title: LANS-Set2_darkToLight_40min_RNA_Rep3

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
For ChIP: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Sequencing adapters on reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 in paired mode. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. In-house scripts were used to limit potential PCR duplicates by limiting reads with the same sequence to a maximum of 5 copies and discarding the copies beyond that limit. Since the previous filtering steps may remove one end of a read pair but not the other, both read-pair fastq files were synced using in-house scripts to ensure proper order for alignment. As the ChIP experiments contained S. pombe spike-in, a chimeric S. cerevisae-S. pombe genome (sacCer3-ASM294v2) was generated using the genomeGenerate tool in STAR (v2.5.2b). This chimeric genome contains the full sequence of both species, allowing reads to align to their best overall fit between the two species. Once generated, read alignment was done using STAR (v2.5.2b) and options --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. Post-alignment, Samtools (v1.31) and bedtools (2.26) were used to generate bigWig files for downstream analyses. To account for S. pombe spike-in, the bigwig signal was normalized by the total number of S. pombe reads per million, using the -scale option within the bedtools genomecov tool. Normalized H3K36me3 signal was obtained by dividing H3K36me3 spike-in normalized signal by H3 spike-in normalized signal for each base pair for each replicate. Some regions were devoid of any H3 signal, and these regions were flagged and excluded from further analyses regardless of H3K36me3 signal.  Deeptools (v2.5.4) was used to generate metagene plots using the normalized H3K36me3 signal. Deeptools was also used to obtain base pair by base pair signal over regions of interest such as genes, introns, and exons. This data was used to calculate the average signal per gene, excluding those regions flagged for lacking H3 signal. We set out to understand H3K36me3 signals over time, however differing levels of normalized H3K36me3 signal within genes made analysis difficult. To account for these differences, we scaled the average signal per gene throughout the time course between 0 (no signal) and 1 (the maximum signal of a gene over the time course). This yielded a relative (proportional) scale for each gene as a fraction of its maximum signal and allowed for easier comparisons of patterns within and across treatments. To yield a comprehensive gene value for plotting, H3K36me3 signal (for both mean or proportional) was the mean of all the replicates for the gene.
For RNA: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 to remove any sequencing adapters. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. Reads were aligned to the sacCer3 genome using STAR (v2.5.4b) with options --quantMode TranscriptomeSAM, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, and --outFilterMultimapNmax 1. To calculate the RNA abundance values, Salmon (v0.8.1) tool quant was used with options -l SR, --incompatPrior 0.0 to account for read strandedness. Samtools (v1.3.1), bedtools (v2.26), and R (v3.3.1) were used to interconvert files for downstream analyses. DESeq2 (v1.14.1) was used to determine which genes had differential expression. Venn diagrams were made using R package Vennerable (v3.0).
Genome_build: sacCer3-ASM294v2
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files for ChIP contain spike-in (S. pombe) scaled ChIP-seq signal for H3 or H3K36me3. Those ending with "normalizedByH3" contain H3K36me3 ChIP-seq signal that is normalized by matched H3 signal (spike-in scaled H3K36me3 / spike-in scaled H3). Bigwigs for RNA contain read depth normalized, non-stranded RNA-seq signal.
Supplementary_files_format_and_content: sf files contain the gene expression data (TPM) as determined by sailfish for all replicates in either Light to Dark (LtD) or Dark to Light (DtL) treatments.
Supplementary_files_format_and_content: Differential abundance files contain the DESeq2 differential genes between 0min and all other timepoints across Light to Dark (LtD) or Dark to Light (DtL) treatments.
Supplementary_files_format_and_content: Model value matrices contain the GLMM model prediction values, errors, and credible intervals for each gene across the time course. High confidence genes are those where credible interval does not cross zero, and are labeled as having a non-zero trend in the table.
Supplementary_files_format_and_content: Histone value matrices contain the average, spike-in scaled, H3 normalized H3K36me3 ChIP-seq signal for each gene and replicate.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: For ChIP-seq: Cells (either WT, set2∆, set2∆ expressing LANS-Set2, rph1∆, or rph1∆ expressing LANS-Set2) were resuspended in YPD (WT, set2∆, and rph1∆) or SC−LEU (set2∆ expressing LANS-Set2 and rph1∆ expressing LANS-Set2) and grown overnight at 30 °C. In the morning cell density was measured at OD600 and cultures were diluted in appropriate media to a final volume of 70 mL and final OD600 of 0.35. Cultures were maintained at 30 °C until the OD600 reached 0.8−1.0.  For RNA-seq: Cells (either WT, rph1∆, or set2∆ expressing LANS-Set2) were resuspended in YPD (WT and rph1∆) or SC−LEU (set2∆ expressing LANS-Set2) and grown overnight at 30 °C. In the morning cell density was measured at OD600 and cultures were diluted in appropriate media to a final volume of 70 mL and final OD600 of 0.3. Cultures were maintained at 30 °C until the OD600 reached 0.8−1.0.

