|
Status |
Public on Aug 07, 2019 |
Title |
Replicate 3 - 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 |
SAMN12501500 |
SRA |
SRX6658755 |