Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

1 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 1004

Reconstituted Epidermis timecourse of barrier formation

ABSTRACT: Data from PeptideAtlas, [[http://www.peptideatlas.org/PASS/PASS00363 PASS00363]]. Experiment: P2-D3, file: P2-D3-F6.mzml. From PeptideAtlas: {{i}} De-cellularized dermis was seeded with neonatal keratinocytes and cultured submerged in media for two days. At this point the cultures were raised to the air/water interface to stimulate differentiation. At the indicated time points, epidermis was removed with forceps. Epidermis was extracted in 50% Trifluoroethanol (TFE), 0.1% SDS, 100 mM Ammonium Bicarbonate (AMBIC). Samples were heated at 60 deg C for 30 minutes, then sonicated at 75 W for 2 minutes process time using a 50% duty cycle. Extracts were cleared by centrifugation. separation: Samples from each timepoint were randomly assigned to 4 pools. Pools of 250 ug peptides were separated with Offgel Electrophoresis, pH 3-10 into 12 fractions. {{/i}}

INSTRUMENT(S): Instrument

ORGANISM(S): Homo_sapiens_viruses, Human, Micavibrio_aeruginosavorus_arl_13

DISEASE(S): Not Available

SUBMITTER: Winget JM, et al.

PROVIDER: GPM32320007927 | GPMDB |

REPOSITORIES: GPMDB

ACCESS DATA

Json Xml

Similar Datasets

Acid exposure

Project description:Two independent exposures (labeled T1 and T2) to pH 5.0. Samples were harvested at 30, 60, 90 and 120 minutes and used to make cDNA. Arrays are set up such that each time point was hybridized to the individual T=0 starting culture. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

2005-12-15 | GSE3833 | GEO

High-resolution proteomics of Zika and Dengue serum samples

Project description:We used data independent acquisition (DIA) mass spectrometry (MS) to profile ~800 proteinsfrom 122 serum samples Dengue or Zika Trinidadian patients. Two time points were collectedper patient. The DIA MS data were matched against a spectral library generated from high pH/low pH separated pooled serum samples.

2021-03-09 | PXD015422 | Pride

Halobacterium NRC-1, EMS Stress Response

Project description:100mM EMS was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of EMS for 30 minutes, cultures were spun down and pellets were re-suspended in same volume of GN101 media. Cultures were then harvested by centrifugation and pellets were snap frozen on a dry-ice ethanol bath. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. Keywords: stress response, dose response

2008-01-03 | GSE7609 | GEO

Hypo-osmotic shock - ppt1 and wildtype

Project description:Wild type and ppt1 mutant under hypo-osmotic shock. Cultures were grown with 1M sorbitol for ~20 hours, cells were collected by centrifugation and resuspended in YPD at time zero. Samples were collected at 0, 7, 15, 30 and 60 minutes after transfer to YPD. Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs. Keywords: time-course

2003-04-15 | GSE407 | GEO

Human Cell 293T BCAT1 IP GC-LC-MS

Project description:To identify the potential interaction protein that interacts with BCAT1 by IP-MS, we established the stable cell line with vector and BCAT1 in AGS. Then ten million cells were collected lysed in ice-cold 0.1% NP-40 buffer (50 mM Na2HPO4, pH 7.5, 150 mM NaCl) with protease inhibitors cocktail (Sigma, p8340). The supernatants were collected by centrifugation and incubated with 10 µL Anti Flag‐beads (Sigma, A2220at 4°C for overnight. After incubation, beads were washed with lysis buffer for 3 times. Precipitates were resuspended in 1 × SDS loading buffer and separated by SDS-PAGE (polyacrylamide gel electrophoresis). Then cut off (about 1cm2) gel for trypsin hydrolysis and collected and dried the peptide for MS analysis (Thermo Fisher Q Exactive).

2024-11-15 | PXD041556 | Pride

Human cerebrospinal fluid analysis by HPLC-MS/MS

Project description:Cerebrospinal fluid samples of patients with Parkinson’s disease and healthy controls were used for this study. Part of the samples consisted of fractions that were separated by gel electrophoresis. After tryptic digestion, all samples were spiked with indexed retention time (iRT) peptides and were measured using a DDA mass spectrometry approach. This data is intended to be used to create a spectral library for DIA analysis.

2020-08-13 | PXD013487 | Pride

Separation of circulating microRNAs using apheresis in patients with systemic lupus erythematosus

Project description:Examined the removal or reduction of circulating miRNAs with apheresis. The levels of expression of a large number of circulating miRNAs were measured in the plasma samples separated by the primary membranes from all 3 patients with systemic lupus erythematosus. This is the first report that circulating miRNAs in peripheral blood can be separated and possibly directly removed using membrane separation apheresis.

2016-04-11 | GSE76241 | GEO

Fluidigm Biomark 96.96 nanofluidic arrays for qRT-PCR of 93 miRNAs: salivary extracellular vesicles

Project description:Crude extracellular vesicles (EVs) from eight healthy volunteers were separated into 6 fractions based on their densities by using the iodixanol-based density gradient centrifugation method. To determine the distribution of miRNAs among these fractions, quantities of 93 miRNAs were quantified by the TaqMan real time PCR method using the BioMark HD system (Fluidigm) equipped with 96.96 dynamic array (Fluidigm).

2016-08-01 | GSE78763 | GEO

Identification and characterization of C4 dicarboxylic acid transporters in Pichia kudriavzevii CY902 strain

Project description:RNA-seq libraries were constructed for three samples, including (I) ΔURA3 strain grown in SD medium containing 2% w/v glucose(pH=5.0);(II)ΔURA3 strain grown in SD medium containing 2%w/v glucose and 2% w/v succinic acid(pH=5.0);(III)ΔURA3 strain grown in SD medium containing 2% w/v succinic acid(pH=5.0). For preparation of RNA samples, ΔURA3 cells grown overnight were inoculated into 50 ml liquid Synthetic Dextrose (SD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 24 hours to the logarithmic growth phase (OD600= 2-3). The cells were collected by centrifugation at 6000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 50 mL SD medium containing carbon sources of different combinations of glucose and succinic acid .The pH of the culture sample is adjusted to 5.0 with NaOH. After flask culturing at 30°C and 250 rpm for an additional three hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA). Each sample contains two biological replicates.

2021-05-05 | GSE159457 | GEO

RNA-seq analysis of various strains of Mycobacterium tuberculosis under glycerol and acetate at acidic Ph

Project description:We have performred RNA-seq analysis of WT under gycerol and acetate at acidic pH to investigate the role of PhoP in maintaning the pH homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. For acid stress, cells at OD600 of 0.6 were pelleted, washed twice with 7H9 medium buffered with 100 mM MOPS or 2N HCl for pH 7.0 or pH 4.5, respectively, re-suspended in media of indicated pH, and finally the cells were grown further for 2 hours at 37°C. After incubation cells were combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Medgenome Labs Private Limited , India. The main purpose of this study is to understand how mycobacteria can sense acidic stress conditions and mount an appropriate stress response.

2025-08-15 | GSE297253 | GEO

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