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Items: 1 to 20 of 1798094

  • The following terms were not found in GEO DataSets: eicosyne, 3-eicosyne.
  • See the search details.
1.

The neurotrophic factor MANF regulates autophagic flux and lysosome function to promote proteostasis in C. elegans

(Submitter supplied) Mesencephalic astrocyte-derived neurotrophic factor (MANF) is the only neurotrophic factor to be conserved between C. elegans and humans. MANF is a unique neutrotophic factor, as it is a resident ER protein in cells that express it and has a role in regulating ER stress response to tunicamycin exposure and pathogenic Pseudomonas exposure. We sought to further understand the role of MANF by comparing a deletion allele, an overexpression line, and the wild-type in this RNAseq experiment.
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18245
9 Samples
Download data: TXT, XLSX
Series
Accession:
GSE278675
ID:
200278675

2.

CRISPR-CLEAR: Nucleotide-Resolution Mapping of Regulatory Elements via Allelic Readout of Tiled Base Editing

(Submitter supplied) CRISPR tiling screens have advanced the identification and characterization of regulatory sequences but are limited by low resolution arising from the indirect readout of editing via guide RNA sequencing. This study introduces CRISPR-CLEAR, an end-to-end experimental assay and computational pipeline, which leverages targeted sequencing of CRISPR-introduced alleles at the endogenous target locus following dense base-editing mutagenesis. more...
Organism:
Homo sapiens; synthetic construct
Type:
Other
Platforms:
GPL24676 GPL26526 GPL15520
49 Samples
Download data: CSV, TSV
Series
Accession:
GSE278581
ID:
200278581

3.

Drosha loss drives pineoblastoma by upregulating Ccnd2 [RNA-seq of Dicer1 tumors]

(Submitter supplied) Mutations in the microRNA processing genes DICER1 and DROSHA drive childhood cancers such as pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. To understand how microRNAs regulate proliferation of these progenitors, we developed a mouse model of pineoblastoma by ablating Drosha or Dicer1 in the developing pineal gland. The tumors that arise in these models resemble proliferative, undifferentiated embryonic progenitors. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30172
3 Samples
Download data: TAB
Series
Accession:
GSE278579
ID:
200278579

4.

Environmental alkalization suppresses deployment of virulence strategies in Pseudomonas syringae pv. tomato DC3000

(Submitter supplied) Plant pathogenic bacteria encounter a drastic increase in apoplastic pH during the early stages of plant immunity. The effects of alkalization on pathogen-host interactions have not been comprehensively characterized. Here we used a global transcriptomic approach to assess the impact of environmental alkalization on Pseudomonas syringae pv. tomato DC3000 in vitro. In addition to the Type 3 Secretion System (T3SS), we found expression of genes encoding other virulence factors such as iron uptake, and coronatine biosynthesis to be strongly affected by environmental alkalization. more...
Organism:
Pseudomonas syringae pv. tomato str. DC3000
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34917
18 Samples
Download data: TXT
Series
Accession:
GSE277531
ID:
200277531

5.

miRNA profile of mice skeletal muscle at 7 days after contusion

(Submitter supplied) Traumatic skeletal muscle fibrosis is disastrous to muscle performance. In this dataset, mice gastrocnemius was subjrct to contusion injury and then measured by miRNA microarray to identify potential therapeutic targets.
Organism:
Mus musculus
Type:
Non-coding RNA profiling by array
Platform:
GPL21265
8 Samples
Download data: TXT
Series
Accession:
GSE277119
ID:
200277119

6.

Detection Of Residual iPSCs Following Differentiation of iPSC-Derived Retinal Pigment Epithelial Cells

(Submitter supplied) PURPOSE: The goal of this study was to develop a lot release assay for iPSC residuals following directed differentiation of iPSCs to retinal pigment epithelial (RPE) cells. METHODS: RNA Sequencing (RNA Seq) of iPSCs and RPE derived from them was used to identify pluripotency markers downregulated in RPE cells. Quantitative real time PCR (qPCR) was then applied to assess iPSC residuals in iPSC-derived RPE. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
6 Samples
Download data: CSV
Series
Accession:
GSE276359
ID:
200276359

7.

