title: 12F3: Foot 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. (12F3_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: Emerin null differentiation T=24 rep1

status: Public on Jul 01 2020

type: SRA

city: Bethlehem

first: Ashvin

last: Iyer

state: Pennsylvania

address: 1325B Johnston Drive

department: Pharmaceutical Sciences

country: USA

institute: University of the Sciences

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

library_source: transcriptomic

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.

molecule: total RNA

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: Del9599 differentiation T=24 rep1

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: TIMELESS_rep_2

city: Cambridge UK

first: Julian

middle: E

last: Sale

address: Cambridge Biomedical Campus, Francis Crick Ave

department: PNAC

country: United Kingdom

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

tag: genotype

value: TIMELESS KO


title: Del9599 differentiation T=0 rep1

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: FANCJ_rep_1

value: FANCJ KO


title: TIMELESS_rep_1


title: 12F2: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 2

city: Davis

first: Jack

last: Cazet

state: CA

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_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. (12F2_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/)

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.

tag: strain

tag: tissue

value: Mid-Body Column

tag: timepoint

value: 12 hours post amputation

tag: regeneration type

value: Foot Regeneration

tag: treatment

value: Untreated


title: WT_rep_3

value: WT


title: 12H1: Head regeneration ATAC-seq, 12 hours post amputation, replicate 1

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. (12H1_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: Head Regeneration


title: Lung, Control A3

city: Groningen

first: Diederik

middle: Eilard

last: van der Feen

address: Antonius Deusinglaan 1

department: Pediatric and Congenital Cardiology

country: Netherlands

institute: University Medical Center Groningen

description: Control

data_processing:
Adapter and polyA sequences and low quality nucleotides were removed using BBDuk.
Trimmed reads were mapped against the Rnor_6.0 rat genome using STAR
htseq-count was used to determine read counts
After quality control with FASTQC, biological replicates were averaged, followed by differential expression analysis using DESeq2.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: htseq-count .txt file

organism: Rattus norvegicus

source_name: Lung, Control

extract_protocol:
From all donor rats, RNA was extracted from whole upper right lobular lung tissue, in 3 biological replicates of 500ng each.
After quality control, the RNAseq library was prepared using the Quantseq 3’mRNA-seq FWD kit (Lexogen). The library was sequenced on 3 HiSeq4000 lanes (Illumina).

treatment_protocol: MCT at day 0, Aorto-caval shunt at day 7. LTx at either day 14, 21 or 28.

tag: disease state

value: Control

tag: time point (day after mct/nacl)

value: 21 days

value: Lung, right middle lobe


title: 12F1: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 1

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. (12F1_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: Wild type differentiation T=0 rep1

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

source_name: Wildtype H2K myogenic precursor cells


title: DDX11_rep_1

value: DDX11 KO


title: THC/SIV [JT80]

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

data_processing:
The BCL file was converted into the fastq file using bcl2fastq 2.19. Raw reads were filtered to remove reads containing adapters or reads of low quality, so that downstream analyses was done based on clean reads. The software used is fastp-0.12.2. The filtering process is as follows: Discard reads (1) with adaptor contamination (2) when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) (3) when low quality nucleotides (base quality less than 20) constitute more than 50 percent of the read.
Genome_build: Macaca_mulatta.Ensembl_release_76
Supplementary_files_format_and_content: abundance measurements/Fold change/p value

organism: Macaca mulatta

source_name: THC/SIV

extract_protocol: Transcriptome profiling by RNA-seq and data analysis were performed by Novogene (Sacremento, CA). cDNA library construction and sequencing were performed by Novogene Co. Ltd, Beijing, CA (http://www.novogene.cn/). For library construction, ~3 μg of total RNA from each sample was used to enrich mRNA with the poly-T oligo-attached magnetic beads. The purified mRNA was then randomly cleaved into small fragments using NEBNEXT RNA fragmentation buffer (35) following the manufacturer’s instructions. First-strand cDNA was synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis by nick translation was subsequently performed using E coli DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. The final cDNA library was prepared after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. The cDNA fragments of preferentially 250−300 bp in length were selected using with AMPure XP system (Beckman Coulter, Beverly, U.S.A.) and PCR amplified using Phusion High-Fidelity DNA polymerase (NEB, Beijing, China), Universal PCR primers and Index (X) Primer. PCR products were then purified using AMPure XP system (Beckman Coulter, U.S.A.), and library quality was assessed on the Agilent Bioanalyzer 2100 system (Agilent Technologies, U.S.A.). The clustering of the index-coded samples was performed on a cBot Cluster Generation System, using TruSeq SR Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2000 platform and 100 bp single end reads were generated.

