Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells and Q175 HET or WT mice. Plus and minus knockdown of PIAS1.

ABSTRACT: HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. four control in duplicate and three HD samples in duplicate with CAG repeat length in juvenile onset range were differentiated as biological growth replicates (separate differentiations) into medium spiny neuron-like cells. Cells were treated with LNPs with siRNA for knockdown of PIAS1 or a luciferase control. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. For mouse data WT and HET GFP+ micro-dissected flash frozen brain regions (striatum) were homogenized in TRIzol reagent (Invitrogen) and RNA were collected and purified using RNEasy Mini kit (Qiagen). Mice were treated with AAV2/1 expressing either a miRNA against Pias1 (miPias1.3), a control scrambled miRNA (miSafe). 1 µg of RNA with RIN values >8 were used for library preparation using the strand specific Illumina TruSeq mRNA protocol. Libraries were sequenced on the HiSeq 4000 using 100 cycles to obtain paired-end 100 reads.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE162349 | GEO | 2021/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Total RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron (MSN)-like cells. Three control in triplicate, one control in duplicate, one HD samples with CAG repeat length in typical adult onset range in triplicate and one in duplicate, and five HD samples with CAG repeat length in typical juvenile onset range in triplicate were differentiated as biological growth replicate (separate differentiations) into medium spiny neuron-like cells. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. 1 µg of RNA with RIN values >9 were used for library preparation using the strand specific Illumina TruSeq Total RNA protocol. Libraries were sequenced on the HiSeq 2500 using 100 cycles to obtain paired-end 100 reads at >50M reads per sample.

2020-03-01 | GSE144559 | GEO

ATAC-Seq for control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. Three control in triplicate, one control in duplicate, one HD samples with CAG repeat length in typical adult onset range in triplicate and one in duplicate, and five HD samples with CAG repeat length in typical juvenile onset range in triplicate were differentiated as biological growth replicate (separate differentiations) into medium spiny neuron-like cells. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. 1 µg of RNA with RIN values >9 were used for library preparation using the strand specific Illumina TruSeq Total RNA protocol. Libraries were sequenced on the HiSeq 2500 using 100 cycles to obtain paired-end 100 reads at >50M reads per sample.

2020-03-01 | GSE144518 | GEO

H3K4me3 ChIP-Seq profiles of control and huntington's disease iPSC-derived medium spiny neuron-like cells

2020-03-01 | GSE144493 | GEO

gene activation by IFNs in wild type and Pias1 null BMMs

Project description:Microarray analysis was designed to study the effect of PIAS1 on interferon (IFN) signaling pathway by comparing the gene activation profiles of wild type and Pias1 null cells in response to IFN treatments. Microarray analysis was performed essentially following the manufacturer’s instructions (Affymetrix). Briefly, bone marrow-derived macrophages (BMMs) from wile type or Pias1 null littermates were either untreated, or treated with IFN-beta (500 U/ml) or IFN-gamma (10 ng/ml) for 2h or 4h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Keywords: parallel sample

2004-07-16 | GSE1552 | GEO

Transcription profiling of mouse wild type and Pias1 null cells in response to IFN treatments to study the effect of PIAS1 on interferon (IFN) signaling pathway

Project description:Microarray analysis was designed to study the effect of PIAS1 on interferon (IFN) signaling pathway by comparing the gene activation profiles of wild type and Pias1 null cells in response to IFN treatments. Microarray analysis was performed essentially following the manufacturer's instructions (Affymetrix). Briefly, bone marrow-derived macrophages (BMMs) from wile type or Pias1 null littermates were either untreated, or treated with IFN-beta (500 U/ml) or IFN-gamma (10 ng/ml) for 2h or 4h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix).

2007-10-10 | E-GEOD-1552 | biostudies-arrayexpress

Effect of PIAS1 on gene expression

2014-02-06 | GSE44024 | GEO

Effect of PIAS1 on gene expression

Project description:To study the effect of PIAS1 on transcriptional regulation, we establishedstable PIAS1 shRNA knockdown cells in breast cancer cell line MDA-MB231. By comparing the expression profiles of control vs PIAS1 knockdown cells, we can identify potential PIAS1 target genes involved in breast tumorigenesis. MDA-MB231 Control shRNA and PIAS1 shRNA2 cells were cultured in DMEM plus 10% FBS (DMEM) or SCM for 30 h, and total RNA was used for microarray.

2014-02-06 | E-GEOD-44024 | biostudies-arrayexpress

Single cell RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. One control and one HD sample with CAG repeat length in typical adult onset range were differentiated into medium spiny neuron-like cells. Cells were dissociated into single cell suspension and single cell viability for each sample was determined (86.9% for control, 80.9% for HD). Cells were processed using 10x genomics single cell platform. Libraries were sequenced on the HiSeq 4000 using 100 cycles to obtain paired-end 100 reads at >50M reads per cell. The estimated number of cells sampled was 5,070 (control) and 3,829 (HD) with an average number of reads per cell at 31,675 (control) and 41,939 (HDQ). After QC filtering, the data were aggregated using Cell Ranger and gene-by-cell expression matrices generated and used as input for Seurat and Scanpy.

2020-03-01 | GSE144477 | GEO

PIAS1 is a target gene selective androgen receptor coregulator in prostate cancer cell chromatin

Project description:To study the importance of PIAS1 (protein inhibitor of activated STAT1) for the androgen-regulated transcriptome of VCaP prostate cancer cells, we silenced its expression by RNAi. Transcriptome analyses revealed that a subset of the androgen-regulated genes is significantly influenced, either activated or repressed, by PIAS1 depletion. The depletion also exposed a completely new set of genes to androgen regulation, suggesting that PIAS1 can mask genes from androgen receptor (AR). Pathway analyses of gene expression data suggest involvement of PIAS1 in VCaP cell proliferation. According to genome-wide ChIP-seq analyses, PIAS1 interacts with the AR on chromatin harboring also SUMO2/3, as androgen exposure multiplied the occupancy of PIAS1 in the chromatin, and resulted in nearly complete overlap with AR chromatin binding events. PIAS1 interacted also with pioneer factor FOXA1 in the chromatin. Our results strongly suggest that PIAS1 is a genuine chromatin-bound coregulator of AR which functions in a target gene selective fashion in prostate cancer cells.

2015-01-02 | GSE56086 | GEO

Genome-wide analysis of the effect of PIAS1 knockdown by siRNA on the androgen regulated gene programs

Project description:Analysis of PIAS1 co-regulation in the androgen signaling pathways in prostate cancer cell line. VCaP cells were exposed to control (siSCR) or PIAS1 (siPIAS1) targeted siRNA for 96h. After 16h of 100 nM testosterone (or without) treatment the total RNA was isolated, each treatment included three replicates.

2013-01-01 | E-GEOD-30316 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data