E-MTAB-4843 - Genotyping by array: Human Developmental Biology Resource (HDBR) expression resource of prenatal human brain development-SNP data

Status
Submitted on 27 November 2015, released on 12 October 2016, last updated on 7 November 2016
Organism
Homo sapiens
Samples (425)
Array (1)
Protocols (6)
Description
The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840) and HDBR expression resource- SNP data (E-MTAB-4843, this submission). It is unique in the age range (4 post conception weeks [PCW] to 17PCW) and number of brains studied, particularly those under 8PCW. It is also unique in that both the large-scale data sets and the corresponding RNA and DNA samples are available, the latter via the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR; www.hdbr.org). There are 628 RNA-seq datasets from different regions of the brains studied. The number of regions depends on the stage and size of the sample and/or the tissue available. Embryos (4-8PCW) have been staged using a modified Carnegie staging system, details can be found at http://database.hudsen.eu/. All the RNAseq datasets from the same embryo/fetus have the same ID number (e.g. RNAseq datasets HDBR251-HDBR254 are from different tissues from embryo number 1406). The embryo/fetus ID number is recorded in the “individual” column. The majority of the brains studied are between 4 and 12PCW. During this time the major brain regions are established and there are the early stages of cortex development. DNA was prepared from all the tissues used for RNA-seq analysis and SNP genotype data generated from one tissue from each brain. RNA-seq data and SNP-data from the same tissue and individual embryo or fetus have the same name (e.g. HDBR469). There are also SNP genotype data from 229 additional specimens in paraffin wax blocks available for individual gene expression studies. For the specimens in wax blocks, the SNP genotype data was generated from DNA from either skin or placenta. The tissues present in the corresponding wax block(s) are given in the biosource type column.
Experiment types
genotyping by array, observational design
Contact
Citation
HDBR Expression: A unique resource for global and individual gene expression studies during early human brain development. Lindsay SJ, Xu Y, Lisgo SN, Harkin L, Copp A, Gerrelli D, Clowry G, Talbot A, Keogh MJ, Coxhead J, Santibanez-Koref M and Chinnery PF. Front. Neuroanat.  (2016)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-4843.idf.txt
Sample and data relationshipE-MTAB-4843.sdrf.txt
Raw data (86)Click to browse raw data
Array designA-GEOD-14157.adf.txt
Links