value: SIV Infected with THC treatment

value: Oropharyngeal mucosa


title: 8F5: Foot regeneration ATAC-seq, 8 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. (8F5_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. (8F_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


title: Emerin null differentiation T=48 rep1

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


title: Lung, Control A2

description: Control


title: WT_rep_1


title: Lung, Reversible PAH 42

description: Reversible PAH

source_name: Lung, Reversible PAH

value: Reversible PAH


title: 12H4: Head 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. (12H4_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/)


title: QH65Z31: CAF15

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Homo sapiens

source_name: MSCs co-cultured with TE-15

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: In order to induce the CAF-like cells, 5 × 104 MSCs were seeded in the bottom chamber of a 6-well plate and co-cultured with 1.5 × 105 TE cells in the upper chamber (0.4-μm pore-size filter; BD Falcon, Lincoln Park, NY) for 7 days. The media and TE cells were changed 4 days after seeding. MSCs were seeded in a same manner without co-culture as control.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tag

value: MSCs co-cultured with TE-15


title: VEH-untreated/SIV [JD59]

source_name: VEH-untreated/SIV

value: SIV Infected without Vehicle treatment


title: QH65Z30: CAF9

source_name: MSCs co-cultured with TE-9

value: MSCs co-cultured with TE-9


title: QH65Z28: MSC

source_name: monocultured MSCs

value: monocultured MSCs


title: TIMELESS_rep_3

value: TIMELESS KO


title: Lung, Control B3

description: Control


title: QH65Z29: CAF8

source_name: MSCs co-cultured with TE-8

value: MSCs co-cultured with TE-8


title: Lung, Reversible PAH 41

description: Reversible PAH


title: Emerin null differentiation T=0 rep1

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: 8F1: Foot regeneration ATAC-seq, 8 hours post amputation, replicate 1

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. (8F1_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. (8F_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: Foot Regeneration

value: Untreated


title: 12H2: Head regeneration ATAC-seq, 12 hours post amputation, replicate 2

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. (12H2_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: 12 hours post amputation

value: Head Regeneration


title: 8H5: Head regeneration ATAC-seq, 8 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. (8H5_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. (8H_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: Z13207_t2

city: Seattle

first: Matthew

middle: Price

last: Wood

state: WA

address: 307 Westlake Ave North

department: Global Infectious Diseases

institute: Seattle Children's Research Institute

hyb_protocol: 100 nanograms of RNA was directly hybridized for 18 hours using the Non-human Primate Immunology v2.0 chipset.

scan_protocol: Images were acquired from 280 fields for each sample

data_processing: Raw data were processed in nSolver 4.0 using Advanced Analysis with R version 3.3.2 by running Normalization with the default settings of a threshold count value of 20 and an observation frequency of 1 with automatic selection of optimal house keeping genes.

source_name: Draining Lymph node 2 weeks before vaccination

extract_protocol: Total RNA was extracted using the Macherey Nagel Nucleospin column purification system following the manufactureres instructions. Lymph node cells were lysed by resuspending the 3.0EE6-cell pellat in 300µL of buffer RA1 with 1% beta-mercaptoethanol and storing long term at -80˚C. Lysed cells were thawed and RNA was purified prior to nanostring analysis.

value: Submandibular Lymph Node


title: THC/SIV [IV90]

value: SIV Infected with THC treatment


title: WT_rep_2

value: WT


title: 8F4: Foot regeneration ATAC-seq, 8 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. (8F4_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. (8F_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


title: VEH-untreated/SIV [JP38]

value: Oropharyngeal mucosa


title: 8F3: Foot regeneration ATAC-seq, 8 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. (8F3_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. (8F_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: 8H4: Head regeneration ATAC-seq, 8 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. (8H4_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. (8H_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: Z13207_t1

source_name: Draining Lymph node 1 week after vaccination


title: THC/SIV [JI45]


title: 8F2: Foot regeneration ATAC-seq, 8 hours post amputation, replicate 2

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. (8F2_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. (8F_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: Z12190_t2


title: Lung, Irreversible PAH 39

description: Irreversible PAH

source_name: Lung, Irreversible PAH

value: Irreversible PAH

value: 21 days

value: Lung, right middle lobe


title: VEH-untreated/SIV [KA05]

value: SIV Infected without Vehicle treatment


title: Lung, Irreversible PAH 26

description: Irreversible PAH

value: 28 days


title: VEH-untreated/SIV [JR15]


