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| Status |
Public on Sep 16, 2021 |
| Title |
HUB-DB-012 |
| Sample type |
SRA |
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| Source name |
Epicardial cells of the Zebrafish heart ventricle
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| Organism |
Danio rerio |
| Characteristics |
line: Tg(tcf21:mCherry)
genotype/variation: prrx1b-/-
treatment: Cryoinjured heart
Stage: 7dpi
cell type: Epicardial cells of adult heart ventricle
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| Treatment protocol |
Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tg(tcf21:mCherry) cells were subsequently FACS sorted based on mCherry expression in 384 well plates, each well containing 1 cell.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Live cells were sorted into 384-well plates with Vapor-Lock oil containing a droplet with barcoded primers, spike-in RNA and dNTPs, followed by heat-induced cell lysis and cDNA syntheses using a robotic liquid handler. After cell lysis for 5 minutes at 65C, RT and second strand mixes were distributed with the Nanodrop II liquid handling platform.
Primers consisted of a 24bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 5' Illumina TruSeq small RNA kit adapter and a T7 promoter. After all cells were pooled in one library, the CEL-seq2 protocol was used for library prep (Hashimony et al., 2016).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sample 4
prrx1b-/- plate 2
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| Data processing |
Paired-end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. (2014) Cell.
(Sample 1,2) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier (UMI) and followed by a 24 nt PolyA stretch and a number (<40) of transcript derived bases. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv", well numbers refer to the 384-well plate in the following order: A1 to A24 - B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2, containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded.
(Sample 3,4) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier (UMI) and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv". Read 1 was not used for quantification. Read 2, containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded.
Genome_build: zv9 (with improved 3' annotation, see Junker et al. (2014) Cell)
Supplementary_files_format_and_content: *.TranscriptCounts.tsv: Tab-delimited read count matrices in which rows correspond to genes and columns to single cells.
Supplementary_files_format_and_content: cel-seq2_barcodes.csv: Comma-separated values
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| Submission date |
Jun 24, 2020 |
| Last update date |
Sep 16, 2021 |
| Contact name |
Dennis de de Bakker |
| E-mail(s) |
dennisdebakker@hotmail.com
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| Phone |
+4915238951188
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| Organization name |
FLI
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| Street address |
Beutenbergstraße 11
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| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
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| Platform ID |
GPL20828 |
| Series (1) |
| GSE153170 |
Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration |
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| Relations |
| BioSample |
SAMN15358109 |
| SRA |
SRX8610203 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4635178_HUB-DB-012_H3HCLBGXC_S4_R2.TranscriptCounts.tsv.gz |
1.2 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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