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| Status |
Public on Sep 25, 2018 |
| Title |
B5 |
| Sample type |
SRA |
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| Source name |
pLN-SPF
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| Organism |
Mus musculus |
| Characteristics |
cell type: skin-draining pLNs (inguinal and axillary)
antibody: CD24- CD45-
index id: SI-GA-B5
index seq: AATAATGG,CCAGGGCA,TGCCTCAT,GTGTCATC
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| Extracted molecule |
total RNA |
| Extraction protocol |
For stromal cell isolation, skin-draining pLNs (inguinal and axillary) or mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase P (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche) as described previously (Fletcher et al., 2011, https://doi.org/10.3389/fimmu.2011.00035). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). CD45- cells were enriched by MACS separation after direct magnetic labeling of CD45+ cells using anti-CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort CD45‑CD24‑ cells by FACS (Aria II)) for single-cell mRNA‑seq analysis.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
library strategy: Drop-Seq
Data were analyzed using Cell Ranger™ v2.0 pipelines and were visualized by Loupe™ Cell Browser v1.0. Both are available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: It includes mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.
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| Submission date |
May 29, 2018 |
| Last update date |
Sep 25, 2018 |
| Contact name |
Joern Pezoldt |
| E-mail(s) |
jorn.pezoldt@epfl.ch
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| Phone |
0041766040171
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| Organization name |
EPFL
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| Department |
SV
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| Lab |
Laboratory Systems Biology and Genetics
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| Street address |
Station 19, SV 3818.A
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE106489 |
Neonatal imprinting of mesenteric lymph node stroma modulates tolerogenic properties of dendritic cells [scRNA-seq] |
| GSE116633 |
Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells |
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| Relations |
| BioSample |
SAMN09274085 |
| SRA |
SRX4134017 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3162136_B5_differential_expression.csv.gz |
2.7 Mb |
(ftp)(http) |
CSV |
| GSM3162136_B5_molecule_info.h5 |
297.8 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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