Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protein phosphorylation of IFNgR1 knockout B16 cells

ABSTRACT: B16 cells were transduced by lentivirus encoding scramble shRNA and engineered to obtain two IFNgR1-knockout cell clones. Proteins from these cells were digested by TPCK-trypsin. Equal amount of peptides were labelled with TMTpro reagents and pooled. Phosphopeptides were enriched from 90% of the pooled peptides using TiO2 beads, and fractionated with the Pierce high pH reversed-phase peptide fractionation kit to get six fractions. The remaining 10% pooled peptides (called total peptides) were fractionated similarly to get five fractions. Peptides from each fraction were analyzed using HPLC-ESI-MS/MS. Some fractions were analyzed twice. TMTpro channels 1-4: four independent samples of scramble shRNA group; channels 5-8: four independent samples of IFNgR1 knockout cell clone 1; channels 9-12: four independent samples of IFNgR1 knockout cell clone 2; channels 13-16: samples not related to this study.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Lewis Zhichang Shi

PROVIDER: MSV000087796 | MassIVE | Mon Jul 12 08:34:00 BST 2021

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A microenvironment-inspired synthetic 3D model for pancreatic ductal adenocarcinoma organoids - PDA Matrisome

Project description:LFQ analysis of matrisome fractions enriched from 12 murine PDA or PanIN samples (samples 1 - 12) and a normal pancreas pool (samples 13) pooled from 10 pancreata of C57-Bl6 animals. Three independent enrichments have been conducted for each sample with each having had four injections.

2021-11-29 | PXD022767 | Pride

Gene expression profiling of Nup98HoxA9 expressing ES cells

2016-01-04 | GSE67967 | GEO

Project description:Pooled BAC clone sequencing of NA12878

| PRJNA342471 | ENA

Gene expression profiling of Nup98HoxA9 expressing ES cells

Project description:To know whether the Nup98-HoxA9 affects global gene expression, we performed DNA microarray analysis using the following four clones: two independent Nup98-HoxA9 ES clones (clone#1 and clone#9), parental ES cells, and HoxA9-Ct ES clone. Two independent Nup98-HoxA9 ES clones (clone#1 and clone#9), and HoxA9-Ct ES clone, was compared with parental ES cells (reference sample).

2016-01-04 | E-GEOD-67967 | biostudies-arrayexpress

Nuclear F-actin Assembly on Damaged Chromatin is Regulated By DYRK1A and Spir1 Phosphorylation

Project description:The uploaded data are described within "DYRK1A promotes nuclear F-actin assembly to effect DSB repair metabolism". Peptides from RPE1 epithelial cells with either, over expression of DYRK1A, normal expression of DYRK1A, or knockout of DYRK1A were labeled with TMTpro-16 reagents and phosphopeptides enriched by TiO2 and Fe-NTA resins.

2024-07-19 | PXD031714 | Pride

Gene expression profiles during the process of differentiation of HL-60 AK2 hetero-knockout clone #47 cells into neutrophils [HL60AK2KO_clone47]

Project description:To investigate the changes in gene expression during the process of differentiation into neutrophils and to evaluate the effect of Ak2 hetero-knockout in the process, microarray analysis was performed. HL-60 Ak2 hetero-knockout clone #47 cells were cultured with all-trans retinoic acid (ATRA) for 4 days. The cells were collected at four different time points and total RNA was prepared for use as a sample for microarray analysis.

2022-12-28 | GSE200825 | GEO

Gene expression profiles during the process of differentiation of HL-60 AK2 hetero-knockout clone #5 cells into neutrophils [HL60AK2KO_clone5]

Project description:To investigate the changes in gene expression during the process of differentiation into neutrophils and to evaluate the effect of Ak2 hetero-knockout in the process, microarray analysis was performed. HL-60 Ak2 hetero-knockout clone #5 cells were cultured with all-trans retinoic acid (ATRA) for 4 days. The cells were collected at four different time points and total RNA was prepared for use as a sample for microarray analysis.

2022-12-28 | GSE200824 | GEO

Identification of Vaccinia Virus HLA Class I Peptides Presented by the Immune System

Project description:Seeking to identify HLA class I peptides that originate from vaccinia virus proteins to understand the mechanism of immune protection. Note that vaccinia-infected B cells will still continue to present (primarily) a wide variety of peptides originating from endogenous proteins; this data set contains evidence for more than 5000 such peptides. The objective and challenge is to detect and identify the peptides that originate from the pathogen (vaccinia virus) in the presence (background) of this large number of endogensous 'self' peptides. Keywords: Peptide search results from multiple injections of multiple strong cation exchange fractions combined into one set of results.

2009-08-31 | GSE10549 | GEO

Identification of PDGF-dependent patterns of gene expression in U87 glioblastoma cells

Project description:Overall study: Identification of PDGF-dependent patterns of gene expression in U87 glioblastoma cells. RNA was obtained from triplicate dishes of 5 different groups of U87 cells, each (total 15) analyzed with one U95 microarray chip. Three different comparisons were made: 1) Clone 3.1 (34580-34582) vs. clone 3.3 (34583-34585) vs. parent U87 (34592-34594). Purpose: demonstrate that the gene expression profiles between these 3 cell lines are not different, so they could be pooled as a single untreated group. 2) Pooled control group (34580-34585, 34592-34594) vs. clone 8.1 (34586-34588). Purpose: identify genes specifically controlled by autocrine PDGF activity. 3) Clone 8.1 (34586-34588) vs. clone 8.1 treated with PDGF (34589-34591) Purpose: Identify genes specifically induced by exogenous PDGF. Keywords = platelet-derived growth factor Keywords = glioblastoma Keywords = brain cancer Keywords = sterol regulatory element binding protein Keywords = SREBP Keywords: ordered

2004-12-10 | GSE1923 | GEO

Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8KO]

Project description:To identify target genes of the histone demethylase Phf8 in oligodendroglial cells in a genome-wide and unbiased approach, RNA-sequencing studies were performed on wildtype CG4 cells and CRISPR/Cas9-edited Phf8 knockout cell lines. We compared three wildtype and one CRISPR/Cas9-treated clone without genome editing with four CRISPR/Cas9 Phf8-knockout clones. Among others we detected substantial changes in the expression of genes associated with cell cycle and replication of DNA.

2024-04-12 | GSE253877 | 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