A Transcriptomic Atlas of Mouse Neocortical Layers

Welcome to the supplementary website for Belgard, et al. (2011).

Please visit the interactive webpage to query specific genes.

Download the Online Supplementary Figures. View or download the Online Supplementary Tables. View the Online Supplementary Notes. Read more about cell types and imprinting.

Download raw sequencing data, read alignments (BAM), wig files giving normalized coverage of uniquely mapping reads, and expression values (with confidence intervals) for all Ensembl and de novo gene models (along with GTF files giving coordinates) from GEO, accession number GSE27243. We used the mm9 build. This archive also includes raw reads and the alignments in BAM format for both replication sets, and estimated fragment sizes and standard deviations for all libraries. Raw reads can also be downloaded here.

Calibrated and uncalibrated layer enrichment probabilities for Ensembl genes, Ensembl transcripts, de novo (cufflinks-built) genes, and de novo (cufflinks-built) transcripts. Note that the uncalibrated layer enrichment probabilities can be used to reconstitute all layer predictions by requiring the uncalibrated probability exceed 0.5. Also, the known genes include additional worksheets for only receptors and ion channels and alternatively-spliced transcripts.

FPKMs across all samples for Ensembl genes & transcripts (release 57) and de novo (cufflinks-built) genes & transcripts. Download the zipped version of all four here.

De novo gene models zipped and in GTF format.

LincRNA gene models in GTF format.

UCSC Genome Browser custom tracks for normalized coverage of all reads and for uniquely mapping reads. These tracks also include lincRNA transcript models.

All significant functional enrichments for sets of genes predicted in layers, along with their contributing genes, are available here. All significant functional differences between patterned and unpatterned genes, along with the contributing genes to each term, are available here. Note that the contributing genes to these enrichments can overwhelm Excel; a text editor may work better. The genes are listed in a comma-space separated format amenable to translation into common gene symbols here.

Data for the dorsal and lateral cortex replications: fastq files of raw reads (only applied Illumina's chastity filter and the base quality filter as described in the Extended Experimental Methods; dorsal cortex; lateral cortex); BAM files (accompanying BAI files are also on this server, so these files can be used for random access; dorsal cortex A B C D E F; lateral cortex A B C D E F); BigWig files appropriate for viewing in the Ensembl genome browser (dorsal cortex A B C D E F; lateral cortex A B C D E F); FPKM values of genes and transcripts with confidence intervals (dorsal cortex, lateral cortex); layer enrichment predicted probabilities (dorsal cortex; lateral cortex); all functional functional terms with contributing genes and p-values (dorsal cortex; lateral cortex); genes sorted by similarity in predicted laminar patterning (Euclidean distance) in dorsal and lateral cortex

The MGI Batch Query is useful for translating to or from Ensembl gene IDs and rapidly linking to other information, such as to relevant Allen Mouse Brain Atlas probes.