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README_data.md

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Available Package Data

Full datasets are too big to include in the package. A small expressed set from embryonic 11.5 day mice (E11.5) has been provided as an example. Full datasets can be downloaded from the Kharchenko lab website due to file size limitations on GitHub.

Generating sample data

load("data-raw/Rdata/E11.5.annot.RData")
load("data-raw/Rdata/E11.5.energy.RData")
load("data-raw/Rdata/sids.RData")

gl <- c("Dcx", "Sox11", "Cited2", "Plxna2", "Neurod6", "Tubb3", "Slc17a6", "Sstr2", "Cxcl12", "Hes6", "Eomes", "Neurog2", "Insm1", "Lrp8", "Mgat5b", "Lrrn3", "Nrn1", "Myt1", "Neurod1", "Sox9", "Fstl1", "Ednrb", "Arx", "Sfrp2", "Mfge8", "Ttyh1", "Dab1", "Fstl1", "Notch2", "Slc1a3", "Sox3", "Sox21", "Ttyh1", "Gli3", "Fgfr3", "Ttyh1", "Notch3", "Igfbp5")
mat <- mat[gl,]

devtools::use_data(structureID, mat, annot3D, gannot3D, vol3D)

Processed Data

Processed data are available for all developing mouse stages under data-raw/RData/:

  • E11.5.*.RData - data for embryonic 11.5 day old mouse
  • E13.5.*.RData - data for embryonic 13.5 day old mouse
  • E15.5.*.RData - data for embryonic 15.5 day old mouse
  • E18.5.*.RData - data for embryonic 18.5 day old mouse
  • P4.*.RData - data for post-natal 4 day old mouse
  • P14.*.RData - data for post-natal 14 day old mouse
  • P28.*.RData - data for post-natal 28 day old mouse
  • P56.*.RData - data for post-natal 56 day old mouse

Each RData file contains:

  • annot3D - 3D array containing structure annotations for each pixel
  • vol3D - 3D array containing stain per pixel for whole mouse
  • gannot3D - 3D array containg structure annotations for each voxel
  • mat - matrix where each row corresponds to the average energy per voxel for a gene

sids.RData contains:

  • structure.id - nested list of structure names to IDs; same for every developing mouse stage

See data-raw/scripts/to_RData.R for more information.

Raw Data

Raw data are too big to included in the package. The following steps were used to download and process data stored in data-raw/. Raw data folders have been zipped to save space. All raw data are publicly available for download through the Allen Brain Atlas website.

Source

This directory is comprised of developing mouse brain ISH data from the Allen Brain Atlas. For more information, please consult the Allen Developing Mouse Brain Atlas technical white apper.

Date

This data was downloaded in March 2014.

Additional resources

Interactive Atlas Viewer - Useful for figuring out what are the comparable regions at different development time points

Gene Search - Useful for searching for gene names to see if they have expression data for that gene

Downloading Gene Expression Data

Official Tutorial

Step 1

Get all gene IDs for all genes by age group. Remove num_row limit by using some really large number.

ex. Embryonic 11.5 days mouse data. Must be non-failed in-situ hybridization experiment. Show gene name and other info just for sanity check:

http://api.brain-map.org/api/v2/data/query.xml?criteria=model::SectionDataSet,rma::criteria,[failed$eq%27false%27],products[abbreviation$eq%27DevMouse%27],treatments[name$eq'ISH'],specimen(donor(age[name$eq'E11.5'])),rma::include,genes,specimen(donor(age))&num_rows=5000000000

Results are saved as XML files under data-raw/xmlQuery/*.xml

Step 2

Parse for gene IDs from XML. See get_data.sh for more info. Results are saved under data-raw/xmlQuery/ids/*

Step 3

Getting the gene expression for each gene requires using the Allen Brain Atlas api. For example, for gene ID 100072942:

http://api.brain-map.org/grid_data/download/100072942?include=energy,intensity,density

Accessing the URL returns a zipped file. Unzip to get:

  • energy.raw - A raw uncompressed float (32-bit) little-endian volume representing average expression energy per voxel. A value of "-1" represents no data. This file is returned by default if the volumes parameter is null.
  • density.raw - A raw uncompressed float (32-bit) little-endian volume representing average expression density per voxel. A value of "-1" represents no data.
  • injection.raw - A raw uncompressed float (32-bit) little-endian volume representing the proportion of pixels within each voxel that were within the manually annotated injection site.
  • and corresponding mhd files with grid size information

Use wget to get gene expression file for each gene ID. Results are stored under data-raw/geneExpression/

Downloading Annotations

Official Tutorial

  • atlasVolume: uchar (8bit) grayscale Nissl or Feulgen-HP yellow volume of the reconstructed brain.
  • annotation: uint (32bit) structural annotation volume matching the atlasVolume. The value represents the ID of the finest level structure annotated for the voxel. Note: the 3-D mask for any structure is composed of all voxels annotated for that structure and all of its descendents in the structure hierarchy.
  • gridAnnotation: uint (32bit) structural annotation volume at grid resolution.

Download directly from site or use wget. See data-raw/csvQuery/*.csv for more details.

Results are stored under data-raw/atlasVolume/, data-raw/atlasAnnotation/, and data-raw/gridAnnotation/ respectively.

Structure IDs

Grid annotation values refer to structure IDs. Get structure IDs from the Atlas Ontologies

wget http://api.brain-map.org/api/v2/structure_graph_download/17.json

Results are stored under data-raw/structureGraph/