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

• RNA-seq. RNA-seq time course experiments for polyA selected transcripts at 2, 4 and 6 hpf in WT and alpha-amanitin (inhibitor of RNA pol II) conditions and RNA-seq time course experiments with ribo-0 selection at 2, 3 and 6 hpf in WT and TinyLNA430 (inhibitor of miR-430) conditions
• Ribo-seq. Ribosome profiling RPKMs and translation efficiencies at 2 hpf in WT and pateamine A (inhibitor of eIF4A and translation initiation) conditions and matching RNA-seq experiment with ribo-0 selection
• DMS-seq accessibility profiles. Table containing transcript UTRs and CDS annotation, transcript sequence, per-transcript DMS-seq raw counts and processed DMS-seq accessibilities for transcripts (protein-coding genes) with >=5 read in average per A and C bases.
• DMS-seq count profiles. Table containing per-transcript DMS-seq raw counts for ALL transcripts.

How to decompress the files

• All files were compressed using XZ. You can obtain a copy at https://tukaani.org/xz if your system doesn’t provide it already.
• To decompress the files xz -d file.csv.xz.
• The Python Data Analysis Library pandas decompresses XZ files transparently.

Replicates

• Labels with B1 (or b1) and B2 (or b2) correspond to biological replicate 1 and 2.
• Labels without B1 (or b1) or B2 (or b2) correspond to sample where reads from both replicates were merged prior to the analysis.

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

RNA-seq and Ribo-seq tables

Label	Stage	Condition
RNA-seq	time course	polyA+ selected or ribo-0 purified	mRNA-seq embryonic development timecourse
Ribo-seq	64-cell (2 hpf)	untreated (column rpf_2h_ctrl_pata) or pateamine A (patA; column rpf_2h_pata) treated (mrna_2h_ctrl_pata and mrna_2h_pata columns for mRNA)	Ribosome profiling

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_92_all_genes.csv.xz
WT_64c_b2	time course	64-cell (2 hpf)	polyA+ selected	WT_64c_b2_accessibility_profiles_92_all_genes.csv.xz
WT_64c	time course	64-cell (2 hpf)	polyA+ selected	WT_64c_accessibility_profiles_92_all_genes.csv.xz
WT_sphere_b1	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_b1_accessibility_profiles_92_all_genes.csv.xz
WT_sphere_b2	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_b2_accessibility_profiles_92_all_genes.csv.xz
WT_sphere	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_accessibility_profiles_92_all_genes.csv.xz
WT_shield_b1	time course	shield (6 hpf)	polyA+ selected	WT_shield_b1_accessibility_profiles_92_all_genes.csv.xz
WT_shield_b2	time course	shield (6 hpf)	polyA+ selected	WT_shield_b2_accessibility_profiles_92_all_genes.csv.xz
WT_shield	time course	shield (6 hpf)	polyA+ selected	WT_shield_accessibility_profiles_92_all_genes.csv.xz
IVT_64c_b1	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_b1_accessibility_profiles_92_all_genes.csv.xz
IVT_64c_b2	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_b2_accessibility_profiles_92_all_genes.csv.xz
IVT_64c	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_accessibility_profiles_92_all_genes.csv.xz
WT_64c_DMS_B1	translation inhibitors	64-cell (2 hpf)	polyA+ selected, untreated	WT_64c_DMS_B1_accessibility_profiles_92_all_genes.csv.xz
WT_64c_DMS_B2	translation inhibitors	64-cell (2 hpf)	polyA+ selected, untreated	WT_64c_DMS_B2_accessibility_profiles_92_all_genes.csv.xz
WT_64c_DMS	translation inhibitors	64-cell (2 hpf)	polyA+ selected, untreated	WT_64c_DMS_accessibility_profiles_92_all_genes.csv.xz
PatA_64c_DMS_B1	translation inhibitors	64-cell (2 hpf)	polyA+ selected, pateamine A treated	PatA_64c_DMS_B1_accessibility_profiles_92_all_genes.csv.xz
PatA_64c_DMS_B2	translation inhibitors	64-cell (2 hpf)	polyA+ selected, pateamine A treated	PatA_64c_DMS_B2_accessibility_profiles_92_all_genes.csv.xz
PatA_64c_DMS	translation inhibitors	64-cell (2 hpf)	polyA+ selected, pateamine A treated	PatA_64c_DMS_accessibility_profiles_92_all_genes.csv.xz
CHX_64c_b1	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_b1_accessibility_profiles_92_all_genes.csv.xz
CHX_64c_b2	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_b2_accessibility_profiles_92_all_genes.csv.xz
CHX_64c	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_accessibility_profiles_92_all_genes.csv.xz

