CONP Portal | Dataset


Keywords: transcriptomics
NIH Blueprint Non-Human Primate Atlas
Creators: The Allen Institute for Brain Science
Contact: http://www.alleninstitute.org#contact-form
Licenses: https://alleninstitute.org/legal/terms-use/
Version: 1.0.0
Modalities: transcriptomics
Formats: CEL JPEG DICOM
Size: 7.0 GB
No of Files: 385
No of Subjects: 36
Primary Publication: Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. https://dx.doi.org/10.1093%2Fnar%2Fgks1042
Metadata file: DATS.json
Is About: Callithrix jacchus
Other Dates: Conp Dats Json Fileset Creation Date: 2019-09-06 13:54:24
Description:
The NIH Blueprint Non-Human Primate (NHP) Atlas consists of a suite of gene expression and neuroanatomical data for exploring the cellular and molecular architecture of the developing rhesus macaque brain.

Dataset README information

README.md

NIH Blueprint Non-Human Primate Atlas

Transcriptome analyses from laser micro-dissection samples of macaque cortical layers from multiple regions at 10 different pre- and post-natal ages using GeneChip microarrays.

This dataset contains the following files:

Dissection Microarray

Downloadable archive files containing all normalized LMD microarray expression values for each brain and probe and sample metadata lmd_expression_matrix_2014-03-06.zip (link)
Downloadable archive files containing all normalized macrodissection microarray expression values for each brain and probe and sample metadata macro_expression_matrix_2014-03-06.zip (link)
Links for downloading both LMD and macrodissection raw microarray files, and some meta-information well_data_files.xml
Neuroanatomical guide files for prenatal LMD sample isolation Neuroanatomical_guides(directory containing 144 JPG file links)

Supplemental data

Supplemental DNA microarray data Transcriptional_Architecture_of_the_Primate_Neocortex (directory containing 229 file links)
MRI zip files, containing the DICOM for the three 48 month specimens used for the ISH data generated serially across a complete hemisphere from adult rhesus macaque. 14349_MRI.zip, 14447_MRI.zip, 14868_MRI.zip (3 links)

Contents of this file adapted from http://blueprintnhpatlas.org/static/download

DOI

Download Using DataLad

CircleCI status

The following instructions require a basic understanding of UNIX/LINUX command lines. A subset of open datasets on the Portal are also available through a browser-based download button. The instructions below regard dataset download with the use of DataLad. To install DataLad on your system, please refer to the install section of the DataLad Handbook .

Note: For maximum compatibility with conp-dataset, the CONP recommends versions 3.12+ of Python, 10.20241202+ of git-annex, and 1.1.4+ of datalad.

1) Initiate the CONP dataset

Run the following command in the directory where you want the CONP dataset (conp-dataset) to be installed:

2) Install the nhpatlas dataset

To install the nhpatlas dataset, run the following commands to move into the "projects" subdirectory under the "conp-dataset" directory (created in the previous step) and run datalad install:

3) Download data from the nhpatlas dataset

Now that the dataset has been installed, go into the nhpatlas dataset directory.

The files visible after installing the dataset but before downloading (in the next step) are symbolic links and need to be downloaded manually using the datalad get command:

If you run datalad get * command, all the files available in the dataset directory will be downloaded.


For more information on how DataLad works, please visit the DataLad Handbook documentation.