GEO DataSets

(Submitter supplied) Regulated translation initiation has the potential to reshape the proteome, but conditions under which start codon selection is altered remain poorly defined. Here, using global translation initiation site profiling, we reveal widespread changes in start codon selection during the mammalian cell cycle. Low-efficiency initiation sites are preferentially repressed in mitosis, resulting in changes in the relative translation of thousands of annotated proteins, alternative translational isoforms, and uORFs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

24 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of human genes, we identified 5 Hox gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

3 Samples

Download data: WIG

(Submitter supplied) The fidelity of start codon recognition by ribosomes is paramount during protein synthesis. The textbook knowledge of eukaryotic translation initiation depicts 5’→3’ unidirectional migration of the pre-initiation complex (PIC) along the 5’UTR. In probing translation initiation from ultra-short 5’UTR, we report that an AUG triplet near the 5’ end can be selected via PIC backsliding. The bi-directional ribosome scanning is supported by competitive selection of closely spaced AUG codons and recognition of two initiation sites flanking an internal ribosome entry site. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

Platforms:

GPL17021 GPL19057 GPL18573

22 Samples

Download data: TXT

(Submitter supplied) Despite this critical role in islet cell development, the precise function and downstream genetic programs regulated directedly by NEUROG3 remain elusive. We therefore mapped genome-wide NEUROG3 occupancy in human induced pluripotent stem cell (iPSC)-derived endocrine progenitors and determined NEUROG3 dependency of associated genes to uncover direct targets. To this aim, we generated a novel hiPSC line (NEUROG3-HA-P2A-Venus), where NEUROG3 is HA-tagged and fused to a self-cleaving fluorescent VENUS reporter. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: XLSX

(Submitter supplied) Despite this critical role in islet cell development, the precise function and downstream genetic programs regulated directedly by NEUROG3 remain elusive. We therefore mapped genome-wide NEUROG3 occupancy in human induced pluripotent stem cell (iPSC)-derived endocrine progenitors and determined NEUROG3 dependency of associated genes to uncover direct targets. To this aim, we generated a novel hiPSC line (NEUROG3-HA-P2A-Venus), where NEUROG3 is HA-tagged and fused to a self-cleaving fluorescent VENUS reporter. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: BW

(Submitter supplied) Purpose: The goals of this study is to analyze the transcriptome change during retinal explant culture treated with pharmacological chaperone of rhodopsin (YC-001). Methods: The WT and RhoP23H/+ mouse eyes were enucleated at post natal day 15 and retinal explant were cultured for 24 hours followed by the 24 hours treatment with pharmacological chaperone of rhodopsin (YC-001) and dmso vehicle control. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: TXT

(Submitter supplied) Understanding the epigenomic evolution and specificity of disease subtypes from complex patient data remains a major biomedical problem. We here present DeCET (Decomposition and Classification of Epigenomic Tensors), an integrative computational approach for simultaneously analyzing hierarchical heterogeneous data, to identify robust epigenomic differences between tissue types, differentiation states, and disease subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TSV

(Submitter supplied) Understanding the epigenomic evolution and specificity of disease subtypes from complex patient data remains a major biomedical problem. We here present DeCET (Decomposition and Classification of Epigenomic Tensors), an integrative computational approach for simultaneously analyzing hierarchical heterogeneous data, to identify robust epigenomic differences between tissue types, differentiation states, and disease subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TSV

(Submitter supplied) Understanding the epigenomic evolution and specificity of disease subtypes from complex patient data remains a major biomedical problem. We here present DeCET (Decomposition and Classification of Epigenomic Tensors), an integrative computational approach for simultaneously analyzing hierarchical heterogeneous data, to identify robust epigenomic differences between tissue types, differentiation states, and disease subtypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: NARROWPEAK

(Submitter supplied) Understanding the epigenomic evolution and specificity of disease subtypes from complex patient data remains a major biomedical problem. We here present DeCET (Decomposition and Classification of Epigenomic Tensors), an integrative computational approach for simultaneously analyzing hierarchical heterogeneous data, to identify robust epigenomic differences between tissue types, differentiation states, and disease subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

