zhu2019EL: Zhu et al. 2019 (eLife): chicken utricle cells
In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package

zhu2019EL

R Documentation

Zhu et al. 2019 (eLife): chicken utricle cells

Description

Single-cell proteomics data from chicken utricle acquired to study the hair-cell development. The cells are isolated from peeled utrical epithelium and separated into hair cells (FM1-43 high) and supporting cells (FM1-43 low). The sample contain either 1 cell (n = 28), 3 cells (n = 7), 5 cells (n = 8) or 20 cells (n = 14).

Usage

zhu2019EL

Format

A QFeatures object with 62 assays, each assay being a SingleCellExperiment object:

XYZw: 60 assays containing PSM data. The sample are annotated as follows. X indicates the experiment, either 1 or 2. Y indicated the FM1-43 signal, either high (H) or low (L). Z indicates the number of cells (0, 1, 3, 5 or 20). w indicates the replicate, starting from a, it can go up to j.
peptides: quantitative data for 3444 peptides in 60 samples (all runs are combined).
proteins_intensity: protein intensities for 840 proteins from 24 samples
proteins_iBAQ: iBAQ values for 840 proteins from 24 samples

Sample annotation is stored in colData(zhu2019EL()).

Acquisition protocol

The data were acquired using the following setup. More information can be found in the source article (see References).

Cell isolation: The cells were taken from the utricles of E15 chick embryos. Samples were stained with FM1-43FX and the cells were dissociated using enzymatic digestion. Cells were FACS sorted (BD Influx) and split based on their FM1-43 signal, while ensuring no debris, doublets or dead cells are retained.
Sample preparation performed using the nanoPOTs device. Cell lysis and protein extraction and reduction are performed using dodecyl beta-D-maltoside + DTT + ammonium bicarbonate. Protein were then alkylated using IAA. Protein digestion is performed using Lys-C and trypsin. Finally samples acidification is performed using formic acid.
Separation: Dionex UltiMate pump with an C18-Packed column (50cm x 30um; 60nL/min)
Ionization: ESI (2,000V)
Mass spectrometry: Orbitrap Fusion Lumos Tribrid. MS1 settings: accumulation time = 246ms; resolution = 120,000; AGC = 3E6. MS/MS settings: accumulation time = 502ms; resolution = 120,000; AGC = 2E5.
Data analysis: Andromeda & MaxQuant (v1.5.3.30) and the search database is NCBI GRCg6a.

Data collection

All data were collected from the PRIDE repository (accession ID: PXD014256).

The sample annotation information is provided in the Zhu_2019_chick_single_cell_samples_CORRECTED.xlsx file. This file was given during a personal discussion and is a corrected version of the annotation table available on the PRIDE repository.

The PSM data were found in the evidence.txt (in the ⁠Experiment 1+ 2⁠) folder. The PSM data were filtered so that it contains only samples that are annotated. The data were then converted to a QFeatures object using the scp::readSCP() function.

The peptide data were found in the peptides.txt file. The column names holding the quantitative data were adapted to match the sample names in the QFeatures object. The data were then converted to a SingleCellExperiment object and then inserted in the QFeatures object. Links between the PSMs and the peptides were added

A similar procedure was applied to the protein data. The data were found in the proteinGroups.txt file. We split the protein table to separate the two types of quantification: summed intensity and intensity based absolute quantification (iBAQ). Both tables are converted to SingleCellExperiment objects and are added to the QFeatures object as well as the AssayLink between peptides and proteins.

Source

The PSM data can be downloaded from the PRIDE repository PXD014256. The source link is: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD014256

References

Zhu, Ying, Mirko Scheibinger, Daniel Christian Ellwanger, Jocelyn F. Krey, Dongseok Choi, Ryan T. Kelly, Stefan Heller, and Peter G. Barr-Gillespie. 2019. “Single-Cell Proteomics Reveals Changes in Expression during Hair-Cell Development.” eLife 8 (November). (link to article).