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Sample GSM4002808 Query DataSets for GSM4002808
Status Public on Feb 12, 2020
Title Remitting_replicate4
Sample type SRA
 
Source name Flow cytometry sorted astrocytes based on TdTomato fluorscence
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype/variation: wild type
Sex: Male
age: P126
mouse status: EAE remission phase
cell type: Flow cytometry sorted astrocytes based on TdTomato fluorscence
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.
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 TdTomato fluorescence. Post-sort, cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out..
Raw reads were aligned to mouse (GRCm38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 100 genes.
 
Submission date Aug 02, 2019
Last update date Feb 13, 2020
Contact name Michael Wheeler
E-mail(s) mwheeler0@bwh.harvard.edu
Organization name Brigham and Women's Hospital
Department Neurology
Street address 60 Fenwood Rd.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL24247
Series (2)
GSE129763 Genome-wide analysis of the transcriptional profile of astrocytes during EAE in Gfap-TdTomato mice by scRNA-seq [scRNA-seq 2]
GSE130119 MAFG-driven astrocytes promote CNS inflammation
Relations
BioSample SAMN12431195
SRA SRX6640580

Supplementary file Size Download File type/resource
GSM4002808_1_H7NF2DRXX.1.TACGCTGC.dge.txt.gz 765.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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