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| Status |
Public on Oct 19, 2022 |
| Title |
SW005 |
| Sample type |
SRA |
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| Source name |
3 dpf HSPCs
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| Organism |
Danio rerio |
| Characteristics |
transgenic line: runx1+23:mCherry
developmental stage: 3 dpf embryo
cell type: HSPCs
morpholino: std MO cells 1-188, irf8 MO cells 189-384
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| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were dissociated using liberase, buffered to 0.1% FBS, and filtered for flow cytometry. Single live mCherry+ cells were sorted into individual wells of 384 well plates, with both sample types represented on each plate to account for potential batch effects. Each well contained 50 nl droplets of barcoded RT primers in 10uL of mineral oil.
RNA libraries were prepared for sequencing using the SORT-seq protocol - see Muraro et al. 2016 (Cell Syst).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
mRNA
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| Data processing |
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the zebrafish GRCz11 with BWA-MEM4. Data was demultiplexed as described in Grün et al. Mapping and generation of count tables were automated using the MapAndGo script. Unsupervised clustering and differential gene expression analysis was performed with the Seurat R toolkit.
Grün D, Kester L, van Oudenaarden A. Validation of noise models for single-cell transcriptomics. Nat Methods. 2014 Jun;11(6):637-40. doi: 10.1038/nmeth.2930.
MapAndGo: https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo
Genome_build: GRCz11
Supplementary_files_format_and_content: *.tsv
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| Submission date |
Feb 10, 2022 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Leonard Zon |
| E-mail(s) |
[email protected]
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| Organization name |
Boston Children's Hospital
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| Department |
Oncology/Hematology
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL20828 |
| Series (2) |
| GSE196552 |
Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality [HSCP] |
| GSE196553 |
Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality |
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| Relations |
| BioSample |
SAMN25854971 |
| SRA |
SRX14137992 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5889063_SW005.tsv.gz |
1006.6 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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