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| Status |
Public on Jun 04, 2021 |
| Title |
Control4 |
| Sample type |
SRA |
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| Source name |
Left Ventricle
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| Organism |
Homo sapiens |
| Characteristics |
gender: Male
tissue: Heart
tissue region: Left Ventricle
age: 21
race: White or Caucasion
disease status: NF
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Five 10 µm curls cut from OCT embedded human cardiac tissue were homogenized using a 2 ml Dounce homogenizer with 1 ml chilled lysis buffer (10mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 and 0.2 U/ml RNase inhibitor). After filtering through a 40 µm cell trainer, nuclei were centrifuged at 700 x g for 5 min at 4oC. The nuclei were subsequently washed with 500 ml and then resuspended in 300 ml of Nuclei Wash/Resuspension Buffer (1x PBS with 2% BSA and 0.2 U/ml RNase inhibitor). 1 ml DRAQ5 (5 mM solution, Thermo Cat #62251) was added, and DRAQ5+ nuclei were sorted (70 mm nozzle on a BD Aria) into 50 ml Nuclei Wash Buffer (3 X 0.2 U/ml RNase inhibitor). Sorted nuclei were directly added to a reverse transcription master mix diluted with water to manufacturer’s specifications
Libraries were prepared using the 10X Chromium Single Cell 3' v3 Gene Expression Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
cell ranger (V3.1.0) mkref package was used to create a “pre-mRNA” reference with pre-built GRCh38 reference package and cell ranger count pipeline was used to align the fastq reads and generated QC matrix and count matrix.
The Count matrix was further analyzed with Seurat R package for batch effect correction by canonical correlation analysis, filtering, normalization, variable features identification and dimensional reduction by Principal Component Analysis (PCA). The top 30 PCAs were used in graph-based clustering based on Louvain, and cluster specific marker genes were identified with FindAllMarkers function in Seurat, cell types were determined by cross-referencing with well-established cell type markers in literature
Genome_build: GRCh38
Supplementary_files_format_and_content: cell.counts.*.txt contain the raw UMI count matrix of all samples with genes in rows and cells in columns, cell.metadata.*.csv contains metainformation of all samples with cells in rows and labels in columns. For each sample, the cell ranger output filtered matrix files including barcodes.tsv, features.tsv and matrix.mtx were included as processed data files as well.
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| Submission date |
Nov 13, 2020 |
| Last update date |
Sep 25, 2021 |
| 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) |
| GSE161470 |
Chamber-Enriched gene expression profiles in failing human hearts with reduced ejection fraction [snRNA-Seq] |
| GSE161473 |
Chamber-Enriched gene expression profiles in failing human hearts with reduced ejection fraction |
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| Relations |
| BioSample |
SAMN16793813 |
| SRA |
SRX9506076 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4907715_Control4.barcodes.tsv.gz |
20.7 Kb |
(ftp)(http) |
TSV |
| GSM4907715_Control4.features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM4907715_Control4.matrix.mtx.gz |
12.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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