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Sample GSM4994841 Query DataSets for GSM4994841
Status Public on Feb 24, 2021
Title Dev_10
Sample type SRA
 
Source name Dictyostelium discoideum
Organism Dictyostelium discoideum
Characteristics strain: AX4
treatment: Starvation 10 hours
Treatment protocol Cells were starve for 30 minutes or 10 hours. Time matched vegetative controls were included.
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.
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Starvation 10 hours
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.
 
Submission date Dec 29, 2020
Last update date Feb 25, 2021
Contact name Immunometabolism Department
E-mail(s) jcurti29@jhmi.edu
Organization name Johns Hopkins University
Department Immunometabolism
Street address 1650 Orleans Street
City Baltimore
State/province Maryland
ZIP/Postal code 21287
Country USA
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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