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| Status |
Public on Jul 13, 2023 |
| Title |
Mouse_HOMER_2 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
disease status: HOMER
Sex: male
tissue: left atrial tissue
cell type: non-cardiomyocytes
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| Treatment protocol |
n/a
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| Growth protocol |
n/a
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| Extracted molecule |
total RNA |
| Extraction protocol |
Viable (DAPI-), metabolically active (Calcein+), nucleated (VDR+), single cells were FACS-purified from digested left atrial tissues, and subsequently loaded on a 10X Genomics Chromium Single Cell B chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NextSeq 500 in high-output mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
FACS-purified left atrial non-cardiomyocytes
mRNA
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| Data processing |
Illumina proprietary software used for basecalling.
10X Genomics Cell Ranger (version 6.0.2 for human samples, version 3.0.2 for mouse samples) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Genome_build: GRCh38 for human samples, GRCm38 (mm10) for mouse samples.
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.tar.gz: tar archives include matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz files; Count matrices in Market Exchange Format for sparse matrices and gzipped tsv files for genes and barcodes corresponding to row and column indices of the count matrices.
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| Submission date |
Feb 26, 2022 |
| Last update date |
Jul 13, 2023 |
| Contact name |
I-Hsiu Lee |
| Organization name |
Mass General Hospital/Harvard University
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| Department |
Center for Systems Biology
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| Street address |
185 Cambridge Street
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE197518 |
The role of stromal and immune cells in atrial disease [I] |
| GSE224959 |
The role of stromal and immune cells in atrial disease |
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| Relations |
| BioSample |
SAMN26278081 |
| SRA |
SRX14299439 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5919357_HOMER_2_filtered_feature_bc_matrix.tar.gz |
35.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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