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Sample GSM3440192 Query DataSets for GSM3440192
Status Public on Nov 02, 2018
Title body column endodermal epithelium -rep 2 (endo1)
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Endo1_S32_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)
 
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 SAMN10267723
SRA SRX4913482

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

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