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| Status |
Public on Jan 24, 2014 |
| Title |
Sample 26 Ring (round) |
| Sample type |
SRA |
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| Source name |
Sample 26
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| Organism |
Amphimedon queenslandica |
| Characteristics |
developmental stage: Ring (round)
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| Treatment protocol |
samples staged by morphology and imaged before being stored in 20 μl RNA later.
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| Growth protocol |
Embryos, larvae and post-larvae were collected individually at Heron Island, the Great Barrier Reef, Australia.
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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 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 (minimum quality of 20, max 1 exception. trimming not required).
RNA-seq, CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing 1 mismatch in the 5 first letters of the barcode.
BWA mapping, version 0.6.1, against A. queenslandica genome Aqu1(bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -M 3 -O 11 -E 4)
Read counting with htseq-count version 0.5.3p1. Using a custom annotation,based on Aqu1 exon annotation (union of overlapping reads).
Genome_build: Aqu1 (Ensembl)
Supplementary_files_format_and_content: read counts
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| Submission date |
Jan 23, 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 |
GPL18214 |
| Series (1) |
| GSE54364 |
A high-resolution Amphimedon queenslandica transriptomic timecourse |
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| Relations |
| BioSample |
SAMN02595539 |
| SRA |
SRX447554 |
| 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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