title: Lung, Reversible PAH 43

description: Reversible PAH

value: Reversible PAH


title: Lung, Irreversible PAH 27

description: Irreversible PAH


title: 8H3: Head regeneration ATAC-seq, 8 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. (8H3_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. (8H_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: VEH-untreated/SIV [JJ71]


title: Lung, Reversible PAH 40

description: Reversible PAH


title: Lung, Reversible PAH 24

description: Reversible PAH


title: 8H2: Head regeneration ATAC-seq, 8 hours post amputation, replicate 2

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. (8H2_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. (8H_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: Uninfected Controls [JD95]

source_name: Uninfected Controls


title: Uninfected Controls [GK22]


title: 8H1: Head regeneration ATAC-seq, 8 hours post amputation, replicate 1

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. (8H1_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. (8H_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: 3F3: Foot regeneration ATAC-seq, 3 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. (3F3_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. (3F_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


title: Uninfected Controls [GK11]


title: Lung, Reversible PAH 25

description: Reversible PAH

data_processing:
Adapter and polyA sequences and low quality nucleotides were removed using BBDuk.
Trimmed reads were mapped against the Rnor_6.0 rat genome using STAR
htseq-count was used to determine read counts
After quality control with FASTQC, biological replicates were averaged, followed by differential expression analysis using DESeq2.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: htseq-count .txt file


title: VEH-untreated/SIV [IJ60]

data_processing:
The BCL file was converted into the fastq file using bcl2fastq 2.19. Raw reads were filtered to remove reads containing adapters or reads of low quality, so that downstream analyses was done based on clean reads. The software used is fastp-0.12.2. The filtering process is as follows: Discard reads (1) with adaptor contamination (2) when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) (3) when low quality nucleotides (base quality less than 20) constitute more than 50 percent of the read.
Genome_build: Macaca_mulatta.Ensembl_release_76
Supplementary_files_format_and_content: abundance measurements/Fold change/p value


title: Lung, Reversible PAH 22

description: Reversible PAH

value: 14 days


title: 3F2: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 2

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. (3F2_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. (3F_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: Foot Regeneration


title: Z11114_t2


title: Z12209_t2


title: Z12209_t1


title: Z12189_t1


title: Z12190_t1


title: Z12189_t2


title: Uninfected Controls [GJ01]

value: Untreated


title: Lung, Control 20

description: Control

value: Control


title: 3F1: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 1

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. (3F1_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. (3F_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: Uninfected Controls [JC65]


title: Lung, Reversible PAH 12

description: Reversible PAH

value: 27 days


title: VEH-untreated/SIV [JR60]


title: 3H3: Head regeneration ATAC-seq, 3 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. (3H3_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. (3H_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: Z11088_t2

value: Submandibular Lymph Node


title: Z11114_t1


title: 3H2: Head regeneration ATAC-seq, 3 hours post amputation, replicate 2

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. (3H2_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. (3H_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: Lung, Irreversible PAH 11

description: Irreversible PAH


title: Lung, Ireversible PAH 10

description: Irreversible PAH

source_name: Lung, Ireversible PAH


title: Lung, Reversible PAH 23

description: Reversible PAH


title: NHP_65_GVHD

city: Boston

first: James

middle: John

last: Kaminski

state: MA

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Boston Children's Hospital

data_processing:
Align with cellranger count (v3.1.0) to MMul10 with Ensembl98 annotations
Combine samples with cellranger aggregate, set “normalization=none”
Load matrix of UMI counts into Seurat v3.1
Retain cells with at least 800 genes detected and 1,500 transcripts detected.
Normalize data with SCTransform function in Seurat, using Lane as batch variable to correct for batch effects
Genome_build: mmul10
Supplementary_files_format_and_content: matrix.mtx.gz contains raw reads after aggregate command in cellranger. Normalized_Count_Matrix.mtx contains normalized counts after SCTransform
barcodes.tsv.gz: Barcodes file output by cellranger count
features.tsv.gz: Features file output by cellranger count
Supplementary_files_format_and_content: matrix.mtx.gz: Count matrix output by cellranger count
Normalized_Count_Matrix.mtx.gz: MatrixMarket formatted matrix of Normalized UMI counts for each gene in each cell, after QC and filtering
Normalized_Count_Matrix__ColumnNames.txt: Cell IDs for Normalized Count Matrix
Normalized_Count_Matrix__RowNames.txt: Genes for Normalized Count Matrix

