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Sample GSM949843 Query DataSets for GSM949843
Status Public on Jul 03, 2012
Title Human VZ4
Sample type SRA
Source name Fetal human neocortex
Organism Homo sapiens
Characteristics tissue: Neocortex
germinal zone: ventricular zone (VZ)
age: 15 w.p.c.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from microdissected germinal zones (VZ, SVZ) and the CP of fetal human and embryonic mouse neocortex using the Qiagen RNeasy Micro Kit. For each zone and human fetus/mouse embryo, a cDNA library was generated from 25 ng of the total RNA using the Illumina TruSeq RNA sample preparation kits. cDNA libraries (10 nM each) were pooled and sequenced on an Illumina Genome Analyzer IIx according to the manufacturer's instructions for Multiplex Single Read sequencing and using 76 + 7 cycles, except that an indexed φX174 control library was added, yielding about 1% of sequencing reads in each lane.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description Sample 22
Data processing The φX174 control reads were aligned to the corresponding reference sequence to obtain a training data set for the base caller IBIS, which was then used to recall bases and quality scores.
Sequencing reads were separated by index, allowing up to one substitution in the index sequence but requiring that all quality scores in the index read were ≥10 (PHRED-scale). Reads of the same sample on different sequencing lanes were combined and represent the submitted raw data.
Raw reads were subjected to adapter trimming, and reads shorter than 60 nucleotides or with more than five bases below a quality score of 15 (PHRED-scale) were removed.
The processed reads were aligned to the human reference genome (hg19/GRCh37, release date Feb. 2009, excluding additional haplotypes) and mouse reference genome (mm9/NCBI37, release date Jul. 2007) using TopHat v1.2.0.
Gene models (Ensembl) were quantified using cufflinks from the alignments of each species. A combined table as created using the 1:1 ortholog assignment from Ensembl.
Genome_build: Fetal human neocortex: h19, Embryonic mouse neocortex: mm9
Supplementary_files_format_and_content: text files with FPKM values, quantified gene models (Ensembl) using cufflinks from the alignments of each species , and combined mouse/human orthologs.
Submission date Jun 19, 2012
Last update date May 15, 2019
Contact name Martin Kircher
Organization name Max Planck Society
Street address Deutscher Platz 6
City Leipzig
ZIP/Postal code 04103
Country Germany
Platform ID GPL10999
Series (1)
GSE38805 Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal.
SRA SRX155068
BioSample SAMN01055282

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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