extract_protocol:
For ChIP-seq: Cells were fixed with a 1% final concentration of formaldehyde, the fixation was quenched, cells were washed, and pellets were frozen at −80 °C. After the completion of each time course, cells were lysed using 140 mM FA lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, pH 7.5, containing protease inhibitor cocktail). Lysed cells were sonicated (Diagenode Bioruptor UCD-200) on high intensity 5 times for 5 minutes each (cycles of 30 seconds “ON” and 30 seconds “OFF”) and clarified by centrifuging at full speed for 15 minutes. Overnight immunoprecipitations of S. cerevisiae chromatin with appropriate antibodies were prepared with S. pombe chromatin spike-in control corresponding to 15% of S. cerevisiae chromatin as estimated by Bradford assay (Bio-Rad). 50 μL of Protein G Dynabeads were added to each 500 μL immunoprecipitation reaction and reactions were incubated for 2 hours. Washes were performed with 1 mL of 140 mM FA-lysis buffer, 500 mM FA-lysis buffer (50 mM HEPES, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, pH 7.5, containing protease inhibitor cocktail), LiCl solution (250 mM LiCl, 10 mM Tris, 0.5% each of NP-40 and sodium doxycholate and 1 mM EDTA) and TE pH 8.0. Elution buffer (1% SDS, 0.1 M NaHCO3) was used to elute the DNA (15 minutes shaking at 65 °C followed by centrifugation at 2,000 RPM for 2 minutes). 10 μL of 5 M NaCl was added to the eluates and 10% inputs and samples were incubated at 65 °C overnight to carry out de-crosslinking. Samples were treated with RNase for 1 hour and proteinase K for 1hour before ChIP DNA Clean & Concentrator (Zymo Research) to extract the DNA.  For RNA-seq: Cells (10 mL of log-phase cultures) were collected by centrifugation and frozen at −80 °C. , RNA was isolated by acid phenol extraction. RNA (10 μg) was treated with DNase (Promega) and purified (RNeasy column, QIAGEN).
For ChIP-seq: Bar-coded sequencing libraries were prepared as recommended by the manufacturer (KAPA Hyper Prep Kit), pooled and sequenced (Hi-Seq 2500, Illumina). Briefly, extracted DNA was end-repaired and A-tailed and adapters were ligated. Bead-based size selection was performed, libraries were amplified, and bead-based size selection was repeated. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.  For RNA-seq: RNA (2.5 μg) was processed using rRNA depletion beads specific to yeast (Illumina). Bar-coded sequencing libraries were prepared as recommended by the manufacturer (TruSeq Stranded Total RNA Library Preparation Kit, Illumina), pooled and sequenced (Hi-Seq 4000, Illumina). Briefly, libraries were constructed by bead-based rRNA depletion, cDNA synthesis, and PCR. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq 4000 following the manufacturer's protocols.

