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| Status |
Public on Nov 07, 2019 |
| Title |
GRN3_lo |
| Sample type |
SRA |
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| Source name |
hippocampus
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| Organism |
Mus musculus |
| Characteristics |
strain: B6.129S4(FVB)-Grntm1.1Far/Mmja
age: 10 month old
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Primary microglia were isolated by gentle dounce homogenization of the brain, Percoll-based myelin removal, and FACS-purification of ~10,000 live CD11b+CD45lo cells. BODIPYlo (=lipid droplet-low) and BODIPYhi (=lipid droplet-high) microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according to the manufacturer’s protocol.
cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
BODIPY-low microglia (lipid-droplet low)
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| Data processing |
Sequencing of isolated microglia was carried out with Novaseq 6000, paired end, 2x 100 bp depth sequencer.
The quality of fastq files was assessed using FASTQC (v 0.11.4).
Reads were mapped to mouse mm9 reference genome using STAR (v 2.5.3a).
Raw read counts were generated with STAR using the GeneCounts function.
Differential expression analysis was performed using DESeq2 with standard settings.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Nov 06, 2019 |
| Last update date |
Nov 08, 2019 |
| Contact name |
Julia Marschallinger |
| E-mail(s) |
[email protected]
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| Phone |
6502839032
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| Organization name |
Stanford University
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| Department |
Neurology
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| Lab |
Tony Wyss-Coray
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| Street address |
1201 Welch Road
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5489 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE140009 |
RNA-seq of lipid droplet-low and lipid droplet-rich microglia isolated from the hippocampi of Progranulin KO mice |
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| Relations |
| BioSample |
SAMN13221420 |
| SRA |
SRX7106630 |
| 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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