40 Samples

Download data: CSV, TSV

(Submitter supplied) Understanding the epigenomic evolution and specificity of disease subtypes from complex patient data remains a major biomedical problem. We here present DeCET (Decomposition and Classification of Epigenomic Tensors), an integrative computational approach for simultaneously analyzing hierarchical heterogeneous data, to identify robust epigenomic differences between tissue types, differentiation states, and disease subtypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

196 Samples

Download data: BROADPEAK, TXT

(Submitter supplied) Celf6 is an RNA binding protein expressed in a subset of neurons in the brain. We conducted an analysis of splicing in RNAseq data derived from Celf6 knockout mice, compared to wildtype littermates. We profiled both total tissue RNAseq from a hindbrain dissection, as well as Translated Ribosome Affinity Purified (TRAP)seq specifically from serotonergic neurons – a population of cells we previously characterized as expressing Celf6. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

24 Samples

Download data: TAB, TXT

(Submitter supplied) Purpose: The goals of this study are to obtain the lncRNA landscape in 6 distinct germ cell types during mouse spermatogenesis. Methods: RNA-seq data of lncRNAs from 6 distinct cell types were generated by deep sequencing using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT-PCR validation was performed using SYBR Green assays. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT

(Submitter supplied) Totipotency is the ability of a single cell to give rise to all the differentiated cells that build the conceptus, yet how to capture this property in vitro remains incompletely understood. Defining totipotency relies upon a variety of assays of variable stringency. Here we describe criteria to define totipotency. We illustrate how distinct criteria of increasing stringency can be used to judge totipotency by evaluating candidate totipotent cell types in the mouse, including early blastomeres and expanded or extended pluripotent stem cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL17021

671 Samples

Download data: CSV, LOOM, TXT

(Submitter supplied) Gene expression analysis was carried out in human T-lymphoma Jurkat cells in order to identify candidate genes showing significant gene expression alterations allowing robust discrimination of the Auger emitter 123I, incorporated into the DNA as 123I-iododeoxyuridine (123IUdR), compared to α- and γ-radiation, which may be useful for biodosimetry purposes. Comparative gene expression analysis was performed employing whole human genome DNA microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

33 Samples

Download data: TXT

(Submitter supplied) Our study shows that CeCas12a nuclease is active in human cells and the stringency of PAM recognition could be an important factor shaping off-target editing in gene editing. Thus, CeCas12a provides a promising candidate with distinctive characteristics for research and therapeutic applications

Organism:

Homo sapiens; synthetic construct

Type:

Other

Platforms:

GPL11154 GPL15228

195 Samples

Download data: TXT, XLSX

(Submitter supplied) We used ChIPseq to identify target genes of BCL6 that are involved in leukemogenesis of E2A-PBX1 and MLL-AF4 pre-B ALL.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: BIGBED, BIGWIG

(Submitter supplied) Here we aim to demonstrate a novel approach enabling standardised and rapid characterisation of transplanted xenografts in the rodent brain. The approach employs bulk tissue dissection, inclusive of the grafted human cells and surrounding host (rodent) tissue, and utilises differences in the RNA sequences between the species to discriminate the xenograft from host gene expression. To demonstrate and validate this technique, we assessed grafts of undifferentiated human stem cells, immature neural progenitors and mature neurons following transplantation into the rodent brain. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16512

9 Samples

Download data: TAB, TXT

(Submitter supplied) Specific interactions between proteins and DNA are essential to many biological processes. Yet it remains unclear how the diversification in DNA-binding specificity was brought about, and what were the mutational paths that led to changes in specificity. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB and Noc: both having roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL18133

30 Samples

Download data: TXT

(Submitter supplied) Despite significant efforts to improve therapies for acute myeloid leukemia (AML), clinical outcomes remain poor. Understanding the mechanisms that regulate the development and maintenance of leukemic stem cells (LSC) is important to reveal new therapeutic opportunities. We have identified CD97, a member of the adhesion class of G-protein coupled receptors (GPCRs), as a frequently upregulated antigen of AML blasts that is a critical regulator of blast function. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

20 Samples

Download data: TXT