Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GFP-fused 53BP1 interacting proteins in HEK293-T cells with and without irradiation

ABSTRACT: Experiment: proteins immunoprecipitated with a GFP-fused 53BP1 fragment. Description: GFP-fused 53BP1 fragment was conditionally expressed (Tet-ON) in HEK293-T cells in duplicate. Cells were irradiated (6 Gy) or not, allowed to recover for 24 hours, cross linked with 0.05% paraformaldehyde, lysed with the EZ-ChIP lysis buffer. Lysates were incubated with anti-GFP beads, washed, and eluted by heating in Laemmli buffer. Eluents were run on an SDS-PAGE gel, lanes were cut into four equally sized sections. Sections were separately in-gel digested with trypsin. Non-Irradiated control sample was labeled with O18 by digesting in the presence of O18 water. Duplicates per section of both samples (non-irradiated and irradiated) were combined to give four samples (one per MW range section). Samples were run on the LTQ Orbitrap XL. Data were searched with Mascot (once including both O16 and O18 at the C-terminus, once allowing only O16, once allowing only O18), and analyzed in Scaffold.

INSTRUMENT(S): LTQ Orbitrap XL

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Laurie Parker Stephen J. Kron

PROVIDER: MSV000083293 | MassIVE | Thu Jan 03 08:41:00 GMT 2019

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Purified touch receptor neurons: expanded polyGlutamine versus control

2015-02-01 | GSE35939 | GEO

NET-seq analysis of pSer2-Pol II profile in shCTRL, shMETTL3 and shDDX21 HeLa cells

Project description:The chromatin fraction was isolated from 5x107 HeLa cells. Chromatin was digested in 100 mL of MNase (40 units/ mL ) reaction buffer for 3 min at 37 °C in a thermomixer (1,400 rpm). After addition of 10 L EGTA (25mM) to inactivate MNase, soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min. 10 mg of Pol II antibody was conjugated to magnetic protein A beads. The supernatant was diluted with 400 mL of NET-2 buffer and pSer2-Pol II antibody-conjugated beads were added. Incubated the IP reaction at 4 °C for 1 hr. The beads were washed with 1 mL of NET-2 buffer six times and 100 mL of 1xPNKT (1xPNK buffer and 0.05% Triton X-100) buffer once. Washed beads were incubated in 50 mL PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/ml T4 PNK (NEB)) in Thermomixer at 37 °C, 1,400 rpm for 6 min. Beads were washed with 1 mL of NET-2 buffer once and RNA was extracted with Trizol reagent. RNA was suspended in urea Dye (7M Urea, 1xTBE, 0.1% BPB and 0.1% XC) and resolved on 6% TBU gel (Invitrogen) at 200 V for 5 min. Gels with 30-160 nt RNAs were collected. 0.2 mL tube was prepared with holes made with 25G needle and placed in a 1.5 mL tube. Gel fragments were placed in the layered tube and broken down by centrifugation at 12,000 rpm for 1 min. The small RNAs were eluted from gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) at 25 °C for 1 hr in Thermomixer (900 rpm). Eluted RNA was puriﬁed with SpinX column (Coster) with 2 glass ﬁlters (Millipore) and the ﬂow-through RNA was ethanol precipitated.

2019-10-15 | GSE134102 | GEO

Purified touch receptor neurons: expanded polyGlutamine versus control

Project description:Transcriptional profiling of C.elegans purified touch receptor neuron precursors, comparing cells expressing mutant Huntingtin N-terminal fragment to normal Huntingtin N-terminal fragment, both fused to GFP under mec-3 promoter. As a control the same experiment has been done with comparing cell expressing normal Huntingtin to GFP only. Goal was to determine the specific effect of expanded polyglutamines on gene expression in purified cell population. Three-condition experiment: mutant Huntingtin (128Q) versus normal Huntingtin (19Q), and normal Huntingtin versus GFP only, 3 biological replicates of each. Cells were purified based on GFP fluorescence using a cell sorter.

2015-02-01 | E-GEOD-35939 | biostudies-arrayexpress

bystander effects from irradiated mouse brain

Project description:control: sham irradiated test1: mouse whole brain irradiated 10Gy for once test2:mouse whole brain irradiated 10Gy for 3 times, once a week

2021-01-24 | MSV000086761 | MassIVE

Transcriptome and protein interaction profiling in cancer cells with mutations in histone H3.3

Project description:This entry contains proteome data extracted from co-immunoprecipitation of engineered H3F3A locus fused to GFP in HEK293 cell line, followed by PAGE separation, in-gel proteolytic digestion and LC-MS/MS identification.

2018-11-07 | PXD009966 | Pride

Ribosome profiling on sections taken from a kidney tumor

Project description:Ribosome profiling on sections taken from a kidney tumor For two tumors: 2 sections of normal tissue and 4 samples of tumor tissue, for another two tumors 1 section of normal tissue and 1 section of tumor tissue

2016-02-17 | E-GEOD-59820 | biostudies-arrayexpress

Secretagogin is expressed by developing neocortical GABAergic neurons in humans but not mice and increases neurite arbor size and complexity

Project description:Analysis of gene expression over serial 150um sections of a single gestational week 18 human neocortical specimen. The hypothesis tested with this dataset was that a transcriptional signature of GABAergic neurons could be isolated via unsupervised gene coexpression analysis due to variation in the abundance of this cell type from section to section. This dataset is the second of its kind generated using this method (Gene Coexpression Analysis of Serial Sections, or GCASS).

2017-04-10 | GSE95639 | GEO

Transient GFP-fused DARPin expression effects on transcription

Project description:Transient GFP-fused DARPin expression effects on transcription

| PRJEB51294 | ENA

Radial glia require PDGFD/PDGFRB signaling in human but not mouse neocortex

Project description:Analysis of gene expression over serial 150um sections of a single gestational week 14.5 human neocortical specimen. The hypothesis tested with this dataset was that a transcriptional signature of radial glia (neural stem cells) could be isolated via unsupervised gene coexpression analysis due to variation in the abundance of this cell type from section to section. This dataset is the first of its kind generated using this method (Gene Coexpression Analysis of Serial Sections, or GCASS).

2014-11-13 | GSE62064 | GEO

Expression data from hESCs expressing RB7LP or T121

Project description:We used microarray analysis to study the expression differences between controls and hESCs expressing RB7LP for 3 days, and controls and hESCs expressing T121 for 3 days. RB7LP is the large pocket fragment of the retinoblastoma protein (RB) fused to GFP, in which seven phosphorylation sites for Cdk have been mutated (Angus, SP et al. Mol Cell Biol 23, 8172 (Nov, 2003). T121 is a truncated form of the SV40 Large T (LT) viral oncoprotein that inactivates the function of the three members of the retinoblastoma (RB) protein family (RB, p107, p130).

2012-06-29 | GSE29783 | 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