Dataset DOI: 10.5061/dryad.70rxwdc9p

We have submitted our gene expression data from PatchSeq experiments including a spreadsheet containing single-cell expression data for 18 lateral olivocochlear (LOC) and 13 medial olivocochlear (MOC) neurons, a report detailing expression profiles of individual cells, and associated patch-clamp data for a subset of cells. This is a standalone dataset, and is not in support of a corresponding manuscript.

Sharing / Access information: Please contact catherine.weisz@nih.gov.

Notes:

Data and File Structure:

• “MOC_LOC_PatchSeq_expression_data.zip” .zip file
  • “LOC_MOC_PatchSeq_expression.xlsx” Excel file
  • “LOC_MOC_PatchSeq_expression_csv.csv” csv file: same as above, csv format
• “MOC_LOC_PatchSeq_Patch_clamp_data.zip” .zip file
  • Patch-clamp data in .dat, .abf, or .txt format
  • “Patch_clamp_text_file_list.xlsx” Excel file
• “PatchSeq_sample_list.xlsx”: Excel file
• PatchSeq_Methods_Frank_Weisz_final.pdf”
• “MultiQC_report”: html doc with expression details, supplemental file (Zenodo)

Spreadsheets:

• LOC MOC PatchSeq expression: This spreadsheet contains the single-cell expression data for 18 LOC and 13 MOC neurons. The first column contains the Ensembl gene id. Columns B-AF contain expression data for an individual cell, with the cell ID at the top of the column. The units are CountsPerMillion_Trimmed Mean of M component (CPM_TMM_Counts). Columb AG contains the entrezgene ID. Column AH “external_gene_name” contains the gene name. Column AI contains the description of the gene.
• PatchSeq sample list: This spreadsheet contains the list of cells that are included in the expression dataset, along with details of cell type, recording date, animal age in post-natal days (P), for which the day of birth = P0, and patch-clamp file name.
• Patch clamp text file list: This spreadsheet contains the recordings types and names for patch-clamp recordings that were collected using HEKA software and were converted to .txt files.

Sub-folder: “MOC LOC PatchSeq expression data”

Contains expression data from LOC and MOC neurons collected using the PatchSeq method. See “spreadsheet” section (above) for details for “LOC MOC PatchSeq expression”. Excel spreadsheets can be opened using Microsoft Excel, the csv version can be opened in any spreadsheet software. Information about gene expression metrics is explained within the supplementary MultiQC report file (stored on Zenodo).

Sub-folder: “PatchSeq Patch clamp data”

Contains patch-clamp electrophysiology data for a subset of the LOC and MOC neurons for which quality single cell expression data was available. It also includes an excel file detailing the recording types for each cell.

These data were recorded using either the Molecular Devices pClamp software version 11 or the HEKA Patchmaster EBC10 software. Files can be opened with various software:

Molecular devices (.abf) files can be opened with Clampfit software. This can be downloaded as part of the pClamp software suite (pClamp, AxoScope, and Clampfit; free download, does not require dongle unless the amplifier is being used to collect new data) at:

-          https://support.moleculardevices.com/s/article/Axon-pCLAMP-11-Electrophysiology-Data-Acquisition-Analysis-Software-Download-Page

-          In addition, various converters can be used to convert .abf files to Matlab or python formats (eg. https://www.mathworks.com/matlabcentral/fileexchange/6190-abfload)

HEKA files (.dat files are the primary data files, if present the .bak, .mrk, .onl, .pul, and .sol files are companion files that automatically get opened with the associated .dat file that has the same name) can be opened with HEKA Patchmaster NEXT, Patchmaster, or HEKA Fitmaster:

-          https://www.heka.com/downloads/downloads_main.html#down_patchmaster_next

-          https://www.heka.com/downloads/downloads_main.html#down_fitmaster

-          https://www.heka.com/downloads/downloads_main.html#down_patchmaster (acquisition software)

-          Full functionality requires purchase of a software dongle, but software can be run in the ‘demo’ mode to open and view data. Note: opening of some files generates a “Too many sample points” error, use the “My risk” button to clear the error and proceed. Open from within the fitmaster software, and load the .dat file.

-          File converters are available for Matlab and python, for example this python converter: https://github.com/campagnola/heka_reader

-          In addition, .dat files were exported as .txt files for opening in any text editor or in Microsoft Excel. For these files, each column represents a ‘sweep’ which can be either a single sweep from a different voltage step in an “IV” experiment, or a single sweep to collect synaptic data. The voltage command (V) data and corresponding current response (I) data are in adjacent columns. Column titles have titles that detail the type of experiment with the numbers responding to the experiment number within the file, and the sweep number. All data from a single cell is included in the same .txt file, including IV curves, drug application, or longer single voltage steps.

File naming conventions: Patch-clamp files are in two formats. For some cells, files were collected in pClamp and have the file naming structure that begins with the cell ID (LOC# or MOC#) followed by LT_year_day_month_file# (LT = experimenter Lester Torres Cadenas). Each set of traces is contained within a single file, and there may be multiple files per cell. All files for a given cell are in a folder. For the remainder of cells, a single file recorded using the HEKA Patchmaster software will have all recordings from a single cell. File naming convention is cell ID (LOC# or MOC#) 2Photon_year-month-day-subfile# (2Photon is the name of the rig and computer that was used for recordings, no multiphoton imaging data is presented in this dataset). The list of file names for each cell (or “none” if no patch-clamp data is included)  can be found in the attached spreadsheet “PatchSeq sample list”

Files are present in the original file formats (.abf for Molecular Devices / pClamp and .dat for HEKA). HEKA files are also exported to .txt.

Variables and abbreviations:

CPM_TMM_Counts = CountsPerMillion_Trimmed Mean of M component”. This is a standard RNA-seq metric, where the number of reads is normalized to the total library size, and then further scaled to take into account large variations in the sample size factors.

mV = milli volts, a unit of electrical potential in neurons

pA = pico-amps, unit of electrical measurement of currents in neurons

mM = milli Molar concentration

Vhold = membrane holding voltage, the voltage that the internal neuron state was set at using the patch-clamp amplifier

IV = current voltage, shorthand for a type of voltage-clamp experiment in which the neuron membrane potential is set to different holding potentials from -110 to ~+20 mV in 10 mV increments while recording the resulting currents in the neuron, or the equivalent protocol in current-clamp in which the neuron is held at a resting membrane potential of ~-60 mV, and the current is stepped to hyperpolarizing and depolarizing potentials by injecting current in 10 pA negative and positive steps.

Code / Software

No additional code was generated for this work.