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Status |
Public on Feb 24, 2021 |
Title |
Dev_10 |
Sample type |
SRA |
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Source name |
Dictyostelium discoideum
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Organism |
Dictyostelium discoideum |
Characteristics |
strain: AX4 treatment: Starvation 10 hours
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Treatment protocol |
Cells were starve for 30 minutes or 10 hours. Time matched vegetative controls were included.
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Growth protocol |
Dictyostelium discoideum (D. discoideum) strain Ax4 was purchased from the Dictybase stock center. Vegetatively growing cells were axenically maintained in shaking culture in HL5 nutrient medium (14.3 g/L bacto peptone, 7.15 g/L yeast extract, 18 g/L maltose monohydrate, 0.641 g/L Na2HPO4, 0.49 g/L KH2PO4, supplemented with biotin, cyanocobalamin, folic acid, lipoic acid, riboflavin and thiamine-HCl). Starvation and consequent aggregation were induced by washing D. discoideum four times in development buffer (DB; 5 mM Na2HPO4, 5 mM KH2PO4, 1 mM CaCl2, 2 mM MgCl2 in autoclaved H2O) and plating at a density of 2 x 106 cells/ml in DB on tissue culture-treated plates, without shaking. As a control, vegetatively growing cells were plated at a density of 2 x 106 cells/ml in HL5 on tissue culture-treated plates, without shaking.
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Extracted molecule |
total RNA |
Extraction protocol |
Single cell RNA sequencing was performed using a 10X Genomics Chromium Controller. Single cells were processed with GemCode Single Cell Platform using GemCode Gel Beads, Chip and Library Kits (v2) following the manufacturer’s protocol. An estimated 10,000 cells were added to each channel with an average of 7,000 cells recovered. Libraries were sequenced on a NovaSeq (Illumina)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Starvation 10 hours
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Data processing |
Samples were demultiplexed and aligned using Cell Ranger 2.2 (10X genomics) Samples were processed and analyzed in R (3.6.0) using Seurat (v3) Genome_build: dicty_2.7 Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells. A list of cell barcodes and detected genes is also included for each sample.
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Submission date |
Dec 29, 2020 |
Last update date |
Feb 25, 2021 |
Contact name |
Immunometabolism Department |
E-mail(s) |
jcurti29@jhmi.edu
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Organization name |
Johns Hopkins University
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Department |
Immunometabolism
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Street address |
1650 Orleans Street
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City |
Baltimore |
State/province |
Maryland |
ZIP/Postal code |
21287 |
Country |
USA |
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Platform ID |
GPL26668 |
Series (2) |
GSE164010 |
Regulated sulfur sequestration promotes multicellularity during nutrient limitation (scRNA-Seq) |
GSE164011 |
Regulated sulfur sequestration promotes multicellularity during nutrient limitation |
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Relations |
BioSample |
SAMN17178671 |
SRA |
SRX9751882 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4994841_Dev_10_barcodes.tsv.gz |
16.8 Kb |
(ftp)(http) |
TSV |
GSM4994841_Dev_10_features.tsv.gz |
133.9 Kb |
(ftp)(http) |
TSV |
GSM4994841_Dev_10_matrix.mtx.gz |
18.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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