NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4632754 Query DataSets for GSM4632754
Status Public on Jul 01, 2020
Title 3H1_RNA: Head regeneration RNA-seq, 3 hours post amputation, replicate 1
Sample type SRA
 
Source name Mid-Body Column Tissue
Organism Hydra vulgaris
Characteristics strain: 105
tissue: Mid-Body Column
timepoint: 3 hours post amputation
regeneration type: Head Regeneration
treatment: Untreated
Treatment protocol For iCRT14 treatment, Hydra were pre-incubated in 5uM iCRT14 for two hours prior to amputation. Following amputation, iCRT14 treatment continued until tissue was collected for library preparation.
Growth protocol Hydra vulgaris strain 105 polyps were cultured according to standard protocol (Lenhoff, 1983) at 18˚C and fed 1-2 times weekly with Artemia nauplii.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from 30 regenerating tissue pieces using a standard trizol extraction. DNA was then removed using a DNaseI digest. A final purification step was then performed using a Zymogen RNA Clean & Concentrator kit.
Illumina TruSeq Stranded mRNA.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: SE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were then mapped to the Hydra vulgaris 2.0 genome and read counts were calculated using rsem (V. 1.2.31) using the following settings: --no-bam-output --bowtie2.
processed data files format and content: Read count matrix for gene models from the Hydra vulgaris 2.0 genome for all RNA-seq samples. Generated using rsem.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)
 
Submission date Jun 22, 2020
Last update date Jul 01, 2020
Contact name Jack Cazet
E-mail(s) jacazet@ucdavis.edu
Organization name University of California, Davis
Department MCB
Street address 1 Shields Ave.
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL25712
Series (1)
GSE152994 Oral Regeneration Is the Default Pathway Triggered by Injury in Hydra
Relations
BioSample SAMN15342860
SRA SRX8598081

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap