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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 10, 2023 |
| Title |
GFAP, EGFR-2, AS (4M67_TGCAGCTA_CTAGTCGA) |
| Sample type |
SRA |
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| Source name |
GFAP, EGFR-2, AS
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: Female
cell type: Astrocytes
genotype: Egfr Knockout
age: 12 weeks
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| Treatment protocol |
Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol and 10X Single Cell V3 as described (Trombetta et al 2014).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The sample is aligned to GRCm38 transcriptome and quantified using Kallisto, Cellranger and RSEM
Assembly: GRCm38
Supplementary files format and content: gzipped abundance.tsv output from Kallisto, Cellranger and RSEM
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| Submission date |
Apr 07, 2022 |
| Last update date |
Mar 10, 2023 |
| Contact name |
Michael Wheeler |
| E-mail(s) |
mwheeler0@bwh.harvard.edu
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| Organization name |
Brigham and Women's Hospital
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| Department |
Neurology
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| Street address |
60 Fenwood Rd.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE200457 |
Droplet-based genome-wide forward genetic screening of astrocyte-microglia communication mechanisms |
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| Relations |
| BioSample |
SAMN27407707 |
| SRA |
SRX14782105 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6034454_4M67_TGCAGCTA_CTAGTCGA.tar.gz |
2.5 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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