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

Latest update: version 12, November 2022 - Ensembl 108

How to decompress the files

• All CSV files are compressed using Zstandard.
• The Python Data Analysis Library pandas decompresses Zstandard files transparently.

Replicates

• Labels with B1 (B2, B3 etc) correspond to biological replicate 1 (2, 3 etc).
• Labels without B1 (B2, B3 etc) correspond to sample where reads from both replicates were merged prior to the analysis.

mRNA-seq embryonic development timecourse

Gene counts

• Reads mapping multiple times on zebrafish genome were included only if mapping up to 1 locus “Unique” (i.e. single mapper) or 2 loci “Up to 2 matches”. “All matches” includes all reads.
• Count were normalized to RPKM:
  • Total count of zebrafish and yeast reads (yeast+zbf)
  • Total count of yeast reads (yeast). Use this run to use yeast spike-in.
  • Total count of zebrafish reads (zbf). Use this run to ignore yeast spike-in.

Set	Type	Normalization	Multi-mapper	File
Gene	All	-	Unique	dev_timecourse_zebrafish_vejnar_giraldez_count_1_gene_all_v12.csv.zst
Gene	Protein-coding	-	Unique	dev_timecourse_zebrafish_vejnar_giraldez_count_1_gene_protein_coding_v12.csv.zst
Transcript	All	-	Unique	dev_timecourse_zebrafish_vejnar_giraldez_count_1_transcript_all_v12.csv.zst
Transcript	Protein-coding	-	Unique	dev_timecourse_zebrafish_vejnar_giraldez_count_1_transcript_protein_coding_v12.csv.zst
Gene	All	-	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_count_2_gene_all_v12.csv.zst
Gene	Protein-coding	-	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_count_2_gene_protein_coding_v12.csv.zst
Transcript	All	-	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_count_2_transcript_all_v12.csv.zst
Transcript	Protein-coding	-	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_count_2_transcript_protein_coding_v12.csv.zst
Gene	All	-	All matches	dev_timecourse_zebrafish_vejnar_giraldez_count_900_gene_all_v12.csv.zst
Gene	Protein-coding	-	All matches	dev_timecourse_zebrafish_vejnar_giraldez_count_900_gene_protein_coding_v12.csv.zst
Transcript	All	-	All matches	dev_timecourse_zebrafish_vejnar_giraldez_count_900_transcript_all_v12.csv.zst
Transcript	Protein-coding	-	All matches	dev_timecourse_zebrafish_vejnar_giraldez_count_900_transcript_protein_coding_v12.csv.zst
Gene	All	RPKM: yeast+zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_all_all_v12.csv.zst
Gene	All	RPKM: yeast	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_all_yst_v12.csv.zst
Gene	All	RPKM: zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_all_zbf_v12.csv.zst
Gene	Protein-coding	RPKM: yeast+zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_protein_coding_all_v12.csv.zst
Gene	Protein-coding	RPKM: yeast	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_protein_coding_yst_v12.csv.zst
Gene	Protein-coding	RPKM: zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_gene_protein_coding_zbf_v12.csv.zst
Transcript	All	RPKM: yeast+zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_all_all_v12.csv.zst
Transcript	All	RPKM: yeast	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_all_yst_v12.csv.zst
Transcript	All	RPKM: zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_all_zbf_v12.csv.zst
Transcript	Protein-coding	RPKM: yeast+zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_protein_coding_all_v12.csv.zst
Transcript	Protein-coding	RPKM: yeast	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_protein_coding_yst_v12.csv.zst
Transcript	Protein-coding	RPKM: zbf	Unique	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_1_transcript_protein_coding_zbf_v12.csv.zst
Gene	All	RPKM: yeast+zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_all_all_v12.csv.zst
Gene	All	RPKM: yeast	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_all_yst_v12.csv.zst
Gene	All	RPKM: zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_all_zbf_v12.csv.zst
Gene	Protein-coding	RPKM: yeast+zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_protein_coding_all_v12.csv.zst
Gene	Protein-coding	RPKM: yeast	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_protein_coding_yst_v12.csv.zst
Gene	Protein-coding	RPKM: zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_gene_protein_coding_zbf_v12.csv.zst
Transcript	All	RPKM: yeast+zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_all_all_v12.csv.zst
Transcript	All	RPKM: yeast	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_all_yst_v12.csv.zst
Transcript	All	RPKM: zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_all_zbf_v12.csv.zst
Transcript	Protein-coding	RPKM: yeast+zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_protein_coding_all_v12.csv.zst
Transcript	Protein-coding	RPKM: yeast	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_protein_coding_yst_v12.csv.zst
Transcript	Protein-coding	RPKM: zbf	Up to 2 matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_2_transcript_protein_coding_zbf_v12.csv.zst
Gene	All	RPKM: yeast+zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_all_all_v12.csv.zst
Gene	All	RPKM: yeast	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_all_yst_v12.csv.zst
Gene	All	RPKM: zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_all_zbf_v12.csv.zst
Gene	Protein-coding	RPKM: yeast+zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_protein_coding_all_v12.csv.zst
Gene	Protein-coding	RPKM: yeast	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_protein_coding_yst_v12.csv.zst
Gene	Protein-coding	RPKM: zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_gene_protein_coding_zbf_v12.csv.zst
Transcript	All	RPKM: yeast+zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_all_all_v12.csv.zst
Transcript	All	RPKM: yeast	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_all_yst_v12.csv.zst
Transcript	All	RPKM: zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_all_zbf_v12.csv.zst
Transcript	Protein-coding	RPKM: yeast+zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_protein_coding_all_v12.csv.zst
Transcript	Protein-coding	RPKM: yeast	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_protein_coding_yst_v12.csv.zst
Transcript	Protein-coding	RPKM: zbf	All matches	dev_timecourse_zebrafish_vejnar_giraldez_rpkm_900_transcript_protein_coding_zbf_v12.csv.zst

Trackhub

Development timecourse genome trackhub

iCLIP

Trackhub

iCLIP genome trackhub

Source code

• FIRE
• Random Forest. Tutorial is included within archive.