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ERX1544443: Illumina HiSeq 2000 paired end sequencing; Human Developmental Biology Resource (HDBR) expression resource-RNAseq
1 ILLUMINA (Illumina HiSeq 2000) run: 38.3M spots, 7.7G bases, 4.7Gb downloads

Design: Human Developmental Biology Resource (HDBR) expression resource-RNAseq
Submitted by: Institute of Genetic Medicine Newcastle University, UK (Institute of Genetic Medicine Newcastle University)
Study: Human Developmental Biology Resource (HDBR) expression resource-RNAseq
show Abstracthide Abstract
"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, this submission) and HDBR expression resource- SNP data (E-MTAB-4843). 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; http://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 brain have the same embryo/fetus 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 brain 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. These data are in the accompanying ""HDBR expression resource- SNP data"" (E-MTAB-4843). "
Sample: HDBR396
SAMEA4050607 • ERS1221717 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: HDBR396
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: Human embryonic and fetal tissues were provided by the Human Developmental Biology Resource (www.HDBR.org). HDBR is a UK tissue bank which is regulated by the UK Human Tissue Authority (HTA; www.hta.gov.uk) and operates in accordance with the relevant HTA Codes of Practice. Tissue samples are collected with appropriate maternal written consent and approval from research ethics committees. Embryonic samples were staged following the staging guidelines outlined in Bullen, P and Willson, D (1997). The Carnegie staging system of human embryos: a practical guide in Molecular Genetics of Early Human Development. T. Strachan, S. Lindsay and D.I. Willson. Fetal samples were staged using foot and knee-heel lengths (Hern WM [1984] Correlation of fetal age and measurements between 10 and 26 weeks of gestations. Obstet. Gynecol.63: 26-32) All nucleic acid preparation was performed by AROS following standardised procedures (AROS – arosab.com). Applied Biotechnology (www.arosab.com). RNA was extracted on the QIAsymphony SP using manufacturer's protocol miRNA v05. Library preparation followed Illumina's guidelines for the TruSeq stranded mRNA stranded LT sample prep kit. (http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf)
Spot descriptor:
forward101  reverse

Experiment attributes:
Experimental Factor: forebrain: organism part
Runs: 1 run, 38.3M spots, 7.7G bases, 4.7Gb
Run# of Spots# of BasesSizePublished
ERR147333238,312,9867.7G4.7Gb2016-10-13

ID:
3290629

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