|
| Status |
Public on Apr 21, 2021 |
| Title |
Vegetative stage replicate 1 (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
Vegetative cells
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
developmental stage: Vegetative
strain: AX4
|
| Growth protocol |
We cultured te strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was extracted from D. Discoedium cells using Dynabeads mRNA direct micro purification kit (Invitrogen)
8 groups were prepared for RNA-seq libraries using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Real-Time Analysis (RTA) software
sequencing reads were aligned to the AX4 genome by Bowtie2(2.2.9)
The analysis pipeline started with pseudo-alignment of the reads using kallisto, followed by building an index and quantification process, which generated h5 files containing the raw binary files for preliminary differential analysis in sleuth.
Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05.
Genome_build: AX4
Supplementary_files_format_and_content: Data matrix was generated by sleuth
|
| |
|
| Submission date |
Sep 17, 2019 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Eric Greer |
| E-mail(s) |
Eric.Greer@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital/Harvard Medical School
|
| Department |
Newborn Medicine/Department of Pediatrics
|
| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL26360 |
| Series (2) |
| GSE137602 |
Transcriptome analysis in D. discoideium (AX2) in different developmental stages |
| GSE137604 |
Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium |
|
| Relations |
| BioSample |
SAMN12775763 |
| SRA |
SRX6862335 |
