CONP Portal | Dataset
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. 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 Brainspan dataset
To install the Brainspan 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 Brainspan dataset
Now that the dataset has been installed, go into the Brainspan 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.
Experiments - Beta