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Sample GSM4006827 Query DataSets for GSM4006827
Status Public on Feb 12, 2020
Title MS patient 3-5
Sample type SRA
 
Source name CNS Percoll pellet
Organism Homo sapiens
Characteristics subject status: Multiple sclerosis (MS) patient
subject group: secondary progressive MS (SPMS)
Treatment protocol Following rapid autopsy, samples were immediately incubated in Hibernate (Life Technologies, #A1247601) for 8-18 hours prior to processing.
Extracted molecule total RNA
Extraction protocol A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. 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 human (GRCh38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 200 genes.
 
Submission date Aug 04, 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 GPL24676
Series (2)
GSE129762 Genome-wide analysis of the transcriptional profile of the CNS in MS patients.
GSE130119 MAFG-driven astrocytes promote CNS inflammation
Relations
BioSample SAMN12495220

Supplementary file Size Download File type/resource
GSM4006827_2_HG37GDMXX.2.ATGCGCAG.dge.txt.gz 36.2 Kb (ftp)(http) TXT
Processed data provided as supplementary file
Raw data are available in SRA

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