ZNF354C is a transcriptional repressor that inhibits angiogenesis in endothelial cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA649218 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12339275.fastq.gz | Fastqsanger.gz | |||
| SRR12339276.fastq.gz | Fastqsanger.gz | |||
| SRR12339277.fastq.gz | Fastqsanger.gz | |||
| SRR12339278.fastq.gz | Fastqsanger.gz | |||
| SRR12339279.fastq.gz | Fastqsanger.gz |
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Samples for proteomics were obtained from HUVECs transduced with the FAT1 intracellular part fused with the extracellular part and transmembrane domain of the IL-2 receptor and carrying a Flag tag on the C terminus (see above) for 36 h followed by lysis in IP buffer. Lysates were incubated with magnetic anti-FLAG beads (M8823, Sigma/Aldrich) overnight at 4Deg. Affinity purified samples were subjected to in-gel (4-12% NuPAGE Bis-Tris gels, ThermoFisher Scientific) digestion as described (DOI: 10.1038/nprot.2006.468). In brief, gel lanes were cut into nine blocks/fractions and finely diced. Embedded proteins were reduced (10 mM dithiothreitol) and alkylated (55 mM iodoacetamide), followed by overnight digestion using trypsin (Serva). Peptides were extracted by increasing concentrations of acetonitrile and lyophilized. Final desalting, concentration and storage utilized "stop and go extraction" (STAGE) tips (DOI: 10.1021/ac026117i). Eluted peptides where subjected to electrospray ionization (ESI)-mediated liquid chromatography/tandem mass spectrometry (LC/MS2) using in house-packed column emitters (15 cm length, 70 um ID, 1.9 um ReprsoSil-Pur 120 C18-AQ, Dr. Maisch) and a buffer system comprising solvent A (0.1% formic acid) and solvent B (80% acetonitrile, 0.1% formic acid). Instrumentation details and parameters were extracted and summarized using MARMoSET (DOI: 10.1074/mcp.TIR119.001505) and are repository deposited. Peptide/spectrum matching and label free quantitation were performed using the MaxQuant suite of algorithms (DOIs: 10.1038/nbt.1511, 10.1021/pr101065j, 10.1074/mcp.M113.031591) against the human UniProt database (canonical & isoforms; downloaded on 2019/01/23). Parameters are included here. Downstream statistical analysis used the limma-based (DOI: 10.1093/nar/gkv007) in-house package autonomics (https://doi.org/doi:10.18129/B9.bioc.autonomics).
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