CONP Portal | Dataset
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
BrainSpan: Atlas of the Developing Human Brain
Is About: | Homo sapiens |
---|---|
Other Dates: | Conp Dats Json Fileset Creation Date: 2019-08-22 13:13:46 |
Description:
Dataset README information
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
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.