|
Status |
Public on Jul 01, 2020 |
Title |
8H3_RNA: Head regeneration RNA-seq, 8 hours post amputation, replicate 3 |
Sample type |
SRA |
|
|
Source name |
Mid-Body Column Tissue
|
Organism |
Hydra vulgaris |
Characteristics |
strain: 105 tissue: Mid-Body Column timepoint: 8 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.
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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/)
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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 |
SAMN15342889 |
SRA |
SRX8598089 |