PT  - JOURNAL ARTICLE
AU  - Julie A. Harris
AU  - Stefan Mihalas
AU  - Karla E. Hirokawa
AU  - Jennifer D. Whitesell
AU  - Joseph Knox
AU  - Amy Bernard
AU  - Philip Bohn
AU  - Shiella Caldejon
AU  - Linzy Casal
AU  - Andrew Cho
AU  - David Feng
AU  - Nathalie Gaudreault
AU  - Nile Graddis
AU  - Peter A. Groblewski
AU  - Alex Henry
AU  - Anh Ho
AU  - Robert Howard
AU  - Leonard Kuan
AU  - Jerome Lecoq
AU  - Jennifer Luviano
AU  - Stephen McConoghy
AU  - Marty T. Mortrud
AU  - Maitham Naeemi
AU  - Lydia Ng
AU  - Seung W. Oh
AU  - Benjamin Ouellette
AU  - Staci A. Sorensen
AU  - Wayne Wakeman
AU  - Quanxin Wang
AU  - Ali Williford
AU  - John W. Phillips
AU  - Allan Jones
AU  - Christof Koch
AU  - Hongkui Zeng
TI  - The organization of intracortical connections by layer and cell class in the mouse brain
AID  - 10.1101/292961
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 292961
4099  - http://biorxiv.org/content/early/2018/04/01/292961.short
4100  - http://biorxiv.org/content/early/2018/04/01/292961.full
AB  - The mammalian cortex is a laminar structure composed of many cell types densely interconnected in complex ways. Recent systematic efforts to map the mouse mesoscale connectome provide comprehensive projection data on inter-areal connections, but not at the level of specific cell classes or layers within cortical areas. We present here a significant expansion of the Allen Mouse Brain Connectivity Atlas, with ~1000 new axonal projection mapping experiments across nearly all isocortical areas in 50 Cre driver lines. Using 13 lines most selective for cortical layer and/or projection neuron class we identify the differential contribution of each layer/class to the overall intracortical connectivity patterns. We find that layer 5 (L5) projection neurons account for essentially all intracortical outputs. L2/3, L4, and L6 neurons contact a subset of the L5 cortical targets. We describe the most common axon lamination patterns in target regions, and their relationships to source layer/class. Most patterns were consistent with previous anatomical rules used to determine hierarchical position between cortical areas (feedforward, feedback), with notable exceptions. We observe a diversity of target patterns arising from every source layer/class, but supragranular (L2/3 and upper L4) neurons are most associated with feedforward type patterns, whereas infragranular (L5 and L6) neurons have both feedforward and feedback. Network analyses revealed a modular organization of the intracortical connectome. Using the cell class-based target lamination patterns, we labeled all connections and intermodule connections as feed-forward or -back, and finally present an integrated view of the intracortical connectome as a hierarchical network.