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Status |
Public on Feb 24, 2021 |
Title |
Dicty_30dg_2 |
Sample type |
SRA |
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Source name |
Dictyostelium discoideum
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Organism |
Dictyostelium discoideum |
Characteristics |
strain: AX4 treatment: Starved 30 minutes plus GSH
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Treatment protocol |
In one experiment, cells were starve for 30 minutes, 4 or 8 hours. In another experiment cells were starved for 30 minutes or 8 hours with or without added reduced glutathione. Time and supplement 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 |
Total RNA was isolated using the RNEasy kit (Qiagen) and quantified using the Qubit 2.0 (ThermoFisher). Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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Description |
Starved 30 minutes plus GSH Experiment 1
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Data processing |
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value. Genome_build: dicty_2.7 Supplementary_files_format_and_content: Processed data is a matrix with raw counts for features in samples, obtained with featureCounts, or individual raw count files for each sample produced the same way
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Submission date |
Dec 29, 2020 |
Last update date |
Feb 24, 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 |
GPL29548 |
Series (2) |
GSE164009 |
Regulated sulfur sequestration promotes multicellularity during nutrient limitation (RNA-Seq) |
GSE164011 |
Regulated sulfur sequestration promotes multicellularity during nutrient limitation |
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Relations |
BioSample |
SAMN17178663 |
SRA |
SRX9751844 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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