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Sample GSM2838916 Query DataSets for GSM2838916
Status Public on Sep 25, 2018
Title L1700566
Sample type SRA
 
Source name pLN-SPF
Organism Mus musculus
Characteristics cell type: skin-draining pLNs (inguinal and axillary)
antibody: CD24- CD45-
index_id: SI-GA-A4
index_seq: TATGATTC,CCCACAGT,ATGCTGAA,GGATGCCG
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.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
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: .csv files include mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.
 
Submission date Nov 03, 2017
Last update date May 15, 2019
Contact name Joern Pezoldt
E-mail(s) jorn.pezoldt@epfl.ch
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 GPL19057
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
Relations
BioSample SAMN07974988
SRA SRX3359238

Supplementary file Size Download File type/resource
GSM2838916_L1700566_differential_expression.csv.gz 2.4 Mb (ftp)(http) CSV
GSM2838916_L1700566_molecule_info.h5 235.6 Mb (ftp)(http) H5
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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