Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic Discovery of Deeply Conserved Protein Complexes, Selaginella

ABSTRACT: The associated files are mass spec data from two HPLC fractionations (Size Exclusion (SEC) or a triple phase ion exchange combination (WaxWaxCat)) of a single native protein extract from Selaginella moellendorfii. The extract was made from frozen powdered green tissue in 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EGTA, 10% glycerol, 1% NP40, phosphatase inhibitors and plant-specific protease inhibitors. 1 mg total protein was separated by SEC and 1.25 mg (diluted to 50 mM NaCl) by a concatenated series of three columns: PolyWaxLP, PolyWaxLP, and poly CAT A (PolyLC, Inc). The triple column series was eluted with a NaCl gradient. The ion exchange fractions # 55-60 were not processed for mass spectrometry becaue the A280 trace from the HPLC indicated insufficient protein present in those fractions.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Selaginella Moellendorffii

SUBMITTER: Ophelia Papoulas

LAB HEAD: Edward M. Marcotte

PROVIDER: PXD013093 | Pride | 2019-10-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Selaginella_SEC_01a_20160309..comet.pep.xml	Pepxml
	Selaginella_SEC_01a_20160309.MSGF.mzid.gz	Mzid
	Selaginella_SEC_01a_20160309.mzXML	Mzxml
	Selaginella_SEC_01a_20160309.pride.mgf.gz	Mgf
	Selaginella_SEC_01a_20160309.raw	Raw

Items per page:

1 - 5 of 648

Similar Datasets

Systematic Discovery of Deeply Conserved Plant Protein Complexes, Quinoa

Project description:The associated files are mass spec data from mixed-bed ion exchange chromatogrphy fractions. Starting extract was 14,000 x g clarified supernatant from extraction of liquid nitrogen powdered Chenopodium quinoa seeds. Extraction buffer was 20 mM HEPES pH 7.6, 130 mM K-acetate, 5 mM Mg-acetate, 0.1 mM EDTA, 10% glycerol, 1 mM DTT, phosphatase inhibitors, and Plant specific protease inhibitors.

2019-10-28 | PXD013080 | Pride

Xenopus laevis Cdc45-FLAG interactions on chromatin during DNA replication

Project description:The aim of the project was to purify Xenopus replisome from replicationg chromatin assembled in Xenopus laevis egg extract. To this end recombinant Cdc45-TEV-His10-FLAG5 was expressed in bacteria and purified. 4 ml of Xenopus laevis egg extract was activated into interphase and supplemented with 10 ng/µl of demembranated sperm DNA, 70 nM recombinant Cdc45, 40 µM aphidicolin, 5 mM caffeine and incubated at 23°C for 60 min. Chromatin was isolated in ANIB100 buffer (50 mM HEPES pH 7.6, 100 mM KOAc, 10 mM MgOAc, 2.5 mM Mg-ATP, 0.5 mM spermidine, 0.3 mM spermine, 1 µg/ml of each aprotinin, leupeptin and pepstatin, 25 mM β-glycerophosphate, 0.1 mM Na3VO4 and 10 mM 2-chloroacetamide) as described previously (Gillespie, Gambus et al. 2012). Chromatin pellets re-suspended in ANIB100 containing 20% sucrose. Protein complexes were released from chromatin by digestion with 4 U/µl benzonase nuclease (E1014-25KU, Sigma) and sonicated for 5 min using a sonicator with settings: 30 sec on, 30 sec off, low power (Bioruptor Diagenode UCD-200). Immunoprecipitation was performed using 100 µl of anti-FLAG M2 magnetic beads (Sigma-Aldrich). Before elution the sample was washed four times with 1 ml of ANIB100 20% sucrose, ANIB100 20% sucrose 0.1% Triton X-100, ANIB100 and elution buffer (25 mM HEPES pH 7.5, 100 mM KAc, 5 mM MgAc, 1 mM ATP and 0.02% NP-40), respectively. The sample was eluted adding 250 µM 3xFLAG peptide (Stratech) to 200 µl of elution buffer and a small proportion of it analysed by mass spectrometry.

2023-10-27 | PXD044422 | Pride

Systematic Discovery of Deeply Conserved Plant Protein Complexes, Tomato

Project description:The associated files are mass spec data from HPLC mixed-bed ion exchange column fractions. Sample loaded was a native extract of tomato leaves.

