Beaudoin et al. Nature Structural Molecular Biology. 2018

For questions, please contact Jean-Denis.Beaudoin@yale.edu or Antonio.Giraldez@yale.edu

Citation

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

mRNA structure dynamics identifies embryonic gene regulatory programs.
Jean-Denis Beaudoin, Eva Maria Novoa, Charles E Vejnar, Valeria Yartseva, Carter Takacs, Manolis Kellis and Antonio J Giraldez.
Nat Structure Mol Biol. 2018

About the datasets

Reference genome and Ensembl annotation

All datasets used in Beaudoin et al. 2018 have been generated using the Zv9 reference genome and Ensembl 78 annotation.

For convenience, we are also providing all datasets using the GRCz11 and Ensembl 92 annotation.

Types of Dataset

How to decompress the samples

Replicates

Datasets using the GRCz11 genome and Ensembl 92 annotation for all annotated transcripts

RNA-seq and Ribo-seq tables

Label Stage Condition File
RNA-seq time course polyA+ selected or ribo-0 purified coming soon
Ribo-seq 64-cell (2 hpf) untreated or pateamine A (patA) treated coming soon

DMS-seq accessibility datasets (processed data, only transcript with >= 5 reads in average per A and C bases for all transcripts (all gene biotypes))

Label Experiment Stage Condition File
WT_64c_b1 time course 64-cell (2 hpf) polyA+ selected WT_64c_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_b2 time course 64-cell (2 hpf) polyA+ selected WT_64c_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c time course 64-cell (2 hpf) polyA+ selected WT_64c_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b1 time course sphere (4 hpf) polyA+ selected WT_sphere_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b2 time course sphere (4 hpf) polyA+ selected WT_sphere_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_sphere time course sphere (4 hpf) polyA+ selected WT_sphere_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_shield_b1 time course shield (6 hpf) polyA+ selected WT_shield_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_shield_b2 time course shield (6 hpf) polyA+ selected WT_shield_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_shield time course shield (6 hpf) polyA+ selected WT_shield_accessibility_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b1 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b2 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
IVT_64c in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_accessibility_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B1_accessibility_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B2_accessibility_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_accessibility_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b1 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b2 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
CHX_64c translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_accessibility_profiles_78_protein_coding_genes.csv.zst

DMS-seq raw count datasets for all transcripts (all gene biotypes)

Label Experiment Stage Condition File
WT_64c_b1 time course 64-cell (2 hpf) polyA+ selected WT_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_b2 time course 64-cell (2 hpf) polyA+ selected WT_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c time course 64-cell (2 hpf) polyA+ selected WT_64c_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b1 time course sphere (4 hpf) polyA+ selected WT_sphere_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b2 time course sphere (4 hpf) polyA+ selected WT_sphere_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_sphere time course sphere (4 hpf) polyA+ selected WT_sphere_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_shield_b1 time course shield (6 hpf) polyA+ selected WT_shield_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_shield_b2 time course shield (6 hpf) polyA+ selected WT_shield_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_shield time course shield (6 hpf) polyA+ selected WT_shield_raw_count_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b1 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b2 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
IVT_64c in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_raw_count_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B1_raw_count_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B2_raw_count_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_raw_count_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b1 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b2 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
CHX_64c translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_raw_count_profiles_78_protein_coding_genes.csv.zst

Datasets using the Zv9 genome and Ensembl 78 annotation for protein coding genes only

RNA-seq and Ribo-seq tables

Label Stage Condition File
RNA-seq time course polyA+ selected or ribo-0 purified RNAseq_table_78_protein_coding_genes.csv
Ribo-seq 64-cell (2 hpf) untreated or pateamine A (patA) treated Ribo_seq_table_78_protein_coding_genes.csv

DMS-seq accessibility datasets (processed data, only transcript with >= 5 reads in average per A and C bases for transcripts with gene biotype = protein coding)

Label Experiment Stage Condition File
WT_64c_b1 time course 64-cell (2 hpf) polyA+ selected WT_64c_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_b2 time course 64-cell (2 hpf) polyA+ selected WT_64c_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c time course 64-cell (2 hpf) polyA+ selected WT_64c_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b1 time course sphere (4 hpf) polyA+ selected WT_sphere_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b2 time course sphere (4 hpf) polyA+ selected WT_sphere_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_sphere time course sphere (4 hpf) polyA+ selected WT_sphere_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_shield_b1 time course shield (6 hpf) polyA+ selected WT_shield_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_shield_b2 time course shield (6 hpf) polyA+ selected WT_shield_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_shield time course shield (6 hpf) polyA+ selected WT_shield_accessibility_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b1 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b2 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
IVT_64c in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B1_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B2_accessibility_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_accessibility_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B1_accessibility_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B2_accessibility_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_accessibility_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b1 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b1_accessibility_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b2 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b2_accessibility_profiles_78_protein_coding_genes.csv.zst
CHX_64c translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_accessibility_profiles_78_protein_coding_genes.csv.zst

DMS-seq raw count datasets for transcripts with gene biotype = protein coding

Label Experiment Stage Condition File
WT_64c_b1 time course 64-cell (2 hpf) polyA+ selected WT_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_b2 time course 64-cell (2 hpf) polyA+ selected WT_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c time course 64-cell (2 hpf) polyA+ selected WT_64c_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b1 time course sphere (4 hpf) polyA+ selected WT_sphere_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_sphere_b2 time course sphere (4 hpf) polyA+ selected WT_sphere_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_sphere time course sphere (4 hpf) polyA+ selected WT_sphere_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_shield_b1 time course shield (6 hpf) polyA+ selected WT_shield_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_shield_b2 time course shield (6 hpf) polyA+ selected WT_shield_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_shield time course shield (6 hpf) polyA+ selected WT_shield_raw_count_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b1 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
IVT_64c_b2 in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
IVT_64c in vitro 64-cell (2 hpf) polyA+ selected IVT_64c_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B1_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_B2_raw_count_profiles_78_protein_coding_genes.csv.zst
WT_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, untreated WT_64c_DMS_raw_count_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B1 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B1_raw_count_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS_B2 translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_B2_raw_count_profiles_78_protein_coding_genes.csv.zst
PatA_64c_DMS translation inhibitors 64-cell (2 hpf) polyA+ selected, pateamine A treated PatA_64c_DMS_raw_count_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b1 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.zst
CHX_64c_b2 translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.zst
CHX_64c translation inhibitors 64-cell (2 hpf) polyA+ selected, cycloheximide treated CHX_64c_raw_count_profiles_78_protein_coding_genes.csv.zst