source_name: Combined host and donor_colon

extract_protocol:
Four colon samples from the allo-HCT cohort and four colon samples from the untransplanted healthy control cohort were aseptically thawed, labeled with the viability dye LIVE/DEAD Violet (Invitrogen), then stained with αCD45 antibodies, conjugated with PerCP-Cy5.5 (BD Biosciences), and PE-conjugated αMAMU-A001 antibodies (NHP Reagent Resource). Viable LIVE/DEAD Violet-negative CD45-positive cells were sorted from two out of four GVHD-derived samples into host and donor fractions, based on MAMU-A001 expression. Sorted samples were also CD45-AF488 (IVas)-negative. Donor- and host-derived cells were defined computationally from two additional GVHD samples (see the corresponding Methods section, below).
Single cell libraries from sorted samples were generated using a UMI-based droplet-partitioning platform with the Chromium single cell 3’ library and gel bead kit v2 and v3 (10X Genomics) and then sequenced using a NovaSeq S2 (Illumina).

tag: sample type

value: Combined host and donor sample

value: colon


title: Z11088_t1


title: NHP_64_GVHD


title: 3H1: Head regeneration ATAC-seq, 3 hours post amputation, replicate 1

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. (3H1_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. (3H_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: Lung, Irreversible PAH 9

description: Irreversible PAH

value: Irreversible PAH


title: Lung, Reversible PAH 8

description: Reversible PAH


title: NHP_61_HC

source_name: Healthy control_colon

value: Healthy control sample


title: Lung, Reversible PAH 7

description: Reversible PAH

value: Lung, right middle lobe


title: Z10070_t1

data_processing: Raw data were processed in nSolver 4.0 using Advanced Analysis with R version 3.3.2 by running Normalization with the default settings of a threshold count value of 20 and an observation frequency of 1 with automatic selection of optimal house keeping genes.


title: Z10070_t2


title: 0F3: Foot regeneration ATAC-seq, 0 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. (0F3_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. (0F_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/)

source_name: Mid-Body Column Tissue

value: 0 hours post amputation


title: 0F4: Foot regeneration ATAC-seq, 0 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. (0F4_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. (0F_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: NHP_60_HC


title: Z10036_t2


title: A16255_t2


title: Lung, Control 1

description: Control

source_name: Lung, Control

value: 21 days


title: NHP_63_HC


title: 0F5: Foot regeneration ATAC-seq, 0 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. (0F5_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. (0F_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: 0H5: Head regeneration ATAC-seq, 0 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. (0H5_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. (0H_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: Z13207.W1

source_name: Buccal mucosa 1 week post IM vaccination

extract_protocol: Total RNA was extracted using the Macherey Nagel Nucleospin column purification system following the manufactureres instructions. Buccal mucosal samples collected by oral cytobrush were stored in 2mL of buffer RA1 with 1% beta-mercaptoethanol and storing long term at -80˚C. Lysed cells were thawed and RNA was purified prior to nanostring analysis.

value: Buccal Mucosa


title: spd_1366-2

city: Houston

first: Nicholas

last: De Lay

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: rRNA depleted (sRNA-seq)

data_processing:
Adapters and low quality bases were trimmed using Cutadapt
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2
Read counting was performed with HTSeq
Differential Gene expression analysis performed with DESeq2
Genome_build: Streptococcus pneumoniae D39 (RefSeq NC_008533) genome and D39 plasmid pDP1 sequence (RefSeq NC_005022)
Supplementary_files_format_and_content: WTvSPD1366DESeq2.xls: differential expression of sRNA genes (all sRNA genes)

organism: Streptococcus pneumoniae D39

source_name: cells

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.15

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
Library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria.  rRNA depleted samples were then subjected to RNA fragmentation using the Ambion RNA fragmentation kit (AM8740). Fragmented RNA was subjected to RNA 5' polyphosphatase (Epicenter) treatment, which was performed to facilitate the 5' adapter ligation step. Small RNA libraries were generated by Macrogen using TruSeq® small RNA library kit (Illumina).

value: {delta}cvfD mutant


title: spd_1366-3

description: rRNA depleted (sRNA-seq)


title: NHP_62_GVHD


title: Lung, Reversible PAH 2

description: Reversible PAH

source_name: Lung, Reversible PAH

value: Reversible PAH

value: 14 days


title: 0H3: Head regeneration ATAC-seq, 0 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. (0H3_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. (0H_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


title: WT3

description: rRNA depleted (sRNA-seq)

value: Wildtype parent