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| Status |
Public on Jan 25, 2019 |
| Title |
PV_Naive_1_5 |
| Sample type |
SRA |
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| Source name |
Perivascular space and parenchyma, naive phase
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Perivascular space and parenchyma (Spinal cord)
age: 8 weeks
cell type: CD45+ cells
disease state: Experimental Autoimmune Encephalomyelitis
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| Treatment protocol |
The mice were subjected to MOG-immunization together with PTX injection in order to induce experimental autoimmune enchepalomyelitis (EAE).
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| Growth protocol |
SPF mouse facility
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| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated myeloid cells were stained with antibodies for lineage gating exclusion (Ly6G, CD3e, CD19 and NK.1.1), CD45 and CD11b. 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
library of 192 cells
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| 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 represent the unique molecular identifier (UMI) and the next six bases represent the cell specific barcode. 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.
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| Submission date |
Aug 22, 2018 |
| Last update date |
Jan 25, 2019 |
| Contact name |
Sagar - |
| E-mail(s) |
sagar@uniklinik-freiburg.de
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| Organization name |
University Medical Center Freiburg
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| Department |
Department of Internal Medicine II
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| Lab |
Sagar
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| Street address |
Hugstetter Straße 55
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| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE118948 |
Single-cell profiling of the myeloid landscape identifies cell subsets with distinct fates during neuroinflammation |
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| Relations |
| BioSample |
SAMN09882831 |
| SRA |
SRX4597720 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3351753_PV_Naive_1_5.coutt.csv.gz |
177.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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