treatment_protocol: For ChIP-seq: WT, set2∆, and rph1∆ cells were collected when the OD600 reached 0.8−1.0. Cells expressing LANS-Set2 (set2∆ and rph1∆) were maintained throughout culturing in 500 μW/cm2 blue light (set2∆ and rph1∆) or in the dark (set2∆) until the OD600 reached 0.8−1.0 when an initial time point was collected then samples were shifted from the dark to light or the light to dark.  For RNA-seq: WT and rph1∆ cells were collected when the OD600 reached 0.8−1.0. set2∆ cells expressing LANS-Set2 were maintained throughout culturing in 500 μW/cm2 blue light or in the dark until the OD600 reached 0.8−1.0 when an initial time point was collected then samples were shifted from the dark to light or the light to dark.

tag: strain

tag: genotype

tag: lans-set2 status

value: Dark to Light

tag: time after light change

value: 40 min

tag: chip antibody

tag: genome build


title: chp_44

status: Public on Jul 01 2020

type: SRA

city: Aurora

first: Ivana

last: Yang

state: CO

country: USA

institute: University of Colorado Anschutz Medical Campus

library_source: transcriptomic

data_processing:
base-calling done by Real-Time Analysis software v3.3.3
fastq file demultiplexing done by bcl2fastq2 Conversion Software v2.20.0.422
genome indexing, pseudoalignments, and counts quantification done by kallisto v0.45.0
Genome_build: GENCODE GRCh38 v27
Supplementary_files_format_and_content: CSV matrix containing all quantified counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Human lung

extract_protocol:
Lung tissue was collected from all participants as either a surgical lung biopsy or at the time of lung transplantation. RNA and DNA were isolated from tissues using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia, CA), according to manufacturer’ s protocol.
To establish RNA library, we used  TruSeq Stranded mRNA Library Prep Kit (San Diego, CA) accoridng to maunfacture`s protocol

tag: tissue

value: lung tissue

tag: Sex

value: female

tag: age

tag: diagnosis

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: UNKNOWN

value: GG

tag: sample type

value: explant

tag: psl

tag: is

value: NO

tag: batch

tag: lane

tag: plate

tag: institution

value: NJH


title: Ctrl_39_6

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

data_processing:
Reads were aligned with BWA aln version 0.7.15 with -l 24
Alignments were demultiplexed with a custom script
UMIs were used to collapse reads and make a count table using a custom script
Genome_build: mm10

molecule: total RNA

source_name: Whole blood

growth_protocol: Human whole peripheral blood from three healthy donors was obtained from Stemcell Technologies (catalog number 70504.5). Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation. 15 mL lymphocyte separation medium (LSM) (Corning 25072CV) was carefully underlaid beneath 35 ml of diluted blood in a 50 ml tube and centrifuged at 400 g for 30 minutes at 20C without break. The upper layer was aspirated leaving the white buffy coat interphase containing PBMCs (lymphocytes, monocytes) undisturbed. The interphase was transferred to a new 50 mL tube containing 10 mL 1XPBS, mixed and centrifuged at 400 g for 10 minutes at 20C. Following the washing step, supernatant was removed and PBMC pellet was resuspended in PBS.  CD14+ Monocytes were then purified from the PBMCs by positive selection with the Monocyte Isolation kit II (Miltenyi Biotec 130-091-153). CD14+ monocytes were plated at 10^6 cells/mL in 10-cm non-tissue culture treated petri in 10 mL of complete RPMI medium supplemented with everything detailed above except sodium pyruvate and MEM non-essential amino acids and containing recombinant human IL-4 (40 ng/ml; Peprotech 200-04µg) and human GM-CSF (100 ng/ml; Peprotech 300-03µg).  Cells were fed at day 3 and 5 with 5 ml of complete RPMI medium supplemented with GM-CSF and IL-4 as described above. At day 7, non-adherent cells were collected by pipetting, centrifuged and resuspended in fresh complete RPMI medium without GM-CSF and IL-4.

