|
| Status |
Public on May 16, 2020 |
| Title |
wasp_infected_48hr_2_dropseq |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Drosophila melanogaster |
| Characteristics |
treatment: wasp infected 48 hr (128 hr AEL)
tissue: blood
technology: Drop-seq
replicate: 2
|
| Treatment protocol |
96 hr AEL larvae were either wounded with clean tungsten needle at the dorso-posterior side of each larva or left unwounded (for controls). For wasp infestations, 72 hr AEL Oregon R larvae were utilized.
|
| Growth protocol |
Precisely staged L3 larvae (96 hr after egg lay [AEL]) were used for the wounded experiments.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Larvae were bled and the hemocytes were were encapsulated at the Single Cell Core from ICCB-Longwood screening facility with inDrops (Zilionis et al., 2017), 10x Genomics, or Drop-seq technologies.
For inDrops samples: Reverse transcription and library preparation were done at the same facility as previously described (Zilionis et al., 2017). 10x cells were prepared following the manufacturer's protocol. All the Drop-seq and cDNA synthesis methods followed a previous study (Macosko et al., 2015).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Drop-seq blood sample 5: wasp infected 48 hr 2 (128 hr AEL)
dropseq-120hr-circulation-merged-expr-all-genes.txt
dropseq_sample_5
|
| Data processing |
inDrops samples: Harvard inDrops v3 library format FASTQ files were processed using the bcbio-nextgen 1.0.6a0-d2b5b522 single-cell RNA-seq pipeline (https://github.com/bcbio/bcbio-nextgen).
Commands: umis fastqtransform; umis demultiplex_samples; umis cb_filter; umis cb_histogram; rapmap quasiindex; rapmap quasimap; samtools index; umis fasttagcount; umis sparse
A sparse matrix of UMI de-duped reads-per-gene-per cell was generated as a gene x cell sparse matrix for all samples combined (tagcounts.mtx).
10x Chromium samples: FASTQ files were aligned with Cell Ranger v3.1.0 against the FlyBase reference genome using default settings.
Drop-seq samples: FASTQ files were processed using the standard pipeline described in Macosko et al., 2015.
Count matrices were filtered for low quality cells, inspecting a combination of genes per cell, UMI counts per cell, mitochondrial content per cell, transcriptome complexity per cell and other metrics.
Genome_build: Drosophila melanogaster, FlyBase release r6.27
Supplementary_files_format_and_content: Matrix Market Exchange Format (sparse matrix)
|
| |
|
| Submission date |
Mar 08, 2020 |
| Last update date |
May 16, 2020 |
| Contact name |
Michael J Steinbaugh |
| E-mail(s) |
[email protected]
|
| Organization name |
Acid Genomics
|
| Street address |
PO Box 1520
|
| City |
Quechee |
| State/province |
VT |
| ZIP/Postal code |
05059 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE146596 |
A single-cell survey of Drosophila blood |
|
| Relations |
| BioSample |
SAMN14330752 |
| SRA |
SRX7869903 |
