title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL02F (DNBSEQ-T7)

description:
ZB4SL02F_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL09H (DNBSEQ-T7)

status: Public on Apr 14 2024

type: SRA

city: beijing

first: Keyong

last: Sun

address: Hai Dian street

department: School of Medicine

country: China

institute: tsinghua university

description:
ZB4SL09H_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

library_source: genomic

data_processing:
Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new Read1 file. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new Read2 file. Round 1, round2 and round3 barcodes are extracted from Read1 and Read2 Fastq files, and are merged and were added into the header of new Read1 and Read2 files. New Read1 and Read2 files were aligned to the reference zebrafish GRCz11 genome assemblyby BWA. The scATAC-seq fragment files were created by sinto (https://timoast.github.io/sinto/index.html) according to standard procedure. Barcodes in fragment file of each sublibrary were tagged with Round4 barcodes (PCR wells), then all sublibrary fragment files were merged into one big fragment file, which were further split into stage-specific fragment files based on Round1 barcodes. For the bulk ATAC-seq data from zebrafish embryos, reads were trimmed with to remove the Nextera sequencing adaptors by trim_galore. The trimmed reads were mapped to the reference zebrafish (GRCz11) genome using BWA. Reads with mapping quality less than 30 and duplication were removed by samtools. BigWig files were generated by bamCoverage.  Fastq files of 10x Genomics scATAC-seq were processed Cell Ranger ATAC Pipeline (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac, v.1.2.0).
Assembly: GRCz11
Supplementary files format and content: bed files, the fragment file of SPATAC-seq, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of 10x Genomics scATAC-seq, the information of each unique fragment within each sample, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of bulk ATAC-seq, the information of each unique fragment, including the chromsome number, start site, end site
Supplementary files format and content: excel file, cell metadata information for the atlas of zebrafish development, including cell types, coordinate and quality metric of each cell
Supplementary files format and content: bigWig file, genome-wide signal for 604 cell types of scATAC-seq datasets
Supplementary files format and content: bigWig file, genome-wide signal for bulk ATAC-seq of zebrafish embryos

molecule: genomic DNA

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
Embryo nuclei were extracted via previously described methods (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019) with some modifications. Briefly, frozen embryos were transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 1 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 200 μl NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB.
Bulk ATAC-seq, 10x Genomics scATAC-seq, and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details.

tag: tissue

value: zebrafish embryos


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL10B (DNBSEQ-T7)

description:
ZB4SL10B_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL02H (DNBSEQ-T7)

description:
ZB4SL02H_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL09A (DNBSEQ-T7)

description:
ZB4SL09A_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL02E (DNBSEQ-T7)

description:
ZB4SL02E_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL02C (DNBSEQ-T7)

description:
ZB4SL02C_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL02B (DNBSEQ-T7)

description:
ZB4SL02B_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL02A (DNBSEQ-T7)

description:
ZB4SL02A_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL10C (DNBSEQ-T7)

description:
ZB4SL10C_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01B (DNBSEQ-T7)

description:
ZB4SL01B_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL09G (DNBSEQ-T7)

description:
ZB4SL09G_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17H (DNBSEQ-T7)

description:
ZB3SL17H_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01D (DNBSEQ-T7)

description:
ZB4SL01D_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01C (DNBSEQ-T7)

description:
ZB4SL01C_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17G (DNBSEQ-T7)

description:
ZB3SL17G_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17F (DNBSEQ-T7)

description:
ZB3SL17F_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17E (DNBSEQ-T7)

description:
ZB3SL17E_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17B (DNBSEQ-T7)

description:
ZB3SL17B_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17A (DNBSEQ-T7)

description:
ZB3SL17A_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17C (DNBSEQ-T7)

description:
ZB3SL17C_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL17D (DNBSEQ-T7)

description:
ZB3SL17D_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10H (DNBSEQ-T7)

description:
ZB3SL10H_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10F (DNBSEQ-T7)

description:
ZB3SL10F_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10G (DNBSEQ-T7)

description:
ZB3SL10G_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL02D (DNBSEQ-T7)

description:
ZB4SL02D_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10C (DNBSEQ-T7)

description:
ZB3SL10C_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10D (DNBSEQ-T7)

description:
ZB3SL10D_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10B (DNBSEQ-T7)

description:
ZB3SL10B_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10A (DNBSEQ-T7)

description:
ZB3SL10A_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01H (DNBSEQ-T7)

description:
ZB4SL01H_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01F (DNBSEQ-T7)

description:
ZB4SL01F_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01G (DNBSEQ-T7)

description:
ZB4SL01G_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01E (DNBSEQ-T7)

description:
ZB4SL01E_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09H (DNBSEQ-T7)

description:
ZB3SL09H_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB4SL01A (DNBSEQ-T7)

description:
ZB4SL01A_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09F (DNBSEQ-T7)

description:
ZB3SL09F_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09E (DNBSEQ-T7)

description:
ZB3SL09E_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09C (DNBSEQ-T7)

description:
ZB3SL09C_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09D (DNBSEQ-T7)

description:
ZB3SL09D_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09B (DNBSEQ-T7)

description:
ZB3SL09B_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09A (DNBSEQ-T7)

description:
ZB3SL09A_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL10E (DNBSEQ-T7)

description:
ZB3SL10E_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07G (DNBSEQ-T7)

description:
ZB2SL07G_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07D (DNBSEQ-T7)

description:
ZB2SL07D_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07A (DNBSEQ-T7)

description:
ZB2SL07A_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07C (DNBSEQ-T7)

description:
ZB2SL07C_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06H (DNBSEQ-T7)

description:
ZB2SL06H_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07B (DNBSEQ-T7)

description:
ZB2SL07B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06G (DNBSEQ-T7)

description:
ZB2SL06G_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06F (DNBSEQ-T7)

description:
ZB2SL06F_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06E (DNBSEQ-T7)

description:
ZB2SL06E_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06D (DNBSEQ-T7)

description:
ZB2SL06D_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06A (DNBSEQ-T7)

description:
ZB2SL06A_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06C (DNBSEQ-T7)

description:
ZB2SL06C_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL06B (DNBSEQ-T7)

description:
ZB2SL06B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05H (DNBSEQ-T7)

description:
ZB2SL05H_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB3SL09G (DNBSEQ-T7)

description:
ZB3SL09G_SPATACseq_Batch3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05E (DNBSEQ-T7)

description:
ZB2SL05E_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05D (DNBSEQ-T7)

description:
ZB2SL05D_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05F (DNBSEQ-T7)

description:
ZB2SL05F_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05G (DNBSEQ-T7)

description:
ZB2SL05G_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05B (DNBSEQ-T7)

description:
ZB2SL05B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05C (DNBSEQ-T7)

description:
ZB2SL05C_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL05A (DNBSEQ-T7)

description:
ZB2SL05A_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07F (DNBSEQ-T7)

description:
ZB2SL07F_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04H (DNBSEQ-T7)

description:
ZB2SL04H_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04F (DNBSEQ-T7)

description:
ZB2SL04F_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07E (DNBSEQ-T7)

description:
ZB2SL07E_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04E (DNBSEQ-T7)

description:
ZB2SL04E_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04C (DNBSEQ-T7)

description:
ZB2SL04C_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04B (DNBSEQ-T7)

description:
ZB2SL04B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04A (DNBSEQ-T7)

