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| Status |
Public on Mar 30, 2018 |
| Title |
R3_left-midbrain_Scar |
| Sample type |
SRA |
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| Source name |
left midbrain single cells
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| Organism |
Danio rerio |
| Characteristics |
cas9 injection: mRNA
FISH id: R3
tissue: left midbrain
sorted plates: 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
After organ isolation, live single cells are sorted into 384 well plates containing mineral oil, uniquely barcoded cell specific primers for independent scar and mRNA detection, Spike-in controls and and RNAse inhibitor.
Scartrace
Illumina TruSeq adapaters
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Scarred GFP
each plate contains 384 sorted cells
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| Data processing |
In scar libraries, first read contains cell barcode (8 first nucleotides) and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries, first read contains UMI (6 first nucleotides) and cell barcode (from 7 to 14 nucleotides) and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome.
Genome_build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9, ensemble 74, extended with ERCC92
Supplementary_files_format_and_content: *scarclones.txt: tabular separated files, with scar percentage (columns) per cell (rows). Cells from the same fish have been named according to barcode ID, plate and organ of origin. Last column (hclust) referes to ID for the clone (cells sharing hclust label have the same scar pattern). *transcriptome.txt.gz: tabular separated files, with transcript count (rows) per cell (columns). Cells in each file are labeled according to barcode ID, plate, organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained after running RaceID (Grun, D. et al. Nature 525, 251-255, 2015) and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.
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| Submission date |
Sep 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Alemany |
| E-mail(s) |
a.alemany@hubrecht.eu
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| Phone |
+31638680750
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| Organization name |
Hubrecht Institue
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| Lab |
AVO
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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 |
GPL20828 |
| Series (1) |
| GSE102990 |
Whole-organism clone-tracing using single-cell sequencing |
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| Relations |
| BioSample |
SAMN07624346 |
| SRA |
SRX3171476 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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