23/11/2021

README for information on raw data files relating to manuscript:

“Identification of a stereotypic molecular arrangement of endogenous glycine receptors at spinal cord synapses” S.A. Maynard, P. Rostaing, N. Schaefer, O. Gemin, A. Candat, A. Dumoulin, C. Villmann, A. Triller, C.G. Specht. eLife 2021.

Animal IDs for Imaging:

>2 months WT
AQ847 EosGlyRb KI/wt mRFP-GPHN KI/KI ♀︎
AQ848 EosGlyRb KI/KI mRFP-GPHN KI/KI ♀︎
AQ858 EosGlyRb wt/wt mRFP-GPHN KI/KI ♀︎
AQ859 EosGlyRb KI/KI mRFP-GPHN KI/wt ♀︎
>10 months WT
BP057 EosGlyRb KI/KI mRFP-GPHN KI/KI ♀︎
BP001 EosGlyRb KI/KI mRFP-GPHN KI/wt ♀︎
BP056 EosGlyRb KI/wt mRFP-GPHN KI/KI ♀︎
>2 months Oscillator
F2-1 EosGlyRb KI/KI  oscillator KI/wt ♀︎
F2-5 EosGlyRb KI/KI  oscillator KI/wt ♀︎
F2-2 EosGlyRb KI/KI  oscillator wt/wt ♀︎ (WT littermate)
F2-3 EosGlyRb KI/KI  oscillator wt/wt ♀︎ (WT littermate)

Confocal Image Data:

>180521 double KI ICC 7a quantified. lif 
>Contains all images for decay, intensity measurements and cross-section quantification of 2 month WT mice
>Figure 1

Decay: 
	AQ848
Intensity measurements:
	AQ847 
	AQ848 
	AQ858 
	AQ859 
Quantification cross-section:
	AQ847
	AQ848

>190117 double KI ICC 7a quantified.lif
>Contains all images for decay, intensity measurements and cross-section quantification of 10 month WT mice
>Figure 1 and supplementary file 3, 4

Intensity measurements:
	BP056
	BP057
Quantification cross-section:
	BP056
	BP057

>210119 osci KI ICC geph7a VGAT.lif
>Contains images for cross-section quantification of 2 month oscillator vs WT littermate mice
>Figure 4 and supplementary file 10

Quantification cross-section:
	F2-1
	F2-2

>210120 osci KI ICC geph7a VGAT.lif
>Contains images for cross-section quantification of 2 month oscillator vs WT littermate mice
>Figure 4 and supplementary file 10

Quantification cross-section:
	F2-3
	F2-5

PALM Image Data:

>PALM IDs:

180919: AQ859
	001-002: Dorsal
180920: AQ859
	003-006: Ventral
	007-009: Dorsal
	010-014: Ventral
180922: AQ859
	015-019: Dorsal
181130: AQ848
	001-009: Dorsal
181201: AQ848
	010-017: Ventral
	018-021: Dorsal
181202: AQ848
	022-027: Ventral
190312: BP057
	001-005: Dorsal
	006-010: Ventral
190313: BP057
	011-015: Dorsal
	016-020: Ventral
190320: BP001
	001-005: Ventral
	006-009: Dorsal
190321: BP001
	010-015: Dorsal
	016-020: Ventral
210120: 
	001-006: Ventral F2-1
	007-012: Dorsal F2-1
	013-015: Ventral F2-2
210122: 
	016-018: Ventral F2-2
	019-024: Dorsal F2-2
210128: 
	038-043: Ventral F2-3
	044-049: Dorsal F2-3
210129: 
	050-055: Ventral F2-5
	056-061: Dorsal F2-5

>PALM images

>Images used for reconstructed image analysis for ICQ and occupancy analysis
>Figure 2, figure 5 and supplementary file 5

MATLAB files contain columns of all the detections. 
	Row titles: 
		frame number
		X position
		Y position
		alpha (intensity under the curve)
		sigma (radius of Gaussian profile)

>PALM detection & synapse area data

>Images used for synapse area, number of synapses and detections
>Figure 2, figure 3, figure 5 and supplementary file 6, 8, 9, 11

Text files (-roi1-counts.txt) contain columns of all the synapses. 
	Column titles: 
		Cluster number
		X position
		Y position
		Cluster area (#10x10np pixels)
		# Bursts
		#Detections per cluster
		#Detections/Burst

>PALM molecule conversion

>Images used for molecule conversion calculation
>Figure 2, figure 3, figure 5 and supplementary file 7, 8, 12

Text files (-roi1-countsbursts.txt) contain columns of burst counts.
	Column titles:
		#Bursts
		Counts
		Mean # of detections

SRRF Images: 

SRRF reconstructed images

>SRRF IDs:
Same as PALM AQ859, AQ848, BP057 and BP001

>Figure 2 and supplementary file 5

Electron Microscopy Images:

>EM Images:

190312 
	Dorsal 1 grid C position G10 (D1 GC G10): Synapses 3, 4, 5
	Ventral 1 grid B position G5 (V1 GB G5): Synapses 1, 2, 4, 5, 7, 8, 9 10, 11, 13
190313 
	Dorsal 2 grid B position E9 (D2 GB E9): Synapses 1, 2, 3, 4, 5, 6, 7
	Dorsal 2 grid B position G9 (D2 GB G9): Synapses 1, 2, 3
	Ventral 2 grid C position E3 (V2 GC E3): Synapses 4, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 22

>Images of serial sections used to measure area of postsynaptic domain of synapses imaged with PALM and SRRF.

>Figure 3 and supplementary file 9

Electrophysiology:

>Cell IDs:

Wt
Exp 1
Contains data from
neuron 1
neuron2
Exp 2
Neuron 4
Neuron 5
Neuron 6
Neuron 7
Neuron 8
Exp 3
Neuron 9
Neuron 10
Neuron 11

Eos
Exp1
Neuron 1
Neuron 2
Exp2
Neuron 3
Neuron 4
Neuron 5
Neuron 6
Neuron 7
Exp 3
Neuron 8
Neuron 9
Neuron 10
Neuron 11

>Electrophysiology data:

>All data files were from HEKA exported into origin, the origin files contain xy date (current versus time).
>The Originlab, Origin 2020 was used to setup the data files.
>Figure 1, supplementary file 2