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| Status |
Public on Feb 08, 2018 |
| Title |
ventralH_Handling_repl5 |
| Sample type |
SRA |
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| Source name |
ventral hippocampus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: ventral hippocampus
age: post natal day 105
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized at 4°C in a tissue lyser bead mill (Qiagen, Germany) for 2 min in 1 ml TrisureTM (Bioline USA Inc., MA), and RNA was extracted according to manufacturer's recommendations. Library was constructed using Illumina TruSeq RNA library preparation using poly(A)-enrichment according to manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Jun 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Johannes Bohacek |
| E-mail(s) |
johannes.bohacek@hest.ethz.ch
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| Organization name |
University of Zurich/ ETH Zurich
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| Street address |
Winterthurerstrasse 190
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| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE100236 |
RNA sequencing of whole, ventral and dorsal hippocampus after different stress conditions |
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| Relations |
| BioSample |
SAMN07257866 |
| SRA |
SRX2935441 |
| 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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