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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-3, MG (4M67_TCGACGTC_AGCTAGAA) |
Sample type |
SRA |
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Source name |
GFAP, EGFR-3, MG
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 Sex: Female cell type: Microglia 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 |
SAMN27407710 |
SRA |
SRX14782102 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6034451_4M67_TCGACGTC_AGCTAGAA.tar.gz |
2.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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