|
| Status |
Public on May 03, 2017 |
| Title |
mel_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Drop-seq of whole embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: mixture stage 10 to 17 batch1
fixation: 80% methanol/PBS
cell type: dissociated cells
|
| Growth protocol |
Egg lays occurred in 2 hour intervals after 3x 1 hour pre-lays; embryos were aged for 6 hours (D. melanogaster) at room temperature.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Methanol-fixation was adapted from Stöckius et al. 2009 (Nat. Methods). To avoid cell clumping, 8 volumes (800 µl) of methanol p. a. (pre-chilled to -20˚C) were added drop-wise, while gently mixing or vortexing the cell suspension. Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
single-cell transcriptomics
|
| Data processing |
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12. Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12. Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j. Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12. Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12. Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2. The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: *txt: Tab-separated text files containing UMI counts per gene and per cell of each sample.
clusters*.txt files generated using Seurat.
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nikos Karaiskos |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE89164 |
Cell fixation and preservation for droplet-based single cell transcriptomics |
|
| Relations |
| BioSample |
SAMN06468920 |
| SRA |
SRX2608929 |
