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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 21, 2020 |
| Title |
Cd98 KO_colon5 |
| Sample type |
SRA |
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| Source name |
colon monocytes and macrophages from tamoxifen induced Cd98 KO (CD98ΔCX3CR1) mouse
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| Organism |
Mus musculus |
| Characteristics |
tissue: colon
cell type: monocytes and macrophages
strain: CD98{delta}CX3CR1
genotype: Cd98 KO
Sex: female
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| Treatment protocol |
100µl tamoxifen (20mg/ml) per mouse was i.p. injected daily over 5 consecutive days. Readout at day 7 (optimum of Cd98 silencing).
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| Growth protocol |
Mice were hold in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were extracted from suspensions of lamina propria of eight individual CD98ΔCX3CR1 female mice
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for Cd11b+ and Ccr2+/Cd64+ expression.
Around 3000 cells per sample were loaded into each well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
UMIsMatrix.txt.gz
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| Data processing |
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.5.3a), and read counting on Ensembl 84 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). Because the mouse strain includes a fluorescent reporter gene, a generic EYFP sequence obtained from https://www.addgene.org/browse/sequence_vdb/6394/ was added to the reference transcriptome before mapping.
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R (v3.5.0). The UMI matrix was filtered to included only cells with a count of at least 100 genes detected, giving a total of 5,949 cells (16,889 genes), and is provided as file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the scran (1.8.4) and scatter (1.8.4) Bioconductor packages, and following the simpleSingleCell Bioconductor workflow (version 1.2.1). Expression values of 11,947 genes for 3,213 cells were obtained after quality filtering and normalization, and used for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 84 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-colon1")
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| Submission date |
Feb 14, 2019 |
| Last update date |
Nov 22, 2021 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
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| Organization name |
University of Basel
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| Department |
Departement of Biomedicine
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| Street address |
Hebelstrasse 20
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| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE126574 |
The Branched-Chain Amino Acid Transporter CD98 Heavy Chain Facilitates the Development of Colonic Macrophages Associated with Decreased Apoptosis in Macrophage Progenitors |
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| Relations |
| BioSample |
SAMN10938566 |
| SRA |
SRX5376151 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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