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Sample GSM5277971 Query DataSets for GSM5277971
Status Public on Jul 23, 2021
Title IP T Naïve 1
Sample type SRA
Source name brain meninges
Organism Mus musculus
Characteristics strain: C57Bl/6j
age: postnatal day 4
pooling: 12 mice, 6 males and 6 females
Extracted molecule total RNA
Extraction protocol Used 10x Genomics kits - GEX 5' Library & Gel Bead Kit (PN-1000014) and 5’ Library & Gel Bead Kit + Single Cell V(D)J Enrichment Kit (Mouse T cells and B cells)
Manufacturer's instructions
droplet scRNA-seq (10x Genomics)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Description Naïve 1
Data processing Genome_build: mouse reference genome: mm10_withIgTCRgenes
Genome_build: V(D)J reference: vdj_GRCm38_alts_ensembl
alignment: CellRanger 2.2.0
main software: Seurat 3.027
general filtering: cells with between 200 and 6000 expressed genes and with mitochondrial counts below 7% were kept for downstream analysis
normalization: data were normalized with a scale factor of 10,000 and were log transformed before identify-ing the 2,000 most highly variable genes
scaling: all genes were scaled using the default settings in Seurat (including cell cycle bias) before performing the principal component analysis
Supplementary_files_format_and_content: for all GEX amples, barcodes.tsv, genes.tsv and matrix.mtx are provided; for V(D)J enrichment analysis, the filtered_contig_annotations file is provided
Supplementary_files_format_and_content: MTX files: The top three lines of this file are header lines. The third line contains the total number of rows in all the three files in this folder (genes.tsv, barcodes.tsv, matrix.mtx). The next lines (line number 4 onwards) have three columns: - The first column refers to the "gene id" index. - The second column refers to "cell id" index.
Submission date May 03, 2021
Last update date Jul 23, 2021
Contact name Xiaoyang Wang
Phone +46 31-786 32 60
Organization name University of Gothenburg
Department Physiology
Street address Medicinaregatan 11
City Gothenburg
ZIP/Postal code 41390
Country Sweden
Platform ID GPL16417
Series (1)
GSE173769 Single-cell atlas reveals meningeal leukocyte heterogeneity in the developing mouse brain
BioSample SAMN18987070
SRA SRX10760252

Supplementary file Size Download File type/resource
GSM5277971_Sample_1_IP_T_filtered_contig_annotations.csv.gz 5.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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