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Sample GSM3529833 Query DataSets for GSM3529833
Status Public on Feb 13, 2019
Title MS_case4_18_Plate2_1.coutt.csv
Sample type SRA
 
Source name Active MS lesion
Organism Homo sapiens
Characteristics tissue: Patietal lobe
Treatment protocol All subjects underwent brain surgery, the healthy samples were located at least 2 cm from the lesion the patients underwent surgery for; the MS samples were taken from the center of an active lesion
Extracted molecule total RNA
Extraction protocol Isolated myeloid cells were stained with antibodies for surface markers (CD45, CD3, CD19, CD20). All CD45+ cells were FACS-sorted in 384-well plates.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description library of 192 cells
Data processing For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
 
Submission date Dec 24, 2018
Last update date Feb 14, 2019
Contact name Sagar -
E-mail(s) sagar@uniklinik-freiburg.de
Organization name University Medical Center Freiburg
Department Department of Internal Medicine II
Lab Sagar
Street address Hugstetter Straße 55
City Freiburg
ZIP/Postal code 79106
Country Germany
 
Platform ID GPL21290
Series (1)
GSE124335 Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution
Relations
BioSample SAMN10642184
SRA SRX5178763

Supplementary file Size Download File type/resource
GSM3529833_MS_case4_18_Plate2_1.coutt.csv.gz 289.8 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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