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| Status |
Public on Dec 31, 2020 |
| Title |
P3-2 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Cyprinus carpio |
| Characteristics |
tissue: embryo
developmental stage: gastrulation (12 hpf)
strain: FFRC No.2 strain
genotype: WT
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| Treatment protocol |
The stages of embryonic development were observed and photographed under an microscope. The test samples consisted of six embryonic stages: cleavage stage(2 hours post-fertilization (hpf) embryos) (P1), blastocyst stage (6 hpf) (P2), gastrulation stage (12 hpf) (P3), organ formation stage (20 hpf) (P4), hatching stage (64 hpf) (P5) and 1 dph larva (P6) (Supplementary fig). All samples were immediately frozen in liquid nitrogen and then stored at −80 °C for further use.
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| Growth protocol |
The common carp used in the experiment is a new fish variety derived from the original parents of Jian carp (C. carpio var. jian), Huanghe carp (C. carpio haematopterus) and Heilongjiang common carp (C. carpio haermatopterus) after five generations combined selection by Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), which is designated as FFRC No.2 strain common carp. Embryos were obtained by natural spawning.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol
Genomic DNA was removed prior to RNA purity and integrity evaluation. An equal amount of total RNA of each stage was pooled separately. The strand-specific cDNA libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) after depletion of rRNA by the Epicentre Ribo-zero rRNA Removal Kit (Epicentre, Madison, WI, USA), according to standard procedures
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
3-2.
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Refseq C. carpio reference genome using Hisat2 aligner with default parameters.
The mapped reads from each sample were assembled using StringTie v1.3.3b, then assembled transcripts were annotated using gffcompare program (v 0.10.1) from the stringTie packageand. The unknown transcripts were used to lncRNA identification using CPAT, NR and Pfam.
Rawcounts of mRNA and lncRNA genes in each sample were quantified using featureCounts program, while RPKM value was used to estimate the relative expression levels among samples.
EdgeR R package was used to identify differentially expressed mRNAs (DE-mRNAs) and differentially expressed lncRNAs (DE-lncRNAs) with rawcounts of genes. The genes with absolute value of |log2 (fold change)| >= 1 and FDR of < 0.05 were considered as significantly differential expressed.
Genome_build: GCF_000951615.1
Supplementary_files_format_and_content: tab-delimited text files include raw count for each Sample
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| Submission date |
May 07, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Lanmei Wang |
| E-mail(s) |
[email protected]
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| Organization name |
Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences
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| Street address |
East Shanshui Road 9
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| City |
Wuxi |
| ZIP/Postal code |
214081 |
| Country |
China |
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| Platform ID |
GPL25715 |
| Series (1) |
| GSE150036 |
A dataset of lncRNAs and mRNAs during embryonic development of common carp, Cyprinus carpio |
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| Relations |
| BioSample |
SAMN14848385 |
| SRA |
SRX8287453 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4521108_3-2.rawCount.txt.gz |
335.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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