RNA-seq reveals ultrasound-guided renal parenchymal infusion of mesenchymal stem cells in chronic kidney disease rat model

(Submitter supplied) Chronic kidney disease (CKD) is a disease characterized by normal or reduced proteinuria, glomerular filtration rate, progressive damage to glomeruli, tubules, and interstitium. In this study, we performed RNA-seq reveals ultrasound-guided renal parenchymal infusion of mesenchymal stem cells in SD rats animal model in chronic kidney disease. Our results indicate that differential genes in the normal group(n=3) VS CKD group(n=3) and normal group(n=3) VS MSCs treatment group(n=3).
Organism:
Rattus norvegicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25947
9 Samples
Download data: TXT
Series
Accession:
GSE275449
ID:
200275449

8.

Cytokine polymorphism in HBV infected patients in Ghanaian population

(Submitter supplied) Genetic variations in drug metabolising enzymes play a role in how individuals respond to drugs. Pharmacogene variation data in the Ghanaian population is limited and this study looks at exploring common variations that exist in our population for commonly used drugs. In addition, the study also looks at the how variations in cytokines and HLA play a role in HBV pathogenesis. Samples were validated with PCR-RFLP for accuracy
Organism:
Homo sapiens
Type:
Genome variation profiling by array
Platform:
GPL33422
185 Samples
Download data: TXT, XML
Series
Accession:
GSE274827
ID:
200274827

9.

Comprehensive profiling of Roquin binding preferences for RNA stem-loops

(Submitter supplied) Roquin proteins target specific RNA stem-loop motifs with their unique ROQ domain for mRNA degradation. The cellular levels of mRNAs are controlled by these post-transcriptional cis-regulatory stem-loop elements in the 3'-untranslated region (3'-UTR). Here, we first provide an RBNS (RNA Bind-n-Seq) experiment using pre-structured RNA libraries as input. This sRBNS (structured RBNS) was used to map Roquin's RNA binding preferences at nucleotide resolution, revealing preferences for loop sizes and consensus motifs for CDEs and ADEs.
Organism:
synthetic construct
Type:
Other
Platform:
GPL27484
10 Samples
Download data: XLSX
Series
Accession:
GSE270841
ID:
200270841

10.

DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A/YTHDF1

(Submitter supplied) RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL34284
8 Samples
Download data
Series
Accession:
GSE264642
ID:
200264642

11.

Smarcd1 is a “Goldilocks” metastasis modifier gene

(Submitter supplied) Breast cancer is the most highly diagnosed cancer worldwide, making up around 12% of all diagnosed cancers in 2020. Mortality caused by breast cancer is largely due to metastasis to distant essential organs, and a lack of metastasis-targeted therapies perpetuates incredibly poor outcomes for late-stage patients. Here we have identified a new class of “Goldilocks” genes for metastasis-targeted therapeutic development, through our focus on meiotic genetics and inherited transcriptional network regulation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
15 Samples
Download data: TXT
Series
Accession:
GSE260680
ID:
200260680

12.

Smarcd1 is a “Goldilocks” metastasis modifier gene [RNA-seq_on_plastic]

(Submitter supplied) Breast cancer is the most highly diagnosed cancer worldwide, making up around 12% of all diagnosed cancers in 2020. Mortality caused by breast cancer is largely due to metastasis to distant essential organs, and a lack of metastasis-targeted therapies perpetuates incredibly poor outcomes for late-stage patients. Here we have identified a new class of “Goldilocks” genes for metastasis-targeted therapeutic development, through our focus on meiotic genetics and inherited transcriptional network regulation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
15 Samples
Download data: TXT
Series
Accession:
GSE260672
ID:
200260672

13.

Smarcd1 is a “Goldilocks” metastasis modifier gene [rnaseq_spheroids]

(Submitter supplied) Breast cancer is the most highly diagnosed cancer worldwide, making up around 12% of all diagnosed cancers in 2020. Mortality caused by breast cancer is largely due to metastasis to distant essential organs, and a lack of metastasis-targeted therapies perpetuates incredibly poor outcomes for late-stage patients. Here we have identified a new class of “Goldilocks” genes for metastasis-targeted therapeutic development, through our focus on meiotic genetics and inherited transcriptional network regulation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
15 Samples
Download data: TXT
Series
Accession:
GSE260622
ID:
200260622

14.

