Vejnar, Abdel Messih, Takacs, Yartseva, Oikonomou et al. Genome Research. 2019

For questions, please contact charles.vejnar@yale.edu, dcb@bu.edu or antonio.giraldez@yale.edu

Citation

Please cite the following manuscript if using any of these datasets:

Genome wide analysis of 3’-UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
Charles E. Vejnar, Mario Abdel Messih, Carter M. Takacs, Valeria Yartseva, Panos Oikonomou, Romain Christiano, Marlon Stoeckius, Stephanie Lau, Miler T. Lee, Jean-Denis Beaudoin, Damir Musaev, Hiba Darwich-Codore, Tobias C. Walther, Saeed Tavazoie, Daniel Cifuentes, Antonio J. Giraldez
Genome Research. 2019

About the datasets

How to decompress the files

Replicates

mRNA-seq embryonic development timecourse

Gene counts

Set Type Normalization Multi-mapper File
Gene All - Unique dev_timecourse_zebrafish_vejnar_giraldez_count_1_gene_all_v11.csv.xz
Gene Protein-coding - Unique dev_timecourse_zebrafish_vejnar_giraldez_count_1_gene_protein_coding_v11.csv.xz
Transcript All - Unique dev_timecourse_zebrafish_vejnar_giraldez_count_1_transcript_all_v11.csv.xz
Transcript Protein-coding - Unique dev_timecourse_zebrafish_vejnar_giraldez_count_1_transcript_protein_coding_v11.csv.xz
Gene All - Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_count_2_gene_all_v11.csv.xz
Gene Protein-coding - Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_count_2_gene_protein_coding_v11.csv.xz
Transcript All - Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_count_2_transcript_all_v11.csv.xz
Transcript Protein-coding - Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_count_2_transcript_protein_coding_v11.csv.xz
Gene All - All matches dev_timecourse_zebrafish_vejnar_giraldez_count_900_gene_all_v11.csv.xz
Gene Protein-coding - All matches dev_timecourse_zebrafish_vejnar_giraldez_count_900_gene_protein_coding_v11.csv.xz
Transcript All - All matches dev_timecourse_zebrafish_vejnar_giraldez_count_900_transcript_all_v11.csv.xz
Transcript Protein-coding - All matches dev_timecourse_zebrafish_vejnar_giraldez_count_900_transcript_protein_coding_v11.csv.xz
Gene All RPKM: yeast+zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_all_all_v11.csv.xz
Gene All RPKM: yeast Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_all_yst_v11.csv.xz
Gene All RPKM: zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_all_zbf_v11.csv.xz
Gene Protein-coding RPKM: yeast+zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_protein_coding_all_v11.csv.xz
Gene Protein-coding RPKM: yeast Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_protein_coding_yst_v11.csv.xz
Gene Protein-coding RPKM: zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_protein_coding_zbf_v11.csv.xz
Transcript All RPKM: yeast+zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_all_all_v11.csv.xz
Transcript All RPKM: yeast Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_all_yst_v11.csv.xz
Transcript All RPKM: zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_all_zbf_v11.csv.xz
Transcript Protein-coding RPKM: yeast+zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_protein_coding_all_v11.csv.xz
Transcript Protein-coding RPKM: yeast Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_protein_coding_yst_v11.csv.xz
Transcript Protein-coding RPKM: zbf Unique dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_protein_coding_zbf_v11.csv.xz
Gene All RPKM: yeast+zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_all_all_v11.csv.xz
Gene All RPKM: yeast Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_all_yst_v11.csv.xz
Gene All RPKM: zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_all_zbf_v11.csv.xz
Gene Protein-coding RPKM: yeast+zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_protein_coding_all_v11.csv.xz
Gene Protein-coding RPKM: yeast Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_protein_coding_yst_v11.csv.xz
Gene Protein-coding RPKM: zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_protein_coding_zbf_v11.csv.xz
Transcript All RPKM: yeast+zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_all_all_v11.csv.xz
Transcript All RPKM: yeast Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_all_yst_v11.csv.xz
Transcript All RPKM: zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_all_zbf_v11.csv.xz
Transcript Protein-coding RPKM: yeast+zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_protein_coding_all_v11.csv.xz
Transcript Protein-coding RPKM: yeast Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_protein_coding_yst_v11.csv.xz
Transcript Protein-coding RPKM: zbf Up to 2 matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_protein_coding_zbf_v11.csv.xz
Gene All RPKM: yeast+zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_all_all_v11.csv.xz
Gene All RPKM: yeast All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_all_yst_v11.csv.xz
Gene All RPKM: zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_all_zbf_v11.csv.xz
Gene Protein-coding RPKM: yeast+zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_protein_coding_all_v11.csv.xz
Gene Protein-coding RPKM: yeast All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_protein_coding_yst_v11.csv.xz
Gene Protein-coding RPKM: zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_protein_coding_zbf_v11.csv.xz
Transcript All RPKM: yeast+zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_all_all_v11.csv.xz
Transcript All RPKM: yeast All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_all_yst_v11.csv.xz
Transcript All RPKM: zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_all_zbf_v11.csv.xz
Transcript Protein-coding RPKM: yeast+zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_protein_coding_all_v11.csv.xz
Transcript Protein-coding RPKM: yeast All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_protein_coding_yst_v11.csv.xz
Transcript Protein-coding RPKM: zbf All matches dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_protein_coding_zbf_v11.csv.xz

Trackhub

Development timecourse genome trackhub

iCLIP

Trackhub

iCLIP genome trackhub

Source code