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| Status |
Public on Sep 30, 2022 |
| Title |
Human left ventricle_1 |
| Sample type |
SRA |
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| Source name |
interventricular septum
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| Organism |
Homo sapiens |
| Characteristics |
tissue: interventricular septum
compartment: nucleus
tissue: heart
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| Treatment protocol |
snap-fozen in liquid nitrogen
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Tissue samples were minced and nuclei extracted in lysis buffer containing 5 mM CaCl2, 3 mM magnesium actetate, 2 mM EDTA, 0.5 mM EGTA, 10 mM Tris, 0.2%, Triton X-100, protease inhibitors and DTT. Nuclei were centrifuged in 1 M sucrose and resuspended in PBS. After staining with Draq7, samples were purified by fluorescence-activated nuclei sorting (FANS). Nuclei were counted under the microscope.
Barcoding, cDNA amplification and gene expression library construction were done using 10x Genomics Chromium Next GEM Single cell 3' Solution v3 according to the manufacturer's recommendation.
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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 |
The libraries generated according to the 10X Genomics protocol v3 were sequenced, demultiplexed and converted to fastq format by EMBL Heidelberg Genomics Core Facilty.
The sequencing parameters were: 28 bp for read1, 8 bp for the index, and 56 bp for informative read2.
The fastq-files were processed with the CellRanger v3 pipeline with standard parameters except for 'pre-mrna' reference file according to the 10x Genomics support file
Gene expression matrix files were subjected to standard Seurat downstream analysis
Genome_build: hg19 GRCh38
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| Submission date |
Nov 06, 2020 |
| Last update date |
Sep 30, 2022 |
| Contact name |
Harald Lahm |
| E-mail(s) |
lahm@dhm.mhn.de
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| Organization name |
German Heart Center Munich
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| Department |
INSURE
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| Street address |
36, Lazarettstraße
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| City |
Munich |
| ZIP/Postal code |
80636 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE161016 |
Expression of candidate genes associated with congenital heart disease in adult human atrial and ventricular tissue |
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| Relations |
| BioSample |
SAMN16689218 |
| SRA |
SRX9452635 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4887878_hLV1_barcodes.tsv.gz |
23.8 Kb |
(ftp)(http) |
TSV |
| GSM4887878_hLV1_features.tsv.gz |
262.5 Kb |
(ftp)(http) |
TSV |
| GSM4887878_hLV1_matrix.mtx.gz |
33.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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