extract_protocol:
Stimulated DCs were lysed with 30 µL of RLT buffer (Qiagen 79216) containing 1% (v/v) b-mercaptoethanol (VWR 97604-848). Total RNA was isolated using Dynabeads MyOne Silane (Thermo Fisher Scientific 37002D) and RLT buffer. Remaining genomic DNA was removed by on-bead DNase I (Thermo Fisher Scientific AM2239) treatment at 37oC for 20 min. After washing two times with 80% ethanol, total RNA was eluted from beads in nuclease-free water.
Total RNA samples obtained from 1x10^4 mouse BMDCs were reverse transcribed to cDNA by denaturing 10-µL RNA samples with 1 µL containing 2 pmoles of a custom RT primer at 72C for 2 min and snap cooled on ice. A 9-µL RT mix containing 4 µL of 5X RT buffer, 1 µL of 10 mM dNTPs, 2 pmoles of template switching oligo, 0.5 µL Maxima H Minus Reverse Transcriptase (ThermoFisher Scientific EP0753) and 3.5 µL of nuclease-free water was added to the denatured RNA samples, and plates were incubated at 42C for 120 min. Double-stranded cDNA samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research D4013), and residual RT primers were removed using exonuclease I (New England Biolabs M0293).  Pooled full-length cDNA was amplified with 4-6 cycles of single-primer PCR with the Advantage 2 PCR Kit (Clontech 639206) in a 50-µL reaction volume. Amplified cDNAs were cleaned up with magnetic beads Agencourt AMPure XP (Beckman Coulter A63880) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851). 1 ng of cDNA was tagmented and amplified by PCR using Nextera XT Kit (Illumina). Libraries were gel purified using E-Gel EX Agarose Gels, 2% (ThermoFisher Scientific G402002), quantified with the Qubit dsDNA High Sensitivity Assay Kit, and sequenced on the NextSeq550 platform (Illumina).

treatment_protocol: 10,000 DCs were plated in 100 µL of medium in non-tissue culture treated 96-well flat bottom plates (ThermoFisher Scientific 260860) and incubated overnight prior to stimulations as indicated. Cells were stimulated with ligands and their combinations for 6 hours.

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 39

tag: prr ligands

value: Ctrl


title: LANS-Set2_darkToLight_20min_RNA_Rep3

tag: strain

tag: genotype

tag: lans-set2 status

tag: time after light change

value: 20 min

tag: chip antibody


title: T101d_Ctrl_M_Liver_5mo

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

library_source: genomic

data_processing:
The sample quality was first assessed with FastQC (v0.11.3), then Trim Galore! (v0.4.5) was used for adapter and quality trimming. More specifically, low-quality bases (quality score lower than 20), adapter sequences (required overlap of 6bp), and end-repair bases from the 3’ end of reads were trimmed, and all reads shorter than 20bp after trimming were discarded.
Bismark was used for alignment and methylation calling, where reads were aligned to mm10 genome using Bowtie2 and methylation calls were reported for all nucleotides with a read depth of at least 5.
Genome_build: mm10
Supplementary_files_format_and_content: bismark coverage files including the percentage of methylation at each position, the number of C bases that are methylated and the number of C bases that are unmethylated

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Upon euthanasia at both 3 weeks and 5 months of age, blood and liver samples were collected. Briefly, blood was collected by cardiac puncture, followed by liver and mesenteric fat. Blood was collected with EDTA anticoagulant, centrifuged, and plasma was removed. Liver was then separated into individual lobes, and the left lobe of the liver was cryo-pulverized and suspended in Buffer RLT (Qiagen, cat # 1053393). Blood and liver DNA extraction were performed using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen #80224).
A total of 50 ng of genomic DNA was digested using restriction enzyme Mspl, and the digested DNA was then purified using phenol:chloroform extraction and ethanol precipitation in the presence of glycogen, before blunt-ending and phosphorylation. A single adenine nucleotide was next added to the 3′ end of the fragments in preparation for the ligation of the adapter duplex with a thymine overhang. The ligated fragments were cleaned, then processed for size selection on agarose gel. Selected fragments were treated with sodium bisulfite to convert unmethylated cytosines to uracils, which are then replaced with thymines during PCR amplification. These libraries were next cleaned up with AMPure XP beads (Product #A63880; Beckman Coulter), quantified using the Agilent TapeStation genomic DNA kit (Catalog #G2991AA; Agilent) and Qubit High Sensitivity dsDNA (Catalog #Q32850; Invitrogen).

