title: MRL/MpJ-Control PBS-spleen

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

source_name: Cultured spleen cells with PBS control

growth_protocol: The spleen of a 6-month-old MRL/MpJ mouse was collected and minced in a culture dish. Next, 10 mL of 1× PBS was added, after which the sample was filtered using 100 μm cell strainers and centrifuged at 210 g for 5 min. After supernatant aspiration, cells were resuspended, incubated with 10 mL of 0.017 M tris buffer containing 0.75% ammonium chloride (pH 7.65) for 5 min, and washed with 10 mL PBS. This solution was filtered using 40 μm cell strainers and centrifuged at 1,000 rpm for 5 min. After washing twice with PBS, the collected cells were resuspended in RPMI1640 with L-glutamine without antibiotics and harvested in 24-well culture plates.

treatment_protocol: These cultured cells were stimulated with PBS or with urine derived from 6-month-old MRL/MpJ or MRL/MpJ-Faslpr/lpr mice. (Urine was collected from male MRL/MpJ or MRL/MpJ-Faslpr/lpr mice at 6 months of age via compressive urination (n = 6), after which samples from each strain were pooled and centrifuged at 1,500 rpm for 5 min. The urine supernatant was filtered using a 0.22 μm syringe filter.) All MLT experiments were performed using 2.5 x 107 cells/mL and 500 μL medium/well.

tag: strain

value: MRL/MpJ

tag: gender

value: Male

value: 6 months

value: spleen

value: Cultured spleen cells

value: control

tag: time

value: 3 hour contact time


title: MRL/MpJ-MRL/MpJ-Faslpr/lpr urine-spleen

status: Public on Apr 15 2024

type: RNA

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

hyb_protocol: Gene Expression Hybridization Kit (Agilent) was used, and 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 25x fragmentation buffer and 10x GE blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μL of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE (G4852A) for 17 hours at 65°C.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Ver.12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

organism: Mus musculus

source_name: Cultured spleen cells with MRL/MpJ-Faslpr/lpr urine stimulation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA from cells was purified using RNeasy Mini Kit (Qiagen)  following the manufacturer's recommendations. RNA samples were checked for RNA integrity on a Bioanalyzer 2100 II (Agilent Technologies).

tag: age

tag: tissue

tag: cell type

tag: treatment

value: MRL/MpJ-Faslpr/lpr urine


title: H9_Control2_d60

type: SRA

city: New York

first: Ryan

last: Walsh

state: NY

address: 430 E 67th St

department: Developmental Biology

country: USA

institute: MSKCC

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger v6.1.2 was used for demultiplexing and generation of a count matrix
Assembly: GRCh38
Supplementary files format and content: comma separated count matrix

organism: Homo sapiens

source_name: organoid

extract_protocol:
Organoids were dissociated with a papain dissociation system (Worthington) according to the manufacturer's protocol for 30min at 37C. The single cell suspension was washed, filtered and resuspended in 0.04% BSA/PBS + Ribolock RNase inhibitor for scRNAseq.
Libraries were constructed with the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to the manufacturer's protocol. In brief, single cell suspensions were loaded onto a Chromium Next GEM Chip G for GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 7,000-15,000 cells. cDNA amplification included 11-12 cycles and 30-240 ng of the material were used to prepare sequencing libraries with 10-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S1 or S4 Reagent Kit (100 or 200 cycles) (Illumina).

value: organoid

tag: cell line

value: progenitors & neurons

tag: genotype

value: WT

value: Control


title: iPSC derived neurons, Ctrl_A

first: Osama

last: Al Dalahmah

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Human Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package (version 1.36.1) (Gautier et al., 2004) included in the Bioconductor software suite (version 2.11) (Gentleman et al., 2004) and an Entrez Gene- specific probeset mapping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan (Dai et al., 2005). Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0).

label: biotin

source_name: iPSC derived neurons from control patient tissue

label_protocol: GeneChipTM Human Gene 2.0 ST microarray procedure

growth_protocol: Neural progenitor cells (NPCs) were generated and cultured as previously described (Hargus et al., 2014; Reinhardt et al., 2013). Briefly, iPSC colonies were detached from MEFs 3–4 days after splitting using 2 mg/ml collagenase IV. Pieces of colonies were collected by sedimentation and resuspended in human ESC media (without FGF2) supplemented with 10 μM SB-431542 (Ascent Scientific), 1 μM dorsomorphin (Tocris), 3 μM CHIR 99021 (Axon Medchem), and 0.5 μM purmorphamine (PMA; Alexis) and subsequently cultured as embryoid bodies (EBs) in Petri dishes. On day 2, media was changed to N2B27 media containing the same small-molecule supplements. N2B27 medium consisted of Dulbecco’s modified Eagle’s media (DMEM)-F12 (Invitrogen)/Neurobasal (Invitrogen) 50:50 with 1:200 N2 supplement (Invitrogen), 1:100 B27 supplement lacking vitamin A (Invitrogen) with1%penicillin/streptomycin/glutamine (PAA). On day 4, SB-431542 and dorsomorphin were withdrawn and 150 mM ascorbic acid (AA; Sigma) was added to the media. On day 6, EBs were triturated into smaller pieces and plated on Matrigel- coated (Matrigel, growth factor reduced, high concentration; BD Biosciences) 12-well plates (Nunc) in NPC expansion media (N2B27 with CHIR, PMA, and AA). Media was changed every other day and cells were typically split 1:10–1:15 every 5–6 days. For splitting, cells were digested to single cells for approximately 10 min at 37C using prewarmed Accutase (PAA). Cells were diluted in DMEM (PAA) and spun down at 1,000 rpm for 5 min. The cell pellet was resuspended in fresh NPC expansion media and plated on Matrigel-coated cell culture dishes.

extract_protocol: RNA from microdissected human nigral tissue or iPSC-derived neurons was extracted using RNeasy columns (QIAGEN)

tag: disease state

value: Ctrl

value: iPSC derived neurons


title: H9_Control1_d60

description: 10x Genomics


title: MRL/MpJ-MRL/MpJ urine-spleen

source_name: Cultured spleen cells with MRL/MpJ urine stimulation

value: MRL/MpJ urine


title: Cardiomyocytes, DOX22h, C2

city: Bogota DC

first: Yohana

last: Dominguez

state: Bogota

address: El Dorado avenue 51-20

department: Sub-Direction of Scientific and Technological Research

country: Colombia

institute: National Institute of Health

library_source: transcriptomic

data_processing:
Read quality assessment was performed using MultiQC and validated in Galaxy using FastQC. Alignments of reads ranging from 17 to 35 nucleotides in length were performed against the Homo sapiens reference genome.
Assembly: Homo sapiens maskedPAR (UCSC hg19)
Supplementary files format and content: Quality control and normalization of the resulting reads was performed using the BaseSpace® Small RNA v1.0 app (Illumina), with subsequent conversion of the sequences to FastQ files. and the quality of the readings was analyzed multiQC and confirmed in Galaxy by FastQC. The alignments for readings obtained between 17 and 35 nt against the reference genome for Homo sapiens.

