|
| Status |
Public on Nov 02, 2018 |
| Title |
homeostatic Hydra, male spike-in (D03-MA) |
| Sample type |
SRA |
| |
|
| Source name |
cell suspension from homeostatic Hydra vulgaris AEP
|
| Organism |
Hydra vulgaris |
| Characteristics |
strain: Hydra vulgaris AEP (transgenic line nGreen, Robert E. Steele)
tissue: whole animal
|
| Treatment protocol |
Prior to Drop-seq cells were dissociated for 90min using Pronase E (VWR, E629-1G) as described previously (Greber et al.,1992) at a concentration of ~75u/mL. 40-50 Hydra were washed twice in sterile filtered Hydra medium and transferred into a 1.5mL eppendorf tube. The medium was removed and 1mL Pronase solution was added. Cells were dissociated for 90min at room temperature (22-24C) with agitation on a nutator. Cells were washed twice and resuspended in resuspended in a salt-adjusted Hydra-PBS (10 mM PO43−, 2mM NaCL, 0.1mM KCl, 0.05% BSA, pH7.6).
|
| Growth protocol |
Hydra vulgaris AEP were cultured according to standard protocol (Lenhoff, 1983) at 18˚C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 14 cycles of PCR amplification and 148 STAMPs per PCR reaction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
D03-MA_S2
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt
|
| Data processing |
library strategy: Drop-seq
Data was processed using Drop-seq tools v1.01, according to Drop-seq protocol v3.1 (http://www.dropseq.org/). Read 2 was aligned with Bowtie2 v 2.2.6 to 1) the Hydra vulgaris 105 2.0 genome using 2.0 genome gene models and 2) a Hydra vulgaris AEP transcriptome reference (aepLRv2)(references available at https://research.nhgri.nih.gov/hydra/). Each aligned read was tagged with its mate-pair UMI and cell barcode (which comprise Read 1). Each aligned exonic read was tagged with a gene name. Cell barcodes were corrected for synthesis errors. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample. Genome UMI counts are provided in supplementary file Hydra_DS_genome_UMICounts.txt. Transcriptome UMI counts are provided in supplementary file Hydra_DS_transcriptome_UMICounts.txt.
genome build: Hydra vulgaris 2.0 genome, Hydra vulgaris AEP transcriptome (aepLRv2)(https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: tab-delimited text files of UMI counts for genome mapping (Hydra_DS_genome_UMICounts.txt) and transcriptome mapping (Hydra_DS_transcriptome_UMICounts.txt)
Supplementary_files_format_and_content: tab-delimited text file of isoform level expression estimates
|
| |
|
| 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 |
GPL25713 |
| Series (1) |
| GSE121617 |
Stem cell differentiation trajectories in Hydra resolved at single cell resolution |
|
| Relations |
| BioSample |
SAMN10267711 |
| SRA |
SRX4913470 |