description:
ZB2SL04A_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04D (DNBSEQ-T7)

description:
ZB2SL04D_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03E (DNBSEQ-T7)

description:
ZB2SL03E_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03H (DNBSEQ-T7)

description:
ZB2SL03H_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03G (DNBSEQ-T7)

description:
ZB2SL03G_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL04G (DNBSEQ-T7)

description:
ZB2SL04G_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03B (DNBSEQ-T7)

description:
ZB2SL03B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02H (DNBSEQ-T7)

description:
ZB2SL02H_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02G (DNBSEQ-T7)

description:
ZB2SL02G_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03C (DNBSEQ-T7)

description:
ZB2SL03C_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03A (DNBSEQ-T7)

description:
ZB2SL03A_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02F (DNBSEQ-T7)

description:
ZB2SL02F_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02D (DNBSEQ-T7)

description:
ZB2SL02D_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02E (DNBSEQ-T7)

description:
ZB2SL02E_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02C (DNBSEQ-T7)

description:
ZB2SL02C_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03D (DNBSEQ-T7)

description:
ZB2SL03D_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02B (DNBSEQ-T7)

description:
ZB2SL02B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL02A (DNBSEQ-T7)

description:
ZB2SL02A_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL07H (DNBSEQ-T7)

description:
ZB2SL07H_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01H (DNBSEQ-T7)

description:
ZB2SL01H_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01E (DNBSEQ-T7)

description:
ZB2SL01E_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01F (DNBSEQ-T7)

description:
ZB2SL01F_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01G (DNBSEQ-T7)

description:
ZB2SL01G_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01D (DNBSEQ-T7)

description:
ZB2SL01D_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 72hpf batch1_replicate1 (MGISEQ-2000RS)

description:
72hpf_10x_batch1_replicate1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 72hpf batch1_replicate2 (MGISEQ-2000RS)

description:
72hpf_10x_batch1_replicate2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01C (DNBSEQ-T7)

description:
ZB2SL01C_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL03F (DNBSEQ-T7)

description:
ZB2SL03F_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01B (DNBSEQ-T7)

description:
ZB2SL01B_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 48hpf batch1_replicate2 (MGISEQ-2000RS)

description:
48hpf_10x_batch1_replicate2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 24hpf batch2_replicate5 (MGISEQ-2000RS)

description:
24hpf_10x_batch2_replicate5
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 48hpf batch1_replicate1 (MGISEQ-2000RS)

description:
48hpf_10x_batch1_replicate1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 24hpf batch2_replicate4 (MGISEQ-2000RS)

description:
24hpf_10x_batch2_replicate4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZB2SL01A (DNBSEQ-T7)

description:
ZB2SL01A_SPATACseq_Batch2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSR8 (DNBSEQ-T7)

description:
ZSR8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSR7 (DNBSEQ-T7)

description:
ZSR7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSR6 (DNBSEQ-T7)

description:
ZSR6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 10x Genomics scATAC-seq with zebrafish embryogenesis in 24hpf batch1_replicate1 (MGISEQ-2000RS)

description:
24hpf_10x_batch1_replicate1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSR4 (DNBSEQ-T7)

description:
ZSR4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSR3 (DNBSEQ-T7)

description:
ZSR3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSR2 (DNBSEQ-T7)

description:
ZSR2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: BW25113 mhpR::km2

city: Martinsired

first: Kilian

last: Schumacher

address: Großhaderner Straße 2-4

country: Germany

institute: LMU Munich

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v20.0.4
Adapter sequence "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" was trimmed using the 'trim-reads' command
The trimmed reads were checked for quality and mapped to the E. coli reference genome using the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1.
Reads mapping in CDS were counted, normalized (rpkm), and transformed (log2). Genes with rpkm values >5 in at least one replicate were considered for analysis.Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 2.0 and a FDR adjusted p-value < 0.01 were considered to be differentially expressed.
Assembly: NC_000913.3, CP009273.1
Supplementary files format and content: Excel file containing rpkm values and edgeR (exact mode) analysis

molecule: total RNA

organism: Escherichia coli BW25113

source_name: bacterial cell

growth_protocol: Cells were inoculated to a starting OD600 of 0.05 from overnight cultures and aerobically grown to exponential phase in 200 ml of unbuffered LB media (pH 7.6) in 1 liter glas flasks.

extract_protocol:
RNA was harvested using the miRNeasy Mini Kit (QIAGEN) in combination with the RNase-Free DNase Set (QIAGEN) following manufacturer's protocols. Ribosomal RNA depletion was performed using the NEBNext rRNA Depletion Kit for bacteria (NEB) following manufacturer's protocols. Integrity of RNA samples was evaluated by using the RNA 6000 Nano Kit (Agilent).
cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocols. cDNA library quality was assessed by using a High Sensitivity DNA Kit (Agilent).

treatment_protocol: Once OD600 = 0.5 was reached, 5M HCl was added to the cultures to adjust the pH to 5.8. After 15, 5M HCl was added again to adjust the pH to 4.4 and cells were incubated for another 15 min.

tag: strain

tag: cell type

value: bacterial cell

tag: genotype

tag: treatment


city: Würzburg

first: Bernardo

last: Papini Gabiatti

address: Sanderring 2

institute: University of Würzburg

description:
polyA total RNA in nutritional stress replicate 3
Sample 62

data_processing:
Sequencing reads were mapped against the T. cruzi Dm28c genome with STAR v2.7.10a with default parameters
Gene counts were obtained for uniquely mapped reads with featureCounts v2.0.1 from the Subread package
To identify mRNAs enriched in the immunoprecipitation eluate relative to the control, the differential expression analysis DESeq2 v1.34.0was used
Assembly: Ensembl Assembly ASM317710v1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (numbered from 1 to 66 according to library names)

molecule: polyA RNA

organism: Trypanosoma cruzi

source_name: whole organism

growth_protocol: Trypanosoma cruzi Dm28c cells were mantained in LIT supplemented in 10% FCS and antibiotics at 28C 5% CO2

extract_protocol:
RNA was extracted from the beads (RIP-seq), directly from the cells (RNA-seq) or from the polysomal fraction (Ribo-seq)
RNA libraries were prepared with TruSeq Stranded mRNA kit following manunfacter's protocols

treatment_protocol:
Nutritional stress was induced by incubation in TAU media for 2 hours
Metacyclic trypomastigotes were differentiated by incubation in TAU for 2 hours, in TAU3AAG for 4 days and subsequently purified by anion exchange chromatography

value: whole organism

value: WT

value: cells (epimastigote stage) in nutritional stress for two hours


description:
Ribo-seq in nutritional stress replicate 2
Sample 64

library_source: other

data_processing:
Sequencing reads were mapped against the T. cruzi Dm28c genome with STAR v2.7.10a with default parameters
Gene counts were obtained for uniquely mapped reads with featureCounts v2.0.1 from the Subread package
To identify mRNAs enriched in the immunoprecipitation eluate relative to the control, the differential expression analysis DESeq2 v1.34.0was used
Assembly: Ensembl Assembly ASM317710v1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (numbered from 1 to 66 according to library names)
Library strategy: Ribo-seq

molecule: other


description:
Ribo-seq in nutritional stress replicate 1
Sample 63


description:
Ribo-seq in nutritional stress replicate 3
Sample 65


description:
polyA total RNA in nutritional stress replicate 2
Sample 61


description:
polyA total RNA in nutritional stress replicate 1
Sample 60

value: cells (epimastigote stage) in exponential growth conditions


title: SPATAC-seq with zebrafish embryogenesis well-ZSR1 (DNBSEQ-T7)