organism: Cavia porcellus

source_name: Heart

extract_protocol:
Total R.N.A. extraction was conducted on isolated guinea pig ventricular cardiomy-ocytes exposed independently to 10 μM of DOX and to the vehicle control (DMSO) for 22 hours at room temperature. We used Trizol reagent to extract following the manufacturer's guidelines (Invitrogen). The extracted R.N.A. was resuspended in H2O DEPC (diethyl py-rocarbonate, Sigma–Aldrich) and quantified via spectrophotometry using the Nanodrop 2000 (Thermo Fisher Scientific).
A small R.N.A. library was constructed using the TruSeq Small R.N.A. Library Prep Kit (Illumina Inc., U.S.A.). . The quality control and the normalization of the readings obtained using the BaseSpace® App, Small RNA v1.0 (Illumina), the sequences converted into FastQ files, and the quality of the readings was analyzed multiQC and confirmed in Galaxy by FastQC (https://usegalaxy.org/).
TruSeq Small R.N.A. Library to miRNAs was sequenced on an Illumina HiSeq2500 platform. Quality control and normalization of the resulting reads was performed using the BaseSpace® Small RNA v1.0 app (Illumina), with subsequent conversion of the sequences to FastQ files.

value: Heart

value: Cardiomyocytes

value: Ventricular cardiomyocytes

value: Mature

value: DOX

tag: time point


title: post-mortem brain tissue, FTD-7

source_name: post-mortem brain tissue from FTD patients

value: FTD

value: post-mortem brain tissue


title: post-mortem brain tissue, FTD-8


title: Patient #159, human colon organoids, differentiation (B+D) medium - control

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

data_processing:
Analyses were performed using Nextpresso RNAseq pipeline.
Sequencing read quality and cross-contamination analysis were performed by FastQC and FastqScreen softwares, respectively.
Raw reads were preprocessed using BBDuk software in order to trim polyA and trueseq adapters contaminant sequences
Raw reads were aligned to hg19 human genome assembly using Bowtie and TopHat aligners. Gene counts were generated from alignment maps using htseq-count function.
Differential expression analysis was performed as paired test using DeSEQ2 R package.
Assembly: hg19

source_name: colon

growth_protocol: Human colon normal organoids were seeded in Matrigel and grown in a culture medium enriched in stemness agents (PROL) according to Fernández-Barral et al. (FEBS J., 2020).

extract_protocol:
Macherey-Nagel RNA extraction Kit was used in combination with TRIZOL. Both large and small RNA was extracted. 500 ng of total RNA was used for the construction of sequencing libraries
RNA samples (500 ng; RQS/RIN average 8.6, range 7.3-9.6) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis.

treatment_protocol: Organoids growing in proliferation (PROL) medium for 5 days were washed twice in PBS and changed to either fresh PROL medium or differentiation (B+D) medium for additional 48 h in the presence of calcitriol (1,25(OH)2D3, 100 nM) or vehicle (ethanol).

value: colon

value: human colon epithelial stem cells

tag: Sex

value: Male

value: Vehicle (ethanol)


title: H9_LIF2_d40

description: 10x Genomics

value: organoid

value: progenitors & neurons

value: LIF


title: Cardiomyocytes, DMSO22h, C2

value: DMSO


title: Patient #159, human colon organoids, proliferation (PROL) medium - control


title: Cardiomyocytes, DOX1h, C2


title: Patient #158, human colon organoids, differentiation (B+D) medium - calcitriol

value: Calcitriol (1,25(OH)2D3)


title: Patient #161, human colon organoids, proliferation (PROL) medium - control

value: Female


title: post-mortem brain tissue, FTD-5


title: H9_LIF1_d40

description: 10x Genomics

value: WT


title: post-mortem brain tissue, FTD-6


title: post-mortem brain tissue, FTD-4


title: H9_Control2_d40

description: 10x Genomics

value: Control


title: Cardiomyocytes, DMSO1h, C2

value: Heart

value: Cardiomyocytes

value: Ventricular cardiomyocytes


title: Patient #158, human colon organoids, differentiation (B+D) medium - control


title: Patient #159, human colon organoids, differentiation (B+D) medium - calcitriol


title: post-mortem brain tissue, FTD-3

value: FTD


title: Cardiomyocytes, DOX22h, C1

value: Mature

value: DOX


title: Patient #158, human colon organoids, proliferation (PROL) medium - control

value: colon

value: human colon epithelial stem cells


title: hiPSC-CM, MYH7 CTRL, Day 30, biol rep2,3,4,5

city: Suwon-si

first: Soah

last: Lee

state: Geonggi-do

address: 2066 Seobu-ro, Jangan-gu, 530502

department: Pharmacy

country: South Korea

institute: Sungkyunkwan University

description:
CTRL-rep2-hashtag (GTCAACTCTTTAGCG); CTRL-rep3-hastag (GTATTCCCTCAGTCA); CTRL-rep4-hashtag (AAGGCAGACGGTGCA); CTRL-rep5-hashtag (GGCTGCGCACCGCCT)
C113C141.D30.rds

data_processing:
scRNA seq data underwent sample demultiplexing, alignment, filtering, barcode processing, and gene counting using cellranger (10X).
Assembly: GRCh38-3.0.0
Supplementary files format and content: RDS (Seurat object)

source_name: iPSC-CM day 30

growth_protocol: hiPSCs were maintained and directed for cardiac differentiation using Wnt-modulating small-molecule-based protocol. Full protocol can be found in the Method section of the manuscript.

