A DNA-nanoassembly-based approach to map membrane protein nanoenvironments
SND-ID: 2020-90-1. Version: 1. DOI: https://doi.org/10.5878/jvvj-1688
Download data
ED_Fig.10_aptamers immobilization.blr (27.5 KB)
ED_Fig.10_CD71 binding sck bis.blr (1.8 MB)
ED_Fig.1a_B1 binding.blr (1.57 MB)
ED_Fig.1a_B2 binding.blr (1.44 MB)
ED_Fig.1a_B3 binding.blr (1.44 MB)
ED_Fig.2a_PAGE 1 comassie.png (613.16 KB)
ED_Fig.2a_PAGE 1.png (565.42 KB)
... Show more..ED_Fig.10_aptamers immobilization.blr (27.5 KB)
ED_Fig.10_CD71 binding sck bis.blr (1.8 MB)
ED_Fig.1a_B1 binding.blr (1.57 MB)
ED_Fig.1a_B2 binding.blr (1.44 MB)
ED_Fig.1a_B3 binding.blr (1.44 MB)
ED_Fig.2a_PAGE 1 comassie.png (613.16 KB)
ED_Fig.2a_PAGE 1.png (565.42 KB)
ED_Fig.2a_PAGE 2 comassie.png (1.99 MB)
ED_Fig.2a_PAGE 2.png (2.33 MB)
ED_Fig.2a_PAGE 3 comassie.png (558.16 KB)
ED_Fig.2a_PAGE 3.png (648.25 KB)
ED_Fig.2b_B1 binding.blr (410.5 KB)
ED_Fig.2b_B1 conjug binding.blr (410.5 KB)
ED_Fig.2b_B2 binding.blr (409.5 KB)
ED_Fig.2b_B2 conjug binding.blr (409.5 KB)
ED_Fig.2b_B3 binding.blr (931 KB)
ED_Fig.2b_B3 conjug binding.blr (409.5 KB)
ED_Fig.3_blocking strand_bis.blr (482.5 KB)
ED_Fig.3_blocking strand.blr (1.1 MB)
ED_Fig.3_Invading strand_bis.blr (57 KB)
ED_Fig.3_Invading strand.blr (45 KB)
ED_Fig.3_NC hybridization_bis.blr (1.1 MB)
ED_Fig.3_NC hybridization.blr (1.1 MB)
ED_Fig.4_B1-NC binding sck.blr (2.09 MB)
ED_Fig.4_B3 - B2 - B1 - invading strand.blr (3.31 MB)
ED_Fig.4_immobilization Her2-Her3-EGFR.blr (79 KB)
ED_Fig.5a_PAGE.png (421.29 KB)
ED_Fig.5b_Ambrosetti_SD_Fig.ED5.xlsx (8.76 KB)
ED_Fig.5b_OD in solution.png (1.55 MB)
ED_Fig.6_Ambrosetti_SD_Fig.ED6.xlsx (9.29 KB)
ED_Fig.6a_immobilization Her2-Her3.blr (76 KB)
ED_Fig.6a_NC-B1 binding sck.blr (638 KB)
ED_Fig.6a_NC-B3 binding sck.blr (637.5 KB)
ED_Fig.6b_analysis.pzfx (25.57 KB)
ED_Fig.6b_analysis.xlsx (19.21 KB)
ED_Fig.6c_analysis.xlsx (9.4 KB)
ED_Fig.6c_sample1.fastq (845.87 MB)
ED_Fig.6c_sample2.gz (166.12 MB)
ED_Fig.6d_analysis.xlsx (17.87 KB)
ED_Fig.7a_Ambrosetti_SD_Fig. ED7.xlsx (8.88 KB)
ED_Fig.7a_analysis.xlsx (20.28 KB)
ED_Fig.7b_sample1_SH-SY5Y_1.fastq.gz (3.3 KB)
ED_Fig.7b_sample2_SH-SY5Y_2.fastq.gz (9.21 KB)
ED_Fig.7b_sample3_SKBR3 positive ctrl.fastq.gz (309.63 MB)
ED_Fig.9_aCD63 binding.blr (651 KB)
ED_Fig.9_aCD63-oligo binding.blr (651 KB)
ED_Fig.9_CD63 immobilization NTA chip.blr (30 KB)
Fig.2c_NC_prongs hybridization.blr (1.59 MB)
Fig.2e_B1 conjug binding.blr (411 KB)
Fig.2e_ECD-Her2 sck.blr (1.05 MB)
Fig.2f_B1conjugate.blr (1.21 MB)
Fig.2f_NC binding.blr (1.13 MB)
Fig.3a_B1-NC binding.blr (756 KB)
Fig.3a_invading strand 2.blr (837.5 KB)
Fig.3b_PAGE_comassie.png (588.07 KB)
Fig.3b_Page_SybrGold.png (1.35 MB)
Fig.4b_Her3 immobilization.blr (74 KB)
Fig.4b_streptavidin.blr (616.5 KB)
Fig.5a_HD_B1-NC binding bis.blr (1.69 MB)
Fig.5a_HD_B1-NC binding sck.blr (2.09 MB)
Fig.5a_HD_B3 - B1 - invading strand.blr (2.55 MB)
Fig.5a_HD_immobilization Her2-Her3.blr (79 KB)
Fig.5a_LD_B1-NC binding bis.blr (1.17 MB)
Fig.5a_LD_B1-NC binding sck.blr (2.09 MB)
Fig.5a_LD_B3 - B1 - invading strand.blr (2.54 MB)
Fig.5a_LD_immobilization Her2-Her3.blr (91.5 KB)
Fig.5b_sample1_bis.fastq (1.81 GB)
Fig.5b_sample1.fastq (1.32 GB)
Fig.5b_sample2.fastq (1.33 GB)
Fig.5b_sample3.fastq (1.36 GB)
Fig.5b_sample4_bis.fastq (2.4 GB)
Fig.5b_sample4.fastq (2.57 GB)
Fig.6a_sample 1.fastq.gz (258.35 MB)
Fig.6a_sample 2.fastq.gz (390.08 MB)
Fig.6a_sample 3.fastq.gz (303.81 MB)
Fig.6b_sample1.fastq.gz (330.05 MB)
Fig.6b_sample2.fastq.gz (277.09 MB)
