G.gallus - Cell line, SC (Muelleretal,nature2020)
Ontology highlight
ABSTRACT:
ORGANISM(S): 9031
SUBMITTER: 
Christian von Mering
PROVIDER: 4245908606 | PAXDB | 2020
REPOSITORIES: PAXDB
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| bioprojects-abundance-files-v4.0.zip | Other |
Items per page: 5 1 - 1 of 1 |
Publications
The proteome landscape of the kingdoms of life.
Müller Johannes B JB Geyer Philipp E PE Colaço Ana R AR Treit Peter V PV Strauss Maximilian T MT Oroshi Mario M Doll Sophia S Virreira Winter Sebastian S Bader Jakob M JM Köhler Niklas N Theis Fabian F Santos Alberto A Mann Matthias M
Nature 20200617 7813
Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported<sup>1</sup>, advances in mass-spectrometry-based proteomics<sup>2</sup> have enabled increasingly comprehensive identification and quantification of the human proteome<sup>3-6</sup>. However, there have been few comparisons across species<sup>7,8</sup ...[more]
Similar Datasets
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys) Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Keywords: amino acid deprivation
2007-12-13 | GSE9517 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE24037: Salivary cytokine alterations in HIV infection part 1 GSE24064: Salivary cytokine alterations in HIV infection part 2 Refer to individual Series
2011-09-08 | E-GEOD-24411 | biostudies-arrayexpress
Project description:We used a machine-learning framework to systematically discover prognostic long non-coding RNAs (lncRNAs) in 9,446 patient tumors of 30 types. We identified 166 prognostic lncRNAs whose transcript abundance correlated with patient risk and improved the performance of common clinical variables and molecular tumor subtypes. In lower-grade gliomas, discrete activation of HOXA10-AS indicated poor patient prognosis, neurodevelopmental pathway activation and a transcriptomic similarity to glioblastomas. To understand the role of HOXA10-AS in the hallmark pathways of glioma, we used RNA-seq to profile the patient-derived G797 glioma cells with siRNA-mediated HOXA10-AS knockdown (KD) and pcDNA3.1-Neomycin-mediated overexpression (OE) phenotypes. Both KD and OE were validated using RT-PCR. We found a pronounced transcriptional response to HOXA10-AS deregulation with 1,715 and 408 differentially expressed protein-coding genes detected in KD and OE cells, respectively (FDR < 0.05, absolute FC > 1.2), including 23 genes detected in both experiments, as well as known genes involved in glioma biology and Hippo signaling. Our study underscores the pan-cancer potential of the non-coding transcriptome for developing molecular biomarkers and innovative therapeutic strategies.
2021-10-02 | E-MTAB-10944 | biostudies-arrayexpress
Project description:Analog-sensitive kinase technology allows for specific inhibition of a given kinase. Here we utilize an analog-sensitive CDK9 cell line to determine the impact of CDK9 inhibition on the phospho-proteome of human cells. Specifically, we aim to identify substrates of CDK9 in a quantitative way using stable isotope labeling by amino acids in cell culture (SILAC) followed by LC-MS/MS.
2019-11-11 | PXD014825 | Pride
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys); Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Experiment Overall Design: First experiment: Three plates of cells were cultured under each condition. Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys). Experiment Overall Design: Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys).