description:
ZSR1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: BW25113 mhpR::km1


description:
Ribo-seq in exponential growing cells replicate 2
Sample 58


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ8 (DNBSEQ-T7)

description:
ZSQ8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
Ribo-seq in exponential growing cells replicate 3
Sample 59


description:
Ribo-seq in exponential growing cells replicate 1
Sample 57


description:
polyA total RNA in exponential growing cells replicate 3
Sample 56


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 24hpf batch2_replicate3 (MGISEQ-2000RS)

description:
24hpf_10x_batch2_replicate3
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: BW25113 WT2

value: Wildtype


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ6 (DNBSEQ-T7)

description:
ZSQ6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: BW25113 WT3


description:
polyA total RNA in exponential growing cells replicate 2
Sample 55


title: BW25113 WT1


title: BW25113 mhpR::km3


title: SPATAC-seq with zebrafish embryogenesis well-ZSR5 (DNBSEQ-T7)

description:
ZSR5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
polyA total RNA in exponential growing cells replicate 1
Sample 54

value: cells fully differentiated to metacyclic trypomastigotes


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ5 (DNBSEQ-T7)

description:
ZSQ5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: eIF4E4 immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 3 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in fully differentiated metacyclic trypomastigotes replicate 3 (extra experiment; experiment number 2 in main text)
Sample 53


title: 10x Genomics scATAC-seq with zebrafish embryogenesis  in 24hpf batch1_replicate2 (MGISEQ-2000RS)

description:
24hpf_10x_batch1_replicate2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 996_Rag2_3DP1

city: New Orleans

first: Jay

last: Kolls

state: Louisiana

address: 333 S. Liberty St

department: Medicine

country: USA

institute: Tulane University

data_processing:
Fastq data were uploaded to Banana Slug Analytics Platform (Slug Genomics, 203  UV Santa Cruz) for trimming.
Trimmed sequence reads were mapped to mm10 using Banana Slug Analytics Platform (Slug Genomics, 203  UV Santa Cruz)
Cuffdif were used for differential expression analysis (Slug Genomics, 203  UV Santa Cruz)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample

organism: Mus musculus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Sample Preparation kit following manufacturer's protocols.


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ7 (DNBSEQ-T7)

description:
ZSQ7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: eIF4E4 immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 2 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in fully differentiated metacyclic trypomastigotes replicate 2 (extra experiment; experiment number 2 in main text)
Sample 52


title: 995_Rag2_3DP1


title: eIF4E4 immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 1 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in fully differentiated metacyclic trypomastigotes replicate 1 (extra experiment; experiment number 2 in main text)
Sample 51


title: IgG (negative control) immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 3 (experiment 2)

description:
IgG (negative control) immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 3 (extra experiment; experiment number 2 in main text)
Sample 50


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ3 (DNBSEQ-T7)

description:
ZSQ3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: IgG (negative control) immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 1 (experiment 2)

description:
IgG (negative control) immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 1 (extra experiment; experiment number 2 in main text)
Sample 48


title: eIF4E4 immunoprecipitation in nutritional stress replicate 3 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 3 (extra experiment; experiment number 2 in main text)
Sample 47


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ4 (DNBSEQ-T7)

description:
ZSQ4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: IgG (negative control) immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 2 (experiment 2)

description:
IgG (negative control) immunoprecipitation in fully differentiated metacyclic trypomastigotes replicate 2 (extra experiment; experiment number 2 in main text)
Sample 49


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ2 (DNBSEQ-T7)

description:
ZSQ2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 994_Rag2_3DP1


title: eIF4E4 immunoprecipitation in nutritional stress replicate 2 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 2 (extra experiment; experiment number 2 in main text)
Sample 46


title: eIF4E4 immunoprecipitation in nutritional stress replicate 1 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 1 (extra experiment; experiment number 2 in main text)
Sample 45


title: 821_B6_3DP1


title: SPATAC-seq with zebrafish embryogenesis well-ZSQ1 (DNBSEQ-T7)

description:
ZSQ1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 820_B6_3DP1


title: SPATAC-seq with zebrafish embryogenesis well-ZSP8 (DNBSEQ-T7)

description:
ZSP8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: 819_B6_3DP1


title: IgG (negative control) immunoprecipitation in nutritional stress replicate 1 (experiment 2)

description:
IgG (negative control) immunoprecipitation in nutritional stress replicate 1 (extra experiment; experiment number 2 in main text)
Sample 42


title: eIF4E4 immunoprecipitation in exponential growth replicate 3 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 3 (extra experiment; experiment number 2 in main text)
Sample 41


title: IgG (negative control) immunoprecipitation in nutritional stress replicate 3 (experiment 2)

description:
IgG (negative control) immunoprecipitation in nutritional stress replicate 3 (extra experiment; experiment number 2 in main text)
Sample 44


title: SPATAC-seq with zebrafish embryogenesis well-ZSP7 (DNBSEQ-T7)

description:
ZSP7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: eIF4E4 immunoprecipitation in exponential growth replicate 2 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 2 (extra experiment; experiment number 2 in main text)
Sample 40


title: eIF4E4 immunoprecipitation in exponential growth replicate 1 (experiment 2)

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 1 (extra experiment; experiment number 2 in main text)
Sample 39


title: SPATAC-seq with zebrafish embryogenesis well-ZSP6 (DNBSEQ-T7)

description:
ZSP6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: IgG (negative control) immunoprecipitation in exponential growth replicate 2 (experiment 2)

description:
IgG (negative control) immunoprecipitation in exponential growth replicate 2 (extra experiment; experiment number 2 in main text)
Sample 38


title: SPATAC-seq with zebrafish embryogenesis well-ZSP5 (DNBSEQ-T7)

description:
ZSP5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: IgG (negative control) immunoprecipitation in exponential growth replicate 1 (experiment 2)

description:
IgG (negative control) immunoprecipitation in exponential growth replicate 1 (extra experiment; experiment number 2 in main text)
Sample 37


title: LSK cells, Flag-Enl-T1, TDI11055, p300, ChIP-seq

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
ChIP-seq and CUT&Tag samples were sequenced using Illumina NextSeq 2000.
Raw reads were mapped to the mouse reference genome (mm10) and transcriptome using Bowtie2 v 2.2.5 with default parameters.
Aligned BAM files were sorted using function samtools v 1.6. Secondary alignments, unmapped reads, and duplicate reads in the sorted bam files were filtered out using samtools v 1.6. The filtered and sorted bam files were then indexed using function indexBam from samtools v 1.6.
Peaks were called using MACS v 2.2.8, peaks were called at q ≤ 1E−2.
Filtered, sorted, indexed BAM files were converted to bigwig files using bamCoverage from deeptools v 3.5.2
Assembly: mm10
Supplementary files format and content: bigWig files are in an indexed binary format

source_name: Blood

growth_protocol: LSK, GMP, L-GMP, cKit+Mac1+ and cKit-Mac1+ cells were fresh sorted from bone marrow ofEnl-WT or T1 mice.