Fig.6b_sample3.fastq.gz (285.41 MB)
Fig.6b_sample4.fastq.gz (251.6 MB)
Fig.6b_sample5.fastq.gz (303.81 MB)
Fig.6b_sample6.fastq (402.33 MB)
Fig.6c_HRG_sample1.fastq (3.34 GB)
Fig.6c_HRG_sample2.fastq (1.5 GB)
Fig.6c_HRG_sample3.fastq (2.33 GB)
Fig.6c_NoL_sample1.fastq (3.75 GB)
Fig.6c_NoL_sample2.fastq (1.46 GB)
Fig.6c_NoL_sample3.fastq (1.49 GB)
Fig.7_Ambrosetti_SD_Fig. 7.xlsx (9.92 KB)
Fig.7_CD71sample1.fastq (1.17 GB)
Fig.7_CD71sample2.fastq (880.28 MB)
Fig.7_sample1.fastq.gz (286.02 MB)
Fig.7_sample2.fastq.gz (268.22 MB)
Fig.7_sample3.fastq.gz (274.25 MB)
Suppl_Fig.1_PAGE.png (482.42 KB)
Show less..Associated documentation
Citation
Creator/Principal investigator(s)
Elena Ambrosetti - Karolinska Institutet, Department of Medical Biochemistry and Biophysics - Biomaterials division
Research principal
Karolinska Institutet - Department of Medical Biochemistry and Biophysics - Biomaterials division
Description
Most proteins at the plasma membrane are not uniformly distributed but localize to dynamic domains of nanoscale dimensions. To investigate their functional relevance, there is a need for methods that enable comprehensive analysis of the compositions and spatial organizations of membrane protein nanodomains in cell populations. Here we describe the development of a non-microscopy based method for ensemble analysis of membrane protein nanodomains. The method, termed NANOscale DEciphEring of membrane Protein nanodomains (NanoDeep), is based on the use of DNA nanoassemblies to translate membrane protein organization information into a DNA sequencing readout. Using NanoDeep, we characterised the nanoenvironments of Her2, a membrane receptor of critical relevance in cancer. Importantly, we were able to modulate by design the inventory of proteins analysed by NanoDeep. NanoDeep has the potential to provide new insights into the roles of the composition and spatial organization of protein nanoenvironments in the regulation of membrane protein function.
The methodology is described in the preprint art
The methodology is described in the preprint article (see publications list).
The methodology for this dataset is available in the preprint (see publication list)
Software for data collection:
Biacore T200 System Control software, NextSeq control software
Software for data analysis:
BIAevaluation v3.0, GraphPad Prism v8.2.1, Fiji ImageJ v1.0, Illumina Sequencing Analysis Viewer software, Python v3.8.0. Show less..
Data contains personal data
No
Language
Population
cell membrane receptors
Study design
Experimental study
Data format / data structure
Responsible department/unit
Department of Medical Biochemistry and Biophysics - Biomaterials division
Research area
Biochemistry and molecular biology (Standard för svensk indelning av forskningsämnen 2011)
Biophysics (Standard för svensk indelning av forskningsämnen 2011)
A DNA nanoassembly-based approach to map membrane protein nanoenvironments (preprint).
Elena Ambrosetti, Giulio Bernardinelli, Ian Hoffecker, Leonard Hartmanis, View ORCID ProfileRickard Sandberg, Björn Högberg, Ana I. Teixeira
doi: https://doi.org/10.1101/836049
DOI:
https://doi.org/10.1101/836049
“A DNA-nanoassembly-based approach to map membrane protein nanoenvironments” E. Ambrosetti, G. Bernardinelli, I. T. Hoffecker, L. Hartmanis, G. Kiriako, A. de Marco, R. Sandberg, B. Högberg, A. I. Teixeira. Nat. Nanotechnol. 2020.
DOI:
https://doi.org/10.1038/s41565-020-00785-0
If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.