extract_protocol:
Detailed protocol can be found in the Method section of the manuscript. Briefly, differentiated cardiomyocytes on differentiation day 30 were harvested and labeled with sample-specific hashtag oligonucleotides according to the manufacturer's protocol (10X Single Cell 3' v3.1 chemistry with feature barcoding technology, CG000206-Rev D). Then, the labeled hiPSC-CMs underwent emulsion-based single cell encapsulation process using 10X Chromium machine, followed by single cell mRNA library construction.
The library was constructed using the manufacturer's protocol (10X Single Cell 3' v3.1 chemistry with feature barcoding technology, CG000206-Rev D). Briefly, the labeled hiPSC-CMs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reversetranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: iPSC-CM day 30

value: cardiomyocyte

value: CTRL


title: Cardiomyocytes, DMSO22h, C1


title: Cardiomyocytes, DOX1h, C1


title: Patient #92, human colon organoids, differentiation (B+D) medium - control

value: Male

value: Vehicle (ethanol)


title: Patient #92, human colon organoids, differentiation (B+D) medium - calcitriol

value: Calcitriol (1,25(OH)2D3)


title: post-mortem brain tissue, FTD-2

value: post-mortem brain tissue


title: post-mortem brain tissue, FTD-1


title: hiPSC-CM, MYH7 G256E, Day 30, biol rep1,2

description:
G256E-rep1-hashtag (AAGGCAGACGGTGCA); G256E-rep2-hashtag (GGCTGCGCACCGCCT)
C113C141.D30.rds

value: G256E mutant


title: Cardiomyocytes, DMSO1h, C1

value: DMSO


title: Patient #92, human colon organoids, proliferation (PROL) medium - control


title: post-mortem brain tissue, Ctrl-2

source_name: post-mortem brain tissue from control patients

value: Ctrl


title: post-mortem brain tissue, Ctrl-3


title: H9_Control1_d40

description: 10x Genomics

value: organoid

value: progenitors & neurons

value: WT

value: Control


title: TBPE-1

status: Public on Apr 14 2024

city: Wuhan

first: Li-Mei

last: Liang

state: Hubei

address: 1277 JieFang Avenue

department: Department of Respiratory and Critical Care Medicine, Union Hospital

country: China

institute: Huazhong University of Science and Technology

description: miRNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference,modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA,  small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified  species itself.
For the samples with biological replicates:Differential expression analysis of two conditions/groups was  performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini& Hochberg  method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: miRNA expression levels were estimated byTPM (transcript per million) through the following criteria ,  Normalizationformula: Normalizedexpression=mappedreadcount/Totalreads*1000000

source_name: exosomes from tuberculous pleural effusions

extract_protocol:
TBPE or TPE specimens were centrifuged at 300 g for 10 min at 4°C. The supernatant was taken and centrifuged at 10,000 g for 30 min at 4°C. Then the supernatant was ultracentrifuged at 100,000 g for 70 min at 4°C. The pellet was resuspended in PBS buffer and ultracentrifuged again at 100,000 g for 70 min. After ultracentrifugation, the pellet was suspended with 50 μl PBS buffer and saved at -80°C.
Libraries were prepared according to Small RNA Sample Pre Kit. Briefly, The special structure of the 3 'and 5' ends of Small RNA (the 5 'end has complete phosphate group and the 3' end has hydroxyl group) was used, and total RNA was used as the starting sample cDNA was synthesized by reverse transcription of Small RNA by adding connectors to both ends of the RNA.

value: exosomes

value: tuberculous pleuritis


title: TPE-3

description: miRNA

source_name: exosomes from transudative pleural effusion

value: cardiac failure


title: CON_input

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
Clean reads were mapped to human genome (UCSC hg19) by using HISAT v2.2.1
Peaks were called uing MACS v3.0.0a7 with the significance cut-off q-value <=0.05
Assembly: hg19
Supplementary files format and content: narrowPeak (except for Input sample)
Library strategy: MeRIP-Seq

molecule: polyA RNA

source_name: primary human endometrial stromal cells

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

treatment_protocol: Primary human endometrial stromal cells (HESCs) were induced to differentiate through treatment with MPA and 8-Br-cAMP.

tag: ip antibody

value: Day 4

value: primary human endometrial stromal cells


title: DEC_input


title: DEC_IP

value: anti-m6a (Synaptic Systems, #202003)


title: hiPSC-CM, MYH7 CTRL, Day 30,biol  rep1

description:
CTRL-rep1-hashtag (GTCAACTCTTTAGCG)
C113C141.D30.rds

value: iPSC-CM day 30

value: cardiomyocyte

value: CTRL


title: siMETTL3_CON

data_processing:
Clean reads were mapped to human genome (UCSC hg19) by using HISAT v2.2.1
The aligned reads were then processed to compute a gene-level expression matrix using HTSeq v2.0.3 software
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include count values for each sample

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Primary human endometrial stromal cells (HESCs) were induced to differentiate through treatment with MPA and 8-Br-cAMP. SiRNA-mediated knockdown of METTL3 was performed on HESCs, 6 h prior to treatment of 8-Br-cAMP and MPA.


title: CON_IP


title: siNC_DEC


title: siMETTL3_DEC


title: post-mortem brain tissue, Ctrl-1

value: post-mortem brain tissue


title: CD45.1/.2 2 days after I/R injury, IZ, S115

city: Munich

first: Markus

last: Joppich

state: Bavaria

address: Amalienstr. 17

department: Department of Informatics

country: Germany

institute: LMU Munich

data_processing:
The obtained reads were trimmed using bbduk from the BBMap (https://sourceforge.net/projects/bbmap/) v38.87 collection using parameters “ktrim=r k=23 mink=11 hdist=1 tpe tbo”. The trimmed reads were aligned with Hisat2 2.2.1 against the Ensembl release 102 reference mouse genome (Yates et al, 2020). Gene expression was quantified per sample and lane using the featureCounts (Liao et al, 2014) application from the subread package (v2.0.1) with parameters “--primary -O -C -B -p -T 8 --minOverlap 5” and finally aggregated per sample.
Assembly: Ensembl release 102 reference mouse genome, GRCm38.p6
Supplementary files format and content: Raw counts excel file

extract_protocol:
Heart tissue was dissected into remote and ischemic tissue as described above and minced into small pieces using forceps and a scalpel. When comparing baseline and I/R injury in FACS analysis, basal heart tissue was used for comparison with remote tissue and apical heart tissue for comparison with ischemia tissue. After enzymatic digestion (Collagenase XI 1200 U/mg, Collagenase I 125 U/mg, Hyaluronidase 500 U/mg, DNase I 1836 U/mg; Sigma Aldrich®) for 30 min at 37°C cells were washed and incubated with purified anti-CD16/32 (FcγRIII/II; dilution 1/50) for 10 min.
For each sample, ~1000 macrophages were sorted into 75µL of RLT buffer (Qiagen, containing 1% beta-mercaptoethanol), vortexed for 1 min and immediately frozen (-80°C). RNA extraction (RNeasy® Plus Micro Kit, Qiagen), cDNA generation (SMART®-Seq v4 Ultra Low Input RNA Kit, Takara Bio)

