|
| Status |
Public on Sep 01, 2017 |
| Title |
mel rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Drop-seq of whole embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: stage 6
cell type: dissociated cells
strain: D.mel y1 w1118 ; P{st.2::Gal4} ; P{vnd::dsRED}
fixation: 80% methanol/PBS
|
| Treatment protocol |
Dechorionated embryos were staged and stage 6 embryos hand-picked into ice-cold PBS-Triton 0.1%.
|
| Growth protocol |
Egg lays occurred in 1 hour intervals; embryos were aged for 2:30 hours (D. melanogaster) or 3:30 hours (D. virilis) at room temperature.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Embryos were dissociated first in a Dounce homogenizer and then further using a syringe with 22G x 2" needle, followed by filtering through 20 um cell strainer and fixation in 80% methanol/PBS
Captured transcriptomes were reverse transcribed while bound on barcoded oligo dT beads; PCR handles added by template switching; cDNA PCR-amplified (4 + 9 cycles); 600 pg cDNA library fragmented and amplified with Nextera XT v2 DNA sample preparation kit using custom primers for 3'-targeted amplification (Macosko et al. 2015 Cell 161)
Drop-seq single-cell transcriptome profiling according to Macosko et al. 2015 Cell 161
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample 4
single-cell transcriptomics
|
| Data processing |
Sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants.
The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices.
Bulk mRNA reads were mapped with STAR. Gene counts were computed with htseq-count.
Genome_build: Drosophila_melanogaster.BDGP6 & Drosophila_virilis.GCA_000005245.1
Supplementary_files_format_and_content: Digital Gene Expression matrices contain UMI counts per cell and per gene. Htseq-counts measure gene abundances in mRNA samples (read counts)
|
| |
|
| Submission date |
Feb 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nikos Karaiskos |
| E-mail(s) |
nikolaos.karaiskos@mdc-berlin.de
|
| Organization name |
Max Delbrück Center for Molecular Medicine
|
| Lab |
Systems Biology of Gene Regulatory Elements
|
| Street address |
Hannoversche Str. 28
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE95025 |
The Drosophila Embryo at Single-Cell Transcriptome Resolution |
|
| Relations |
| BioSample |
SAMN06344994 |
| SRA |
SRX2573623 |
