Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [bulk RNA-seq]

ABSTRACT: Purpose:To asses changes in gene expression profiles from the P0 wild type littermate controls cortex, hGFAP-Cre, SmoM2f/+ mice cortex and ShhN IUE (ShhN palsmid were electroporated to wild type mice cortex at E13.5 and the cortex were dissected at P0) mice. Methords:Total RNA was isolated and sequenced using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered significantly changed whicn perform fold-change>=2 and P value <= 0.05 Results: Compared to controls, 2466 genes were significantly down-regulated, and 5289 genes were up regulated in the RNA expression level of the SmoM2 mice; 3492 genes were significantly down-regulated, and 3577 genes were up regulated in the RNA expression level of the cortex of ShhN IUE mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE138878 | GEO | 2020/02/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [single-cell RNA-seq]

Project description:Purpose:To asses changes in gene expression profiles of single cell from the E16.5 wild type littermate controls cortex, and ShhN IUE (ShhN palsmid were electroporated to wild type mice cortex at E13.5 and the cortex were dissected at E16.5) mice. Methords: E16.5 wild type and ShhN-IUE cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension. The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions. The cDNA libraries were purified, quantified using Agilent 2100 Bioanalyzer, and sequenced on the Illumina Hiseq4000 Results: 7834 cells (2368 median genes per cell) captured for the Control cortex. And 8538 cells with 2422 median genes per cell captured for Shh-IUE mice.

2020-02-19 | GSE140816 | GEO

Sequential regulation of glutamatergic and subtype-specific projection neuron identities in the developing cerebral cortex

Project description:Purpose:To asses changes in gene expression profiles of cortices from the P0 wild type littermate controls and Tle4-/- null mutant mice. Methords:Total RNA was isolated and sequenced using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered significantly changed whicn perform P value <= 0.05 Results: Compared to controls, 306 genes were significantly down-regulated in the Tle4 null mutant mice, and 338 genes were significantly up-regulated in the Tle4 null mutant mice.

2019-12-18 | GSE142269 | GEO

BMP7 expression in mammalian cortical radial glial cells increases the length of the neurogenic period

Project description:Purpose:To asses changes in gene expression profiles of single cell from the E39 Ferret Cortex. Mouse E18 littermate controls cortex, and Smo CKO (SmoF/F hGFAP-Cre) mice. Methords: E39 ferret cortex, E18 wild type and Smo CKO cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension. The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions. The cDNA libraries were purified, quantified using Agilent 2100 Bioanalyzer, and sequenced on the Illumina Hiseq4000 Results: E18 SmoF/F (control) cortex, 10524 cells, 1954 genes/cell; hGFAP-Cre; SmoF/F cortex, 7596 cells, 2104 genes/cell; E39 ferret cortex, 23482 cells, 1759 genes/cell.

2023-06-12 | GSE221389 | GEO

Enhancing CDK4/6 inhibitor therapy for medulloblastoma using nanoparticle delivery and scRNA-seq-guided combination with sapanisertib

Project description:We report scRNA-seq data showing the effect of palbociclib treatment on medulloblastomas that form in Smo-mutant mice. We generate tumor-bearing mice by breeding hGFAP-Cre and SmoM2 mouse lines to prodce tumor-prone progeny heterozygous for both transgenes (G-Smo mice). We compare tumors from untreated G-Smo mice to tumors from G-Smo ice treated with nanoparticle--delievered palbociclib, using Drop-seq-based scRNA-seq.

2021-11-16 | GSE188672 | GEO

Chronic AMPK inactivation slows SHH medulloblastoma progression by inhibiting mTORC1 and depleting tumor stem cell populations

Project description:We report scRNA-seq data showing the effect of Prkaa1/2 deletion on medulloblastomas that form in Smo-mutant mice. We generate tumor-bearing mice by breeding hGFAP-Cre/Prkaa1fl/fl/Prk112fl/fl and Prkaa1fl/fl/Prk112fl/fl/SmoM2 mouse lines to prodce tumor-prone progeny with homozygous, conditional deletion of Prkaa1 and Prkaa2 (G-SmoAMPK mice). We compared tumors from G-Smo mice withintact Prkaa1 and Prkaa2 to tumors from G-SmoAMPK mice, using Drop-seq-based scRNA-seq.

2021-12-08 | GSE190297 | GEO

Snf2h and Satb2-dependent chromatin remodeling establishes callosal projection neuron identity through clustered protocadherin gene regulation.

Project description:Mouse cortex (dorsal telencephalon) analysis from Snf2h cKO-Emx1 mice versus control littermates at birth (P0). P0 mouse cortex, 3 cortices pooled per sample, n=2 per genotype.

2014-12-31 | GSE59152 | GEO

Transcription profiling of mouse medulloblastoma

Project description:Dysregulatio of Hh signaling has been shown to be involved in the formation of human medulloblastoma. We generated a mouse model (CAGGS-CreER;R26-SmoM2) of Hh related tumors. We used microarray to profile gene expression in Hh induced mouse medulloblastoma and identified distinct classes of up-regulated or down-regulated genes during Hh dependent tumorigenesis . Experiment Overall Design: Medulloblastoma samples and adjacent wild type cerebellar tissue from CAGGS-CreER;R26-SmoM2 mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

2008-06-16 | E-GEOD-9299 | biostudies-arrayexpress

Transcriptional profiling of SmoM2 expressing IFE cells at different stages of basal cell carcinoma formation

Project description:Basal cell carcinoma initiating cells undergo profound and rapid reprogramming into embryonic hair follicle progenitor like fate upon SmoM2 expression. Activation of Wnt/M-NM-2-catenin signaling pathways is required in a cell autonomous manner for the reprogramming of adult IFE progenitors into EHFP-like fate as well as for tumor initiation. We used MA to define the molecular changes that occur in basal cell carcinoma initiating cells form the first oncogenic hit to the development of invasive tumor and further on to investigate the role of Wnt/M-NM-2-catenin signaling activation in molecular changes occurring early during BCC development. Basal interfollicular cells expressing SmoM2 were FACS isolated at different stages of tumor development and in M-NM-2-catenin LOF condition for RNA extraction and hybridization on Affymetrix microarrays. By comparing the transcriptional profile of SmoM2 expressing cells with FACS-isolated cells from littermate control mice, we determined a list of genes differentially regulated by SmoM2 expression as specific SmoM2 signature.

2012-09-06 | E-GEOD-40612 | biostudies-arrayexpress

Transcription Factors Sp8 and Sp9 Coordinately Regulate Olfactory Bulb Interneuron Development [RNA-seq 2]

Project description:Purpose: To asses changes in gene expression profiles from the P30 wild type littermate control olfactory bulbs and conditional double knockout olfactory bulbs of hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox mice. Methods: Total RNA was isolated and sequenced from the olfactory bulbs of the P30 wild type littermate controls or hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox mice in tetrad using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=2 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of Sp8 and Sp9. Results: 31 genes were significantly increased and 74 genes were significantly decreased in expression level due to the loss of Sp9 and Sp8 expression.

2017-01-04 | GSE93061 | GEO

Cortical gene expression profiles in the forebrain-specific Foxp1 conditional knockout (cKO) mice at P0 and P7.

Project description:Examination of 2 different developmental time points (P0 and P7) in the cortex of control and Foxp1 cKO mice.

2018-09-14 | GSE98913 | GEO