|
| Status |
Public on Apr 21, 2021 |
| Title |
Vegetative stage replicate 3 [NovaSeq] |
| Sample type |
SRA |
| |
|
| Source name |
Vegetative cells
|
| Organism |
Dictyostelium discoideum AX4 |
| Characteristics |
developmental stage: Vegetative
genotype: WT
|
| Growth protocol |
We cultured te strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were dissociated into single cells from different stages by physical pipetting with PBS + 0.04% BSA. The cell numbers were counted using a microscope.
Cell from each sample were subject to Chromium Single Cell Gene Expression kit V3 (10x Genomics) for library construction according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
V3
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv
|
| Data processing |
Sequence reads were aligned, quantified by Cell Ranger with default setting except using normalized="none" for aggr function.
Low quality cellsor outliers were filtered out from the data by the following threshold: 200 < total Gene count < 7000, 500 <total UMI count <30000.
Normalization (SCTransform), batch correction (Harmony) and dimension reduction (PCA and UMAP) were conducted in Seurat.
raw_sc_Dicty_3_stage.tsv was generated by removing streaming stage cells from the matrix.
raw_sc_Dicty_3_stage_ds.tsv (used for pseudotime analysis) was generated by downsampling the raw_sc_Dicty_3_stage.tsv.
Genome_build: AX4
Supplementary_files_format_and_content: Matrix of UMI counts per gene for each cell.
Supplementary_files_format_and_content: The information (cell stage, batch…) of each cell barcode in the quantification matrix file.
|
| |
|
| Submission date |
Jul 04, 2020 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Eric Greer |
| E-mail(s) |
Eric.Greer@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital/Harvard Medical School
|
| Department |
Newborn Medicine/Department of Pediatrics
|
| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL28816 |
| Series (2) |
| GSE137604 |
Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium |
| GSE153795 |
Single-cell transcriptome analysis in D. discoideum (AX4) in different developmental stages |
|
| Relations |
| BioSample |
SAMN15447782 |
| SRA |
SRX8666619 |
