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| Status |
Public on Nov 24, 2017 |
| Title |
Control, SP |
| Sample type |
SRA |
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| Source name |
Hippocampus, SP
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: hippocampal SP
age: postnatal 12 weeks
genotype: Rng105flox/flox
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
SP and SR in the CA1 region in the hippocampus were microdissected, and RNA was extracted from the tissues using ISOGEN (Nippon Gene).
Total RNA (200 ng per sample) was used as the starting material to prepare cDNA using TruSeq RNA sample Preparation Kit v2 (Illumina) at a half scale compared with the manufacturer's protocols, as follows. Poly-A-containing mRNAs were purified using Oligo dT magnetic beads. After the mRNAs were denatured and fragmented, first-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific), and then second-strand cDNA was synthesized. After the ends of the fragments were blunted, an adenine nucleotide was added to the 3'-end. RNA adapter index was ligated to the 5'- and 3'-ends of the ds cDNA, and the cDNA was amplified with 10 PCR cycles.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
cont_SP-vs-SR_gene_exp.diff
SP_cont-vs-cKO_gene_exp.diff
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| Data processing |
Illumina CASAVA version 1.8 software used for basecalling.
Sequence reads were mapped to mouse genome (Mus musculus Ensemble NCBIM37) using TopHat (v 2.0.11) with parameters -p 4 -G.
The mapped reads were assembled by Cufflinks (v 2.2.1), and differential gene enrichment analysis was conducted by Cuffdiff.
Genome_build: Mus musculus Ensemble NCBIM37
Supplementary_files_format_and_content: diff files (tab-delimited text files) include test id, gene id, gene name, locus, test status, FPKM value, log2 (fold change), test statistic value, p value, q value and significant for each sample.
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| Submission date |
Mar 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Rie Ohashi |
| E-mail(s) |
ohashi@nibb.ac.jp
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| Organization name |
National Institute for Basic Biology
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| Street address |
Nishigonaka 38, Myodaiji
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| City |
Okazaki |
| ZIP/Postal code |
444-8585 |
| Country |
Japan |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE96552 |
Genome-wide profiling of somato-dendritic mRNA distribution in the hippocampus in RNG105/caprin1 conditional knockout (cKO) mice |
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| Relations |
| BioSample |
SAMN06564593 |
| SRA |
SRX2636873 |
| 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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