value: Heart

value: macrophages

value: infarcted

value: 2 days after I/R injury, IZ


title: CD45.1/.2 2 days after I/R injury, IZ, S113


title: CD45.1/.2 2 days after I/R injury, RZ, S112

value: 2 days after I/R injury, RZ


title: CD45.1/.2 2 days after I/R injury, IZ, S111


title: CD45.1/.2 2 days after I/R injury, RZ, S110


title: CD45.1/.2 2 days after I/R injury, IZ, S109


title: CD45.1/.2 2 days after I/R injury, RZ, S108


title: CD45.1/.2 2 days after I/R injury, RZ, S106


title: post-mortem brain tissue, Ctrl-4

value: Ctrl


title: CD45.1/.2 2 days after I/R injury, IZ, S107


title: TBPE-3

description: miRNA


title: siNC_CON

value: DMSO+siNC


title: TBPE-2

description: miRNA

value: exosomes


title: CD45.1/.2 2 days after I/R injury, IZ, S105


title: CD45.1/.2 2 days after I/R injury, RZ, S104


title: TPE-2

description: miRNA


title: TPE-1

description: miRNA


title: CD45.1/.2 2 days after I/R injury, RZ, S114


title: SPATAC-seq with zebrafish embryogenesis well-ZB5SLC09 (Novaseq 6000)

city: beijing

first: Keyong

last: Sun

address: Hai Dian street

department: School of Medicine

institute: tsinghua university

description:
ZB5SLC09_SPATACseq_Batch5
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.

value: zebrafish embryos


title: SPATAC-seq with zebrafish embryogenesis well-ZB5SLB09 (Novaseq 6000)

description:
ZB5SLB09_SPATACseq_Batch5
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-ZB5SLA09 (Novaseq 6000)

description:
ZB5SLA09_SPATACseq_Batch5
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 (Novaseq 6000)

description:
ZSR7_SPATACseq_Batch1_illumina
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-ZSQ5 (Novaseq 6000)

description:
ZSQ5_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSR6_SPATACseq_Batch1_illumina
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-ZSR5 (Novaseq 6000)

description:
ZSR5_SPATACseq_Batch1_illumina
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-ZSQ7 (Novaseq 6000)

description:
ZSQ7_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSR3_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSR2_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSR4_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSR8_SPATACseq_Batch1_illumina
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-ZSQ3 (Novaseq 6000)

description:
ZSQ3_SPATACseq_Batch1_illumina
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-ZSQ6 (Novaseq 6000)

description:
ZSQ6_SPATACseq_Batch1_illumina
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-ZSR1 (Novaseq 6000)

description:
ZSR1_SPATACseq_Batch1_illumina
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-ZSQ2 (Novaseq 6000)

description:
ZSQ2_SPATACseq_Batch1_illumina
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-ZSQ1 (Novaseq 6000)

description:
ZSQ1_SPATACseq_Batch1_illumina
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-ZSP8 (Novaseq 6000)

description:
ZSP8_SPATACseq_Batch1_illumina
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-ZSP7 (Novaseq 6000)

description:
ZSP7_SPATACseq_Batch1_illumina
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-ZSP6 (Novaseq 6000)

description:
ZSP6_SPATACseq_Batch1_illumina
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-ZSP5 (Novaseq 6000)

description:
ZSP5_SPATACseq_Batch1_illumina
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-ZSP3 (Novaseq 6000)

description:
ZSP3_SPATACseq_Batch1_illumina
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-ZSQ8 (Novaseq 6000)

description:
ZSQ8_SPATACseq_Batch1_illumina
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-ZSO8 (Novaseq 6000)

description:
ZSO8_SPATACseq_Batch1_illumina
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-ZSP4 (Novaseq 6000)

description:
ZSP4_SPATACseq_Batch1_illumina
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-ZSO7 (Novaseq 6000)

description:
ZSO7_SPATACseq_Batch1_illumina
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-ZSP1 (Novaseq 6000)

description:
ZSP1_SPATACseq_Batch1_illumina
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-ZSQ4 (Novaseq 6000)

description:
ZSQ4_SPATACseq_Batch1_illumina
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-ZSO6 (Novaseq 6000)

description:
ZSO6_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSO4_SPATACseq_Batch1_illumina
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-ZSO3 (Novaseq 6000)

description:
ZSO3_SPATACseq_Batch1_illumina
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-ZSO5 (Novaseq 6000)

description:
ZSO5_SPATACseq_Batch1_illumina
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-ZSN7 (Novaseq 6000)

description:
ZSN7_SPATACseq_Batch1_illumina
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-ZSN5 (Novaseq 6000)

description:
ZSN5_SPATACseq_Batch1_illumina
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-ZSN8 (Novaseq 6000)

description:
ZSN8_SPATACseq_Batch1_illumina
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-ZSN2 (Novaseq 6000)

description:
ZSN2_SPATACseq_Batch1_illumina
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-ZSN3 (Novaseq 6000)

description:
ZSN3_SPATACseq_Batch1_illumina
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-ZSM8 (Novaseq 6000)

description:
ZSM8_SPATACseq_Batch1_illumina
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-ZSO2 (Novaseq 6000)

description:
ZSO2_SPATACseq_Batch1_illumina
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-ZSM5 (Novaseq 6000)

description:
ZSM5_SPATACseq_Batch1_illumina
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-ZSM4 (Novaseq 6000)

description:
ZSM4_SPATACseq_Batch1_illumina
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-ZSO1 (Novaseq 6000)

description:
ZSO1_SPATACseq_Batch1_illumina
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-ZSN6 (Novaseq 6000)

description:
ZSN6_SPATACseq_Batch1_illumina
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-ZSN4 (Novaseq 6000)

description:
ZSN4_SPATACseq_Batch1_illumina
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-ZSP2 (Novaseq 6000)

description:
ZSP2_SPATACseq_Batch1_illumina
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-ZSM7 (Novaseq 6000)

description:
ZSM7_SPATACseq_Batch1_illumina
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-ZSM2 (Novaseq 6000)

description:
ZSM2_SPATACseq_Batch1_illumina
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-ZSN1 (Novaseq 6000)

description:
ZSN1_SPATACseq_Batch1_illumina
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-ZSM3 (Novaseq 6000)

description:
ZSM3_SPATACseq_Batch1_illumina
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-ZSM1 (Novaseq 6000)

description:
ZSM1_SPATACseq_Batch1_illumina
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-ZSL8 (Novaseq 6000)

description:
ZSL8_SPATACseq_Batch1_illumina
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-ZSL4 (Novaseq 6000)

