Description
Single-cell and pooled cell proteomic data from alveolar type II epithelial cell line (C10) and axillary lymph node cell line (SVEC). Cells were sorted using cellenONE onto several nanoSPLITS chips. Cell lysates were then split for parallel RNAseq and proteomic analysis. For the proteomic sample prep all steps utilized the nanoPOTS sample handling robot. Lysates were reduced, treated with IAA, digested overnight with trypsin/Lys-C at 37C, and vacuum dried / stored at -20C. LC-MS/MS data was acquired using TIFF DDA methodology on a Thermo Tribrid mass spectrometer. Data was searched using FragPipe version 17.1 before downstream analysis in R.
[doi:10.25345/C5VH5CN69]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: nanoPOTS ; nanoSPLITS ; single-cell ; multiomics ; multimodal ; scRNAseq ; scProteomics
Contact
Principal Investigators:
(in alphabetical order)
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Ying Zhu, Pacific Northwest National Laboratory, United States
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Submitting User: |
alchemistmatt
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Publications
James M. Fulcher, Lye Meng Markillie, Hugh D. Mitchell, Sarah M. Williams, Kristin M. Engbrecht, Ronald J. Moore, Joshua Cantlon-Bruce, Johannes W. Bagnoli, Anjali Seth, Ljiljana Paša-Toli?, Ying Zhu.
Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting.
bioRxiv. Epub 2022 May 18. doi: https://doi.org/10.1101/2022.05.17.492137.
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Technical Replicates:
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Identification Results |
Proteins (Human, Remapped):
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Proteins (Reported):
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Number of distinct conditions across all analyses (original submission and reanalyses)
associated with this dataset.
Distinct condition labels are counted across all files submitted in the "Metadata" category
having a "Condition" column in this dataset.
"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses)
associated with this dataset.
Distinct replicate labels are counted across all files submitted in the "Metadata" category
having a "BioReplicate" or "Replicate" column in this dataset.
"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses)
associated with this dataset.
The technical replicate count is defined as the maximum number of times any one distinct
combination of condition and biological replicate was analyzed across all files submitted in the
"Metadata" category. In the case of fractionated experiments, only the first fraction is
considered.
"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically
remapped by MassIVE to proteins in the
SwissProt
human reference database.
"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and
reanalyses) associated with this dataset.
"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original
submission and reanalyses) associated with this dataset.
"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported
across all analyses (original submission and reanalyses) associated with this dataset.
"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all
analyses (original submission and reanalyses) associated with this dataset.
"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses)
associated with this dataset.
Distinct protein accessions are counted across all files submitted in the "Statistical Analysis
of Quantified Analytes" category having a "Protein" column in this dataset.
"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison
across all analyses (original submission and reanalyses) associated with this dataset.
A protein is differentially abundant if its change in abundance across conditions is found
to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated
with statistical tests for differential abundance.
Distinct protein accessions are counted across all files submitted in the "Statistical Analysis
of Quantified Analytes" category having a "Protein" column in this dataset.
"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE.
It has been imported to MassIVE for reanalysis purposes, so its spectra data here may
consist solely of processed peak lists suitable for reanalysis with most software.