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| Status |
Public on Feb 12, 2020 |
| Title |
MS patient 4-1 |
| Sample type |
SRA |
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| Source name |
CNS Percoll pellet
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| Organism |
Homo sapiens |
| Characteristics |
subject status: Multiple sclerosis (MS) patient
subject group: secondary progressive MS (SPMS)
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| Treatment protocol |
Following rapid autopsy, samples were immediately incubated in Hibernate (Life Technologies, #A1247601) for 8-18 hours prior to processing.
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| 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.
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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 |
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.
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| Submission date |
Aug 04, 2019 |
| Last update date |
Feb 13, 2020 |
| 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 |
GPL24676 |
| Series (2) |
| GSE129762 |
Genome-wide analysis of the transcriptional profile of the CNS in MS patients. |
| GSE130119 |
MAFG-driven astrocytes promote CNS inflammation |
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| Relations |
| BioSample |
SAMN12495219 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4006828_1_HJJ3WDMXX.1.TAAGGCGA.dge.txt.gz |
404.0 Kb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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