description:
ZSL4_SPATACseq_Batch1_illumina
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-ZSL5 (Novaseq 6000)

description:
ZSL5_SPATACseq_Batch1_illumina
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-ZSL7 (Novaseq 6000)

description:
ZSL7_SPATACseq_Batch1_illumina
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-ZSL3 (Novaseq 6000)

description:
ZSL3_SPATACseq_Batch1_illumina
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-ZSL6 (Novaseq 6000)

description:
ZSL6_SPATACseq_Batch1_illumina
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-ZSK8 (Novaseq 6000)

description:
ZSK8_SPATACseq_Batch1_illumina
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-ZSL1 (Novaseq 6000)

description:
ZSL1_SPATACseq_Batch1_illumina
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-ZSK7 (Novaseq 6000)

description:
ZSK7_SPATACseq_Batch1_illumina
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-ZSM6 (Novaseq 6000)

description:
ZSM6_SPATACseq_Batch1_illumina
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-ZSK6 (Novaseq 6000)

description:
ZSK6_SPATACseq_Batch1_illumina
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-ZSL2 (Novaseq 6000)

description:
ZSL2_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSK5_SPATACseq_Batch1_illumina
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-ZSK3 (Novaseq 6000)

description:
ZSK3_SPATACseq_Batch1_illumina
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-ZSK1 (Novaseq 6000)

description:
ZSK1_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSJ7_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSK4_SPATACseq_Batch1_illumina
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-ZSJ8 (Novaseq 6000)

description:
ZSJ8_SPATACseq_Batch1_illumina
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-ZSJ4 (Novaseq 6000)

description:
ZSJ4_SPATACseq_Batch1_illumina
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-ZSK2 (Novaseq 6000)

description:
ZSK2_SPATACseq_Batch1_illumina
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-ZSJ1 (Novaseq 6000)

description:
ZSJ1_SPATACseq_Batch1_illumina
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-ZSI8 (Novaseq 6000)

description:
ZSI8_SPATACseq_Batch1_illumina
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-ZSJ2 (Novaseq 6000)

description:
ZSJ2_SPATACseq_Batch1_illumina
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-ZSI7 (Novaseq 6000)

description:
ZSI7_SPATACseq_Batch1_illumina
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-ZSI6 (Novaseq 6000)

description:
ZSI6_SPATACseq_Batch1_illumina
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-ZSI3 (Novaseq 6000)

description:
ZSI3_SPATACseq_Batch1_illumina
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-ZSI5 (Novaseq 6000)

description:
ZSI5_SPATACseq_Batch1_illumina
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-ZSI4 (Novaseq 6000)

description:
ZSI4_SPATACseq_Batch1_illumina
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-ZSH8 (Novaseq 6000)

description:
ZSH8_SPATACseq_Batch1_illumina
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-ZSI2 (Novaseq 6000)

description:
ZSI2_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSH6_SPATACseq_Batch1_illumina
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-ZSI1 (Novaseq 6000)

description:
ZSI1_SPATACseq_Batch1_illumina
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-ZSH4 (Novaseq 6000)

description:
ZSH4_SPATACseq_Batch1_illumina
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-ZSH5 (Novaseq 6000)

description:
ZSH5_SPATACseq_Batch1_illumina
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-ZSH3 (Novaseq 6000)

description:
ZSH3_SPATACseq_Batch1_illumina
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-ZSH1 (Novaseq 6000)

description:
ZSH1_SPATACseq_Batch1_illumina
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-ZSG8 (Novaseq 6000)

description:
ZSG8_SPATACseq_Batch1_illumina
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-ZSH2 (Novaseq 6000)

description:
ZSH2_SPATACseq_Batch1_illumina
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-ZSJ5 (Novaseq 6000)

description:
ZSJ5_SPATACseq_Batch1_illumina
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 (Novaseq 6000)

description:
ZSJ3_SPATACseq_Batch1_illumina
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-ZSG7 (Novaseq 6000)

description:
ZSG7_SPATACseq_Batch1_illumina
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-ZSJ6 (Novaseq 6000)

description:
ZSJ6_SPATACseq_Batch1_illumina
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-ZSG5 (Novaseq 6000)

description:
ZSG5_SPATACseq_Batch1_illumina
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-ZSG4 (Novaseq 6000)

description:
ZSG4_SPATACseq_Batch1_illumina
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-ZSG2 (Novaseq 6000)

description:
ZSG2_SPATACseq_Batch1_illumina
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-ZSG6 (Novaseq 6000)

description:
ZSG6_SPATACseq_Batch1_illumina
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-ZSF8 (Novaseq 6000)

description:
ZSF8_SPATACseq_Batch1_illumina
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-ZSF5 (Novaseq 6000)

description:
ZSF5_SPATACseq_Batch1_illumina
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-ZSF7 (Novaseq 6000)

description:
ZSF7_SPATACseq_Batch1_illumina
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-ZSG3 (Novaseq 6000)

description:
ZSG3_SPATACseq_Batch1_illumina
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-ZSF4 (Novaseq 6000)

description:
ZSF4_SPATACseq_Batch1_illumina
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-ZSH7 (Novaseq 6000)

description:
ZSH7_SPATACseq_Batch1_illumina
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-ZSF6 (Novaseq 6000)

description:
ZSF6_SPATACseq_Batch1_illumina
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-ZSF1 (Novaseq 6000)

description:
ZSF1_SPATACseq_Batch1_illumina
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-ZSF2 (Novaseq 6000)

description:
ZSF2_SPATACseq_Batch1_illumina
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-ZSF3 (Novaseq 6000)

description:
ZSF3_SPATACseq_Batch1_illumina
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-ZSG1 (Novaseq 6000)

description:
ZSG1_SPATACseq_Batch1_illumina
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-ZSE8 (Novaseq 6000)

description:
ZSE8_SPATACseq_Batch1_illumina
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-ZSE7 (Novaseq 6000)

description:
ZSE7_SPATACseq_Batch1_illumina
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-ZSE5 (Novaseq 6000)

description:
ZSE5_SPATACseq_Batch1_illumina
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-ZSE6 (Novaseq 6000)

description:
ZSE6_SPATACseq_Batch1_illumina
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-ZSE4 (Novaseq 6000)

description:
ZSE4_SPATACseq_Batch1_illumina
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-ZSE2 (Novaseq 6000)

description:
ZSE2_SPATACseq_Batch1_illumina
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-ZSE3 (Novaseq 6000)

description:
ZSE3_SPATACseq_Batch1_illumina
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-ZSE1 (Novaseq 6000)