2008-06-16 | E-GEOD-9517 | biostudies-arrayexpress
Project description:This series is a supplementary data set for the manuscript titled "Cohesin relocation from sites of chromosomal loading to places of convergent transcription" All data shown in the paper were registered (30 ChIP-chip and one transcription data). Experimental design: 1. Type of experiment: a. ChIP (Chromatin immunoprecipitation) analysis hybridised to a high density oligonucleotide array. The S. cerevisiae chromosome VI array described by Katou et al. (2003) Nature 424, 1078-83 has been used. Newly developed S. cerevisiae chromosomes III-V and S. pombe chromosomes 2-3 oligonucleotide arrays produced by Affymetrix have also been used. b. Gene expression profile analysis of S. cerevisiae. 2. Experimental factors: a. Distribution of different proteins related to sister chromatid cohesion or condensation during the cell cycle, mainly in G1 (alpha-factor arrested cells), S-phase (HU arrested cells) and metaphase (Nocodazole arrested cells). b. Gene expression profile analysis of logarithmically growing cells. 3. Number of hybridizations performed: a. ChIP analysis: 32 b. Gene expression: 1 4. Hybridisation design: ChIP analysis: comparison of ChIP fraction with SUP (supernatant) fraction 5. Quality control: Duplication, confirmation using different tags, different subunits of the same complex, and different yeast strain backgrounds (W303, BY4741, and SK1). Checking of the ChIP fraction by Western blotting. Checking amount of mRNA by RT-PCR. 6. URL of supplemental website: GEO Accession number: GSE1461 Web site: http://chromosomedynamics.bio.titech.ac.jp Samples used, extract preparation and labeling: 1. Origin of the biological sample Budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) 2. Manipulation of the samples and the protocols used: a. Mitotic budding yeast cells were synchronised in G1 with alpha-factor (2uM) and then released at 23ºC into medium containing 200 mM HU or 7.5 ug/ml Nocodazole for 60 min and 150 min, respectively. scc2-4 cells were shifted to 37ºC 60 min before alpha-factor release. Heat-shock treatment has been done at 37ºC for 15 minutes. b. Meiotic budding yeast cells were collected 4 hours after meiosis induction at 23ºC. c. Mitotic fission yeast cells were grown logarithmically in minimum medium (MM). Cells were fixed over night in 1% formaldehyde at 4ºC. 3. Protocols for preparing extracts: a. ChIP analysis: Extract preparation was processed following the Shirahige lab protocol (http://chromosomedynamics.bio.titech.ac.jp ). 5x10^8 cells were disrupted using Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka). Whole cell extract was sonicated to obtain 400-600 bp genomic DNA fragments. Anti-HA monoclonal antibody (clone 16B12, CRP Inc., Denver, PA) and anti-Flag monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) coupled to Dynabeads (Dynal, protein A Dynabeads) were used for chromatin immunoprecipitation. The immunprecipates were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp. After Dnase I inactivation at 95ºC, fragments were labelled as detailled below. b. Gene expression analysis: Total RNA was prepared using FastRNA Pro Red Kit (BIO 101 Systems) according to the manufacturerâs instructions. 10 ug of total RNA was reverse transcribed according to the protocol recommended by Affymetrix. In vitro transcription was performed on 1 ug of cDNA. cRNA was cleaned and fragmented by heating. 20 ug of fragmented cRNA were hybridised. 4. Labelling protocol DNA fragments were end-labelled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) for 1 hour at 37ºC as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization. Hybridization procedures and parameters: Hybridization, blocking and washing were carried out as previously described (http://chromosomedynamics.bio.titech.ac.jp). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3âbiotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100ºC for 10 minutes, and then put on ice before being hybridized for 16 hours at 42ºC in an hybridization oven (GeneChip Hybri. Oven 320, Affymetrix). Washing and scanning protocol (FlexMidi-euk2v3-450) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix). Measurement data and specifications: S. cerevisiae arrays were scanned using the HP GeneArray Scanner (Affymetrix) at an emission wavelength of 560 nm, resolution 7.5 uM. S. pombe arrays were scanned by GeneChip Scanner 3000 (Affymetrix) at an emission wavelength of 570 nm, resolution 2.5 uM. Grids were aligned to scans following the library array description. Primary data analyses were carried out using Affymetrix Microarray Suite Ver.5.0 software to obtain signal intensity, fold change value, change p-value and detection p-value. The