GEO DataSets

(Submitter supplied) To gain a deeper insight into dynamic changes of histone lysine crotonylation and lactylation during embryonic neurogenesis, ChIP-seq, ATAC-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and Kla in the developing telencephalon.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

22 Samples

Download data: BW, TXT

(Submitter supplied) To gain a deeper insight into dynamic changes of histone lysine crotonylation and lactylation during embryonic neurogenesis, ChIP-seq, ATAC-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and Kla in the P19 embryonal carcinoma cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL24247

28 Samples

Download data: BW, TXT

(Submitter supplied) To gain a deeper insight into dynamic changes of H3K9cr and H3K9ac during cell fate commitment, ChIP-seq was performed to analyze the genome-wide changes of H3K9cr and H3K9ac during neuroectodermal differentiation of the P19 embryonal carcinoma cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW, TXT

(Submitter supplied) In this work, we detected lysinebutyrylation (Kbu) and crotonylation(Kcr) sites in rice histone proteins by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells. Comparative analysis of genome-wide histone Kbu, Kcr, and H3K9ac in combination of RNA-sequencing revealed that a large number of rice genes are marked by both Kbu and Kcr, most of which overlap with H3K9ac and are active genes. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13834

41 Samples

Download data: TXT, XLSX

(Submitter supplied) To gain a deeper insight into how crotonate regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, CUT&Tag was performed to analyze the genome-wide changes of H3K4me3 and H3K27me3 stimulated with crotonate in E13.5 NSPCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW, TXT

(Submitter supplied) To gain a deeper insight into how crotonate regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, ChIP-seq was performed to analyze the genome-wide changes of H3K4me3, H3K27ac and H3K27me3 stimulated with crotonate in E13.5 NSPCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: BW, TXT

(Submitter supplied) To gain a deeper insight into how histone lysine crotonylation regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, ChIP-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and transcriptiome changes stimulated with crotonate and MS-275 in E13.5 NSPCs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL24247 GPL23479

30 Samples

Download data: BED, BW, TXT

(Submitter supplied) Histone lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. To assess relevance in histone Kcr and genome, we performed on genomic localization analysis of histone Kcr by ChIP-seq analysis.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18525

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: BW, MTX, TSV

(Submitter supplied) We examined the genome-wide distribution of histone crotonylation and H3K27ac in human embryonic stem cells and induced endoderm cells, by obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA. When compared to H3K27ac, histone crotonylation was more enriched in metabolic genes and in promoters at pluripotent state, while H3k27ac was enriched in the enhancers of endoderm genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

14 Samples

Download data: BW

(Submitter supplied) In this study we report that histone crotonylation promotes human embryonic stem cell differentiation to endoderm cells. Addition of crotonate, a precursor for crotonyl-CoA and therefore histone crotonylation, dramatically enhanced endoderm cell differentiation from human embryonic stem cells, while incubation of acetate, a precursor of acetyl-CoA and therefore histone acetylation, did not change the efficiency of endoderm differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: MTX, TSV

(Submitter supplied) Purpose: The goal of this study is to identify the whole-genome transcriptome profiling of differentially expressed genes during human embryonic stem cell differentiation. Methods: Triplicate RNA profiles were generated from hESCs and induced endoderm cells, by deep sequencing with Illumina NextSeq 500. Results: We identified 6320 genes differentially expressed between hESCs and induced endoderm cells, with foldchange  1.5 and P < 0.05. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11002 GPL9052

9 Samples

Download data: BED

(Submitter supplied) The transition from transcription initiation to elongation is a key regulatory step in gene expression, which requires RNA polymerase II (Pol II) to escape promoter proximal pausing on chromatin. While elongation factors promote pause release leading to transcription elongation, the role of epigenetic modifications during this critical transition step is poorly understood. Two histone marks on histone H3, lysine 4 trimethylation (H3K4me3) and lysine 9 acetylation (H3K9ac), co-localize on active gene promoters and are associated with active transcription. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: BW

(Submitter supplied) Chronic kidney disease (CKD) is characterized by sustained inflammation and progressive fibrosis, however therapies to slow CKD progression are limited. Histone lysine crotonylation (Kcr) as a novel post-translational modification is widespread as acetylation (Kac), but its roles in CKD are largely unknown. In the study, we firstly reported that the nuclear histone Kcr in tubular epithelial cells was significantly elevated in fibrotic kidney of patients and mice, which was positively correlated with the progression of disease. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: BED

(Submitter supplied) Chronic kidney disease (CKD) is characterized by sustained inflammation and progressive fibrosis, however therapies to slow CKD progression are limited. Histone lysine crotonylation (Kcr) as a novel post-translational modification is widespread as acetylation (Kac), but its roles in CKD are largely unknown. In the study, we firstly reported that the nuclear histone Kcr in tubular epithelial cells was significantly elevated in fibrotic kidney of patients and mice, which was positively correlated with the progression of disease. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: XLSX

(Submitter supplied) Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. Interestingly, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on TSSs and the regulated Kla can facilitate in signaling pathways and progress of tumorigenesis. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: BW

(Submitter supplied) Cancer-augmented lactogenesis has been described by the Warburg effect, and is associated with several major hallmarks of neoplasia. However, the non-metabolic functions of elevated lactate in physiology and disease remain unknown. Here we report histone lysine lactylation as a new type of epigenetic mechanism and as a functional destination for lactate. Histone lactylation is induced under glycolytic conditions such as hypoxia and M1 macrophage polarization. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21103

38 Samples

Download data: BROADPEAK, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) H3K9 acetylation was enriched in pluripotency genes in hESCs and in neural genes in neural progenitor cells

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BEDGRAPH, TXT