description:
ZSE1_SPATACseq_Batch1_illumina
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-ZSD8 (Novaseq 6000)

description:
ZSD8_SPATACseq_Batch1_illumina
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-ZSD7 (Novaseq 6000)

description:
ZSD7_SPATACseq_Batch1_illumina
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-ZSD6 (Novaseq 6000)

description:
ZSD6_SPATACseq_Batch1_illumina
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-ZSD5 (Novaseq 6000)

description:
ZSD5_SPATACseq_Batch1_illumina
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-ZSD4 (Novaseq 6000)

description:
ZSD4_SPATACseq_Batch1_illumina
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-ZSD2 (Novaseq 6000)

description:
ZSD2_SPATACseq_Batch1_illumina
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-ZSD3 (Novaseq 6000)

description:
ZSD3_SPATACseq_Batch1_illumina
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-ZSD1 (Novaseq 6000)

description:
ZSD1_SPATACseq_Batch1_illumina
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-ZSC8 (Novaseq 6000)

description:
ZSC8_SPATACseq_Batch1_illumina
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-ZSC6 (Novaseq 6000)

description:
ZSC6_SPATACseq_Batch1_illumina
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-ZSC5 (Novaseq 6000)

description:
ZSC5_SPATACseq_Batch1_illumina
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-ZSC4 (Novaseq 6000)

description:
ZSC4_SPATACseq_Batch1_illumina
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-ZSC3 (Novaseq 6000)

description:
ZSC3_SPATACseq_Batch1_illumina
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-ZSC2 (Novaseq 6000)

description:
ZSC2_SPATACseq_Batch1_illumina
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-ZSC1 (Novaseq 6000)

description:
ZSC1_SPATACseq_Batch1_illumina
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-ZSB8 (Novaseq 6000)

description:
ZSB8_SPATACseq_Batch1_illumina
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-ZSB7 (Novaseq 6000)

description:
ZSB7_SPATACseq_Batch1_illumina
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-ZSB6 (Novaseq 6000)

description:
ZSB6_SPATACseq_Batch1_illumina
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-ZSB4 (Novaseq 6000)

description:
ZSB4_SPATACseq_Batch1_illumina
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-ZSB3 (Novaseq 6000)

description:
ZSB3_SPATACseq_Batch1_illumina
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-ZSA7 (Novaseq 6000)

description:
ZSA7_SPATACseq_Batch1_illumina
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-ZSB2 (Novaseq 6000)

description:
ZSB2_SPATACseq_Batch1_illumina
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-ZSA8 (Novaseq 6000)

description:
ZSA8_SPATACseq_Batch1_illumina
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-ZSA6 (Novaseq 6000)

description:
ZSA6_SPATACseq_Batch1_illumina
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-ZSB5 (Novaseq 6000)

description:
ZSB5_SPATACseq_Batch1_illumina
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-ZSB1 (Novaseq 6000)

description:
ZSB1_SPATACseq_Batch1_illumina
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-ZSA4 (Novaseq 6000)

description:
ZSA4_SPATACseq_Batch1_illumina
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-ZSA5 (Novaseq 6000)

description:
ZSA5_SPATACseq_Batch1_illumina
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-ZSA3 (Novaseq 6000)

description:
ZSA3_SPATACseq_Batch1_illumina
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-ZSA2 (Novaseq 6000)

description:
ZSA2_SPATACseq_Batch1_illumina
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-ZS0G (Novaseq 6000)

description:
ZS0G_SPATACseq_Batch1_illumina
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-ZS0H (Novaseq 6000)

description:
ZS0H_SPATACseq_Batch1_illumina
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-ZSA1 (Novaseq 6000)

description:
ZSA1_SPATACseq_Batch1_illumina
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-ZSC7 (Novaseq 6000)

description:
ZSC7_SPATACseq_Batch1_illumina
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-ZS0F (Novaseq 6000)

description:
ZS0F_SPATACseq_Batch1_illumina
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-ZS0D (Novaseq 6000)

description:
ZS0D_SPATACseq_Batch1_illumina
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-ZS0E (Novaseq 6000)

description:
ZS0E_SPATACseq_Batch1_illumina
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-ZS0C (Novaseq 6000)

description:
ZS0C_SPATACseq_Batch1_illumina
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-ZS0A (Novaseq 6000)

description:
ZS0A_SPATACseq_Batch1_illumina
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: HUVECs_PNUTS siRNA_3

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

data_processing:
fastqc, 0.10.1; bowtie2, 2.2.6; tophat, 2.1.0; samtools, 1.2; picard, v1.139; cufflinks, 2.2.1; cuffmerge, 1.0.0; cuffquant, 2.2.1; featureCounts, v1.4.6-p4; cuffnorm, 2.2.1; cuffdiff, 2.2.1;
Assembly: GRCh37
Supplementary files format and content: Microsoft Excel Spreadsheet containing FPKM values per strand for each sample

source_name: HUVEC human umbilical vein endothelial cells

growth_protocol: HUVECs were transfected at a confluency of 70% and harvested 48h after transfection.

extract_protocol:
All samples were prepared using miRNeasy Kit (Qiagen) including DNase treatment.
Illumina TruSeq stranded total RNA sample preparation kit (Illumina) with rRNA depletion

value: PNUTS siRNA


title: SPATAC-seq with zebrafish embryogenesis well-ZS0B (Novaseq 6000)

description:
ZS0B_SPATACseq_Batch1_illumina
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: HUVECs_PNUTS siRNA_1

value: HUVEC human umbilical vein endothelial cells


title: HUVECs_PNUTS siRNA_2


title: HUVECs_control siRNA_1

value: control siRNA


title: MG1655 dmhpR3

city: Martinsired

first: Kilian

last: Schumacher

address: Großhaderner Straße 2-4

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

organism: Escherichia coli str. K-12 substr. MG1655

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.

