CONP Portal | Dataset


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BrainSpan: Atlas of the Developing Human Brain
  • Creators: The Allen Institute for Brain Science
  • Version: 1.0.0
  • Date Added: 2019-08-21
  • Date Updated: 2021-11-29
  • Modalities: genomics
  • License: https://alleninstitute.org/legal/terms-use/
  • Files: 26
  • Size: 1.7 GB
  • Subjects: 4
  • Formats: CSV
ARK ID : https://n2t.net/ark:/70798/d76473rr7886x28g1r
Keywords: genomics
BrainSpan: Atlas of the Developing Human Brain
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: genomics
Formats: CSV
Size: 1.7 GB
No of Files: 26
No of Subjects: 4
Primary Publication: Transcriptional landscape of the prenatal human brain. https://doi.org/10.1038/nature13185
Metadata file: DATS.json
Is About: Homo sapiens
Other Dates: Conp Dats Json Fileset Creation Date: 2019-08-22 13:13:46
Description:
This resource describes an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions.

Dataset README information

README.md

Brainspan

This dataset contains links to the following files:

Developmental Transcriptome Dataset

Downloadable archive files containing normalized expression values and meta-data (as displayed in heatmap) for analysis:

RNA-Seq Gencode v10 summarized to exons exons_matrix_csv.zip
RNA-Seq Gencode v10 summarized to genes genes_matrix_csv.zip
Exon microarray summarized to probe sets exon_array_matrix_csv.zip
Exon microarray summarized to genes gene_array_matrix_csv.zip

White paper describing normalisation procedures: Transcription_Profiling.pdf

Prenatal LMD Microarray Dataset

Downloadable archive files containing normalized expression values for each brain and meta-data for analysis:

H376.IIIA.02, male, 15 pcw lmd_matrix_12840.zip
H376.IIIB.02. female, 16 pcw lmd_matrix_14751.zip
H376.IV.02, female, 21 pcw lmd_matrix_12566.zip
H376.IV.03, female, 21 pcw lmd_matrix_12690.zip

Locations for downloading raw misroarray data: LMD_microarray_link_and_tissue_sample_metadata.csv

3-D Fiber Tract and Developmental Transcriptome Sampling Annotation

3-D expert annotation of 22 major fiber tracts across 8 developmental stages accompanied by annotation of the Developmental Transcriptome survey sampling sites.

14 pcw annotation fiber tracts Stage_3A_14_pcw_Fiber_tracts.zip
14 pcw annotation structures Stage_3A_14_pcw_Transcriptome_structures.zip
17 pcw annotation fiber tracts Stage_3B_17_pcw_Fiber_tracts.zip
17 pcw annotation structures Stage_3B_17_pcw_Transcriptome_structures.zip
19 pcw annotation fiber tracts Stage_4_19_pcw_Fiber_tracts.zip
19 pcw annotation structures Stage_4_19_pcw_Transcriptome_structures.zip
37 pcw annotation fiber tracts Stage_5_37_pcw_Fiber_tracts.zip
37 pcw annotation structures Stage_5_37_pcw_Transcriptome_structures.zip
3 yrs annotation fiber tracts Stage_8_3_year_Fiber_tracts.zip
8 yrs annotation fiber tracts Stage_9_8_year_Fiber_tracts.zip
15 yrs annotation fiber tracts Stage_10_15_year_Fiber_tracts.zip
32 yrs annotation fiber tracts Stage_11_32_year_Fiber_tracts.zip

Data description taken from http://brainspan.org/static/download.html

https://doi.org/10.5281/zenodo.3385150

Download Using DataLad

CircleCI status

The following instructions require a basic understanding of UNIX/LINUX command lines. Future portal functionality may include downloads directly from the web browser. Dataset download is currently enabled through DataLad.

Note: The conp-dataset requires version >=0.12.5 of DataLad and version >=8.20200309 of git-annex.

To install DataLad on your system, please refer to the install section of the DataLad Handbook (installation via miniconda is recommended in order to obtain the latest version of DataLad).

1) Initiate the CONP dataset

To initiate the CONP dataset (conp-dataset), run the following command in the directory where you want CONP datasets to be installed:

datalad install https://github.com/CONP-PCNO/conp-dataset.git
2) Install the Brainspan dataset

To install the dataset, go into the created conp-dataset directory and run datalad install on the dataset Brainspan:

cd conp-dataset
datalad install projects/Brainspan
3) Download the Brainspan dataset

Now that the DataLad dataset has been installed, go into the dataset directory under projects/Brainspan.

cd projects/Brainspan

Note that files visible in the dataset are symlinks and will need to be downloaded manually using the datalad get command in the dataset directory:

datalad get <filepath>

Note, if you run datalad get * command, all the files present in the dataset directory will be downloaded.

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