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Sample GSM4524179 Query DataSets for GSM4524179
Status Public on May 29, 2021
Title B lymphocytes (D7_2 + VDJ_D4_2)
Sample type SRA
 
Source name B lymphocytes
Organism Mus musculus
Characteristics tissue: heart
strain: C57BL/6
kit: Chromium Next GEM Single Cell 5’ v1.1
Extracted molecule total RNA
Extraction protocol The heart samples were enzymatically digested in type II collagenase (1,000 IU/ml, Worthington Biochemical Corporation, Lakewood, NJ, USA) for 30 minutes at 37°C. The digested hearts and the med-LNs were gently filtered through a 30-µm mesh (Miltenyi Biotec, Bergisch Gladbach, Germany). Following a washing step, all samples were resuspended in FACS buffer (PBS containing 1% BSA, 0.1% sodium azide and 1 mM EDTA), and surface staining was performed in the presence of FC-blocking antibody (anti-CD16/CD32, clone 2.4G2, BD Pharmingen). The following fluorophore-conjugated antibodies (obtained from Biolegend [San Diego, CA, USA], unless otherwise indicated) were used for surface staining: anti-CD45 (clone 30-F11), anti-CD45.2 (clone 104), anti-CD19 (clone 6D5), anti-CD45/B220 (clone RA3-6B2), anti-CXCR5 (clone L138D7), anti-CD69 (clone H1.2F3), anti-CD95 (clone SA367H8), and anti-GL7 (clone GL7). Additionally, AmCyan Zombie Aqua fixable viability dye (Biolegend, San Diego, CA, USA) was used to exclude dead cells. Flow cytometry measurements were performed on an Attune-NxT (Thermo Scientific, Darmstadt, Germany) or on a FACS Canto (BD, Heidelberg, Germany). Cell sorting for single-cell RNA sequencing was performed using a FACS Aria III (BD, Heidelberg, Germany), and no sodium azide was included in the buffers used for sorting purposes. Post-sorting, the cells were washed once in PBS containing 1% FCS, and each sample was labelled separately with anti-CD45/H2-K hashtag antibody (Biolegend TotalSeq-C antibodies, San Diego, CA, USA). Following a washing step, all the samples were pooled and resuspended in 100 µl of PBS/0.05% BSA, filtered through a 40 µm cell strainer and loaded in the 10x Genomics Chromium system as one multiplexed sample.
Cells were loaded in the 10X Genomics Chromium with the aim of recovering 10,000 cells. Libraries were generated with the Chromium Next GEM Single Cell 5’ Reagents Kit v1.1 Chemistry according to manufacturer ´s instructions.
Chromium Next GEM Single Cell 5’ v1.1 (10xGenomics)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Multiplexed: Gene expression library (GEX)
Multiplexed: V(D)J library
Data processing Library strategy: RNA-seq + VDJ
Data were analyzed using Cell Ranger™ v3.1.0 pipelines which is available in 10xGenomics website.
Genome_build: mm10 3.0.0 for GEX and GRCm38 3.1.0 for V(D)J
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
Supplementary_files_format_and_content: csv;High-level descriptions of each clonotype and annotations of each high-confidence, cellular contig.
 
Submission date May 08, 2020
Last update date May 29, 2021
Contact name Antoine-Emmanuel Saliba
E-mail(s) emmanuel.saliba@helmholtz-hzi.de
Phone +49-931-31-81341
Organization name Helmholtz Institute for RNA-based Infection Research
Street address Josef-Schneider-Straße 2 / D15
City Würzburg
ZIP/Postal code 97080
Country Germany
 
Platform ID GPL24247
Series (1)
GSE150140 The healing myocardium mobilizes a distinct B-cell subset through a CXCL13-CXCR5-dependent mechanism
Relations
BioSample SAMN14856607
SRA SRX8294655

Supplementary file Size Download File type/resource
GSM4524179_D7_2_filtered_feature_bc_matrix.tar.gz 56.5 Mb (ftp)(http) TAR
GSM4524179_D7_2_molecule_info.h5 411.2 Mb (ftp)(http) H5
GSM4524179_VDJ_D4_2_clonotypes.csv.gz 203.9 Kb (ftp)(http) CSV
GSM4524179_VDJ_D4_2_filtered_contig_annotations.csv.gz 701.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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