|
Status |
Public on Apr 21, 2021 |
Title |
Vegetative stage replicate 1 [NovaSeq] |
Sample type |
SRA |
|
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
V1 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.
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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 |
SAMN15447786 |
SRA |
SRX8666615 |