detailed information of this analysis is available at http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf and http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf To discriminate significant signals for binding to DNA (dark grey signals), signals from the ChIP fraction scan were compared to the SUP (supernatant) fraction scan using the 3 following criteria: first, the signal reliability was judged by the detection p-value of each locus (p-value â¤0.025); secondly, reliability of binding ratio was judged by change p-value (p-value â¤0.025); thirdly, only clusters of at least 3 contiguous loci responding to the 2 previous criteria were selected as significantly enriched locus. The light grey signals represent the statistically not significantly enriched signals. The software to present the result (chr6viewer) is available at http://everythingchromovi.gsc.riken.go.jp. The raw and transformed data files are available at GEO database website and at our web site http://chromosomedynamics.bio.titech.ac.jp. Array Design 1. General array design: in situ synthesized arrays by Affymetrix 2. Availability of arrays: commercially available from Affymetrix 3. Location and ID of each spot on arrays: available at our web site (http://chromosomedynamics.bio.titech.ac.jp) and from Affymetrix on request 4. Probe type: oligonucleotide 5. The arrays used in this study can be purchased from Affymetrix: Chromosome VI S.cerevisiae: rikDACF, P/N# 510636 Chromosome III,IV,V S.cerevisiae: SC3456a520015F, P/N# 520015 Chromosome II,III S.pombe: S_pombea520106F, P/N# 520106 YGS98 GeneChipsT oligonucleotide arrays: P/N# 900256 Keywords = Yeast Cohesin Condensin Loading Distribution Keywords: other
2010-06-09 | E-GEOD-1461 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE18023: Mice with FIA develop anti-native and anti-in vitro citrullinated fibrinogen antibodies GSE18024: FIA plasma induces arthritis in naïve mice GSE18025: Fibrinogen-reactive T cells transfer disease to naïve mice Refer to individual Series
2010-05-05 | E-GEOD-18073 | biostudies-arrayexpress
Project description:Synovial antigen arrays were probed with 1:150 dilutions of plasma derived from SJL mice immunized with fibrinogen emulsified in CFA or with CFA alone. Autoantibody binding was detected with a Cy3-conjugated goat-anti-mouse IgG/M secondary antibody. SAM was applied to identify antigens with statistically significant differences in array reactivity between FIA and CFA control plasma (q < 0.01) obtained from mice before boosting. The SAM hits were subjected to hierarchical cluster analysis and are displayed as a heatmap. Synovial array profiling of FIA plasma demonstrated autoreactive B-cell responses against peptides representing native fibrinogen, and B-cell epitope spreading resulting in additional targeting of citrullinated fibrinogen in the samples obtained before boosting. Custom-spotted protein slides were probed with plasma samples from individual mice. Four slides were probed with plasma derived from mice immunized with CFA and six slides were probed with plasma derived from mice immunized with fibrinogen emulsified in CFA.
2010-05-05 | E-GEOD-18023 | biostudies-arrayexpress
Project description:Plasma collected from mice with FIA were pooled, and 0.3 ml was injected intravenously into 6-week-old naïve SJL mice on days 0 and 2. Synovial antigen array profiling of plasma from the arthritic recipient mice demonstrated autoreactive B-cell responses against peptides representing native fibrinogen and citrullinated fibrinogen, and further epitope spreading resulting in additional targeting of fibronectin, collagen type V, cartilage gp39, and clusterin. Custom-spotted protein slides were probed with plasma samples from individual mice. Four slides were probed with plasma derived from naïve mice and four slides were probed with plasma derived from mice injected with FIA plasma.
2010-05-05 | E-GEOD-18024 | biostudies-arrayexpress
Project description:Splenocytes harvested from mice with FIA were cultured in vitro and stimulated with 0.01 mg/ml fibrinogen for 3 days. Enriched T cells were transferred into 6-week-old naïve SJL mice, which developed visible signs of arthritis within 2 weeks. Synovial array profiling of plasma from the arthritic recipient mice demonstrated autoreactive B cell responses against peptides representing native fibrinogen, and further spreading of the responses to target collagen type V, cartilage gp39, and citrullinated vimentin. Custom-spotted protein slides were with plasma samples from individual mice. Four slides were probed with plasma derived from naïve mice and five slides were probed with plasma derived from mice injected with FIA T cells.
2010-05-05 | E-GEOD-18025 | biostudies-arrayexpress