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| Status |
Public on Apr 21, 2021 |
| Title |
Transcriptome analysis in D. discoideium (AX2) in different developmental stages |
| Organism |
Dictyostelium discoideum |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The goal of RNA-seq is to identify the differential expressed genes in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Two biological replicates were assigned for each group and in total 8 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped about 20 - 30 million reads per sample to D. discoideum with bowtie2 workflow. 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. Our results showed stage-specific gene expression profiles in different developmental stages.
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| Overall design |
Messenger RNA from vegetative, streaming, mound and fruiting body stages were extacted and cDNA libraries were generated for deep sequencing, in duplicate, using Nextseq500
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| Contributor(s) |
Yuan Wang S, Liberman Greer E |
| Citation(s) |
33947439 |
| |
| Submission date |
Sep 17, 2019 |
| Last update date |
Jul 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 |
| |
|
| Platforms (1) |
| GPL26360 |
Illumina NextSeq 500 (Dictyostelium discoideum) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE137604 |
Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium |
|
| Relations |
| BioProject |
PRJNA565993 |
| SRA |
SRP222094 |
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