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| Status |
Public on Nov 04, 2020 |
| Title |
M-ctrl-1 |
| Sample type |
SRA |
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| Source name |
brain CD11b+
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 12 weeks
Sex: male
tumor stage: -
implanted cell line: -
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Animals were perfused with PBS and brains taken out. Brain tissue was enzymatically dissociated to single cell suspension with Neural Tissue Dissociation Kit [Miltenyi Biotec] and gentleMACS Octo Dissociator [Miltenyi Biotec]. Myelin was removed by density gradient centrifugation and CD11b+ cells FACS sorted to 20% FBS in PBS. Cell suspension from FACS was loaded directly onto Chromium™ Single Cell A Chip [10x Genomics].
Preparation of Gel Beads in Emulsion and libraries were performed with Chromium Controller and Single Cell Gene Expression v2 Chemistry [10x Genomics, USA] according to the Chromium Single Cell 3’ Reagent Kits v2 User Guide provided by the manufacturer. Libraries quality and quantity was verified with High Sensitivity DNA Kit [Agilent Technologies, USA] on 2100 Bioanalyzer [Agilent Technologies, USA]. Next, sequencing was run in the rapid run flow cell and paired-end sequenced (read 1 – 26 bp, read 2 – 100 bp) on HiSeq 1500 [Illumina, USA]
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
male control replicate 1
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| Data processing |
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v3.0.1 (10x Genomics) and bcl2fastq v2.20.0.422 (Illumina)
Cell Ranger v3.0.1 count was used to align the demultiplexed reads to the reference genome (mm10), perform filtering, barcode counting, UMI (unique molecule identifier) counting and estimate the number of cells.
Data analysis was performed in R using Seurat v3 package.
Genome_build: mm10
Supplementary_files_format_and_content: cell barcodes list: barcode sequences correspond to column indices of feature-barcode matrices. Each barcode sequence includes a suffix with a dash separator followed by a number.
Supplementary_files_format_and_content: cell features (genes) list: features correspond to row indices of feature-barcode matrices. For each feature, its feature ID and name are stored in the first and second column of the (unzipped) features.tsv file, respectively. The third column identifies the type of feature, which in this case will be Gene Expression (the feature ID corresponds to gene_id in the annotation field of the reference GTF).
Supplementary_files_format_and_content: feature-barcode count matrix: each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. Contains only cellular barcodes detected by CellRanger.
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| Submission date |
Aug 19, 2019 |
| Last update date |
Nov 04, 2020 |
| Contact name |
Jakub Mieczkowski |
| E-mail(s) |
jmieczkowski@jmieczkowski.pl
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| Organization name |
Medical University of Gdansk
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| Street address |
Debinki 12
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| City |
Gdansk |
| ZIP/Postal code |
80-211 |
| Country |
Poland |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE136001 |
Single cell RNA sequencing reveals functional heterogeneity and sex differences of glioma-associated brain macrophages |
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| Relations |
| BioSample |
SAMN12601679 |
| SRA |
SRX6742908 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4039245_m-ctrl-1-filtered-barcodes.tsv.gz |
19.8 Kb |
(ftp)(http) |
TSV |
| GSM4039245_m-ctrl-1-filtered-features.tsv.gz |
244.7 Kb |
(ftp)(http) |
TSV |
| GSM4039245_m-ctrl-1-filtered-matrix.mtx.gz |
14.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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