Single Human Neuron Expression Data

 

Overview:

Normalized expression data (transcripts per million or TPM) is provided for 4039 data sets deposited in dbGaP (accession phs000833.v4.p1) as part of a study to characterize neuronal diversity across six distinct cerebral cortical regions of a single individual [1].  After filtering low mapping outliers and potential doublets [1], 3083 annotated single nuclei data sets were classified into distinct excitatory (Ex1-Ex8) and inhibitory (In1-In8) neuronal subtypes.  We provide TPM values derived from both exon and intron reads (Lake-2016_Gene_TPM.dat ), as well as TPM values derived from only exon reads (Lake-2016_Exon_TPM.dat).  Associated with each TPM file is an annotation file for the 3083 single nuclei described [1] including the TPM file sample name, associated subtype, Brodmann Area (BA) origin and designated dbGaP sample name.   Raw data and additional information for each sample is available from dbGaP.

 

Recommendations:

Use provided annotation files to generate a subset containing only the 3083 quality filtered data sets for subsequent analyses.  Exclude genes starting with “MT- ” which represent mitochondrial transcripts that may have randomly associated with the nuclear membrane. 

 

Provided Files:

Lake-2016_Gene_TPM.dat

Lake-2016_Gene_TPM_Sample-annotation.txt

Lake-2016_Exon_TPM.dat

Lake-2016_Exon_TPM_Sample-annotation.txt

 

Citation: 

1. Lake, B.B. et al. Science 352, 1586-1590 (2016). 10.1126/science.aaf1204

 

Full Data Availability:

dbGaP (accession phs000833.v4.p1); www.scap-t.org