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| Status |
Public on Apr 04, 2017 |
| Title |
MA_EVO_DEVO_115 |
| Sample type |
SRA |
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| Source name |
pool of 10 whole embryos
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: 536
time after 4-cell embryo (minutes): 180
tissue: whole embryo
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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 |
polyA 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 2500 |
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| Description |
536C
Sample name: 536C
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| Data processing |
Libraries were sequenced on the Illumina HiSeq2500 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
Genome_build: WS230
Supplementary_files_format_and_content: tabular Expression matrix. See sample description for sample ID.
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| Submission date |
Sep 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Harel Zalts |
| Organization name |
Technion
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| Street address |
Technion city
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| City |
Haifa |
| State/province |
Israel |
| ZIP/Postal code |
12345 |
| Country |
Israel |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE87528 |
Developmental constraints shape the evolution of the nematode mid-developmental transition |
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| Relations |
| BioSample |
SAMN05855891 |
| SRA |
SRX2203151 |
| 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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