|
| Status |
Public on Nov 24, 2021 |
| Title |
WT_LG_sample_3 |
| Sample type |
SRA |
| |
|
| Source name |
strain AX3_WT_liquid growth
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
strain background: AX3
genotype: WT
growth condition: liquid growth
|
| Treatment protocol |
None
|
| Growth protocol |
Amebae were grown under axenic conditions in growth medium until approximately 80% confluence was reached in the case of cells in surface cultures, or approximately 2 million cells/ml in the case of liquid cultures. They were then frozen until RNA extraction was performed.
|
| 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 NovaSeq 6000 |
| |
|
| 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 2.6.0c
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 |
GPL26668 |
| Series (2) |
| GSE156812 |
RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae in surface and liquid growth |
| GSE156813 |
RNA-Seq analysis of wild-type and mutant D. discoideum amebae |
|
| Relations |
| BioSample |
SAMN15897280 |
| SRA |
SRX9002321 |