extract_protocol:
Lysates were clarified from nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq sample libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, #E7645L) following the manufacturer's instructions.  After adapter ligation, DNA was PCR amplified with Illumina primers for indicated cycles and the DNA size distribution was quantified on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504). Then samples were sequenced using Illumina NextSeq2000.
CUT&Tag sample libraries were prepared using the CUTANA™ CUT&Tag Kit (EpiCypher, #14-1102) following the manufacturer's instructions.  After getting the library, the DNA size distribution was quantified on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504). Then samples were sequenced using Illumina NextSeq2000.

treatment_protocol: invivotreatment ofEnl-WT or T1 mice with DMSO or TDI-11055 for 4 weeks

value: Blood

tag: cell line

value: LSK

value: hematopoietic stem cell


title: LSK cells, Flag-Enl-WT, DMSO, input, ChIP-seq

value: DMSO


description:
eIF4E4 immunoprecipitation (episomal using GFP antibodies) in nutritional stress replicate 1
Sample 34

value: episomal eIF4E4-GFP


description:
eIF4E4 immunoprecipitation (episomal using GFP antibodies) in nutritional stress replicate 2
Sample 35


description:
eIF4E4 immunoprecipitation (episomal using GFP antibodies) in nutritional stress replicate 3
Sample 36


title: LSK cells, Flag-Enl-T1-H116P, DMSO, p300, ChIP-seq


title: SPATAC-seq with zebrafish embryogenesis well-ZSP4 (DNBSEQ-T7)

description:
ZSP4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
eIF4E3 immunoprecipitation (episomal using GFP antibodies) in nutritional stress replicate 3
Sample 33

value: episomal eIF4E3-GFP


title: SPATAC-seq with zebrafish embryogenesis well-ZSP3 (DNBSEQ-T7)

description:
ZSP3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: LSK cells, Flag-Enl-T1, DMSO, p300, ChIP-seq


title: SPATAC-seq with zebrafish embryogenesis well-ZSP2 (DNBSEQ-T7)

description:
ZSP2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
GFP-FLAG (negative control) immunoprecipitation in nutritional stress replicate 3
Sample 30

value: episomal GFP-FLAG


description:
eIF4E3 immunoprecipitation (episomal using GFP antibodies) in nutritional stress replicate 2
Sample 32


title: LSK cells, Flag-Enl-T1, TDI11055, H3K27ac, CUT&Tag

data_processing:
ChIP-seq and CUT&Tag samples were sequenced using Illumina NextSeq 2000.
Raw reads were mapped to the mouse reference genome (mm10) and transcriptome using Bowtie2 v 2.2.5 with default parameters.
Aligned BAM files were sorted using function samtools v 1.6. Secondary alignments, unmapped reads, and duplicate reads in the sorted bam files were filtered out using samtools v 1.6. The filtered and sorted bam files were then indexed using function indexBam from samtools v 1.6.
Peaks were called using MACS v 2.2.8, peaks were called at q ≤ 1E−2.
Filtered, sorted, indexed BAM files were converted to bigwig files using bamCoverage from deeptools v 3.5.2
Assembly: mm10
Supplementary files format and content: bigWig files are in an indexed binary format
Library strategy: CUT&Tag


title: LSK cells, Flag-Enl-WT, DMSO, p300, ChIP-seq


description:
GFP-FLAG (negative control) immunoprecipitation in nutritional stress replicate 2
Sample 29


title: SPATAC-seq with zebrafish embryogenesis well-ZSP1 (DNBSEQ-T7)

description:
ZSP1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
eIF4E4 immunoprecipitation (episomal using GFP antibodies) in exponential growth replicate 3
Sample 27


title: IgG (negative control) immunoprecipitation in nutritional stress replicate 2 (experiment 2)

description:
IgG (negative control) immunoprecipitation in nutritional stress replicate 2 (extra experiment; experiment number 2 in main text)
Sample 43


description:
eIF4E3 immunoprecipitation (episomal using GFP antibodies) in nutritional stress replicate 1
Sample 31


title: SPATAC-seq with zebrafish embryogenesis well-ZSO8 (DNBSEQ-T7)

description:
ZSO8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
GFP-FLAG (negative control) immunoprecipitation in nutritional stress replicate 1
Sample 28


title: LSK cells, Flag-Enl-WT, DMSO, H3K27ac, CUT&Tag


description:
eIF4E3 immunoprecipitation (episomal using GFP antibodies) in exponential growth replicate 3
Sample 24


description:
eIF4E4 immunoprecipitation (episomal using GFP antibodies) in exponential growth replicate 2
Sample 26


title: LSK cells, Flag-Enl-T1, DMSO, H3K27ac, CUT&Tag


title: KLF5KO ES for differentiation

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

institute: Nankai University

library_source: transcriptomic single cell

data_processing:
Using cellranger to analyse fastq data
Assembly: mm10
Supplementary files format and content: Cellranger processed data

source_name: ES

extract_protocol:
Cells were wash twice with PBS containing 5% FBS. Then 10X Genomics platform was using to generate scRNA library
10X Genomics

value: ES

value: KLF5KO no 2i no lif


title: SPATAC-seq with zebrafish embryogenesis well-ZSO5 (DNBSEQ-T7)

description:
ZSO5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: LSK cells, Flag-Enl-T1-H116P, Flag, CUT&Tag


title: LSK cells, Flag-Enl-T1, Flag, CUT&Tag


title: SEKO ES for differentiation

value: SEKO no 2i no lif


title: SPATAC-seq with zebrafish embryogenesis well-ZSO6 (DNBSEQ-T7)

description:
ZSO6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSO4 (DNBSEQ-T7)

description:
ZSO4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
eIF4E3 immunoprecipitation (episomal using GFP antibodies) in exponential growth replicate 1
Sample 22

value: whole organism


title: LSK cells, Flag-Enl-T1-H116P, H3K27ac, CUT&Tag


title: SPATAC-seq with zebrafish embryogenesis well-ZSO3 (DNBSEQ-T7)

description:
ZSO3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: LSK cells, Flag-Enl-WT, Flag, CUT&Tag

value: WT


description:
GFP-FLAG (negative control) immunoprecipitation in exponential growth replicate 3
Sample 21


description:
eIF4E4 immunoprecipitation (episomal using GFP antibodies) in exponential growth replicate 1
Sample 25


title: LSK cells, Flag-Enl-T1, H3K27ac, CUT&Tag


description:
GFP-FLAG (negative control) immunoprecipitation in exponential growth replicate 2
Sample 20


title: LSK cells, Flag-Enl-WT, H3K27ac, CUT&Tag


title: SPATAC-seq with zebrafish embryogenesis well-ZSO7 (DNBSEQ-T7)

description:
ZSO7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
GFP-FLAG (negative control) immunoprecipitation in exponential growth replicate 1
Sample 19


title: SPATAC-seq with zebrafish embryogenesis well-ZSO1 (DNBSEQ-T7)

description:
ZSO1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: APAP_72h_Hep

city: Kansas City

first: David

middle: S

last: Umbaugh

email: dumbaug@gmail.com, hjaeschke@kumc.edu

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
Data was analyzed using the 10x Genomics Chromium Single cell software suite
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (GRCm38: refdata-cellranger-GRCm38-3.0.0) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated raw feature-barcode matrix file

source_name: liver

extract_protocol:
Single cell suspension was generated using a collagenase perfusion method. Cell viability and concentration were measured by Countess II FL Automated cell counter. Hepatocytes or NPCs were separated using percoll gradient in combination with centrifugation.
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).
scRNA-seq 10x Genomics

treatment_protocol: APAP 300mg/kg, i.p., in saline or vehicle control (saline)

value: liver

value: hepatocytes

value: APAP 300 mg/kg


title: APAP_72h_NPC

value: non-parenchymal cells of liver


title: ES for differentiation

value: E14 no 2i no lif


description:
eIF4E3 immunoprecipitation (episomal using GFP antibodies) in exponential growth replicate 2
Sample 23

value: cells (epimastigote stage) in exponential growth conditions


title: L-GMP cells, Enl-T1, A485, 24h, H3K27ac, CUT&Tag

value: Blood

value: L-GMP

value: hematopoietic stem cell


title: SPATAC-seq with zebrafish embryogenesis well-ZSN8 (DNBSEQ-T7)

description:
ZSN8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: eIF4E4 immunoprecipitation in nutritional stress replicate 3

