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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 03, 2021 |
| Title |
CD11c-YFP rep1 |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: thymus
cell type: myeloid cell
age: 9-weeks-old
genotype: Itgax-Venus
treatment: Mice were sacrified by CO2
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| Treatment protocol |
Mice were sacrified by CO2.
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| Growth protocol |
All mice were maintained under specific pathogen-free conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For myeloid cell isolation, mouse thymuses were cut into small pieces and digested with 0.2 mg/mL DNase I (Roche) and 0.2 mg/mL collagenase P (Roche) in complete DMEM for 20 min at 37˚C with frequent agitation.Thymic myeloid cells were enriched by 57% Percoll PLUS (GE Healthcare) discontinuous gradient centrifugation at 4˚C, 1800 rpm, for 20 min without brake. Cells at the interface were collected and washed with PBS to remove residual silica particles. GFP+ and YFP+ cells were then sorted on BD FASC Melody. The sorted cells were resuspended in PBS with 0.5% BSA (HM Biological), filtered through 70 µm filter, and used for encapsulation and library preparation.
RNA libraries were prepared for sequencing follow the Single Cell 3' v3 Gene Expression Library protocol of 10x Genomics.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Paired-end sequencing. Read1 used to read cell and molecule barcodes and Read2 contained cDNA sequences.
bcl2fastq v2.20 for base-calling.
Sequenced reads were mapped to GRCm39 mouse genome using STAR 2.7.9a with parameters --limitOutSJcollapsed 5000000 --outFilterMultimapNmax 1 --quantMode GeneCounts --soloType CB_UMI_Simple --soloUMIlen 12 --soloBarcodeReadLength 0 --soloCBmatchWLtype 1MM_multi_pseudocounts --soloUMIfiltering MultiGeneUMI; CB whitelist was obtained from Cell Ranger of 10x Genomics (3M-february-2018.txt).
Count matrices were read and downsampled by DropletUtils (Morgan M, et al., Nat Methods, 2020) and analyzed SingleCellExperiment (Robert R.A, et al., Nat Methods, 2019) workflow.
Genes were annotated by biomaRT (Durinck S, et al., Nat Protoc, 2009); cell-level and feature-level QC were done by Scater (McCarthy DJ, et al., Bioinformatics, 2017).
Normalized expression values were calculated by Scran (Lun ATL, et al., F1000Research, 2016)
Genome_build: GRCm39 (mm39)
Supplementary_files_format_and_content: matrix.mtx files of count matrices.
Supplementary_files_format_and_content: features.tsv files of gene ID correspond to row indices of matrix.
Supplementary_files_format_and_content: barcodes.tsv files of barcode sequences correspond to column indices of matrix.
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| Submission date |
Oct 06, 2021 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Tyng-An Zhou |
| E-mail(s) |
tyngan@hotmail.com
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| Organization name |
National Yang Ming Chiao Tung University
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| Department |
Institute of Microbiology and Immunology
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| Lab |
Ivan Dzhagalov
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| Street address |
No.155, Sec.2, Linong Street
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| City |
Taipei |
| State/province |
Taiwan |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE185460 |
Single-cell RNA-sequencing of thymic myeloid cells from Csf1rgfp/gfp (MaFIA) and Cd11cyfp/yfp mice |
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| Relations |
| BioSample |
SAMN22104317 |
| SRA |
SRX12511003 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5615676_Cd11cyfp__1_barcodes.tsv.gz |
31.5 Kb |
(ftp)(http) |
TSV |
| GSM5615676_Cd11cyfp__1_features.tsv.gz |
427.0 Kb |
(ftp)(http) |
TSV |
| GSM5615676_Cd11cyfp__1_matrix.mtx.gz |
87.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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