Series Summary for DCD000336SR

RNA-seq data from 4 early developmental stages

Survey

10.1186/1471-213X-11-30

PRJEB2512

In this study we use RNA-Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped to the zebrafish genome and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development.

True

mickael.dong

June 1, 2017, 4:06 a.m.

Aug. 14, 2018, 7:52 a.m.

Assays

Biosample ID Series biosample_type biosample_lab genetic_background
DCD006937BS DCD000336SR whole organism Kere Lab, Karolinska Institute WT
Applied Assay ID Biosample Replicate Assay
DCD001924AA DCD013449BR small-RNA-seq_Kere_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002275SQ DCD002282TR Kere Lab, Karolinska Institute SOLiD AB SOLiD System unstranded 06/09/2011
DCD004746DT: FASTQ
DCD008836DT: BIGWIG GRCz10/danRer10
DCD009455DT: LOG GRCz10/danRer10
DCD009457DT: TSV GRCz10/danRer10
DCD009458DT: TSV GRCz10/danRer10
DCD009459DT: BEDGRAPH GRCz10/danRer10
DCD009460DT: BEDGRAPH GRCz10/danRer10
DCD009461DT: BEDGRAPH GRCz10/danRer10
DCD009462DT: BEDGRAPH GRCz10/danRer10
DCD009463DT: PDF GRCz10/danRer10
DCD009464DT: LOG GRCz10/danRer10
DCD009465DT: PDF GRCz10/danRer10
DCD009466DT: LOG GRCz10/danRer10
DCD009547DT: BAM GRCz10/danRer10
Biosample ID Series biosample_type biosample_lab genetic_background
DCD006938BS DCD000336SR whole organism Kere Lab, Karolinska Institute WT
Applied Assay ID Biosample Replicate Assay
DCD001923AA DCD013450BR small-RNA-seq_Kere_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002274SQ DCD002281TR Kere Lab, Karolinska Institute SOLiD AB SOLiD System unstranded 06/09/2011
DCD004745DT: FASTQ
DCD008835DT: BIGWIG GRCz10/danRer10
DCD009491DT: LOG GRCz10/danRer10
DCD009492DT: TSV GRCz10/danRer10
DCD009493DT: TSV GRCz10/danRer10
DCD009494DT: BEDGRAPH GRCz10/danRer10
DCD009496DT: BEDGRAPH GRCz10/danRer10
DCD009497DT: BEDGRAPH GRCz10/danRer10
DCD009498DT: PDF GRCz10/danRer10
DCD009499DT: LOG GRCz10/danRer10
DCD009500DT: PDF GRCz10/danRer10
DCD009501DT: LOG GRCz10/danRer10
DCD009502DT: BEDGRAPH GRCz10/danRer10
DCD009562DT: BAM GRCz10/danRer10
Biosample ID Series biosample_type biosample_lab genetic_background
DCD006939BS DCD000336SR whole organism Kere Lab, Karolinska Institute WT
Applied Assay ID Biosample Replicate Assay
DCD001922AA DCD013451BR small-RNA-seq_Kere_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002273SQ DCD002280TR Kere Lab, Karolinska Institute SOLiD AB SOLiD System unstranded 06/09/2011
DCD004744DT: FASTQ
DCD008841DT: BIGWIG GRCz10/danRer10
DCD009431DT: LOG GRCz10/danRer10
DCD009433DT: TSV GRCz10/danRer10
DCD009434DT: TSV GRCz10/danRer10
DCD009435DT: BEDGRAPH GRCz10/danRer10
DCD009436DT: BEDGRAPH GRCz10/danRer10
DCD009437DT: BEDGRAPH GRCz10/danRer10
DCD009438DT: PDF GRCz10/danRer10
DCD009439DT: LOG GRCz10/danRer10
DCD009440DT: PDF GRCz10/danRer10
DCD009441DT: LOG GRCz10/danRer10
DCD009442DT: BEDGRAPH GRCz10/danRer10
DCD009507DT: BAM GRCz10/danRer10
Biosample ID Series biosample_type biosample_lab genetic_background
DCD006940BS DCD000336SR whole organism Kere Lab, Karolinska Institute WT
Applied Assay ID Biosample Replicate Assay
DCD001921AA DCD013452BR small-RNA-seq_Kere_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002272SQ DCD002279TR Kere Lab, Karolinska Institute SOLiD AB SOLiD System unstranded 06/09/2011
DCD004743DT: FASTQ
DCD008833DT: BIGWIG GRCz10/danRer10
DCD009503DT: LOG GRCz10/danRer10
DCD009504DT: TSV GRCz10/danRer10
DCD009505DT: TSV GRCz10/danRer10
DCD009506DT: BEDGRAPH GRCz10/danRer10
DCD009508DT: BEDGRAPH GRCz10/danRer10
DCD009509DT: BEDGRAPH GRCz10/danRer10
DCD009510DT: PDF GRCz10/danRer10
DCD009511DT: LOG GRCz10/danRer10
DCD009512DT: PDF GRCz10/danRer10
DCD009513DT: LOG GRCz10/danRer10
DCD009514DT: BEDGRAPH GRCz10/danRer10
DCD009577DT: BAM GRCz10/danRer10