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 3
Sample 18

value: cells (epimastigote stage) in nutritional stress for two hours


title: APAP_48h_Hep


title: L-GMP cells, Enl-T1, A485, 6h, H3K27ac, CUT&Tag


title: eIF4E4 immunoprecipitation in nutritional stress replicate 2

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 2
Sample 17


title: Control_72h_NPC

value: saline vehicle


title: L-GMP cells, Enl-T1, A485, 3h, H3K27ac, CUT&Tag


title: SPATAC-seq with zebrafish embryogenesis well-ZSN6 (DNBSEQ-T7)

description:
ZSN6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Control_72h_Hep


title: L-GMP cells, Enl-T1, DMSO, 24h, H3K27ac, CUT&Tag

value: DMSO, 24h


title: SPATAC-seq with zebrafish embryogenesis well-ZSO2 (DNBSEQ-T7)

description:
ZSO2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: eIF4E3 immunoprecipitation in nutritional stress replicate 3

description:
eIF4E3 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 3
Sample 15


title: ES-2i_lif

value: ES

value: E14 2i+lif


title: Control_48h_NPC


title: SPATAC-seq with zebrafish embryogenesis well-ZSN5 (DNBSEQ-T7)

description:
ZSN5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: L-GMP cells, Enl-WT, DMSO, 24h, H3K27ac, CUT&Tag


title: APAP_48h_NPC


title: Control_48h_Hep


title: SPATAC-seq with zebrafish embryogenesis well-ZSN4 (DNBSEQ-T7)

description:
ZSN4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: eIF4E3 immunoprecipitation in nutritional stress replicate 1

description:
eIF4E3 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 1
Sample 13

value: whole organism


title: SPATAC-seq with zebrafish embryogenesis well-ZSN3 (DNBSEQ-T7)

description:
ZSN3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: GMP cells, Enl-WT, input, ChIP-seq

value: GMP

value: hematopoietic progenitor cell

value: WT

value: DMSO


description:
IgG (negative control) immunoprecipitation in nutritional stress replicate 3
Sample 12


title: SPATAC-seq with zebrafish embryogenesis well-ZSN2 (DNBSEQ-T7)

description:
ZSN2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 8, multiplexed scRNASeq

city: Nijmegen

first: Mumin

last: Ozturk

address: Geert Groote Plein Zuid 30

department: Cell Biology

country: Netherlands

institute: Radboud University

description: ParseBio Evercode

data_processing:
The conversion of BCL to FASTQ files was executed using Illumina’s bcl2fastq (version 2.20.0.422). ParseBio’s analysis pipeline split-pipe (version 1.0.5p) facilitated demultiplexing, alignment of sequencing reads, and the compilation of the cell-by-gene count matrix
Assembly: mm10
Supplementary files format and content: Compressed comma separated value files
Supplementary files format and content: Compressed matrix file
Supplementary files format and content: Sample loading table file for ParseBio experiment

source_name: Bone marrow

extract_protocol:
Femur bones from HFD-exposed and non-exposed Ldlr-/- mice (n=4/group) were dissected. Bone marrow cells were flushed with DMEM + 10%FCS, washed once and passed through 70 um cell strainers. CD11b+ cells were first depleted with CD11b magnetic microbeads (Miltenyi Biotec, Bergish Gladbach, Germany) and flow through was collected. The cells were later applied to the mouse lineage cell depletion kit (Miltenyi Biotec) to enrich progenitor cells. On average, around 9x105 Lin- cells were isolated per mouse. Lin- cells were fixed according to Evercode Fixation (ParseBiosciences, Seattle, USA) protocol
Library preparation was performed following manufacturer’s instructions for the Single Cell Whole Transcriptome Mega Kit, where total 12500 cells per sample were projected to be barcoded. After the third round of barcoding, eight sublibraries were prepared with the barcoded cDNA.
SPLIT-Seq based Evercode scRNA-Seq

value: Bone marrow

value: Lin negative cells

value: Progenitor cells

value: Ldlr-/-

value: Regular chow and high fat diet mixed


title: L-GMP cells, Enl-T1, p300, ChIP-seq

value: Blood

value: L-GMP


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 7, multiplexed scRNASeq

description: ParseBio Evercode


description:
IgG (negative control) immunoprecipitation in nutritional stress replicate 2
Sample 11

value: cells (epimastigote stage) in nutritional stress for two hours


title: SPATAC-seq with zebrafish embryogenesis well-ZSN7 (DNBSEQ-T7)

description:
ZSN7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: eIF4E4 immunoprecipitation in nutritional stress replicate 1

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 1
Sample 16


title: L-GMP cells, Enl-WT, p300, ChIP-seq


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 6, multiplexed scRNASeq

description: ParseBio Evercode


title: SPATAC-seq with zebrafish embryogenesis well-ZSN1 (DNBSEQ-T7)

description:
ZSN1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
IgG (negative control) immunoprecipitation in nutritional stress replicate 1
Sample 10


title: GMP cells, Enl-T1, p300, ChIP-seq


title: eIF4E3 immunoprecipitation in nutritional stress replicate 2

description:
eIF4E3 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 2
Sample 14


title: GMP cells, Enl-WT, p300, ChIP-seq


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 5, multiplexed scRNASeq

description: ParseBio Evercode


title: eIF4E4 immunoprecipitation in exponential growth replicate 3

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 3
Sample 9

value: cells (epimastigote stage) in exponential growth conditions


title: eIF4E4 immunoprecipitation in exponential growth replicate 2

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 2
Sample 8


title: SPATAC-seq with zebrafish embryogenesis well-ZSM7 (DNBSEQ-T7)

description:
ZSM7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: GMP cells, Enl-T1, H3K27ac, TDI11055, CUT&Tag


title: SPATAC-seq with zebrafish embryogenesis well-ZSM6 (DNBSEQ-T7)

description:
ZSM6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: LSK cells, Enl-T1, H3K27ac, TDI11055, CUT&Tag

value: LSK

value: hematopoietic stem cell


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 3, multiplexed scRNASeq

description: ParseBio Evercode


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 4, multiplexed scRNASeq

description: ParseBio Evercode


title: eIF4E4 immunoprecipitation in exponential growth replicate 1

description:
eIF4E4 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 1
Sample 7


title: SPATAC-seq with zebrafish embryogenesis well-ZSM5 (DNBSEQ-T7)

description:
ZSM5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: eIF4E3 immunoprecipitation in exponential growth replicate 3

description:
eIF4E3 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 3
Sample 6

value: whole organism


title: SPATAC-seq with zebrafish embryogenesis well-ZSM4 (DNBSEQ-T7)

description:
ZSM4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: cKit-Mac1+ cells, Enl-WT, H3K27me3, CUT&Tag

value: hematopoietic myeloid cell


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 1, multiplexed scRNASeq

description: ParseBio Evercode


title: eIF4E3 immunoprecipitation in exponential growth replicate 2

description:
eIF4E3 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 2
Sample 5


title: SPATAC-seq with zebrafish embryogenesis well-ZSM3 (DNBSEQ-T7)

description:
ZSM3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: cKit+Mac1+ cells, Enl-T1, H3K27me3, CUT&Tag


title: SPATAC-seq with zebrafish embryogenesis well-ZSM2 (DNBSEQ-T7)

description:
ZSM2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: U2OS cells，siSRSF1-3 rep2

city: GuangZhou

first: Shuqi

last: Li

state: GuangDong

address: #58, Zhongshan Road II, Guangzhou, China.

