 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 04, 2022 |
| Title |
exp10_idx1GGTTATCGAA_idx2GACCGTAGCA |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: Drosophila embryo (0-20 hrs)
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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).
|
| |
|
| Submission date |
Dec 03, 2021 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Diego Calderon |
| E-mail(s) |
dcal@uw.edu
|
| Organization name |
University of Washington
|
| Street address |
3720 15th Ave NE
|
| City |
Seattle |
| ZIP/Postal code |
98105 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE190147 |
sci-RNA-seq data |
| GSE190149 |
The continuum of Drosophila embryonic development at single cell resolution |
|
| Relations |
| BioSample |
SAMN23608082 |
| SRA |
SRX13308002 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
