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| Status |
Public on Aug 04, 2022 |
| Title |
exp10_idx1GCATCGTATG_idx2CAAGCTTGGC |
| Sample type |
SRA |
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| Source name |
whole embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: Drosophila embryo (0-20 hrs)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Drosophila melanogaster embryos were collected as previously described (Sandmann, Jakobsen, and Furlong 2006; Cusanovich et al. 2018).
We performed sci-RNA-seq3 as previously described (Cao et al. 2019), except for using a Tn5 enzyme loaded with N7 adapter only. Several experiments were done and each one included samples from multiple time windows. Associated time-windows for nuclei batches were tracked through specific wells. Additionally, for a subset of the data we included mouse nuclei to serve as a control to determine the rate of cell doublets.
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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 |
For sci-RNA-seq processing, the read alignment and gene count matrix generation was performed as was done in earlier studies (Cao et al. 2020, 2019) with minor modifications: reads were mapped with STAR v2.7.3a to the dm6 drosophila genome and the BDGP6.28.102 gene annotation.
Genome_build: dm6
Supplementary_files_format_and_content: MM sparse matrix containing the sci-RNA-seq read count for genes (rows) by nuclei (cols).
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| Submission date |
Dec 03, 2021 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Diego Calderon |
| E-mail(s) |
dcal@uw.edu
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| Organization name |
University of Washington
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| ZIP/Postal code |
98105 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE190147 |
sci-RNA-seq data |
| GSE190149 |
The continuum of Drosophila embryonic development at single cell resolution |
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| Relations |
| BioSample |
SAMN23607049 |
| SRA |
SRX13306654 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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