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| Status |
Public on Jul 01, 2024 |
| Title |
NHDF_72h_IL1b |
| Sample type |
SRA |
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| Source name |
adult human dermal fibroblasts (NHDF-Ad, Lonza, CC-2511)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: adult human dermal fibroblasts (NHDF-Ad, Lonza, CC-2511)
library type: mRNA
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| Treatment protocol |
For cytokine treatment, cells were seeded in 6-well plates and allowed to attach for 24hr. Thereafter, cells were equilibrated for 16 hr in low serum medium (0.2% FBS for NHDF-Ad, and 0.5% for NHCF-V and iHCF), and then treated with 10 ng/mL of recombinant human TGF-b (R&D Systems; 240-B-002) or 10 ng/mL of recombinant human IL-1β (R&D Systems; 201-LB-005) for the indicated times.
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| Growth protocol |
Human ventricular cardiac fibroblasts (NHCF-V, Lonza, CC-2904), adult human dermal fibroblasts (NHDF-Ad, Lonza, CC-2511), and immortalized human cardiac fibroblasts (iHCF, Applied Biological Materials Inc., T0446) were grown in FibroGRO LS medium supplemented with 2% (NHDF-Ad) or 10% (NHCF-V and iHCF) FBS. Cells were maintained in a humidified atmosphere (95% air, 5% CO2) at 37°C and passaged every 2-3 days.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
After trypsinization, cell suspensions were labeled with barcoded lipids from the 3' CellPlex Kit Set A (10x Genomics PN:1000261) following manufacturer’s instructions (Protocol CG000391). After labeling, technical replicates were pooled and loaded onto a Chromium Controller (10x Genomics) at a concentration to capture 6-10,000 cells.
Single-cell libraries were prepared using the Single Cell 3’ Kit v3.1 (10x Genomics PN:1000268) according to manufacturer’s instructions (User Guide CG000388). Gene expression and cellplex libraries were indexed with Dual Index Kit TT Set A and NN Set A indexes (PN:1000215, 3000482) respectively.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
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| Data processing |
Raw fastq files were aligned to the human GRCh38 reference genome (v) using CellRanger (10x Genomics, v6) multi pipeline with the provided cell multiplexing CMO tags
Subsequent quality control, SCTransform normalization, dimensional reduction, and clustering was performed in Seurat v4.0. Processed data were reference mapped to human CITE-seq fibroblast data within this study by MapQuery function to impute cell annotations.
Assembly: GRCh38
Supplementary files format and content: CellPlex_Multiplex_count_feature_reference.csv with detailed cell multiplexing CMO tags information. 10x Genomics cellranger multi output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
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| Submission date |
Nov 20, 2022 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Xin Luo |
| E-mail(s) |
xluo01@amgen.com
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| Organization name |
Amgen Inc
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| Department |
Research and Development
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| Street address |
750 Gateway Blvd
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE218391 |
Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis II |
| GSE218392 |
Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis |
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| Relations |
| BioSample |
SAMN31805284 |
| SRA |
SRX18322241 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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