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| Status |
Public on Oct 31, 2020 |
| Title |
APP/PS1 group rep3 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: APP/PS1
Sex: Male
age: 6 months
tissue: Brain
cell type: Endothelial cells (CD31+CD45-)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brain endothelial cells were isolated by FACS (CD31+CD45-) from brain homogenates.
20000 cells were collected and RNA was extracted from isolated cerebral ECs using Quick-RNA MiniPrep kit (Zymo Research) with the in-column DNase treatment. Each library was prepared using the Smart-seq2 protocol with a tagged oligo (dT) primer to make first strand cDNA from 1.5ng total RNA input.
Double-stranded cDNA was generated for library construction with 12 cycles of PCR and 0.075 ng of cDNA was used as input in a ΒΌ volume of standard NexteraXT (Illumina) reaction. Libraries were sequenced on an Illumina NextSeq500 instrument with 50 bases for read1 and 25 bases read2.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
6-month-old male APP/PS1 mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 6
X6
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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 mm10 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 and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: nextseq_170608_rsem.genes.counts.matrix: Tab-delimited text file includes RPKM values for all samples. The column names 1, 2, 3, 4, 5, 6, 7, 8 and 9 represent Sample 1, Sample 2, Sample 3, Sample 4, Sample 5, Sample 6, Sample 7, Sample 8 and Sample 9, respectively.
Supplementary_files_format_and_content: APPPS1vsWT.txt: Differential gene expression of APP/PS1vs WT mice, calculated by edgeR (version 3.10.2).
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| Submission date |
Oct 30, 2020 |
| Last update date |
Oct 31, 2020 |
| Contact name |
Chengyu Zou |
| E-mail(s) |
chengyuzou@gmail.com
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| Phone |
6174324171
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| Organization name |
Harvard medical school
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| Street address |
240 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE160528 |
Bulk sequencing of isolated endothelial cells in AD |
| GSE160529 |
Single-cell and bulk sequencing of endothelial cells of WT and APP/PS1 mice |
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| Relations |
| BioSample |
SAMN16607259 |
| SRA |
SRX9407947 |
| 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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