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork.
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: tab-detailed text file includes raw counts for each Sample
Supplementary files format and content: tab-detailed text files include RPKM values for each Sample

source_name: osteosarcoma

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3 ug of total RNA was usedfor the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: osteosarcoma

value: U2OS cell line

value: tumor cell


title: U2OS cells，siSRSF1-3 rep3


title: eIF4E3 immunoprecipitation in exponential growth replicate 1

description:
eIF4E3 immunoprecipitation (endogenous using specific antibodies) in exponential growth replicate 1
Sample 4

value: WT


title: cKit+Mac1+ cells, Enl-WT, H3K27me3, CUT&Tag

value: DMSO


title: SPATAC-seq with zebrafish embryogenesis well-ZSM8 (DNBSEQ-T7)

description:
ZSM8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


description:
IgG (negative control) immunoprecipitation in exponential growth replicate 3
Sample 3


title: SPATAC-seq with zebrafish embryogenesis well-ZSM1 (DNBSEQ-T7)

description:
ZSM1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: U2OS cells，siSRSF1-3 rep1


description:
IgG (negative control) immunoprecipitation in exponential growth replicate 2
Sample 2


title: SPATAC-seq with zebrafish embryogenesis well-ZSL7 (DNBSEQ-T7)

description:
ZSL7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: L-GMP cells, Enl-WT, H3K27me3, CUT&Tag

value: hematopoietic progenitor cell


title: U2OS cells，siSRSF1-2 rep3


description:
IgG (negative control) immunoprecipitation in exponential growth replicate 1
Sample 1


title: SPATAC-seq with zebrafish embryogenesis well-ZSL8 (DNBSEQ-T7)

description:
ZSL8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Mix of Lin- cells , Non-exposed and HFD-exposed mice, sublibrary 2, multiplexed scRNASeq

description: ParseBio Evercode

value: Bone marrow

value: Lin negative cells

value: Progenitor cells

value: Ldlr-/-


title: GMP cells, Enl-T1, H3K27me3, CUT&Tag

value: Blood

value: GMP


title: L-GMP cells, Enl-T1, H3K27me3, CUT&Tag

value: L-GMP


title: SPATAC-seq with zebrafish embryogenesis well-ZSL6 (DNBSEQ-T7)

description:
ZSL6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: U2OS cells，siSRSF1-2 rep1


title: GMP cells, Enl-WT, H3K27me3, CUT&Tag


title: cKit-Mac1+ cells, Enl-T1, H3K27me3, CUT&Tag


title: U2OS cells，siSRSF1-2 rep2


title: U2OS cells，OE-LINC01134 re3


title: F hOss, scRNAseq

city: Paris

first: Chloé

last: Friedrich

address: 8 rue Méchain

country: France

institute: Cochin Institute

description: 10x Genomics

data_processing:
The Galaxy interface was used to construct the gene-barcode expression matrix. FastQ files were aligned to the reference genome (GRCh38) via STAR (Spliced Transcripts Alignment to a Reference), with gene annotation from ENSEMBL. After quantifying the UMIs (Unique molecular identifiers) for each barcode, the unfiltered gene-barcode matrix was generated. From this unfiltered matrix, we created a filtered matrix (without empty cells and cells with a low number of UMIs (UMI < 50)).
The rest of the analysis was carried out using Seurat (Version 4.1.0)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: HSPC

extract_protocol:
To enrich samples in CD34+ fraction, immunomagnetic sorting was performed (130-046-703, CD34 MicroBead Kit, human, Miltenyi Biotec). After checking the purity and viability of the sorted cells, Human CD34+ cells were washed with PBS containing 0.04% BSA.
Libraries were prepared with the Chromium system of 10× Genomics, with the Chromium Single Cell 3’ v3.1 kit according to the manufacturer’s protocol (www.10xgenomics.com). The samples were processed on the same chromium chip. The number of cells targeted was 8000 per sample.

value: HSPC

value: NOD.Cg-Prkdcscid Il2rgtm1WjI/SzJ

tag: age

value: 6-8 weeks old


title: SPATAC-seq with zebrafish embryogenesis well-ZSL5 (DNBSEQ-T7)

description:
ZSL5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: SPATAC-seq with zebrafish embryogenesis well-ZSL4 (DNBSEQ-T7)

description:
ZSL4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: mBM Wo hOss, scRNAseq

description: 10x Genomics


title: U2OS cells，OE-LINC01134 re1

value: osteosarcoma


title: U2OS cells，OE-LINC01134 re2

value: U2OS cell line


title: LSK cells, Enl-WT, H3K27me3, CUT&Tag

value: LSK

value: hematopoietic stem cell


title: SPATAC-seq with zebrafish embryogenesis well-ZSL3 (DNBSEQ-T7)

description:
ZSL3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-45

city: Seoul

first: Sun Ha

last: Paek

address: 101, Daehak-ro, Jongno-gu

department: Department of Neurosurgery

country: South Korea

institute: Seoul National University College of Medicine, Seoul National University Hospital

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4d, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

growth_protocol: Patient-derived primary GBM cell lines were cultured in Dulbecco’s modified Eagle’s high glucose medium (SH30243.01, Hyclone) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (2357664RP, Gibco) and 1% antibiotic-antimycotic (15240062, Gibco). All cells were maintained at 37 °C in a 5% CO2 incubator and tested regularly for mycoplasma contamination by Mycoplasma Detection Kit (rep-mys-20, InvivoGen).

