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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 03, 2012 |
| Title |
Mouse SVZ3 |
| Sample type |
SRA |
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| Source name |
Embryonic mouse neocortex
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: E14.5
tissue: Neocortex
germinal zone: subventricular zone (SVZ)
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Sample 32
SVZ3
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| 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.
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| Submission date |
Jun 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Kircher |
| Organization name |
Max Planck Society
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| Street address |
Deutscher Platz 6
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| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE38805 |
Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. |
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| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX155078 |
| BioSample |
SAMN01055292 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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