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| Status |
Public on Feb 14, 2018 |
| Title |
Control 5dpf zebrafish embryos replicate 2 run 1 |
| Sample type |
SRA |
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| Source name |
Zebrafish whole embryos 5dpf
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| Organism |
Danio rerio |
| Characteristics |
genotype/variation: Wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was purified using QIAGEN RNA purification kit for zebrafish and AMBION kit for sea urchin
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Embr_5dpf_ESRP_WT_b
cRPKM-Dre4.tab
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| Data processing |
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences were downloaded from Ensembl for zebrafish and from Echinobase from sea urchin. For each gene, the canonical transcript was selected for gene expression analysis based on ORF lenght.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: zebrafish: danRer10. sea urchin: Spur_v3.1
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above) for each gene's canonical transcript in each condition
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| Submission date |
Mar 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Demian Burguera |
| E-mail(s) |
dburghez@gmail.com
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| Organization name |
University of Barcelona
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| Department |
Genetics, Faculty of Biology
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| Street address |
Diagonal 643
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| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
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| Platform ID |
GPL18413 |
| Series (1) |
| GSE97267 |
Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes |
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| Relations |
| BioSample |
SAMN06671010 |
| SRA |
SRX2693200 |
| 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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