GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3162137 Query DataSets for GSM3162137
Status Public on Sep 25, 2018
Title B6
Sample type SRA
Source name mLN-SPF
Organism Mus musculus
Characteristics cell type: mLNs (small intestinal and colon/caecum-draining)
antibody: CD24- CD45-
index id: SI-GA-B6
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, 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.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
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.
Submission date May 29, 2018
Last update date Apr 21, 2021
Contact name Joern Pezoldt
Phone 0041766040171
Organization name EPFL
Department SV
Lab Laboratory Systems Biology and Genetics
Street address Station 19, SV 3818.A
City Lausanne
ZIP/Postal code 1015
Country Switzerland
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
Reanalyzed by GSM5258270
BioSample SAMN09274084
SRA SRX4134018

Supplementary file Size Download File type/resource
GSM3162137_B6_differential_expression.csv.gz 2.9 Mb (ftp)(http) CSV
GSM3162137_B6_molecule_info.h5 222.5 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap