title: 8iH1: Head regeneration ATAC-seq, 8 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iH1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (8iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: AHR KD - AHR KD 3 [C2_siA1]

status: Public on Jul 01 2020

type: SRA

city: Stanford

first: Juyong

middle: Brian

last: Kim

state: CA

address: 300 Pasteur Dr.

country: USA

institute: Stanford University

description: processed data file: mastertable.genename.siAHR.txt

library_source: transcriptomic

data_processing:
RNA-seq: QC of sequencing data was performed using fastqc. Then, STAR was used to map the reads to the reference genome (hg19). FeatureCounts from the Subread package was then used to count the number of reads mapped, and deseq2 was used to generate the list of differentially regulated genes.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: HCASMC_AHR KD - AHR KD

growth_protocol: HCASMC media, passages 5-8

extract_protocol: HCASMC between passages 5-8 were used to transfect scrambled RNA or siRNA. Then RNA was collected after 48 hours using the Rneasy kit from Qiagen, and sent for library construction and sequencing performed at Novogene. 250-300bp cDNA library was constructed , and sequenced.

tag: cell line

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

tag: tissue

value: coronary artery

tag: genotype/treatment

value: AHR knockdown


title: Q133H differentiation T=0  rep2

city: Bethlehem

first: Ashvin

last: Iyer

state: Pennsylvania

address: 1325B Johnston Drive

department: Pharmaceutical Sciences

institute: University of the Sciences

description:
Q133H differentiation T=0
Emerin-null cells transduced with Q133H emerin mutant
Q133H_T0-VS-Q133H_T24.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-Q133H_T0.DEseq2_Method.GeneDiffExp.xls

data_processing:
Purity of RNA was assessed using Nanodrop (ND-2000) and quantification was done using the Quant-IT RNA assay kit (ThermoFisher Scientific, #Q10213). BGI Genomics performed library preparation and sequencing using BGISEQ-500 platform.
BGI Genomics filtered reads using SOAPnuke and genome mapping was done to the mouse genome (mm10) using hierarchical indexing for spliced alignment of Transcripts-2 (HISAT2).
Differentially expressed genes was detected using DEseq2. Transcripts were considered to be significantly differentially expressed if the q-value <0.05. The q-value is a p-value corrected for the False Discovery Rate (FDR) and represents the standard in the field for determining significance.
All differentially expressed transcripts were also >= 2-fold increased or decreased.
KEGG pathway enrichment analysis was done using phyper, a function of R.

organism: Mus musculus

source_name: Emerin-null H2K myogenic precursor cells

growth_protocol: Proliferating myogenic progenitors  were cultured in plates coated with gelatin at 37°C and 10% CO2 in DMEM containing 20% HI-FBS, 2% L-glutamine, 2% Chick embryo extract , 1% Pen/Strep and 20 units/ml γ-interferon . Differentiating cells were cultured in plates coated with gelatin in proliferative conditions for 24 h, then switched to differentiation media consisting of DMEM supplemented with 5% horse serum and 2% L-glutamine and grown at 37°C and 5% CO2.  For EDMD mutant cell lines, puromycin was added to the media during proliferation and differentiation.

extract_protocol:
RNA was isolated using the mRNeasy Plus Kit (Qiagen, Germantown, MD. USA, #74136) per manufacturer’s instructions. Three technical replicates per sample were performed for each biological replicate (n=2).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached  magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent  cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using  reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA  Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and  subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle  (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle  by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs  were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq  platform for the following data analysis study. For this step, the DNBseq platform combines the DNA  nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis  Sequencing Method.

tag: cell type

value: H2K myogenic precursor cells


title: CTRL 1 [WTCHG_281991_273_1CTRL_1]

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

country: United Kingdom

institute: King's College London

description: mRNA fraction selected from total RNA before conversion to cDNA

data_processing:
Quality of raw sequencing files was checked using FastQC version 0.11.2 and trimming of adaptor sequences and the first 12 bases from the 5’ end of all reads was performed using Trim Galore! Version 0.4.1
Reads were aligned to mouse genome mm10 using TopHat version 2.1.0 with parameters  -bowtie1 -r 150, -mate-std-dev=50, -p 8
Reads were counted using FeatureCounts version 1.5.0 with parameters -p -T 8 -F GTF
Read counts from technical replicates (i.e. from both lanes) were summed using the Deseq2  CollapseReplicates function.  Deseq2 was used for differential expression testing, using the DESeq command. The results command with the “contrast” argument was used to compare expression profiles between control and test genotypes.
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Text file containing read counts for all samples assigned to features (genes)

source_name: Chd8 +/+_E12.5_cortex

extract_protocol:
Total RNA was extracted from brain tissue samples using Trizol Reagent. RNA was purified using the Direct-Zol RNA Miniprep Kit (Zymo Research, CA, USA; Catalogue No. R2050) according to the manufacturer's recommendations.
Library Prep was performed by the Oxford Genomics Centre (Oxford, United Kingdom). mRNA was selected from total RNA and converted to cDNA. dUTP was incorporated during second strand cDNA synthesis. CDNA was end-repaired, A-tailed and adaptor ligated. Uridine digestion was performed before amplification of samples. Prepared libraries were size selected and multiplexed and paired-end sequencing was performed across 2 lanes of a flow cell on the Illumina HiSeq 4000 platform.

tag: strain

tag: developmental stage

value: Embryonic day 12.5

tag: genotype/variation

value: Cortex


title: 3iF5: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 5, iCRT14 treated

city: Davis

first: Jack

last: Cazet

address: 1 Shields Ave.

department: MCB

institute: University of California, Davis

library_source: genomic

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iF5_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

molecule: genomic DNA

organism: Hydra vulgaris

source_name: Mid-Body Column Tissue

growth_protocol: Hydra vulgaris strain 105 polyps were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C and fed 1-2 times weekly with Artemia nauplii.

extract_protocol:
15 regenerating tips were homogenized using a dounce homogenizer and cells were lysed using a cocktail of mild detergents as described in the OMNI-ATAC-seq protocol (Corces et al., 2017). ~50000 nuclei were then spun down and used for tagmentation.
Libraries were prepared as described in the original ATAC-seq publication (Buenrostro et al., 2013)

treatment_protocol: For iCRT14 treatment, Hydra were pre-incubated in 5uM iCRT14 for two hours prior to amputation. Following amputation, iCRT14 treatment continued until tissue was collected for library preparation.

value: Mid-Body Column

tag: timepoint

value: 3 hours post amputation

tag: regeneration type

value: Foot Regeneration

tag: treatment

value: treated with  5uM iCRT14 for 5 hours


title: Del9599 differentiation T=0 rep2

description:
Del9599 differentiation T=0
Emerin-null cells transduced with del9599 emerin mutant
9599_T0-VS-9599_T24.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-9599_T0.DEseq2_Method.GeneDiffExp.xls


title: AHR OE - Control 2 [C2]

description: processed data file: all_genes_exp.txt

source_name: HCASMC_AHR OE - control

value: Control


title: Control 3 for AHR KD and TCF21 KD [C2_NC1]

source_name: HCASMC_AHR KD - control


title: 8iH4: Head regeneration ATAC-seq, 8 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iH4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (8iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: 8 hours post amputation

value: Head Regeneration

value: treated with  5uM iCRT14 for 10 hours


title: AHR OE - Control 1 [C1]

description: processed data file: all_genes_exp.txt


title: CTRL 2 [WTCHG_281991_274_1CTRL_2]


title: S54F differentiation T=0 rep2

description:
S54F differentiation T=0
Emerin-null cells transduced with S54F emerin mutant
S54F_T0-VS-S54F_T24.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-S54F_T0.DEseq2_Method.GeneDiffExp.xls


title: 3iF4: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iF4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: 8iH2: Head regeneration ATAC-seq, 8 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iH2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (8iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: Wild type differentiation T=48 rep2

description:
Wild type differentiation T=48
WT_T24-VS-WT_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-9599_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-EMD_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-Enull_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-Q133H_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-S54F_T48.DEseq2_Method.GeneDiffExp.xls

source_name: Wildtype H2K myogenic precursor cells


title: Control 4 for AHR KD and TCF21 KD [C2_NC2]


title: 8iH3: Head regeneration ATAC-seq, 8 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iH3_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (8iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: Del9599 differentiation T=24 rep2

description:
Del9599 differentiation T=24
Emerin-null cells transduced with del9599 emerin mutant
9599_T24-VS-9599_T48.DEseq2_Method.GeneDiffExp.xls
9599_T0-VS-9599_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-9599_T24.DEseq2_Method.GeneDiffExp.xls


title: SUMO2-cKO rep3

city: Durham

first: Wei

last: Yang

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

data_processing:
TrimGalore toolkit which employed Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads . Only reads that were 20 nt or longer after trimming were reserved for further analysis.
STAR RNA-Seq for alignment. Reads were reserved for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression were performed using the DESeq2 Bioconductor package with the R statistical programming environment .
Genome_build: GRCm38v68 version of the mouse genome
Supplementary_files_format_and_content: Excel file with normalized expression values.

source_name: hippocampus

extract_protocol:
Hippocampus were removed and snap frozen in liquid nitrogen. RNA was prepared using Trizol reagent (Invitrogen), treated with DNase, and purified with RNA Cleanup kit (Qiagen). The KAPA Stranded mRNA-Seq Kit (KapaBioSystems) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

tag: age

value: 2-month old

tag: genotype

value: Sumo2 f/f;Emx1-Cre


title: SUMO2-cKO rep4


title: Del9599 differentiation T=48 rep2

description:
Del9599 differentiation T=48
Emerin-null cells transduced with del9599 emerin mutant
9599_T24-VS-9599_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-9599_T48.DEseq2_Method.GeneDiffExp.xls


title: AHR KD - AHR KD 4 [C2_siA2]

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)


title: AHR KD - AHR KD 1 [C1_siA1]

value: coronary artery


title: Wild type differentiation T=24 rep2

description:
Wild type differentiation T=24
WT_T24-VS-9599_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-EMD_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-Enull_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-Q133H_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-S54F_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-WT_T48.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-WT_T24.DEseq2_Method.GeneDiffExp.xls


title: Control rep4

value: Sumo2 f/f


title: 3iH3: Head regeneration ATAC-seq, 3 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iH3_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: AHR KD - AHR KD 2 [C1_siA2]

value: AHR knockdown


title: Control rep2


title: 3iF3: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iF3_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: Emerin null differentiation T=0 rep2

description:
Emerin null differentiation T=0
Enull_T0-VS-Enull_T24.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-Enull_T0.DEseq2_Method.GeneDiffExp.xls

value: H2K myogenic precursor cells


title: 3iH4: Head regeneration ATAC-seq, 3 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iH4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: Control rep1


title: Control 1 for AHR KD and TCF21 KD [C1_NC1]


title: 0iF4: Foot regeneration ATAC-seq, 0 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iF4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: 0 hours post amputation

value: treated with  5uM iCRT14 for 2 hours


title: EMD differentiation T=24 rep1

description:
EMD differentiation T=24
Emerin-null cells transduced with wildtype emerin
EMD_T24-VS-EMD_T48.DEseq2_Method.GeneDiffExp.xls
EMD_T0-VS-EMD_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-EMD_T24.DEseq2_Method.GeneDiffExp.xls


title: TCF21 KD - TCF21 KD 4 [C2_siT2]

description: processed data file: mastertable.genename.siTCF21.txt

source_name: HCASMC_TCF21 KD - TCF21 KD

value: TCF21 knockdown


title: 12iH4: Head regeneration ATAC-seq, 12 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iH4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Mid-Body Column

value: 12 hours post amputation

value: treated with  5uM iCRT14 for 14 hours


title: Control 2 for AHR KD and TCF21 KD [C1_NC2]

value: Control


title: 3iF1: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iF1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: 3 hours post amputation

value: Foot Regeneration

value: treated with  5uM iCRT14 for 5 hours


title: HUVEC KRAS-U0126 rep3

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Next, Fastq files were aligned to GRCh38 (or hg19) and transcript abundance estimates were quantified using Salmon 1.1.0.
Normalized counts and differential expression were acquired using tximport and DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Plain-text, tab-separated file with a single header line (which names all of the columns) that contains Name, Length, EffectiveLength, TPM and NumReads

source_name: Human umbilical vein endothelial cell

growth_protocol: HUVEC were electroporated with 2.5 µg of pCS2+ (control) or pCS2-KRAS4AG12V together with 0.2 µg of pmaxGFP (Lonza) using the P5 Primary Cell Kit (Lonza, Cat#: V4XP-5024) and a 4D-nucleofector (Lonza). Electroporation efficiency was typically ~70%, as assessed by pmaxGFP expression the following day. Cells from each electroporation were plated in two wells of a 12-well plate (pre-coated with attachment factor). Media was changed 1 h after plating.

extract_protocol:
RNA was isolated using Trizol and stored at -80oC until processing.
Upon processing, RNA from all samples was thawed and following confirmation of integrity and concentration using a Bioanalyzer, 100 ng was used for low-input library preparation using the NEBNext Ultra II RNA Library Prep kit for Illumina.
The libraries were then quantified and sequenced using an Illumina NovaSeq 6000 at a depth of 20 million reads per sample.

treatment_protocol: After ~18 h, serum-starve media (basal media [ScienCell], no growth factors, 0.1% FBS) containing 20 µM U0126 (InvivoGen), 10 µM LY294002 (Cell Signaling) or an equivalent amount of DMSO (vehicle control, 0.1%) was added to confluent cells for 6 h.

value: Human umbilical vein endothelial cell

tag: electroporated construct


title: HUVEC KRAS-U0126 rep2


title: CTRL 1 [WTCHG_282157_273_1CTRL_1]

value: Embryonic day 12.5

value: Cortex


title: hy5_3

city: Berlin

first: Henrik

last: Johansson

address: Albrecht-Thaer-Weg 6

country: Germany

institute: Freie Universität Berlin

description: deetiolated/red light

data_processing:
Base-calling was done with BGISEQ500, version 1.1.2.29164.
After removal of adaptors and low quality reads, the obtained clean reads (approximately 23 million) were stored as FASTQ format SOAPnuke, version v1.5.2, parameters: -I15 -q 0.5 -n0.1.
The clean reads were mapped to the reference genome (TAIR10) using HISAT, version v2.0.4, parameters: -p8 --phred64 --sensitive -I 1 -X10000.
For gene expression analysis clean reads were mapped to reference using Bowtie2, v2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Gene expression levels based on the FPKM method were quantified using RSEM v1.2.12, Parameters: default.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.gene.fpkm.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seeds were surface sterilized, sown on half MS medium without sucrose and stratified in darkness for 2 days at 4°C before given a two hours white light pulse (90 µmol m-2 s-1) and returned to darkness for 22 h. Seedlings were grown for 3 more days in red light [80 µmol m-2 s-1] at 22 °C.

extract_protocol:
Total RNA was extracted from seedlings flash-frozen in liquid nitrogen using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) as described in the user’s manual including an on-column DNase treatment.
RNA libraries were prepared by the BGISEQ-500 RNA-Seq Library Preparation Protocol. In brief, mRNA was purified with oligo(dt) magnetic beads, mRNA was chemically fragmented and cDNA was generated using random hexamer-primed reverse transcription. End-repair and 3'adenylation was done and adapters were ligated to the adenylated cDNA. Adapter-ligated was amplified via PCR and purified with Ampure XP Beads (Agencourt). The library was validated on the Agilent Technologies 2100 Bioanalyzer and the double stranded PCR products were denaturized and circularized.

value: Whole seedling

value: 4 days after germination


title: Wild type differentiation T=0 rep2

description:
Wild type differentiation T=0
WT_T0-VS-Enull_T0.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-EMD_T0.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-9599_T0.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-S54F_T0.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-Q133H_T0.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-WT_T24.DEseq2_Method.GeneDiffExp.xls


title: SUMO2-cKO rep1

value: hippocampus

value: 2-month old

value: Sumo2 f/f;Emx1-Cre


title: 3iH2: Head regeneration ATAC-seq, 3 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iH2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Head Regeneration


title: Emerin null differentiation T=48 rep2

description:
Emerin null differentiation T=48
Enull_T24-VS-Enull_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-Enull_T48.DEseq2_Method.GeneDiffExp.xls

data_processing:
Purity of RNA was assessed using Nanodrop (ND-2000) and quantification was done using the Quant-IT RNA assay kit (ThermoFisher Scientific, #Q10213). BGI Genomics performed library preparation and sequencing using BGISEQ-500 platform.
BGI Genomics filtered reads using SOAPnuke and genome mapping was done to the mouse genome (mm10) using hierarchical indexing for spliced alignment of Transcripts-2 (HISAT2).
Differentially expressed genes was detected using DEseq2. Transcripts were considered to be significantly differentially expressed if the q-value <0.05. The q-value is a p-value corrected for the False Discovery Rate (FDR) and represents the standard in the field for determining significance.
All differentially expressed transcripts were also >= 2-fold increased or decreased.
KEGG pathway enrichment analysis was done using phyper, a function of R.

value: H2K myogenic precursor cells


title: HUVEC KRAS-U0126 rep1


title: Emerin null differentiation T=24 rep2

description:
Emerin null differentiation T=24
Enull_T0-VS-Enull_T24.DEseq2_Method.GeneDiffExp.xls
Enull_T24-VS-Enull_T48.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-Enull_T24.DEseq2_Method.GeneDiffExp.xls


title: Q133H differentiation T=48 rep1

description:
Q133H differentiation T=48
Emerin-null cells transduced with Q133H emerin mutant
Q133H_T24-VS-Q133H_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-Q133H_T48.DEseq2_Method.GeneDiffExp.xls


title: 0iF2: Foot regeneration ATAC-seq, 0 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iF2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Mid-Body Column

value: 0 hours post amputation

value: treated with  5uM iCRT14 for 2 hours


title: 3iF2: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iF2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: HUVEC KRAS-LY294002 rep2


title: HUVEC KRAS-LY294002 rep3


title: SUMO2-cKO rep2


title: hy5_1

description: deetiolated/red light


title: HUVEC KRAS-LY294002 rep1


title: EMD differentiation T=48 rep1

description:
EMD differentiation T=48
Emerin-null cells transduced with wildtype emerin
EMD_T24-VS-EMD_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-EMD_T48.DEseq2_Method.GeneDiffExp.xls


title: 3iH1: Head regeneration ATAC-seq, 3 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (3iH1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (3iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: HUVEC KRAS-DMSO rep2

value: DMSO


title: Control rep3

value: Sumo2 f/f


title: 0iH3: Head regeneration ATAC-seq, 0 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iH3_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: 0iH4: Head regeneration ATAC-seq, 0 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iH4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: HUVEC PCS2-DMSO rep3


title: EMD differentiation T=0 rep1

description:
EMD differentiation T=0
Emerin-null cells transduced with wildtype emerin
EMD_T0-VS-EMD_T24.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-EMD_T0.DEseq2_Method.GeneDiffExp.xls


title: bbx202122_1

description: deetiolated/red light


title: S54F differentiation T=24 rep1

description:
S54F differentiation T=24
Emerin-null cells transduced with S54F emerin mutant
S54F_T24-VS-S54F_T48.DEseq2_Method.GeneDiffExp.xls
S54F_T0-VS-S54F_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-S54F_T24.DEseq2_Method.GeneDiffExp.xls


title: Q133H differentiation T=0  rep1

description:
Q133H differentiation T=0
Emerin-null cells transduced with Q133H emerin mutant
Q133H_T0-VS-Q133H_T24.DEseq2_Method.GeneDiffExp.xls
WT_T0-VS-Q133H_T0.DEseq2_Method.GeneDiffExp.xls


title: 0iF3: Foot regeneration ATAC-seq, 0 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iF3_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Foot Regeneration


title: HUVEC KRAS-DMSO rep1


title: hy5_2

description: deetiolated/red light


title: 0iH2: Head regeneration ATAC-seq, 0 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iH2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: HUVEC KRAS-DMSO rep3


title: 0iF1: Foot regeneration ATAC-seq, 0 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iF1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: bbx202122_3

description: deetiolated/red light


title: 0iH1: Head regeneration ATAC-seq, 0 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (0iH1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: treated with 5uM iCRT14 for 2 hours


title: S54F differentiation T=0 rep1


title: HUVEC PCS2-DMSO rep1

value: Human umbilical vein endothelial cell


title: Q133H differentiation T=24 rep1

description:
Q133H differentiation T=24
Emerin-null cells transduced with Q133H emerin mutant
Q133H_T24-VS-Q133H_T48.DEseq2_Method.GeneDiffExp.xls
Q133H_T0-VS-Q133H_T24.DEseq2_Method.GeneDiffExp.xls
WT_T24-VS-Q133H_T24.DEseq2_Method.GeneDiffExp.xls


title: 12F5: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 5

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (12F5_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12F_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: 12 hours post amputation

value: Untreated


title: FANCJ_rep_3

city: Cambridge UK

first: Julian

middle: E

last: Sale

address: Cambridge Biomedical Campus, Francis Crick Ave

department: PNAC

institute: MRC Laboratory of Molecular Biology

data_processing:
RNA sequencing reads were aligned to the GRCg6a chicken genome using Bowtie 2
Expression estimates were calculated using the rsem-calculate-expression command of RSEM and the version 96 of the chicken genome gene annotation from Ensembl
Genome_build: GRCg6a
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each transcript

molecule: polyA RNA

organism: Gallus gallus

source_name: DT40 cells

growth_protocol: All DT40 cell lines were cultured at 37°C in a humidified 10% CO2 atmosphere in RPMI 1640 with Glutamax (Thermo Fisher Scientific) supplemented with 7% fetal bovine serum (Thermo Fisher Scientific), 3% chicken serum (Sigma-Aldrich), 50 μM 2-mercaptoethanol and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN), according to the manufacturer’s instructions.
750 ng RNA were used to build the next generation sequencing libraries with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs), NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2), according to the manufacturer’s intructions.
poly(A) capture

