RNA sequencing of (1) isolated retinal endothelial cells from wildtype and Zmiz1-KO endothelial cells and (2) control and Zmiz1 shRNA treated MS1 cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1041428 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR25919200_1.fastq.gz | Fastqsanger.gz | |||
| SRR25919200_2.fastq.gz | Fastqsanger.gz | |||
| SRR25919202_1.fastq.gz | Fastqsanger.gz | |||
| SRR25919202_2.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 association with vascular system, its role in physiological and pathological angiogenesis is significantly unknown. Here, we use (1) MS1 cell line treated with control shRNA and Zmiz1 shRNA and (2) murine model to knockout Zmiz1 in endothelial cells using Cdh5CreERT2 and isolate retinal endothelial cells (iRECs) then performed RNA sequencing to profile transcriptional changes upon Zmiz1 deletion. Retinal ECs were isolated from P7 pups as previously described (Patel et al., 2022. JCI Insight). Briefly, isolation of ECs from the retinas was performed using the Miltenyi Neural tissue Dissociation Kit (P) (Miltenyi, 130-092-628). For each sample, 8-10 retinas were pooled and digested to obtain a single cell suspension. CD31+ cells were separated from the cell mixture via magnetic activated cell sorting. MS1 cells were transfected with 20μM of either control-shRNA or Zmiz1-shRNA using Lipofectamine3000 (Thermofisher, L3000015). Next, RNA was isolated from the cells and used for downstream RNA-sequencing. RNA concentration and RNA integrity number were determined. RNA library was prepared, quantified, and verified using TruSeq RNA Library Prep Kit v2, Qubit dsDNA High Sensitivity Assay kit and Bioanalyzer DNA1000 assay kit respectively. Verified samples were sequenced on a Nextseq 500/550 platform. RNA-seq data analysis was performed using illumina BaseSpace Sequence Hub. Results: For iRECs , we found 2,364 differentially expressed genes of which 834 genes were upregulated while 1530 genes were downregulated. Downregulated genes were enriched in biological processes such as angiogenesis, vascular development, and cell growth. For MS1 cells, we found 1,711 differentially expressed genes of which 718 genes were upregulated while 993 genes were downregulated. Downregulated genes were enriched in biological processes such as regulation of angiogenesis. Conclusions: We assessed changes in transcriptional landscape in MS1 and iRECs following Zmiz1 deletion.
2025-05-28 | GSE242406 | GEO
Project description:Human T-cell Acute lymphoblastic Leukemia cell line CEM was transfected with either shRNA against ZMIZ1 or scrambled shRNA. Four (non-paired) biological replicates of each condition had mRNA assays performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets. A supplementary Excel workbook holding the same processed data as the series matrix file is provided, with some probe set annotation, and a simple statistical comparison. The raw (.CEL) files are also provided. Keywords: Expression profiling by array Human T-cell Acute lymphoblastic Leukemia cell line CEM was transfected with either shRNA against ZMIZ1 or scrambled shRNA. Four (non-paired) biological replicates of each condition had mRNA assays performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets.
2012-12-13 | E-GEOD-32523 | biostudies-arrayexpress
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Project description:TAZ-CAMTA1 is a defining genetic aberration in the vascular cancer epithelioid hemangioendothelioma. We studied the transcriptome of TAZ-CAMTA1 and compared it to that of control or activated TAZ (TAZ4A)-expressing endothelial cells. We utilized an immortalized, mouse endothelial cell line known as MS1. We present and make available the first RNA-sequencing data of TAZ-CAMTA1's transcriptome in endothelial cells
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Project description:Human T-cell Acute lymphoblastic Leukemia cell line CEM was transfected with either shRNA against ZMIZ1 or scrambled shRNA. Four (non-paired) biological replicates of each condition had mRNA assays performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets. A supplementary Excel workbook holding the same processed data as the series matrix file is provided, with some probe set annotation, and a simple statistical comparison. The raw (.CEL) files are also provided. Keywords: Expression profiling by array
2012-12-13 | GSE32523 | GEO
Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profileepigenetic changes upon Zmiz1 knockdown using siRNA. Methods: ATAC sequencing library was prepared as per manufacturer instruction (Active Motif, 53150). Briefly, intact nuclei were isolated from control and Zmiz1 siRNA transfected HDLECs. Samples were treated with a hyperactive Tn5 transposase which tag the target DNA with sequencing adapters and fragment the DNA simultaneously. Library was then quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA High Sensitivity Assay Kit (Agilent, 5067-4626). Validated samples were sequenced using the NextSeq1000/2000 P2 Reagents (100 Cycles) v3 (Illumina, 20046811) on a Nextseq1000/2000. Resulting sequencing data were analyzed using basepairtech ATAC-Seq pipeline (www.basepairtech.com). Briefly, sequenced reads were aligned to the human (hg19) reference genome using Bowtie2. ATAC-Seq peaks and differentially accessible regions were quantified using MACS2 and DESeq2. Results: ATAC seq peaks analysis using MACS2 identified 576 peaks of which are mostly located in intergenic regions followed by introns. We found significantly reduced open chromatin near Prox1 loci upol loss of Zmiz1. Conclusions: We identify Zmiz1 regulates chromatin accessibility near Prox1 genomic loci in lymphatic endothelial cells
2023-11-29 | GSE225130 | GEO
Project description:Effect of transforming growth factor-beta (TGF-b) on miRNA expression profile in MS1 endothelial cells.
2016-07-31 | GSE76028 | GEO
Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profile transcriptional changes upon Zmiz1 knockdown using siRNA. Methods: Total RNA was extracted from control and Zmiz1 siRNA transfected HDLECs using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732) following the manufacturer instructions. RNA concentration and RNA integrity (RIN) number were determined using Qubit RNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32852) and Bioanalyzer RNA 6000 Nano assay kit (Agilent, 5067-1511) respectively. RNA library was prepared using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505). Verified samples were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 (Illumina, 20046812) on a Nextseq1000/2000. Sequenced reads were aligned to the human (hg19) reference genome with RNA-Seq alignment tool (STAR aligner). The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-Seq Differential Expression tool (version 1.0.1). Both alignment and differential expression analysis were performed using the tools in the illumina BaseSpace Sequence Hub. Results: We found 2,228 differentially expressed genes of which 1,115 genes were upregulated while 1,113 genes were downregulated. Downregulated genes were enriched in biological processes such as lymph vessel development, cell migration and heart valve development. Conclusions: We identify Zmiz1 regulates Prox1 in lymphatic endothelial cells
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Project description:Transgenic mice expressing a truncated form of Zmiz1 in the skin develop spontaneous keratoacanthomas. In this experiment, a Cre-inducible transgene expressing a truncated form of Zmiz1 was introduced into mice. Activation of the transgene in these mice was achieved by breeding to K14-Cre transgenic animals. Double transgenic mice formed spontaenous keratoacanthomas with short latency. In this experiment, we generated gene expression profiles for five Zmiz1-induced keratoacanthomas and six normal skin samples.
2012-10-01 | E-GEOD-39360 | biostudies-arrayexpress