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Sample GSM4039245 Query DataSets for GSM4039245
Status Public on Nov 04, 2020
Title M-ctrl-1
Sample type SRA
Source name brain CD11b+
Organism Mus musculus
Characteristics strain: C57BL/6
age: 12 weeks
Sex: male
tumor stage: -
implanted cell line: -
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]
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description male control replicate 1
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.
Submission date Aug 19, 2019
Last update date Nov 04, 2020
Contact name Jakub Mieczkowski
Organization name Medical University of Gdansk
Street address Debinki 12
City Gdansk
ZIP/Postal code 80-211
Country Poland
Platform ID GPL18480
Series (1)
GSE136001 Single cell RNA sequencing reveals functional heterogeneity and sex differences of glioma-associated brain macrophages
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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