treatment_protocol: DT40 timeless and ddx11mutants were generated by CRISPR-Cas9-mediated gene disruption

value: FANCJ KO


title: S54F differentiation T=48 rep1

description:
S54F differentiation T=48
Emerin-null cells transduced with S54F emerin mutant
S54F_T24-VS-S54F_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-S54F_T48.DEseq2_Method.GeneDiffExp.xls


title: bbx202122_2

description: deetiolated/red light

value: Whole seedling

value: 4 days after germination


title: 12F4: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 4

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (12F4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12F_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: HUVEC PCS2-DMSO rep2


title: Y-organ C1

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

country: China

institute: College of Life Sciences, Tianjin Normal University

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw reads and saved as fastq files
Filter dirty raw reads to obtain clean reads.1.Remove reads with adaptors;2.Remove reads in which unknown bases are more than 10%;3.Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read)
Clean reads were mapped to reference sequences (ENA accession number: PRJEB4541) using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression is calculated by the numbers of reads mapped to the reference sequence and every gene.The gene expression level was calculated by RPKM
The statistical analysis of reads frequency was performed in C0 and C1 to screen the differentially expressed unigenes in E. sinensis Y-organ. P-value, FDR and log2 Ratio(C1/C0) were calculated for the further screening of the differentially expressed unigenes.
Genome_build: Alignment was to the transcriptome  (ENA accession number: PRJEB4541)
Supplementary_files_format_and_content: The gene expression is calculated by the numbers of reads mapped to the reference sequence and every gene.The gene expression level was calculated by RPKM

organism: Eriocheir sinensis

source_name: Y-organ

growth_protocol: Healthy crabs (body weight 5-6g) with good vitality were hold in fresh water at 18-20°C for 3-5 days.

extract_protocol:
The total RNA from the Y-organ was extracted using the TRIzol method (Invitrogen,USA) according to the manufacturer's protocol.
After extracting the total RNA from the samples, mRNA is enriched by using the oligo(dT) magnetic beads. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.

treatment_protocol: Sixty crabs were randomly selected and equally divided into two groups. The eyestalk of experimental group was ablated and 48 hours later the Y-organ was taken as sample C1. The sample was stored in -80°C liquid nitrogen until RNA was extracted. The eyestalk of control group was not treated and the Y-organ was taken as sample C0 48 hours later

value: Y-organ

value: removing of eyestalk

tag: culture time


title: FANCJ_rep_2


title: Y-organ C0

value: untreated


title: Wild type differentiation T=48 rep1

description:
Wild type differentiation T=48
WT_T24-VS-WT_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-9599_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-EMD_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-Enull_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-Q133H_T48.DEseq2_Method.GeneDiffExp.xls
WT_T48-VS-S54F_T48.DEseq2_Method.GeneDiffExp.xls

value: H2K myogenic precursor cells


title: DDX11_rep_3

value: DDX11 KO


title: Wild type differentiation T=24 rep1


title: Col-0_3

description: deetiolated/red light

tag: ecotype

value: WT


title: DDX11_rep_2


title: 12H5: Head regeneration ATAC-seq, 12 hours post amputation, replicate 5

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (12H5_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12H_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Mid-Body Column

value: Head Regeneration


title: Del9599 differentiation T=48 rep1


title: Col-0_2

description: deetiolated/red light

data_processing:
Base-calling was done with BGISEQ500, version 1.1.2.29164.
After removal of adaptors and low quality reads, the obtained clean reads (approximately 23 million) were stored as FASTQ format SOAPnuke, version v1.5.2, parameters: -I15 -q 0.5 -n0.1.
The clean reads were mapped to the reference genome (TAIR10) using HISAT, version v2.0.4, parameters: -p8 --phred64 --sensitive -I 1 -X10000.
For gene expression analysis clean reads were mapped to reference using Bowtie2, v2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Gene expression levels based on the FPKM method were quantified using RSEM v1.2.12, Parameters: default.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.gene.fpkm.txt: Tab-delimited text files include FPKM values for each Sample.


title: Col-0_1

description: deetiolated/red light


title: 12H3: Head regeneration ATAC-seq, 12 hours post amputation, replicate 3

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (12H3_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12H_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)