|
Status |
Public on Nov 02, 2018 |
Title |
body column endodermal epithelium -rep 3 (endo3) |
Sample type |
SRA |
|
|
Source name |
body column endodermal epithelium
|
Organism |
Hydra vulgaris |
Characteristics |
strain: Hydra vulgaris AEP (transgenic line expressing RFP in ectoderm, GFP in endoderm, Glauber et al., 2013) tissue: endoderm
|
Treatment protocol |
Viable Hydra endoderm and ectoderm layers were obtained as described previously (Lesh-Laurie, 1983). Hydra were allowed to relax for approximately 30 sec to 1 min in M solution (Muscatine, 1961) that was adjusted to pH 2.5. The head was then excised by a cut directly below the tentacle ring, followed by the excision of the lower peduncle. The remaining cylinder of tissue was transferred to Haynes solution (Davis et al. 1966). Shortly after being placed in Haynes solution the ectoderm contracts until it forms a small ring surrounding a column of extended endodermal tissue. The ectodermal annulus and the endodermal tissue were immediately transferred to Trizol (Invitrogen). Eight to ten tissue samples were pooled prior to total RNA extraction.
|
Growth protocol |
Hydra vulgaris AEP were cultured according to standard protocol (Lenhoff, 1983) at 18˚C.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Trizol (Invitrogen) QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen)
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
Endo3_S33_L003 processed data file: DGE_ecto_endo_aepLRv2.matrix
|
Data processing |
library strategy: Tag-seq
Poly-A stretches and sequencing adapters were trimmed using the script bbduk.sh (Joint Genome Institute) using the following parameters: k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20. Ribosomal reads were excluded using bbduk.sh and a set of Hydra rRNA sequences. Epithelium specific expression levels were estimated using RSEM v1.2.31 and bowtie v1.1.2.
genome build: Hydra vulgaris AEP transcriptome (aepLRv2) (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: tab-delimited text file of isoform level expression estimates for endoderm and ectoderm (DGE_ecto_endo_aepLRv2.txt)
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|
|
Submission date |
Oct 22, 2018 |
Last update date |
Jul 30, 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 |
GPL25712 |
Series (1) |
GSE121617 |
Stem cell differentiation trajectories in Hydra resolved at single cell resolution |
|
Relations |
BioSample |
SAMN10267722 |
SRA |
SRX4913483 |