Molecular properties

This sub-section evaluates the usage of gene expression data to classify and model single neurons.

The frequency of expression of commonly expressed calcium binding proteins and neuropeptides obtained from RT-PCR experiments were evaluated in the reconstructed microcircuit.

The results of the consistency check were categorized as consistent, inconsistent, possibly consistent, not implemented or not applicable based on agreement with a given evaluation criterion.

paper(s)
paper(s)
paper(s)
paper(s)
paper(s)

consistent - Nathaniel Heintz - Application of a translational profiling approach for the comparative analysis of CNS cell types. ext_link

input/validation/consistent
consistent
evaluation criterion
The single cell transcriptome is essential to classify and characterize neuronal populations
id
1
should be in
mol
feedback
follow if time
species
mouse
age
adult
brain region
Cortex, cerebellum, striatum, brain stem, spinal cord
layer
-
cell
Expressing molecular marker: PcP2, NeuroD1, Grm2, Lypd6, Grp, Olig2, Cmtm5, Sept4, Aldh1L1, Chat, Drd1,Ntsr1, Glt25d2, Etv1, Pnoc, Cort, Aldh1L1 or Cck
aspect
Transcriptome study of cell types defined by single molecular markers
statement
We present transcriptional profiles for 24 CNS cell populations and identify known cell-specific and enriched transcripts for each population. We report thousands of cell-specific mRNAs that were not detected in whole-tissue microarray studies
pmid
19013282
title
Application of a translational profiling approach for the comparative analysis of CNS cell types.
contact Name
Nathaniel Heintz
contributed by
J. Ryge
checked by
DK

consistent - Burkhalter, A - Axo-axonic synapses formed by somatostatin-expressing GABAergic neurons in rat and monkey visual cortex. ext_link

input/validation/consistent
consistent
evaluation criterion
We have incorporated the capability for axo-axonic contacts for ceertain types of inhibitory cells.
id
2
should be in
mol
feedback
follow if time
species
rat
age
adult
brain region
V1
layer
2/3,4
cell
IN, PC
aspect
Neuropeptide markers
statement
Electron microscopic examination directly demonstrated that SOM axon terminals form symmetric synapses with the initial segments of pyramidal cells in supragranular layers of rat and monkey primary visual cortex. These SOM synapses differed ultrastructurally from the more numerous unlabeled symmetric synapses found on initial segments
pmid
11793343
title
Axo-axonic synapses formed by somatostatin-expressing GABAergic neurons in rat and monkey visual cortex.
contact Name
Burkhalter, A
contributed by
SR
checked by
DK

consistent - Cauli, B - Classification of NPY-expressing neocortical interneurons. ext_link

input/validation/consistent
consistent
evaluation criterion
The reporetd gene-types were used to validate the m-type composition of the reconstructed microcircuit
id
3
should be in
mol
feedback
follow if time
species
rat
age
P17-21
brain region
barrel cortex
layer
each
cell
interneurons NPY expressing
aspect
morphology, neurochemical, electrical
statement
To classify reliably cortical NPY neurons, used unsupervised clustering algorithms based on laminar location and electrophysiological and molecular properties. These classification schemes confirmed that NPY neurons are nearly exclusively GABAergic and are three main types (1) Neurogliaform-like neurons exhibiting a dense axonal arbor, were the most frequent and superficial, and substantially expressed the neuronal isoform of nitric oxide synthase. (2) Martinotti-like cells characterized by an ascending axon ramifying in layer I coexpressed somatostatin and were the most excitable type. (3) Among fast-spiking and parvalbumin-positive basket cells, NPY expression was correlated with pronounced spike latency.
pmid
19295167
title
Classification of NPY-expressing neocortical interneurons.
contact Name
Cauli, B
contributed by
Monica Favre
checked by
DK

consistent - Andreas Bosio - Gene expression analysis defines differences between region-specific GABAergic neurons. ext_link

input/validation/consistent
consistent
evaluation criterion
We use a similar technique based on single cell transcripts to classify inhibitory cells
id
4
should be in
mol
feedback
follow if time
species
mouse
age
P1
brain region
cortex, olfactory bulb, striatum and cerebellum
layer
NA
cell
GABAergic IN (Gad67)
aspect
Gene expression in GABAergic cells
statement
Expression profiles available for GABAergic cells in different brain regions. Clustering of our gene expression results revealed major differences between hind and forebrain GABAergic neurons indicating that the development of GABAergic neurons depends on their regional location.
pmid
18725299
title
Gene expression analysis defines differences between region-specific GABAergic neurons.
contact Name
Andreas Bosio
contributed by
J.Ryge
checked by
DK

consistent - Sacha B Nelson - Molecular taxonomy of major neuronal classes in the adult mouse forebrain. ext_link

input/validation/consistent
consistent
evaluation criterion
We use a similar technique to classify cells
id
5
should be in
mol
feedback
follow if time
species
Mouse
age
P57-107
brain region
cingulate cortex, S1, hippocampus, amygdala and thalamus
layer
Layer 1-6, CA1-CA3, Dorsal LGN
cell
PC, Gabaergic,
aspect
Gene expression and electrophysiology of 12 well defined neuronal populations across the brain
statement
Expression profiles together with ephys propertis available for 12 neuronal populations across the brain. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements.
pmid
16369481
title
Molecular taxonomy of major neuronal classes in the adult mouse forebrain.
contact Name
Sacha B Nelson
contributed by
J.Ryge
checked by
DK

consistent - Yasuo Kawaguchi - Selective coexpression of multiple chemical markers defines discrete populations of neocortical GABAergic neurons. ext_link

input/validation/consistent
consistent
evaluation criterion
The reported gene-types were used to validate the m-type composition of the reconstructed microcircuit
id
6
should be in
mol
feedback
follow if time
species
rat
age
PNW4-8
brain region
medial agranular frontal cortex
layer
each
cell
GABAergic interneurons
aspect
CRF, NPY, SPR, and NOS
statement
To better clarify GABAergic neuron diversity, assessed colocalization of 6 chemical markers (parvalbumin, calretinin, alpha-actinin-2, somatostatin, vasoactive intestinal polypeptide, and cholecystokinin) with corticotropin-releasing factor (CRF), neuropeptide Y (NPY), the substance P receptor (SPR), and nitric oxide synthase (NOS).
pmid
21220766
title
Selective coexpression of multiple chemical markers defines discrete populations of neocortical GABAergic neurons.
contact Name
Yasuo Kawaguchi
contributed by
Monica Favre
checked by
DK