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini Kit (74106, QIAGEN) according to the manufacturer’s instructions
Libraries for bulk RNA-seq were prepared using the TruSeq Stranded Total RNA Library Prep Kit

value: Brain

value: Primary

value: Human glioblastoma multiforme

value: Untreated

tag: sex/age


title: cKit-Mac1+ cells, Enl-T1, H3K27ac, CUT&Tag

value: hematopoietic myeloid cell

value: DMSO


title: SPATAC-seq with zebrafish embryogenesis well-ZSL2 (DNBSEQ-T7)

description:
ZSL2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-44

value: Recurrent


title: U2OS cells，blank rep3

value: tumor cell


title: cKit-Mac1+ cells, Enl-WT, H3K27ac, CUT&Tag

value: Blood

value: WT


title: Patient-derived GBM cell line-43


title: P-N hOss, scRNAseq

description: 10x Genomics

value: HSPC

value: NOD.Cg-Prkdcscid Il2rgtm1WjI/SzJ


title: SPATAC-seq with zebrafish embryogenesis well-ZSL1 (DNBSEQ-T7)

description:
ZSL1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: U2OS cells，blank rep1

value: osteosarcoma


title: Patient-derived GBM cell line-42


title: cKit+Mac1+ cells, Enl-T1, H3K27ac, CUT&Tag


title: Patient-derived GBM cell line-41


title: L-GMP cells, Enl-T1, H3K27ac, CUT&Tag

value: L-GMP

value: hematopoietic progenitor cell


title: SPATAC-seq with zebrafish embryogenesis well-ZSK7 (DNBSEQ-T7)

description:
ZSK7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: APX-8

city: Chengdu

first: Hongyan

last: Gao

address: 1166 Liutai Avenue

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: adipose tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose tissue

tag: Sex

value: male

value: EA

tag: time

value: Day 21


title: cKit+Mac1+ cells, Enl-WT, H3K27ac, CUT&Tag


title: Patient-derived GBM cell line-40

value: Brain

value: Primary

value: Human glioblastoma multiforme

value: Untreated


title: SPATAC-seq with zebrafish embryogenesis well-ZSK6 (DNBSEQ-T7)

description:
ZSK6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: APX-7


title: LSK cells, Enl-T1, H3K27me3, CUT&Tag

value: LSK

value: hematopoietic stem cell

value: DMSO


title: Patient-derived GBM cell line-39


title: Patient-derived GBM cell line-38


title: MPX-7


title: SPATAC-seq with zebrafish embryogenesis well-ZSK8 (DNBSEQ-T7)

description:
ZSK8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSK5 (DNBSEQ-T7)

description:
ZSK5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSK4 (DNBSEQ-T7)

description:
ZSK4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: U2OS cells，blank rep2

value: U2OS cell line

value: tumor cell


title: APX-5


title: Patient-derived GBM cell line-37


title: GMP cells, Enl-T1, H3K27ac, CUT&Tag

value: Blood

value: GMP


title: GMP cells, Enl-WT, H3K27ac, CUT&Tag

value: WT


title: SPATAC-seq with zebrafish embryogenesis well-ZSK3 (DNBSEQ-T7)

description:
ZSK3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: CPX-8

value: adipose tissue


title: MPX-5

value: male


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ8 (DNBSEQ-T7)

description:
ZSJ8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Sublibraries-7 of species-mixing experiment using SPATAC

library_source: genomic single cell

data_processing:
We reformated raw Fastq file to Cell Ranger ATAC (v1.2) format. Round 1, round2 and round3 barcodes are extracted from Read1 and Read2 Fastq files, and are megred and transformed to new read2 barcode file of Cell Ranger ATAC format. Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new read1 file of Cell Ranger ATAC format. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new read2 file of Cell Ranger ATAC format. Finally, the resulting three  reformated Fastq files were processed using Cell Ranger ATAC v1.2 with GRCh38_and_mm10 reference.
Assembly: GRCh38_and_mm10 Reference
Supplementary files format and content: CSV file, cell metadata information within each sublibrary, including high-quality cell number and doublet rate; Fragment file, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.

organism:
Homo sapiens
Mus musculus

source_name: Genome DNA of mammalian cell lines

growth_protocol: Two cell lines Hepa (Mouse), K562 (Human) cells were obtained from Dr. Xin Lin (Tsinghua University, Beijing, China). K562 cells were maintained in RPMI 1640 (C11875500BT, Gibco) containing 10% FBS (04-001-1ACS, Biological Industries) and 1% penicillin-streptomycin (15140122, ThermoFisher). Hepa cells were maintained in DMEM (C11995500CP, Gibco) containing 10% FBS and 1% penicillin-streptomycin. Cells were cultured in a humidified 5% CO2 atmosphere, at 37℃.

extract_protocol:
Nuclei of Hepa and K562 cell lines were isolated according to the Omni-ATAC protocol. In brief, 10 million cells were pelleted by centrifugation at 500 x g for 5 min at room temperature. Supernatant was discarded and the cell pellet was lysed with the Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin (G9441, Promega), 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl pH 7.4 for 3 min on ice. Then, 10ml NWB (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma))  were added to lysed cells. Nuclei were spun down for 5 min at 500 x g at 4°C, and resuspended in 10ml NWB. The following steps were processed according to the fixation protocol of embryo nuclei above. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB.
SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details.For species-mixing experiment, we just used the first eight indexed Tn5 transposome.
Illumina NovaSeq 6000 System and Hiseq X Ten System

value: K562 (Human)

value: Hepa (Mouse)


title: Patient-derived normal tissue-4

value: Brain

value: Normal

value: Normal brain


title: Patient-derived normal tissue-3

value: Untreated


title: SPATAC-seq with zebrafish embryogenesis well-ZSK1 (DNBSEQ-T7)

description:
ZSK1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: MPX-2

value: Day 21


title: SPATAC-seq with zebrafish embryogenesis well-ZSK2 (DNBSEQ-T7)

description:
ZSK2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: CPX-4


title: SPATAC-seq with mouse organogenesis well-E8H

data_processing:
Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new Read1 file. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new Read2 file of Cell Ranger ATAC format. Round 1, Round2 and Round3 barcodes are extracted from raw Read1 and Read2 Fastq files, are merged after correcting 1bp mismatch. Then merged barcodes were attached in the read name of new Read1 and Read2 fastq files by software sinto (https://timoast.github.io/sinto/index.html), which were aligned to the reference mouse (mm10) genome (https://cf.10xgenomics.com/supp/cell-atac/refdata-cellranger-atac-mm10-1.2.0.tar.gz) using BWA. The bam file of each sublibrary was converted to scATAC-seq fragment file by sinto according to standard procedure. Finnaly, the barcodes in fragment file of each sublibrary were tagged with Round4 barcodes (PCR wells).
Assembly: mm10
Supplementary files format and content: bed files, the fragment file of SPATAC-seq, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: CSV file, cell metadata information for the atlas of zebrafish development, including cell types, coordinate and quality metric of each cell

source_name: mouse embryo

extract_protocol:
Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment.
Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details.

value: mouse embryo


title: Sublibraries-8 of species-mixing experiment using SPATAC


title: LSK cells, Enl-T1, H3K27ac, CUT&Tag

value: LSK

value: hematopoietic stem cell

value: DMSO


title: Patient-derived normal tissue-2


title: Patient-derived GBM cell line-33

value: Primary

value: Human glioblastoma multiforme


title: L-GMP cells, Enl-WT, H3K27ac, CUT&Tag

value: Blood

value: L-GMP

value: hematopoietic progenitor cell

value: WT


title: SPATAC-seq with mouse organogenesis well-E8G


title: Sublibraries-6 of species-mixing experiment using SPATAC

value: K562 (Human)


title: LSK cells, Enl-WT, H3K27ac, CUT&Tag


title: Patient-derived GBM cell line-35


title: Sublibraries-5 of species-mixing experiment using SPATAC

value: Hepa (Mouse)


title: Patient-derived GBM cell line-36

value: Brain


title: Patient-derived GBM cell line-34


title: Patient-derived GBM cell line-32


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ4 (DNBSEQ-T7)

description:
ZSJ4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: CPX-6

value: adipose tissue

value: male


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ5 (DNBSEQ-T7)

description:
ZSJ5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E8E


title: Sublibraries-3 of species-mixing experiment using SPATAC


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ6 (DNBSEQ-T7)

description:
ZSJ6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ3 (DNBSEQ-T7)

description:
ZSJ3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Sublibraries-2 of species-mixing experiment using SPATAC


