|
| Status |
Public on Jun 12, 2023 |
| Title |
Anthox8_60h_rep1_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Whole planula larvae
|
| Organism |
Nematostella vectensis |
| Characteristics |
tissue: Whole planula larvae
developmental stage: 60hpf planula
genotype/variation: F3 Anthox8 homozygous mutant
protocol: PolyA Selected RNA-seq
|
| Treatment protocol |
Anthox1a, Anthox8, Anthox6a mutants were generated using CRISPR/Cas9 (500ng/uL RNP complex). shRNAs targeting Pbx or carrying a scrambled sequence were injected at a final concentration of 600ng/uL into unfertilized oocytes.
|
| Growth protocol |
All animals used in this study were raised at 22°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
200 planula larvae were collected into a 1.5mL eppendorf tube. 500uL of TRIzol reagent was added to each tube and vortexed until samples is homogenized. Total mRNA extraction was performed using Directzol RNA Miniprep kits following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Bulk RNA-seq data used to identify potential landmark genes
|
| Data processing |
Bulk RNA-seq:Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were then aligned to Nematostella genome NV2 using STAR. Raw reads count table was generated with FeatureCounts
Genome_build: NV2
Supplementary_files_format_and_content: Gene count table in csv file for RNA-seq data, single cell expression matrix in h5 format
|
| |
|
| Submission date |
May 03, 2021 |
| Last update date |
Jun 12, 2023 |
| Contact name |
Shiyuan (Cynthia) Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Department |
Computational Biology
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL23029 |
| Series (1) |
| GSE173786 |
Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis |
|
| Relations |
| BioSample |
SAMN18989259 |
| SRA |
SRX10761302 |
