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| Status |
Public on Jun 20, 2021 |
| Title |
PKP2 mutant hiPSC-epicardial cells rep1 |
| Sample type |
SRA |
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| Source name |
epicardial cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived epicardial cells
genotype: PKP2 c.2013delC
age: day 70 of differentiation
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| Growth protocol |
Epicardal cells were genarated from hiPSCs according to the protocol described in Bao et al., 2017
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| Extracted molecule |
total RNA |
| Extraction protocol |
Day 70 PKP2 c.2013delC and reverted hiPSC-epicardial cells were dissociated and single-cell sorted using the FACSJazz™ Cell Sorter (BD Biosciences) into 384-well plates containing 384 primers and Mineral oil (Sigma-Aldrich). After sorting, plates were snap-frozen on dry ice and stored at -80°C.
Libraries were constructed by Single Cell Discoveries according to an adapted version of the SORT-seq protocol (Muraro et al. (2016), A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Syst).
scRNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cell barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA
Data was demultiplexed.
Raw read counts (included as count tables "ReadCounts") were converted to umi counts (referred to as "barcode counts"); an additional correction was performed based on binominal statistics, resulting in "transcript counts".
Post-processing of count tables: after loading count tables mitochondrial transcript counts were removed, as were genes expressed in less than 10 cells. Consecutively, cells with a remaining transcript count < 5000 were removed. The count tables in the data attached here do contain those cells and genes.
Genome_build: Hg19
Supplementary_files_format_and_content: Count tables of raw reads ("readcounts"), umi counts ("barcode counts"), and corrected umi counts ("transcript counts"). Columns are single cells (and each file corresponds to one sample), rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. S1-4 enumerates the samples. (HUB = Hubrecht, AK = Arwa Kohela)
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| Submission date |
Apr 24, 2020 |
| Last update date |
Jun 20, 2021 |
| Contact name |
Eva van Rooij |
| E-mail(s) |
E.vanrooij@hubrecht.eu
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| Organization name |
Hubrecht Institute
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE149331 |
Epicardial Differentiation Drives Fibro-fatty Remodeling in Arrhythmogenic Cardiomyopathy [scRNA-seq] |
| GSE152747 |
Epicardial Differentiation Drives Fibro-fatty Remodeling in Arrhythmogenic Cardiomyopathy |
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| Relations |
| BioSample |
SAMN14692139 |
| SRA |
SRX8173925 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4498064_HUB-AK-005_HLWF5BGX9_S3_R2.BarcodeCounts.tsv.gz |
1.9 Mb |
(ftp)(http) |
TSV |
| GSM4498064_HUB-AK-005_HLWF5BGX9_S3_R2.ReadCounts.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSM4498064_HUB-AK-005_HLWF5BGX9_S3_R2.TranscriptCounts.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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