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ2 (DNBSEQ-T7)

description:
ZSJ2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ7 (DNBSEQ-T7)

description:
ZSJ7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E8D


title: SPATAC-seq with zebrafish embryogenesis well-ZSJ1 (DNBSEQ-T7)

description:
ZSJ1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Sublibraries-1 of species-mixing experiment using SPATAC


title: SPATAC-seq with mouse organogenesis well-E8C


title: Sublibraries-4 of species-mixing experiment using SPATAC


title: Patient-derived GBM cell line-31

value: Recurrent

value: Untreated


title: SPATAC-seq with zebrafish embryogenesis well-ZSI8 (DNBSEQ-T7)

description:
ZSI8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-30


title: Patient-derived GBM cell line-29


title: SPATAC-seq with mouse organogenesis well-E8F

value: mouse embryo


title: SPATAC-seq with zebrafish embryogenesis well-ZSI7 (DNBSEQ-T7)

description:
ZSI7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E8B


title: Lungs, LCMV+glucose, biol rep 3

city: Rijeka

first: Felix

middle: Martinus

last: Wensveen

address: Braće Branchetta 20

department: Histology & Embryology

country: Croatia

institute: University of Rijeka faculty of medicine

data_processing:
Sequence reads were mapped to the mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 (Langmeadand Salzberg, 2012) and EnsEMBL annotation release 67.
Gene expression was quantified by featureCounts and analyzed using DESeq2 within R based on an adjusted P (padj) < 0.05 and, where applied, fold change > 1.2.
As an input for the analysis the raw counts table was used.
Assembly: mm10
Supplementary files format and content: tab-delimited .tsv file contains raw counts for each sample
Supplementary files format and content: Tab-delimited .xlsx file includes comparison between IFNg/IL-1b treated and untreated samples

source_name: Lung

growth_protocol: Mice were infected with LCMV and fasted for 3 days in presence or absence of glucose in drinking water.

extract_protocol:
RNA was extracted using standard TRIzol (Invitrogen) protocol
Sequencing libraries were generated using the CEL-seq2 protocol, rendering barcoded samples.

treatment_protocol: Next, lungs were isolated and total RNA was isolated of lung homogenates.

value: Lung

value: 3 days post infection

value: LCMV+glucose


title: Lungs, LCMV+glucose, biol rep 1


title: Lungs, LCMV+glucose, biol rep 2


title: Patient-derived GBM cell line-28

value: Primary

value: Human glioblastoma multiforme


title: Lungs, LCMV, biol rep 3

value: LCMV only


title: SPATAC-seq with mouse organogenesis well-E8A


title: SPATAC-seq with zebrafish embryogenesis well-ZSI5 (DNBSEQ-T7)

description:
ZSI5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

data_processing:
Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new Read1 file. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new Read2 file. Round 1, round2 and round3 barcodes are extracted from Read1 and Read2 Fastq files, and are merged and were added into the header of new Read1 and Read2 files. New Read1 and Read2 files were aligned to the reference zebrafish GRCz11 genome assemblyby BWA. The scATAC-seq fragment files were created by sinto (https://timoast.github.io/sinto/index.html) according to standard procedure. Barcodes in fragment file of each sublibrary were tagged with Round4 barcodes (PCR wells), then all sublibrary fragment files were merged into one big fragment file, which were further split into stage-specific fragment files based on Round1 barcodes. For the bulk ATAC-seq data from zebrafish embryos, reads were trimmed with to remove the Nextera sequencing adaptors by trim_galore. The trimmed reads were mapped to the reference zebrafish (GRCz11) genome using BWA. Reads with mapping quality less than 30 and duplication were removed by samtools. BigWig files were generated by bamCoverage.  Fastq files of 10x Genomics scATAC-seq were processed Cell Ranger ATAC Pipeline (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac, v.1.2.0).
Assembly: GRCz11
Supplementary files format and content: bed files, the fragment file of SPATAC-seq, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of 10x Genomics scATAC-seq, the information of each unique fragment within each sample, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of bulk ATAC-seq, the information of each unique fragment, including the chromsome number, start site, end site
Supplementary files format and content: excel file, cell metadata information for the atlas of zebrafish development, including cell types, coordinate and quality metric of each cell
Supplementary files format and content: bigWig file, genome-wide signal for 604 cell types of scATAC-seq datasets
Supplementary files format and content: bigWig file, genome-wide signal for bulk ATAC-seq of zebrafish embryos


title: SPATAC-seq with zebrafish embryogenesis well-ZSI6 (DNBSEQ-T7)

description:
ZSI6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E7H


title: Patient-derived GBM cell line-27


title: SPATAC-seq with mouse organogenesis well-E7G


title: Patient-derived GBM cell line-26


title: SPATAC-seq with zebrafish embryogenesis well-ZSI4 (DNBSEQ-T7)

description:
ZSI4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E7F


title: Lungs, LCMV, biol rep 2


title: Patient-derived GBM cell line-25


title: SPATAC-seq with mouse organogenesis well-E7E


title: Beta cells, IFNg/IL1b, biol rep 4

source_name: Pancreas

growth_protocol: After purification, beta cells were cultured for 48h in complete RPMI medium (supplemented with 10% FBS, 1% HEPES, sodium pyruvate, glutamine, streptomycin and penicillin).

treatment_protocol: 3x104 beta cells were incubated with 10ng/ml of IFNg and 2ng/ml of IL-1b. 4h later, cells were incubated for 1h in KBR medium (115mM Nacl, 4.7mM of KCl, 2.6mM CaCl2x2H2O, 1.2mM KH2PO4, 1.2mM MgSO4x2H2O, 10mM of Hepes,0.5% of BSA and with 2.8mM of Glucose), after which cells were harvested

value: Pancreas

value: beta cells


title: Patient-derived GBM cell line-24


title: SPATAC-seq with zebrafish embryogenesis well-ZSI2 (DNBSEQ-T7)

description:
ZSI2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived normal tissue-1

value: Normal

value: Normal brain


title: SPATAC-seq with mouse organogenesis well-E7D


title: Beta cells, IFNg/IL1b, biol rep 3

value: WT


title: Lungs, LCMV, biol rep 1


title: SPATAC-seq with zebrafish embryogenesis well-ZSI3 (DNBSEQ-T7)

description:
ZSI3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: Patient-derived GBM cell line-23

value: Brain


title: Beta cells, IFNg/IL1b, biol rep 2


title: SPATAC-seq with zebrafish embryogenesis well-ZSI1 (DNBSEQ-T7)

description:
ZSI1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E7C


title: Patient-derived GBM cell line-22


title: Patient-derived GBM cell line-21


title: SPATAC-seq with zebrafish embryogenesis well-ZSH7 (DNBSEQ-T7)

description:
ZSH7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E7B


title: Patient-derived GBM cell line-20


title: Beta cells, control, biol rep 4

value: glucose only


title: SPATAC-seq with zebrafish embryogenesis well-ZSH8 (DNBSEQ-T7)

description:
ZSH8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSH6 (DNBSEQ-T7)

description:
ZSH6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Beta cells, control, biol rep 3