|
| Status |
Public on May 09, 2019 |
| Title |
NC34.2_slug_a |
| Sample type |
SRA |
| |
|
| Source name |
Slug stage of Dictyostelium discoideum NC34.2 grown clonally
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
strain: NC34.2
developmental stage: Slug
|
| Growth protocol |
Cells of each strain were grown in association with Klebsiella aerogenes, before washing by centrifugation in KK2 buffer. Washed cells were then plated on non-nutrient L28 purified agar (agar) at a density of x cells/cm2. For chimeric combinations we mixed equal numbers of cells from each strain. Aggregations were harvested after fourteen hours of development, when slugs had formed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ten agar plates per sample were pooled for RNA extraction using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were trimmed and filtered using Skewer v0.2.2 (min. length of 20bp, mean Quality score of 20). Chimerism genes are then defined as those that are significantly up-regulated in chimeric slugs (FDR adjusted p-value < 0.05).
Segmental duplication specific to AX4 on chromosome 2 between bases 3002337 and 375508 was masked from the reference genome prior to mapping.
Reads were pseudo-aligned to D. discoideum transcripts obtained from Ensembl Protists database release 36 and quantified using Kallisto v0.43.0. One hundred bootstrap samples were generated for each replicate to compute uncertainty estimates for the expression levels.
Genes with less than 5 reads in at least 47% of the libraries were discarded.
Estimates of expression were then normalized and summarized to gene level using sleuth v0.29.0
Wald test for differential expression was conducted using sleuth v0.29.0
Genome_build: Genome assembly: dicty_2.7
Supplementary_files_format_and_content: tab-delimited text files include estimated counts and transcripts per million for each Sample
|
| |
|
| Submission date |
Aug 03, 2018 |
| Last update date |
May 09, 2019 |
| Contact name |
Atahualpa Castillo Morales |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Bath
|
| Department |
Biology and Biochemistry
|
| Street address |
Claverton Down
|
| City |
Bath |
| ZIP/Postal code |
BA2 3AS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15643 |
| Series (1) |
| GSE118081 |
Transcriptome profile of Dictyostelium discoideum slugs in clonal and chimeric development |
|
| Relations |
| BioSample |
SAMN09763680 |
| SRA |
SRX4505216 |
