Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cryo-EM study of bovine retinal pigment epithelium cell lysate

ABSTRACT: This is the proteomic analysis data of bovine retinal pigment epithelium cell lysate subjected to cryo-EM study.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Bos Taurus (bovine)

TISSUE(S): Epithelial Cell, Retinal Pigment Epithelium Cell

SUBMITTER: zhemin zhang

LAB HEAD: Edward W. Yu

PROVIDER: PXD037186 | Pride | 2023-01-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Lum_21nov3011.raw	Raw
	Lum_21nov3012.raw	Raw
	mzTab.mzTab	Mztab
	proteinGroups.txt	Txt

Items per page:

1 - 4 of 4

Publications

Toward structural-omics of the bovine retinal pigment epithelium.

Morgan Christopher E CE Zhang Zhemin Z Miyagi Masaru M Golczak Marcin M Yu Edward W EW

Cell reports 20221201 13

The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven differe ...[more]

PMID: 36577381

Similar Datasets

Whole genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration

Project description:Illumina Infinium HumanMethylation450 BeadChip data from genomic DNA of retinal pigment epithelium from Age-related Macular Degeneration patients or age-matched controls.

2019-08-01 | E-MTAB-7183 | biostudies-arrayexpress

Pigment Epithelium Derived Factor (PEDF) secreted from iPSC derived-RPE facilitates apoptotic causes cell death, not the differentiation, of iPSCs

Project description:We show that Retinal pigment epithelium (RPE) secreted-factor, pigment epithelium derived factor (PEDF) secreted/derived from primary or iPSC-derived retinal pigment epithelium (RPE)RPE, dramatically inhibitsed the cell growth of iPSCs. PEDF was detected abundantly in culture supernatant media of primary and iPSC-derived RPE. We examined the gene expression in primary RPE and iPS-derived RPE. Two samples: RPE derived from 253G1 iPSC, Primary RPE.

2013-01-03 | E-GEOD-43257 | biostudies-arrayexpress

RNA-seq of retinal pigment epithelium (RPE) derived from human induced pluripotent stem cells (iPSCs): healthy control and USH1B patient iPSCs

Project description:Compare transcriptomes of control and USH1B patient iPSC-derived retinal pigment epithelium (RPE) to elucidate disease mechanisms of Usher syndrome type IB (USH1B). USH1B patient fibroblasts were collected at Great Ormond Street Hospital (GOSH) and reprogrammed to iPSCs. Control and patient iPSCs differentiated in vitro to generate retinal pigment epithelium (RPE) and collected for RNA-seq at 24 week. Sequencing was performed at University College London (UCL) Genomics on a NovaSeq 6000 system. Data aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b.

2023-08-22 | E-MTAB-12165 | biostudies-arrayexpress

Transcription profiling of zebrafish embryonic retinal pigment epithelium in vivo

Project description:Eye development and photoreceptor maintenance requires the retinal pigment epithelium (RPE), a thin layer of cells that underlies the neural retina. Despite its importance, RPE development has not been studied by a genomic approach. A microarray expression profiling methodology was established in this study for studying RPE development. The intact retina with RPE attached was dissected from developing embryos, and differentially expressed genes in RPE were inferred by comparing the dissected tissues with retinas without RPE using microarray and statistical analyses. We found 8810 probesets to be significantly expressed in RPE at 52 hours post-fertilization (hpf), of which 1443 might have biologically meaningful expression levels. Further, 78 and 988 probesets were found to be significantly over- or under-expressed in RPE respectively compared to retina. Also, 79.2% (38/48) of the known over-expressed probesets have been independently validated as RPE-related transcripts. The results strongly suggest that this methodology can obtain in vivo RPE specific gene expression from the zebrafish embryos and identify novel RPE markers. Experiment Overall Design: The gene expression levels of three independent replicates of retina with RPE attached consisting of ten samples each at 52hpf (WRR52) were compared with three independent pure retinal samples consisting of ten retinas each at 52hpf (WR52). The yield-adjusted WR52 expression values were assumed to be equivalent to the retinal contribution in WRR52 samples and deducted from WRR52 expression values to obtain estimations of RPE gene expression at 52hpf (RPE52). Differential gene expressions between RPE and retina were inferred by comparing the RPE52 estimates and WR52 expression values.

2008-06-13 | E-GEOD-5048 | biostudies-arrayexpress

Functional Retinal Pigment Epithelium-like Cells from Human Fibroblasts

Project description:The retinal pigment epithelium (RPE) provides vital support to photoreceptor cells and its dysfunction is associated with the onset and progression of age-related macular degeneration (AMD). Surgical provision of RPE cells may ameliorate AMD and thus it would be valuable to develop sources of patient-matched RPE cells for this application of regenerative medicine. We describe here the generation of functional RPE-like cells from fibroblasts that represent an important step toward that goal. We identified candidate master transcriptional regulators of RPEs using a novel computational method and then used these regulators to guide exploration of the transcriptional regulatory circuitry of RPE cells and to reprogram human fibroblasts into RPE-like cells. The RPE-like cells share key features with RPEs derived from healthy individuals, including morphology, gene expression and function, and thus represent a step toward the goal of generating patient-matched RPE cells for treatment of macular degeneration. Expression analysis was performed on induced retinal pigment epithelium-like cells.

2015-09-23 | E-GEOD-64264 | biostudies-arrayexpress

cryo-EM study of human liver mitochondria lysate

Project description:This is the proteomic analysis data of Human liver mitochondria lysate subjected to cryo-EM study.

2024-01-26 | PXD044860 | Pride

cryo-EM study of human liver cell lysate

Project description:This is the proteomic analysis data of Human liver cell lysate subjected to cryo-EM study.

2024-01-26 | PXD040733 | Pride

Transcriptomic analysis of human retinal detachment (RD) reveals both inflammation and photoreceptor death

Project description:We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment. Data analysis reveals major involvement of the immune response in the disease and interindividual variation was monitored to unravel a second crucial aspect of the pathological process, the death of photoreceptor cells. In total 38 surgical specimens (samples) were analyzed, 19 represent biopsies from patients with retinal detachment (RD) and 19 represent contral samples without retinal detachment.

2012-03-06 | E-GEOD-28133 | biostudies-arrayexpress

Transcription profiling of mouse Nxnl1-/- retina

Project description:Rod-derived Cone Viability Factor (RdCVF, alias nxnl1) is a retina-specific protein identified for its therapeutic potential in supporting cone survival during retinal degeneration. A nxnl1 knockout mouse model was created and the transcriptome used to demonstrate that the retina is compromised by the absence of nxnl1. Experiment Overall Design: In total 9 samples were analyzed, they represent three different genotypes (wt/wt, ko/wt, ko/ko) that were tested in triplicate each.

2010-02-17 | E-GEOD-13869 | biostudies-arrayexpress

RNA-seq of human hTERT-RPE1 and RPE1-MYCN-ER cells with treatment of EtOH (0h) or tamoxifen for 24h, 48h and 72h to activate MYCN

Project description:RNA-seq upon MYCN activation in the hTERT-immortalized MYCN retinal pigmented epithelial cell line (RPE1–MYCN-ER). The parental hTERT-immortalized retinal pigment epithelium (hTERT-RPE1) was used as a control as this cell line does not carry the MYCN:ER expression construct. Both cell lines were treated with tamoxifen (400nM; 4-OHT) for MYCN induction (with 4-OHT or not). Analysis was performed 24 h, 48 h and 72 h upon MYCN activation, including four biological replicates per condition.

2021-06-03 | E-MTAB-9667 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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