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| Status |
Public on Apr 23, 2019 |
| Title |
K03FC.1D7 |
| Sample type |
SRA |
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| Source name |
Cortex
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| Organism |
Mus musculus |
| Characteristics |
ngene: 2607
numi: 490458
percentmito: 0.0106
age: 3
Sex: Female
genotype: APP_NL-F-G
plate: 1
lane: mglia25
set: K03FC
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| Growth protocol |
3, 6 and 12 month old time points: homozygous AppNL-G-F (Saito et al., 2014) mice, backcrossed for at least 2 generations with C57Bl/6 mice in the De Strooper lab ; Wild type C57Bl/6 mice. 21 month old time point: AppNL-G-F and C57Bl/6 mice were transferred from the Saido lab to the De Strooper lab, and housed at least 1 month before being used for experiments.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The dissection and microglia isolation steps were carried out on ice or at +4°C. Cortex and hippocampus were dissected and finely chopped, and transferred to a tuve containing ice-cold Hibernate A medium without phenol red. Single cell suspension prepared using the Adult Brain Dissociation kit. Single live microglia cells (CD11b+/DAPI-) were sorted using BD FACSAria III
Single cell retrotranscription and preparation of sequencing libraries was performed using a modified SmartSeq2 protocol (Picelli et al., 2013, 2014; Trombetta et al., 2014). We used 5’-biotinylated primers throughout the protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
Demultiplexed FASTQ files were aligned to the mouse genome (mm10 build) using STAR version 2.5.2 (Dobin et al., 2013) with default options.
Reads aligned to each gene were counted using featureCounts version 1.5.1 (Liao et al., 2014)
Filtered out cells outside the limits of median ± 4 * median absolute deviations for both reads number and genes detected; and excluded cells with more than 10% of reads aligning to mitochondrial genes
Further downstream processing was performed using Seurat (version 2.3.1 (Butler et al., 2018)) and Monocle2 (version 2.6.4 (Qiu et al., 2017a, 2017b; Trapnell et al., 2014))
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files of raw count data
Supplementary_files_format_and_content: tab-delimited text files of normalised count data (log normalised, scaled by 10000)
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| Submission date |
Mar 05, 2019 |
| Last update date |
Apr 23, 2019 |
| Contact name |
Bart de Strooper |
| E-mail(s) |
[email protected]
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| Organization name |
KULeuven
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| Department |
VIB-KU Leuven Center for Brain & Disease Research
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| Street address |
Campus Gasthuisberg, Herestraat 49, bus 602
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| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE127892 |
The major risk factors for Alzheimer’s disease: Age, Sex and Genes, modulate the microglia response to Aβ plaques (KW) |
| GSE127893 |
The major risk factors for Alzheimer’s disease: Age, Sex and Genes, modulate the microglia response to Aβ plaques |
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| Relations |
| BioSample |
SAMN11060912 |
| SRA |
SRX5477082 |
| 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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