 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 24, 2021 |
| Title |
Dicty_8d_3 |
| Sample type |
SRA |
| |
|
| Source name |
Dictyostelium discoideum
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
strain: AX4
treatment: Starved 8 hours control
|
| 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.
|
| 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 |
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)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Starved 8 hours control
Experiment 1
|
| 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
|
| |
|
| Submission date |
Dec 29, 2020 |
| Last update date |
Feb 24, 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 |
GPL29548 |
| Series (2) |
| GSE164009 |
Regulated sulfur sequestration promotes multicellularity during nutrient limitation (RNA-Seq) |
| GSE164011 |
Regulated sulfur sequestration promotes multicellularity during nutrient limitation |
|
| Relations |
| BioSample |
SAMN17178678 |
| SRA |
SRX9751854 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
