in surface and liquid growth

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26668
24 Samples
Download data: TXT
Series
Accession:
GSE156812
ID:
200156812
3.

RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae during short-term nutrient deprivation

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26000
35 Samples
Download data: TXT
Series
Accession:
GSE156811
ID:
200156811
4.

RNA-Seq analysis of wild-type and ttpA-D450trx mutant D. discoideum amebae

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26668
8 Samples
Download data: TXT
Series
Accession:
GSE156810
ID:
200156810
5.

RNA-Seq analysis of wild-type and ttpA-C231S, ttpA-E236fsx, and ttpA-Y242fsx mutant D. discoideum amebae

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26668
16 Samples
Download data: TXT
Series
Accession:
GSE156809
ID:
200156809
6.

Transcriptional milestones in Dictyostelium development

(Submitter supplied) Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis,. These strains exhibit developmental arrest at different stages, accelerated development, or atypical morphologies. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing; Third-party reanalysis
Platforms:
GPL9379 GPL26668 GPL22784
486 Samples
Download data: TAB, XLSX
Series
Accession:
GSE152851
ID:
200152851
7.

RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16

(Submitter supplied) Purpose: Global survey of the transcriptome and comparison to the proteome in autophagy-deficient strains of D. discoideum. Results: Our RNAseq analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2. Conclusions: Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells and adds to our knowledge of functions of these proteins in Dictyostelium discoideum.
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15643
36 Samples
Download data: XLS
Series
Accession:
GSE162070
ID:
200162070
8.

Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II]

(Submitter supplied) The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Three biological replicates were assigned for each group and in total 13 groups were prepared for ATAC-seq libraries. We mapped about 30 million reads per sample to D. discoideum with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. more...
Organism:
Dictyostelium discoideum
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26000
13 Samples
Download data: NARROWPEAK
Series
Accession:
GSE153733
ID:
200153733
9.

Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Dictyostelium discoideum; Dictyostelium discoideum AX4
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms
117 Samples
Download data: H5, NARROWPEAK
Series
Accession:
GSE137604
ID:
200137604
10.

Transcriptome analysis in D. discoideium (AX2) in different developmental stages

(Submitter supplied) The goal of RNA-seq is to identify the differential expressed genes in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Two biological replicates were assigned for each group and in total 8 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26360
8 Samples
Download data: H5, XLSX
Series
Accession:
GSE137602
ID:
200137602
11.

Determine the genome-wide localization of histone and histone marks in different stages of D. discoideum

(Submitter supplied) We report the chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) on H3, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, and H3K36me3. ChIP-seq were sequenced to a depth of at least 8 million total reads/sample. We found that H3K4me3, H3K27ac and H3K4me1 show separation between unicellular and multicellular stages in principal component analysis (PCA); other marks were unable to show a clear separation in PCA.
Organism:
Dictyostelium discoideum
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26360
64 Samples
Download data: NARROWPEAK
Series
Accession:
GSE137599
ID:
200137599
12.

Chromatin accessibility in D. discoideium (AX2) in different developmental stages

(Submitter supplied) The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Two biological replicates were assigned for each group and in total 8 groups were prepared for ATAC-seq libraries. We mapped about 10 million reads per sample to D. discoideum with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. more...
Organism:
Dictyostelium discoideum
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26360
8 Samples
Download data: NARROWPEAK
Series
Accession:
GSE137598
ID:
200137598
13.

Regulated sulfur sequestration promotes multicellularity during nutrient limitation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL26668 GPL29548
46 Samples
Download data: MTX, TSV
Series
Accession:
GSE164011
ID:
200164011
14.

Regulated sulfur sequestration promotes multicellularity during nutrient limitation (scRNA-Seq)

(Submitter supplied) Dictyostelium discoideum behavior depends on nutrients1. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism2,3. This unique biology makes D. discoideum an ideal model for investigating how fundamental metabolic pathways command cell differentiation and function. We show here that reactive oxygen species (ROS), generated as a consequence of nutrient limitation, lead to the sequestration of the amino acid cysteine in the antioxidant glutathione, limiting the use of its sulfur atom for processes such as protein translation and FeS cluster-containing enzyme activity that contribute to mitochondrial metabolism and cellular proliferation. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26668
4 Samples
Download data: MTX, TSV
Series
Accession:
GSE164010
ID:
200164010
15.

Regulated sulfur sequestration promotes multicellularity during nutrient limitation (RNA-Seq)

(Submitter supplied) Dictyostelium discoideum behavior depends on nutrients1. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism2,3. This unique biology makes D. discoideum an ideal model for investigating how fundamental metabolic pathways command cell differentiation and function. We show here that reactive oxygen species (ROS), generated as a consequence of nutrient limitation, lead to the sequestration of the amino acid cysteine in the antioxidant glutathione, limiting the use of its sulfur atom for processes such as protein translation and FeS cluster-containing enzyme activity that contribute to mitochondrial metabolism and cellular proliferation. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29548
42 Samples
Download data: TSV, TXT
Series
Accession:
GSE164009
ID:
200164009
16.

Cell and molecular transitions during efficient dedifferentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26360
154 Samples
Download data: CSV
Series
Accession:
GSE144892
ID:
200144892
17.

Cell and molecular transitions during efficient dedifferentiation: testing transcription factor mutants

(Submitter supplied) Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum: comparing wild type with bzpS-, mybD-, nfyA-, DDB_G0281091-, DDB_G0269374- and DDB_G0272386- mutant cells dedifferentiating in growth medium
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26360
42 Samples
Download data: TXT, XLS
Series
Accession:
GSE144891
ID:
200144891
18.

Cell and molecular transitions during efficient dedifferentiation: single cell RNAseq

(Submitter supplied) Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum by single cell RNAseq
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26360
4 Samples
Download data: CSV
Series
Accession:
GSE144890
ID:
200144890
19.

Cell and molecular transitions during efficient dedifferentiation: testing forG- mutant

(Submitter supplied) Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum: comparing wild type and forG- (formin-) mutant cells dedifferentiating in growth medium
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26360
24 Samples
Download data: TXT, XLS
Series
Accession:
GSE144889
ID:
200144889
20.

Cell and molecular transitions during efficient dedifferentiation: population timecourses

(Submitter supplied) Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum, with comparison to forward development
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26360
84 Samples
Download data: TXT, XLS
Series
Accession:
GSE144888
ID:
200144888
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