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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 23, 2021 |
| Title |
IP T Naïve 1 |
| Sample type |
SRA |
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| Source name |
brain meninges
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6j
age: postnatal day 4
pooling: 12 mice, 6 males and 6 females
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
Naïve 1
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| 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.
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| Submission date |
May 03, 2021 |
| Last update date |
Jul 23, 2021 |
| Contact name |
Xiaoyang Wang |
| E-mail(s) |
xiaoyang.wang@fysiologi.gu.se
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| Phone |
+46 31-786 32 60
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| Organization name |
University of Gothenburg
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| Department |
Physiology
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| Street address |
Medicinaregatan 11
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| City |
Gothenburg |
| ZIP/Postal code |
41390 |
| Country |
Sweden |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE173769 |
Single-cell atlas reveals meningeal leukocyte heterogeneity in the developing mouse brain |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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