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_92_all_genes.csv.xz
WT_64c_b2	time course	64-cell (2 hpf)	polyA+ selected	WT_64c_b2_raw_count_profiles_92_all_genes.csv.xz
WT_64c	time course	64-cell (2 hpf)	polyA+ selected	WT_64c_raw_count_profiles_92_all_genes.csv.xz
WT_sphere_b1	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_b1_raw_count_profiles_92_all_genes.csv.xz
WT_sphere_b2	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_b2_raw_count_profiles_92_all_genes.csv.xz
WT_sphere	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_raw_count_profiles_92_all_genes.csv.xz
WT_shield_b1	time course	shield (6 hpf)	polyA+ selected	WT_shield_b1_raw_count_profiles_92_all_genes.csv.xz
WT_shield_b2	time course	shield (6 hpf)	polyA+ selected	WT_shield_b2_raw_count_profiles_92_all_genes.csv.xz
WT_shield	time course	shield (6 hpf)	polyA+ selected	WT_shield_raw_count_profiles_92_all_genes.csv.xz
IVT_64c_b1	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_b1_raw_count_profiles_92_all_genes.csv.xz
IVT_64c_b2	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_b2_raw_count_profiles_92_all_genes.csv.xz
IVT_64c	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_raw_count_profiles_92_all_genes.csv.xz
WT_64c_DMS_B1	translation inhibitors	64-cell (2 hpf)	polyA+ selected, untreated	WT_64c_DMS_B1_raw_count_profiles_92_all_genes.csv.xz
WT_64c_DMS_B2	translation inhibitors	64-cell (2 hpf)	polyA+ selected, untreated	WT_64c_DMS_B2_raw_count_profiles_92_all_genes.csv.xz
WT_64c_DMS	translation inhibitors	64-cell (2 hpf)	polyA+ selected, untreated	WT_64c_DMS_raw_count_profiles_92_all_genes.csv.xz
PatA_64c_DMS_B1	translation inhibitors	64-cell (2 hpf)	polyA+ selected, pateamine A treated	PatA_64c_DMS_B1_raw_count_profiles_92_all_genes.csv.xz
PatA_64c_DMS_B2	translation inhibitors	64-cell (2 hpf)	polyA+ selected, pateamine A treated	PatA_64c_DMS_B2_raw_count_profiles_92_all_genes.csv.xz
PatA_64c_DMS	translation inhibitors	64-cell (2 hpf)	polyA+ selected, pateamine A treated	PatA_64c_DMS_raw_count_profiles_92_all_genes.csv.xz
CHX_64c_b1	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_b1_raw_count_profiles_92_all_genes.csv.xz
CHX_64c_b2	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_b2_raw_count_profiles_92_all_genes.csv.xz
CHX_64c	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_raw_count_profiles_92_all_genes.csv.xz

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

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.xz
WT_64c_b2	time course	64-cell (2 hpf)	polyA+ selected	WT_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.xz
WT_64c	time course	64-cell (2 hpf)	polyA+ selected	WT_64c_raw_count_profiles_78_protein_coding_genes.csv.xz
WT_sphere_b1	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_b1_raw_count_profiles_78_protein_coding_genes.csv.xz
WT_sphere_b2	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_b2_raw_count_profiles_78_protein_coding_genes.csv.xz
WT_sphere	time course	sphere (4 hpf)	polyA+ selected	WT_sphere_raw_count_profiles_78_protein_coding_genes.csv.xz
WT_shield_b1	time course	shield (6 hpf)	polyA+ selected	WT_shield_b1_raw_count_profiles_78_protein_coding_genes.csv.xz
WT_shield_b2	time course	shield (6 hpf)	polyA+ selected	WT_shield_b2_raw_count_profiles_78_protein_coding_genes.csv.xz
WT_shield	time course	shield (6 hpf)	polyA+ selected	WT_shield_raw_count_profiles_78_protein_coding_genes.csv.xz
IVT_64c_b1	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.xz
IVT_64c_b2	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.xz
IVT_64c	in vitro	64-cell (2 hpf)	polyA+ selected	IVT_64c_raw_count_profiles_78_protein_coding_genes.csv.xz
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.xz
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.xz
WT_64c_DMS	translation inhibitors	64-cell (2 hpf)	polyA+ selected, untreated	WT_64c_DMS_raw_count_profiles_78_protein_coding_genes.csv.xz
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.xz
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.xz
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.xz
CHX_64c_b1	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_b1_raw_count_profiles_78_protein_coding_genes.csv.xz
CHX_64c_b2	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_b2_raw_count_profiles_78_protein_coding_genes.csv.xz
CHX_64c	translation inhibitors	64-cell (2 hpf)	polyA+ selected, cycloheximide treated	CHX_64c_raw_count_profiles_78_protein_coding_genes.csv.xz