|
| Status |
Public on Nov 24, 2021 |
| Title |
WT_2hr_sample_A |
| Sample type |
SRA |
| |
|
| Source name |
strain AX3_WT_2hr
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
strain background: AX3
genotype: WT
timepoint: 2hr
|
| Treatment protocol |
None
|
| Growth protocol |
Wild-type and mutant amebae were grown under axenic conditions in growth medium until approximately 80% confluence was reached. Eight samples were then frozen until RNA extraction was performed. Other samples of the same type were subjected to nutrient deprivation for 2 and 6 hours, after which the samples were frozen and RNA extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using the Illustra RNAspin Kit (GE Healthcare Life Sciences) following the manufacturer’s protocol.
Total cellular RNA was quantitated with a Qubit fluorometer, and 250 ng of each sample was transcribed to generate cDNA libraries using the Illumina TruSeq RNA Kit (Illumina Inc, San Diego, CA) following the manufacturer's Low Sample (LS) protocol, with the following modifications: 2 minutes of centrifugation were used during the bead drying steps and 12 cycles were used to enrich DNA fragments.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling and generation of FASTQ files was performed with Illumina bcl2fastq2
Read pairs were filtered to remove those where either mate's mean quality score fell below 20
Reads were aligned to D. discoideum reference assembly using STAR 2.5.2b
Counts per gene were determined using featureCounts 1.5.1 based on dictyBase.org gene annotations downloaded in March 2018
Normalized counts were determined using the estimateSizeFactors function
Genome_build: dictyBase.org D. discoideum Chromosomal DNA created 05-13-2009
Supplementary_files_format_and_content: tab-delimited text, raw and normalized read counts per gene
|
| |
|
| Submission date |
Aug 24, 2020 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Melissa Wells |
| E-mail(s) |
wellsme@niehs.nih.gov
|
| Phone |
919-541-7867
|
| Organization name |
NIEHS
|
| Department |
LST
|
| Street address |
111 TW Alexander Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27103 |
| Country |
USA |
| |
|
| Platform ID |
GPL26000 |
| Series (2) |
| GSE156811 |
RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae during short-term nutrient deprivation |
| GSE156813 |
RNA-Seq analysis of wild-type and mutant D. discoideum amebae |
|
| Relations |
| BioSample |
SAMN15897286 |
| SRA |
SRX9002302 |
