|
| Status |
Public on Nov 30, 2012 |
| Title |
gastrula stage embryo 12C CD1_12 |
| Sample type |
SRA |
| |
|
| Source name |
gastrula stage embryo
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
developmental stage: gastrula stage embryo
female parent: C
male parent: D
temperature: 12
|
| Treatment protocol |
Growth chambers were set to either 12C or 18C, and water was equilibrated prior to adding the fertilized embryos.
|
| Growth protocol |
Adult urchins were spawned by injecting 0.5M KCl. Eggs and sperm were mixed, fertilization rates assessed, washed, and then moved to larger culture dishes for growth. Embryos were cultured at low density until they reached the mid-point of gastrulation in artificial sea water at 18C or 12C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
6.5 − 8.5μg of DNase-treated total RNA was used as the input sample. mRNA was isolated via two rounds of poly-A selection using 100μl of Dynabeads (Invitrogen). Bar- coded SOLiD libraries were prepared using the RNA-seq protocol for the SOLiD Total RNA-Seq kit and the SOLiD Transcriptome Multiplexing Kit (Applied Biosystems). Library quality was assessed using a 2100 Bioanalyzer (Agilent). Libraries were quantitated using qPCR, and prepared for standard stand-specific SOLiD sequencing in equimolar concentrations. 50bp single-end reads were generated on 2 slides by the IGSP Genome Sequencing and Analysis Core Resource at Duke University.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
Initial filtering by Corona
Reads were mapped to the S purpuratus genome with Bowtie v0.12.7. Mapping parameters were -C -n 2 -l 9 -e 100 -M 1 -t -best -trim3 15
Reads were counted in gene models using Htseq with the parameters --mode=intersection-nonempty --stranded=yes
Genome_build: Spur_3.1.LinearScaffold.fa from www.SpBase.org
Supplementary_files_format_and_content: SPU_counts.txt countains total counts of reads per gene model per sample, as generated by Htseq
|
| |
|
| Submission date |
Jun 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Runcie |
| E-mail(s) |
der7@duke.edu
|
| Organization name |
Duke University
|
| Department |
Biology Department
|
| Street address |
Box 90338
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL15679 |
| Series (2) |
| GSE29504 |
Genetics of gene expression responses to temperature stress in a sea urchin gene network |
| GSE38606 |
Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS) |
|
| Relations |
| SRA |
SRX152587 |
| BioSample |
SAMN01041925 |
