|
| Status |
Public on Aug 07, 2019 |
| Title |
Replicate 2 - hywi knockdown |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Hydra vulgaris |
| Characteristics |
tissue: whole animal
strain: AEP
genotype/variation: transgenic line expressing hywi hairpin transgene in epithelial stem cells
|
| Treatment protocol |
Offspring (with transgene) from the hywi RNAi-1 transgenic line were collected 4 days post hatching. 10 animals were used in RNA extractions.
|
| Growth protocol |
Hydra were cultured according to standard protocol (Lenhoff, 1983) at 18˚C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol (Invitrogen)
TruSeq stranded RNA (RS-122-2201)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapters (Truseq3) were trimmed and reads filtered using trimmomatic-0.33 (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). RSEM v1.2.31/bowtie v1.1.2 were used to estimate expression levels using a transcriptome reference (rsem-calculate-expression --forward-prob 0).
tab-delimited text file of isoform level raw expression estimates - Differential_Gene_Expression_Count_Matrix.txt
Genome_build: Hydra vulgaris AEP transcriptome (aepLRv2) (Transcriptome Shotgun Assembly project: GHHG01000000)
|
| |
|
| Submission date |
Aug 06, 2019 |
| Last update date |
Aug 07, 2019 |
| Contact name |
Celina E Juliano |
| E-mail(s) |
cejuliano@ucdavis.edu
|
| Organization name |
University of California Davis
|
| Department |
MCB
|
| Lab |
Julianolab
|
| Street address |
149 Briggs Hall
|
| City |
Davis |
| State/province |
California |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL27013 |
| Series (1) |
| GSE135440 |
PIWI-piRNA pathway mediated transposon repression in Hydra somatic stem cells |
|
| Relations |
| BioSample |
SAMN12501489 |
| SRA |
SRX6658754 |
