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Sample GSM5715553

Query DataSets for GSM5715553

Status

Public on Aug 04, 2022

Title

exp10_idx1AGTCCGCTGC_idx2AAGATCCAAC

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)

[email protected]

Organization name

University of Washington

Street address

3720 15th Ave NE