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Status |
Public on May 29, 2021 |
Title |
B lymphocytes (D7_2 + VDJ_D4_2) |
Sample type |
SRA |
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Source name |
B lymphocytes
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Organism |
Mus musculus |
Characteristics |
tissue: heart strain: C57BL/6 kit: Chromium Next GEM Single Cell 5’ v1.1
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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)
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Multiplexed: Gene expression library (GEX) Multiplexed: V(D)J library
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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.
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Submission date |
May 08, 2020 |
Last update date |
May 29, 2021 |
Contact name |
Antoine-Emmanuel Saliba |
E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
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Phone |
+49-931-31-81341
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Organization name |
Helmholtz Institute for RNA-based Infection Research
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Street address |
Josef-Schneider-Straße 2 / D15
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City |
Würzburg |
ZIP/Postal code |
97080 |
Country |
Germany |
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Platform ID |
GPL24247 |
Series (1) |
GSE150140 |
The healing myocardium mobilizes a distinct B-cell subset through a CXCL13-CXCR5-dependent mechanism |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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