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| Status |
Public on Feb 18, 2016 |
| Title |
Metazome_Echinodermata_timecourse_sample_0086 |
| Sample type |
SRA |
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| Source name |
single embryo 86
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| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
time: : 2760
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| Growth protocol |
Schmidtea polychroa embryos were collected at the lab of Jochen Rink (Max Planck Institute CBG, Dresden, Germany). A population of S.polychroa was maintained in the lab at 20°C as described elsewhere (PMID 18942102). Egg capsules were regularly collected just after deposition and kept in Petri dishes at 20°C. Once at the desired time of development (evenly spread over 15 days of development), capsules were carefully opened using two fine forceps. Embryos were released from capsules and collected individually into eppendorf tubes. After assessment of stage of development (according to system established by Martin-Duran PMID 20100474) excess water was removed and embryos flash-frozen in liquid nitrogen.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps.
The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. The library was treated with DSN treatment
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0 using parameters "--mp 3,1 -N 1 -L 15"
Read counting with htseq-count version 0.5.4p3.
Genome_build: WHL22 transcriptome (NCBI BioProject PRJNA81157)
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| Submission date |
Jun 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Itai Yanai |
| E-mail(s) |
yanai@technion.ac.il
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| Organization name |
Technion - Israel Institute of Technology
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| Department |
Biology
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| Lab |
Yanai
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| Street address |
Technion City
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| City |
Haifa |
| ZIP/Postal code |
30200 |
| Country |
Israel |
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| Platform ID |
GPL19892 |
| Series (2) |
| GSE70185 |
The mid-developmental transition and the evolution of animal body plans |
| GSE70372 |
Strongylocentrotus purpuratus high resolution developmental transcriptomic time-course |
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| Relations |
| BioSample |
SAMN03799959 |
| SRA |
SRX1075454 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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