Smarcd1 is a “Goldilocks” metastasis modifier gene [ATAC_on_plastic]

(Submitter supplied) Breast cancer is the most highly diagnosed cancer worldwide, making up around 12% of all diagnosed cancers in 2020. Mortality caused by breast cancer is largely due to metastasis to distant essential organs, and a lack of metastasis-targeted therapies perpetuates incredibly poor outcomes for late-stage patients. Here we have identified a new class of “Goldilocks” genes for metastasis-targeted therapeutic development, through our focus on meiotic genetics and inherited transcriptional network regulation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
15 Samples
Download data: TXT
Series
Accession:
GSE260621
ID:
200260621

15.

Drosha loss drives pineoblastoma by upregulating Ccnd2

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
Platforms:
GPL24247 GPL30172 GPL19057
64 Samples
Download data: BED, BIGWIG, BW, NARROWPEAK
Series
Accession:
GSE255914
ID:
200255914

16.

Drosha loss drives pineoblastoma by upregulating Ccnd2 [RNAseq of ceritinib treatment]

(Submitter supplied) Mutations in the microRNA processing genes DICER1 and DROSHA drive childhood cancers such as pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. To understand how microRNAs regulate proliferation of these progenitors, we developed a mouse model of pineoblastoma by ablating Drosha or Dicer1 in the developing pineal gland. The tumors that arise in these models resemble proliferative, undifferentiated embryonic progenitors. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30172
4 Samples
Download data: TAB
Series
Accession:
GSE255910
ID:
200255910

17.

Drosha loss drives pineoblastoma by upregulating Ccnd2 [RNA-seq of palbociclib treatment]

(Submitter supplied) Mutations in the microRNA processing genes DICER1 and DROSHA drive childhood cancers such as pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. To understand how microRNAs regulate proliferation of these progenitors, we developed a mouse model of pineoblastoma by ablating Drosha or Dicer1 in the developing pineal gland. The tumors that arise in these models resemble proliferative, undifferentiated embryonic progenitors. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30172
4 Samples
Download data: TAB
Series
Accession:
GSE255907
ID:
200255907

18.

T-lymphocyte recruitment and retention in lichen planus

(Submitter supplied) Lichen planus (LP) is a chronic, debilitating, inflammatory disease of the skin and mucous membranes that affects 1-2% of Americans. Its molecular pathogenesis remains poorly understood, and there are no FDA-approved treatments. We performed single cell RNA sequencing on blood and affected and unaffected skin from 7 LP patients. LP affected skin exhibited a robust immune infiltrate primarily composed of CD8 T-cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28038
20 Samples
Download data: ZIP
Series
Accession:
GSE254542
ID:
200254542

19.

CaClust: a probabilistic model for intraclonal heterogeneity (K6B)

(Submitter supplied) Clones in the cancer tissue exhibit different genotypes and phenotypes, which can be linked with their evolution, future progression, and possible treatment methods. The development of single-cell RNA sequencing allowed for the measurement of single-cell phenotypes, but without a genotype-phenotype map the phenotypes of the clones cannot be obtained. We introduce CaClust, a probabilistic graphical model that integrates whole exome, ultra-deep single-cell RNA and B-cell receptor sequencing data, to infer clonal genotypes, cell-to-clone mapping, and single-cell genotyping, enabling the combined study of clonal genotypes and phenotypes. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL28352 GPL20301
3 Samples
Download data: CSV, FASTA, MTX, TSV
Series
Accession:
GSE252416
ID:
200252416

20.

CaClust: a probabilistic model for intraclonal heterogeneity (K7B)

(Submitter supplied) Clones in the cancer tissue exhibit different genotypes and phenotypes, which can be linked with their evolution, future progression, and possible treatment methods. The development of single-cell RNA sequencing allowed for the measurement of single-cell phenotypes, but without a genotype-phenotype map the phenotypes of the clones cannot be obtained. We introduce CaClust, a probabilistic graphical model that integrates whole exome, ultra-deep single-cell RNA and B-cell receptor sequencing data, to infer clonal genotypes, cell-to-clone mapping, and single-cell genotyping, enabling the combined study of clonal genotypes and phenotypes. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other; Genome variation profiling by high throughput sequencing
Platforms:
GPL28352 GPL20301
3 Samples
Download data: CSV, FASTA, MTX, TSV
Series
Accession:
GSE252344
ID:
200252344

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