value: bacterial cell

value: dmhpR


title: MG1655 dmhpR2


title: HUVECs_control siRNA_2


title: MG1655 dmhpR1


title: MG1655 WT3

value: Wildtype


title: MG1655 WT1


title: Bulk ATAC-seq with zebrafish embryogenesis in 72hpf with replicate 1 (DNBSEQ-T7)

description:
hpf72-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 48hpf with replicate 1 (DNBSEQ-T7)

description:
hpf48-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 48hpf with replicate 2 (DNBSEQ-T7)

description:
hpf48-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: MG1655 WT2


title: Bulk ATAC-seq with zebrafish embryogenesis in 38hpf with replicate 2 (DNBSEQ-T7)

description:
hpf38-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 72hpf with replicate 2 (DNBSEQ-T7)

description:
hpf72-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 42hpf with replicate 2 (DNBSEQ-T7)

description:
hpf42-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 42hpf with replicate 1 (DNBSEQ-T7)

description:
hpf42-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 30hpf with replicate 2 (DNBSEQ-T7)

description:
hpf30-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 38hpf with replicate 1 (DNBSEQ-T7)

description:
hpf38-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: HUVECs_control siRNA_3


title: Bulk ATAC-seq with zebrafish embryogenesis in 34hpf with replicate 1 (DNBSEQ-T7)

description:
hpf34-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 24hpf with replicate 2 (DNBSEQ-T7)

description:
hpf24-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 24hpf with replicate 1 (DNBSEQ-T7)

description:
hpf24-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 30hpf with replicate 1 (DNBSEQ-T7)

description:
hpf30-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 34hpf with replicate 2 (DNBSEQ-T7)

description:
hpf34-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 22hpf with replicate 2 (DNBSEQ-T7)

description:
hpf22-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 20hpf with replicate 1 (DNBSEQ-T7)

description:
hpf20-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 18hpf with replicate 2 (DNBSEQ-T7)

description:
hpf18-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 18hpf with replicate 1 (DNBSEQ-T7)

description:
hpf18-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 14hpf with replicate 1 (DNBSEQ-T7)

description:
hpf14-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 12hpf with replicate 2 (DNBSEQ-T7)

description:
hpf12-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 12hpf with replicate 1 (DNBSEQ-T7)

description:
hpf12-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 11hpf with replicate 1 (DNBSEQ-T7)

description:
hpf11-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 22hpf with replicate 1 (DNBSEQ-T7)

description:
hpf22-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 9hpf with replicate 2 (DNBSEQ-T7)

description:
hpf09-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 9hpf with replicate 1 (DNBSEQ-T7)

description:
hpf09-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 8hpf with replicate 1 (DNBSEQ-T7)

description:
hpf08-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 6hpf with replicate 2 (DNBSEQ-T7)

description:
hpf06-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 10hpf with replicate 1 (DNBSEQ-T7)

description:
hpf10-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 8hpf with replicate 2 (DNBSEQ-T7)

description:
hpf08-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 6hpf with replicate 1 (DNBSEQ-T7)

description:
hpf06-Bulk-rep1
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 14hpf with replicate 2 (DNBSEQ-T7)

description:
hpf14-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 5hpf with replicate 1 (DNBSEQ-T7)

description:
hpf05-Bulk-rep1
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-ZB5SLH07 (DNBSEQ-T7)

description:
ZB5SLH07_SPATACseq_Batch5
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 5hpf with replicate 2 (DNBSEQ-T7)

description:
hpf05-Bulk-rep2
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-ZB5SLH06 (DNBSEQ-T7)

description:
ZB5SLH06_SPATACseq_Batch5
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 20hpf with replicate 2 (DNBSEQ-T7)

description:
hpf20-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 7hpf with replicate 1 (DNBSEQ-T7)

description:
hpf07-Bulk-rep1
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-ZB5SLH08 (DNBSEQ-T7)

description:
ZB5SLH08_SPATACseq_Batch5
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 4hpf with replicate 2 (DNBSEQ-T7)

description:
hpf04-Bulk-rep2
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-ZB5SLH05 (DNBSEQ-T7)

description:
ZB5SLH05_SPATACseq_Batch5
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-ZB5SLH04 (DNBSEQ-T7)

description:
ZB5SLH04_SPATACseq_Batch5
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 4hpf with replicate 1 (DNBSEQ-T7)

description:
hpf04-Bulk-rep1
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-ZB5SLH01 (DNBSEQ-T7)

description:
ZB5SLH01_SPATACseq_Batch5
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-ZB5SLH03 (DNBSEQ-T7)

description:
ZB5SLH03_SPATACseq_Batch5
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-ZB5SLG08 (DNBSEQ-T7)

description:
ZB5SLG08_SPATACseq_Batch5
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-ZB5SLH02 (DNBSEQ-T7)

description:
ZB5SLH02_SPATACseq_Batch5
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 11hpf with replicate 2 (DNBSEQ-T7)

description:
hpf11-Bulk-rep2
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 10hpf with replicate 2 (DNBSEQ-T7)

description:
hpf10-Bulk-rep2
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-ZB5SLG06 (DNBSEQ-T7)

description:
ZB5SLG06_SPATACseq_Batch5
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-ZB5SLG05 (DNBSEQ-T7)

description:
ZB5SLG05_SPATACseq_Batch5
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Bulk ATAC-seq with zebrafish embryogenesis in 7hpf with replicate 2 (DNBSEQ-T7)

description:
hpf07-Bulk-rep2
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-ZB5SLG03 (DNBSEQ-T7)

description:
ZB5SLG03_SPATACseq_Batch5
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-ZB5SLG04 (DNBSEQ-T7)

description:
ZB5SLG04_SPATACseq_Batch5
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-ZB5SLG02 (DNBSEQ-T7)

description:
ZB5SLG02_SPATACseq_Batch5
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-ZB5SLG01 (DNBSEQ-T7)

description:
ZB5SLG01_SPATACseq_Batch5
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-ZB5SLF08 (DNBSEQ-T7)

description:
ZB5SLF08_SPATACseq_Batch5
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-ZB5SLF07 (DNBSEQ-T7)

description:
ZB5SLF07_SPATACseq_Batch5
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-ZB5SLF06 (DNBSEQ-T7)

description:
ZB5SLF06_SPATACseq_Batch5
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-ZB5SLF04 (DNBSEQ-T7)

description:
ZB5SLF04_SPATACseq_Batch5
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-ZB5SLE08 (DNBSEQ-T7)

description:
ZB5SLE08_SPATACseq_Batch5
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-ZB5SLD08 (DNBSEQ-T7)

description:
ZB5SLD08_SPATACseq_Batch5
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-ZB5SLF02 (DNBSEQ-T7)

description:
ZB5SLF02_SPATACseq_Batch5
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-ZB5SLE07 (DNBSEQ-T7)

description:
ZB5SLE07_SPATACseq_Batch5
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-ZB5SLF01 (DNBSEQ-T7)

description:
ZB5SLF01_SPATACseq_Batch5
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-ZB5SLE02 (DNBSEQ-T7)

description:
ZB5SLE02_SPATACseq_Batch5
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-ZB5SLF03 (DNBSEQ-T7)

description:
ZB5SLF03_SPATACseq_Batch5
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-ZB5SLF05 (DNBSEQ-T7)

