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| Status |
Public on Feb 18, 2016 |
| Title |
Metazome_Annelida_timecourse_sample_0020 |
| Sample type |
SRA |
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| Source name |
single embryo 20
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| Organism |
Platynereis dumerilii |
| Characteristics |
time (minutes after fertilization): 1200
tissue: whole embryo
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| Growth protocol |
Platynereis dumerilii embryos were collected by ML and NM at the lab of Detlev Arendt (EMBL Heidelberg, Germany). In each of several containers, a gravid male and a female were mixed in a small container containing North Sea water. The classical breeding dance was observed after several minutes and the females and males released oocytes and sperm. Fertilized eggs were incubated at 18°C and embryos were collected every hour after fertilization for a period of 5 days. Individual embryos were collected on the cap of a 1.5 ml Eppendorf tube using a micro-mouth pipette. Excessive water was removed and the sample was 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.
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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, against Pdum_transcriptome_v1
Read counting with htseq-count version 0.5.4p3.
Genome_build: Pdum_transcriptome_v1 (NCBI BioProject PRJNA271451)
Supplementary_files_format_and_content: tabular expression matrix
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| Submission date |
Jan 13, 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 |
GPL19648 |
| Series (2) |
| GSE64943 |
Platynereis dumerilii high resolution developmental transcriptomic time-course |
| GSE70185 |
The mid-developmental transition and the evolution of animal body plans |
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| Relations |
| BioSample |
SAMN03283433 |
| SRA |
SRX840399 |
| 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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