2019-10-28 | PXD013004 | Pride

Protein interaction AP-MS data for TAP-CSAG1 and TAP-CSAG2 from HEK293 cells

Project description:Ten 15 cm2 plates of HEK293 cells stably expressing TAP-vector, TAP-CSAG1, or TAP-CSAG2 were lysed with TAP lysis buffer (10% (v/v) glycerol, 50 mM HEPES-KOH pH 7.5, 100 mM KCl, 2 mM EDTA, 0.1% (v/v) NP-40, 10 mM NaF, 0.25 mM Na3VO4, 50 mM β-glyerolphosphate, 2 mM DTT, and 1X protease inhibitor cocktail (Sigma)) and cleared supernatants were bound to IgG-Sepharose beads (GE Amersham) and then washed in lysis buffer and TEV buffer (10 mM HEPES-KOH pH 8.0, 150 mM NaCl, 0.1% (v/v) NP-40, 0.5 mM EDTA, 1 mM DTT, and 1X protease inhibitor cocktail). Protein complexes were cleaved off the beads by TEV protease (Sigma) and incubated with calmodulin-Sepharose beads (GE Amersham) in calmodulin binding buffer (10 mM HEPES-KOH pH 8.0, 150 mM NaCl, 1 mM Mg acetate, 1 mM imidazole, 0.1% (v/v) NP-40, 6 mM CaCl2, 10 mM 2-mercaptoethanol) and then washed in calmodulin rinse buffer (50 mM Ammonium bicarbonate pH 8.0, 75 mM NaCl, 1 mM Mg Acetate, 1 mM Imidazole, 2 mM CaCl2) before eluted with SDS sample buffer, subjected to SDS-PAGE, and stained with GelCode Blue stain (Thermo Fisher Scientific) before protein identification by LC-MS/MS.

2020-09-01 | PXD020231 | Pride

Systematic Discovery of Plant Protein Complexes, fern

Project description:The associated files are mass spec data from Size exlusion and Triple-phase ion exchange chromatographic separations of native fern (Ceratopteris richardii) frond extract. The ion exchange separation used a concatenated series of 3 columns (WAX, WAX, CAT).

2019-10-28 | PXD013320 | Pride

Proteomics of SEC and IEX fractionated Mouse Embryonic Stem Cells

Project description:Mouse embryonic stem cells were lysed in Pierce IP Lysis buffer and 2 mg of the clarified extract was fractionated on an HPLC SEC column and 2 mg was fractionated on an HPLC IEX mixed bed column. All fractions were reduced, alkylated, and trypsin digested for mass spectrometry as in Mallam et al. 2019 (PMID: 31665645). Data were collected on an Orbitrap Fusion mass spectrometer using a data dependent 75 minute topspeed method. Dissociation for SEC fractions was by CID, and for IEX fractions was by HCD. RAW files were converted to mzXML and searched using an MSBlender analysis pipeline.

2023-05-01 | MSV000091831 | MassIVE

Transcriptional analysis of live and hybridized J1 and NIH-3T3 cells

Project description:J1 mouse embryonic stem cells (mESCs) and NIH-3T3 fibroblasts were grown in standard media conditions. Hybridized cells were fixed with 4% paraformaldehyde; permeabilized in 70% ethanol; incubated for 12 hours at 30C in an RNA preserving hybridization (RPH) buffer (300 mM Sodium chloride, 30mM Sodium citrate, 2.1M Ammonium sulfate, 25% formamide, 10 mM EDTA, 1 mg/ml E. Coli tRNA, 500 μg/ml BSA); and reverse cross-linked for 1 hour at 50C with Sodium dodecyl sulfate (SDS) and Proteinase K (100 mM NaCl, 10 mM Tris pH 8.0, 1 mM EDTA, 0.5% SDS, 500 μg/ml Proteinase K).

2014-03-20 | GSE55919 | GEO

Fly_wing_disc_600_mM_Salt_Extracted_Chromatin_Pellet

Project description:modENCODE_submission_2516 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: ML-DmD16-c3; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Cell Line ML-DmD16-c3; biochemical fraction (extract) precipitate; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1-2 hours

2010-11-18 | E-GEOD-25384 | biostudies-arrayexpress

Kc_600_mM_Salt_Extracted_Chromatin_Pellet

Project description:modENCODE_submission_2757 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Cell Line Kc167; biochemical fraction (extract) precipitate; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1 to 2 hours

2010-11-18 | E-GEOD-25386 | biostudies-arrayexpress

Kc_600_mM_Salt_Extracted_Chromatin

Project description:modENCODE_submission_2756 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Cell Line Kc167; biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1 to 2 hours

2010-11-18 | E-GEOD-25385 | 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