description:
ZB5SLF05_SPATACseq_Batch5
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-ZB5SLE04 (DNBSEQ-T7)

description:
ZB5SLE04_SPATACseq_Batch5
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-ZB5SLD06 (DNBSEQ-T7)

description:
ZB5SLD06_SPATACseq_Batch5
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-ZB5SLE06 (DNBSEQ-T7)

description:
ZB5SLE06_SPATACseq_Batch5
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-ZB5SLE03 (DNBSEQ-T7)

description:
ZB5SLE03_SPATACseq_Batch5
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-ZB5SLD07 (DNBSEQ-T7)

description:
ZB5SLD07_SPATACseq_Batch5
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-ZB5SLE05 (DNBSEQ-T7)

description:
ZB5SLE05_SPATACseq_Batch5
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-ZB5SLE01 (DNBSEQ-T7)

description:
ZB5SLE01_SPATACseq_Batch5
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-ZB5SLG07 (DNBSEQ-T7)

description:
ZB5SLG07_SPATACseq_Batch5
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-ZB5SLD03 (DNBSEQ-T7)

description:
ZB5SLD03_SPATACseq_Batch5
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-ZB5SLD04 (DNBSEQ-T7)

description:
ZB5SLD04_SPATACseq_Batch5
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-ZB5SLD02 (DNBSEQ-T7)

description:
ZB5SLD02_SPATACseq_Batch5
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-ZB5SLC08 (DNBSEQ-T7)

description:
ZB5SLC08_SPATACseq_Batch5
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-ZB5SLC05 (DNBSEQ-T7)

description:
ZB5SLC05_SPATACseq_Batch5
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-ZB5SLC06 (DNBSEQ-T7)

description:
ZB5SLC06_SPATACseq_Batch5
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-ZB5SLC03 (DNBSEQ-T7)

description:
ZB5SLC03_SPATACseq_Batch5
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-ZB5SLC07 (DNBSEQ-T7)

description:
ZB5SLC07_SPATACseq_Batch5
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-ZB5SLC04 (DNBSEQ-T7)

description:
ZB5SLC04_SPATACseq_Batch5
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-ZB5SLC02 (DNBSEQ-T7)

description:
ZB5SLC02_SPATACseq_Batch5
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-ZB5SLB08 (DNBSEQ-T7)

description:
ZB5SLB08_SPATACseq_Batch5
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-ZB5SLC01 (DNBSEQ-T7)

description:
ZB5SLC01_SPATACseq_Batch5
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-ZB5SLD05 (DNBSEQ-T7)

description:
ZB5SLD05_SPATACseq_Batch5
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-ZB5SLB03 (DNBSEQ-T7)

description:
ZB5SLB03_SPATACseq_Batch5
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-ZB5SLB06 (DNBSEQ-T7)

description:
ZB5SLB06_SPATACseq_Batch5
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-ZB5SLB05 (DNBSEQ-T7)

description:
ZB5SLB05_SPATACseq_Batch5
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-ZB5SLB04 (DNBSEQ-T7)

description:
ZB5SLB04_SPATACseq_Batch5
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-ZB5SLB07 (DNBSEQ-T7)

description:
ZB5SLB07_SPATACseq_Batch5
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-ZB5SLA05 (DNBSEQ-T7)

description:
ZB5SLA05_SPATACseq_Batch5
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-ZB5SLB01 (DNBSEQ-T7)

description:
ZB5SLB01_SPATACseq_Batch5
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-ZB5SLA01 (DNBSEQ-T7)

description:
ZB5SLA01_SPATACseq_Batch5
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-ZB4SL16C (DNBSEQ-T7)

description:
ZB4SL16C_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-ZB5SLB02 (DNBSEQ-T7)

description:
ZB5SLB02_SPATACseq_Batch5
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-ZB5SLD01 (DNBSEQ-T7)

description:
ZB5SLD01_SPATACseq_Batch5
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-ZB5SLA06 (DNBSEQ-T7)

description:
ZB5SLA06_SPATACseq_Batch5
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-ZB5SLA07 (DNBSEQ-T7)

description:
ZB5SLA07_SPATACseq_Batch5
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-ZB5SLA02 (DNBSEQ-T7)

description:
ZB5SLA02_SPATACseq_Batch5
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-ZB4SL16B (DNBSEQ-T7)

description:
ZB4SL16B_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-ZB5SLA04 (DNBSEQ-T7)

description:
ZB5SLA04_SPATACseq_Batch5
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-ZB4SL16A (DNBSEQ-T7)

description:
ZB4SL16A_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-ZB4SL11H (DNBSEQ-T7)

description:
ZB4SL11H_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-ZB4SL11G (DNBSEQ-T7)

description:
ZB4SL11G_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-ZB4SL11F (DNBSEQ-T7)

description:
ZB4SL11F_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-ZB4SL11E (DNBSEQ-T7)

description:
ZB4SL11E_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-ZB4SL11D (DNBSEQ-T7)

description:
ZB4SL11D_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-ZB4SL11C (DNBSEQ-T7)

description:
ZB4SL11C_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-ZB4SL11B (DNBSEQ-T7)

description:
ZB4SL11B_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-ZB4SL11A (DNBSEQ-T7)

description:
ZB4SL11A_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-ZB4SL10H (DNBSEQ-T7)

description:
ZB4SL10H_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-ZB5SLA03 (DNBSEQ-T7)

description:
ZB5SLA03_SPATACseq_Batch5
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-ZB5SLA08 (DNBSEQ-T7)

description:
ZB5SLA08_SPATACseq_Batch5
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-ZB4SL10G (DNBSEQ-T7)

description:
ZB4SL10G_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-ZB4SL10F (DNBSEQ-T7)

description:
ZB4SL10F_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-ZB4SL10E (DNBSEQ-T7)

description:
ZB4SL10E_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-ZB4SL10D (DNBSEQ-T7)

description:
ZB4SL10D_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-ZB4SL10A (DNBSEQ-T7)

description:
ZB4SL10A_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-ZB4SL09F (DNBSEQ-T7)

description:
ZB4SL09F_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-ZB4SL09E (DNBSEQ-T7)

description:
ZB4SL09E_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-ZB4SL02G (DNBSEQ-T7)

description:
ZB4SL02G_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-ZB4SL09C (DNBSEQ-T7)

description:
ZB4SL09C_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-ZB4SL09B (DNBSEQ-T7)

description:
ZB4SL09B_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-ZB4SL09D (DNBSEQ-T7)

description:
ZB4SL09D_SPATACseq_Batch4
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file