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| Status |
Public on Feb 18, 2016 |
| Title |
Metazome_CE_timecourse_sample_0133 |
| Sample type |
SRA |
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| Source name |
single embryo 133
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| Organism |
Caenorhabditis elegans |
| Characteristics |
time point (minutes after 4-cell): 360
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| Treatment protocol |
For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.
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| Growth protocol |
Standard C. elegans techniques were followed to grow worms (Stiernagle 2006).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol as previously described (Levin et al., 2012).
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. 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 C. elegans genome WS230
Read counting with htseq-count version 0.5.4p3. Using on WS230 annotations
Genome_build: WormBase WS230
Supplementary_files_format_and_content: tabular Expression matrix
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| Submission date |
Aug 26, 2014 |
| 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 |
GPL13657 |
| Series (2) |
| GSE60755 |
Caenorhabditis elegans high resolution developmental transcriptomic time-course |
| GSE70185 |
The mid-developmental transition and the evolution of animal body plans |
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| Relations |
| BioSample |
SAMN03008855 |
| SRA |
SRX686644 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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