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Links from GEO DataSets

Items: 20

1.

Zebrafish 24hpf mutant sk8 gene expression

(Submitter supplied) The production of functional mRNA involves multiple steps including transcription initiation, elongation, and termination. spt5 encodes a conserved essential transcription elongation factor that controls RNAPII processivity in vitro and co-localizes with RNAPII in vivo. We used microarrays to detail the global expression of gene expression at 24 hours post fertilization in wild-type and Spt5 mutant (fog-sk8) to identify Spt5 transcriptionally dependent genes and affected pathways. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Dataset:
GDS3464
Platform:
GPL1319
6 Samples
Download data: CEL
Series
Accession:
GSE12826
ID:
200012826
2.
Full record GDS3464

SPT5 mutant embryos

Analysis of fog-sk8 mutant embryos containing a severe truncation of Spt5. Spt5 regulates transcription elongation. Results identify Spt5 target genes during development.
Organism:
Danio rerio
Type:
Expression profiling by array, transformed count, 2 genotype/variation sets
Platform:
GPL1319
Series:
GSE12826
6 Samples
Download data: CEL
3.

Gene expression in unfertilized eggs and the MBT stage of zebrafish embryos

(Submitter supplied) Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL9998
7 Samples
Download data: TXT
Series
Accession:
GSE20137
ID:
200020137
4.

Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window in elongation

(Submitter supplied) Spt5 is a highly conserved RNA polymerase II (Pol II)-associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in the absence of Spt5, a fraction of Pol II molecules are dislodged during elongation thus decreasing the number of Pol II complexes that complete the transcription cycle. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL17021 GPL13112
20 Samples
Download data: BW, TXT
5.

The expression of Spt5 targeted genes

(Submitter supplied) The Spt4-Spt5 complex, and its human homolog DSIF (DRB sensitivity-inducing factor), is unique in its ability to regulate Pol II processivity. Previous studies have shown that Spt5 has the characteristics of a general transcription-elongation factor. However, mutagenesis of Spt5 showed specific phenotypes during development, which were far less severe than those of Pol II defects or TBP deficient embryos. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL1319
6 Samples
Download data: CEL
Series
Accession:
GSE6127
ID:
200006127
6.

Targeting Spt5-Pol II small-molecule inhibitors uncouple distinct activities and reveal additional regulatory roles

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL16791
27 Samples
Download data
Series
Accession:
GSE136026
ID:
200136026
7.

Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on transcription [4sU-seq]

(Submitter supplied) We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. Using SPIs we identified Spt5 target genes that responded with profoundly diverse kinetics and a novel regulatory element of proximal-promoter-pausing. To validate that the effects of SPIs are at the transcriptional level, cellular RNA was metabolically labeled with 4-thio-uridine (4sU) for 2 hours in the presence of DMSO or SPI-21 in the presence or absence of TNFα. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL16791
8 Samples
Download data: XLSX
Series
Accession:
GSE136025
ID:
200136025
8.

Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on transcription [GRO-Seq]

(Submitter supplied) We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. Using SPIs we identified Spt5 target genes that responded with profoundly diverse kinetics and a novel regulatory element of proximal-promoter-pausing. To obtain a genome-wide view of the impact of SPIs on transcription, we performed Global run-on sequencing (GRO-seq) using nuclei of HeLa cells treated with either DMSO (control) or SPI-21.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL16791
3 Samples
Download data: XLSX
Series
Accession:
GSE136024
ID:
200136024
9.

Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on mRNA levels [RNA-Seq 24h]

(Submitter supplied) We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. We determined the global effect of short and long-term SPI-21 treatment by RNA-seq and compared the affected genes between the two treatments. The results revealed that temporary and constitutive Spt5-regulated genes can be distinguished by SPIs.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
8 Samples
Download data: XLSX
Series
Accession:
GSE136023
ID:
200136023
10.

Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on mRNA levels [RNA-Seq 2h]

(Submitter supplied) We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. We determined the global effect of short and long-term SPI-21 treatment by RNA-seq and compared the affected genes between the two treatments. The results revealed that temporary and constitutive Spt5-regulated genes can be distinguished by SPIs.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
8 Samples
Download data: CSV, TSV
Series
Accession:
GSE136022
ID:
200136022
11.

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [ChIP-seq_round2]

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...
Organism:
Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20584
32 Samples
Download data: BEDGRAPH
Series
Accession:
GSE93803
ID:
200093803
12.

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Schizosaccharomyces pombe
Type:
Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20584 GPL13988 GPL17225
70 Samples
Download data: BEDGRAPH, BIGWIG, TXT, WIG
Series
Accession:
GSE85182
ID:
200085182
13.

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [4tU-seq]

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...
Organism:
Schizosaccharomyces pombe
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17225
6 Samples
Download data: BIGWIG, TXT
Series
Accession:
GSE85181
ID:
200085181
14.

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [ChIP-seq_round1]

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...
Organism:
Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17225
16 Samples
Download data: BEDGRAPH
Series
Accession:
GSE85127
ID:
200085127
15.

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [RNA-seq]

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...
Organism:
Schizosaccharomyces pombe
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17225
12 Samples
Download data: WIG
Series
Accession:
GSE85125
ID:
200085125
16.

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [NET-seq]

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...
Organism:
Schizosaccharomyces pombe
Type:
Other; Expression profiling by high throughput sequencing
Platform:
GPL13988
4 Samples
Download data: WIG
17.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [TT-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20795
6 Samples
Download data: BW
Series
Accession:
GSE183506
ID:
200183506
18.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [PRO-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20795
25 Samples
Download data: BW
Series
Accession:
GSE183505
ID:
200183505
19.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL20795
69 Samples
Download data: BW
Series
Accession:
GSE180845
ID:
200180845
20.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ATAC-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20795
4 Samples
Download data: BW
Series
Accession:
GSE180844
ID:
200180844
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