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| Status |
Public on Nov 29, 2023 |
| Title |
LUNG scRNASEQ pre-cDCs |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mus musculus |
| Characteristics |
cell type: pre-cDC
tissue: Lung
strain: C57BL6
age: 6-8 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens, and lungs were cut into small pieces and digested with collagenase VIII (1 mg/ml; Sigma-Aldrich) and deoxyribonuclease I (0.4 mg/ml; Roche) in RPMI 1640 for 15 min (spleen) or 25 min (lung) at 37°C. Digested tissues were passed through a 70-μm cell strainer (BD Biosciences) and washed with FACS buffer (3% FCS and 5 mM EDTA in PBS). For lung, leukocytes were enriched by Percoll gradient centrifugation (GE Healthcare). For BM, the femur, tibia and hip extremities were cut and spun for 30 s at 10,000 rpm. Cells were resuspended in FACS buffer after centrifugation. Single cell suspensions from the bone marrow, spleen and lung were enriched for pre-cDCs by staining lineage-restricted markers with FITC-conjugated antibodies (CD3, Ly6G, SiglecF, B220, CD19, Ly6D, NK1.1, and Ter119) and depleting T, B, plasmacytoid, and red blood cells, neutrophils, eosinophils, and their precursors using the EasySep Mouse FITC Positive Selection Kit II (Stemcell technologies). Cells were stained and FACS sorted on an Aria Fusion (BD) with a 100um nozzle.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10x Genomics
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| Data processing |
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the mm10 transcriptome + eGFP sequence using STAR (v.2.5.1b)
All subsequent analyses were performed in R v.3.6.1 using the Seurat (v3) package
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files
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| Submission date |
Nov 04, 2022 |
| Last update date |
Nov 29, 2023 |
| Contact name |
Probir Chakravarty |
| E-mail(s) |
probir.chakravarty@crick.ac.uk
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| Organization name |
Francis Crick Institute
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| Street address |
1 Midland Road
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| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE217328 |
Gene expression profile at single cell level of pre-cDCs from the bone marrow, spleen and lung of mice |
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| Relations |
| BioSample |
SAMN31611807 |
| SRA |
SRX18175130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6711830_MIN636A9.barcodes.tsv.gz |
4.2 Kb |
(ftp)(http) |
TSV |
| GSM6711830_MIN636A9.features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM6711830_MIN636A9.matrix.mtx.gz |
6.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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