tag: Sex

value: Male

tag: treatment

tag: time

value: 5 months


title: Ctrl_39_5


title: SHAM2

city: Beijing

first: Gaoyan

last: La

address: Huayuan North Road NO.49

department: The Department of Rehabilitation Medicine

country: China

institute: Peking University Third Hospital

data_processing:
base-calling using GATK
Data Filtering using SOAPnuke
alignment using HISAT2 to map clean reads to reference genome
Gene quantification using RSEM
Screening of differentially expressed genes using NOISeq
Genome_build: ucsc,rn6
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: gastrocnemius muscle

growth_protocol: 8 weeks old male rats, the specific pathogen free rats were housed in at 20℃,with alternating 12:12 of light/darkness cycles, and consumed a standard chow diet and water ad libitum.

extract_protocol:
Total RNA was harvested using Trizol reagent. BGISEQ-500 was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNA library was prepared following DNase I digest, mRNA isolation, mRNA fragment, cDNA synthesis, repair and validated on the Agilent Technologies 2100 bioanalyzer.

treatment_protocol: The animals in the group of DN-SM accepted daily electrical stimulation for 4 weeks immediately after the surgery day. 15 minutes after anesthesia by sodium pentobarbital, the left leg skin above the gastrocnemius muscle region were shaved and wetted by warm saline, and two surface electrodes were put on the skin. The stimulator (ZS Dichuang, China) connected to the electrodes were set as: voltage 25 V , current 1mA, square pulse 2 Hz, pulse width 300 ms. Apparent heel lifting movement could be observed while being stimulated. The animals in SHAM and DN groups were also anesthetized, shaved, wetted and placed with the two electrodes for 10 minutes, which was in the same way with the DN-SM group, but no electricity was provided.

tag: age

value: 8 weeks

value: male

tag: tissue

value: gastrocnemius muscle

tag: operation

value: sham operation

tag: treatmant

value: no treatment


title: T101d_Ctrl_M_Blood_5mo

source_name: Blood


title: chp_43

value: lung tissue

value: female

tag: diagnosis

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

tag: psl

tag: is

tag: batch

tag: lane

tag: plate


title: LANS-Set2_darkToLight_40min_RNA_Rep2

tag: strain

tag: genotype

tag: lans-set2 status

value: Dark to Light

tag: time after light change

value: 40 min

tag: genome build


title: LANS-Set2_darkToLight_0min_RNA_Rep3

value: 0 min

tag: chip antibody


title: T102b_Lead_M_Blood_PND21

tag: Sex

tag: treatment

value: Lead

tag: time


title: Ctrl_39_2

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 39

tag: prr ligands


title: LANS-Set2_darkToLight_20min_RNA_Rep2

value: 20 min


title: Ctrl_45_2

value: Donor 45

value: Ctrl


title: chp_38

tag: tissue

tag: age

tag: diagnosis

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: biopsy

tag: psl

value: NO

value: YES

tag: institution

value: LTRC


title: chp_37

value: lung tissue

value: male

value: no

value: explant

tag: is

tag: batch

tag: lane

tag: plate


title: T101b_Ctrl_M_Liver_PND21

tag: Sex

value: Male


title: T101b_Ctrl_M_Blood_PND21

tag: treatment


title: chp_36

value: female

value: chp


title: T101c_Ctrl_F_Liver_5mo

value: Female

tag: time

value: 5 months


title: T101c_Ctrl_F_Blood_5mo


title: LANS-Set2_darkToLight_0min_RNA_Rep2

tag: strain

tag: genotype

tag: lans-set2 status

value: Dark to Light

tag: time after light change

value: 0 min

tag: chip antibody

tag: genome build


title: LANS-Set2_darkToLight_40min_RNA_Rep1

value: 40 min


title: chp_34

tag: tissue

tag: age

tag: diagnosis

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT


title: Ctrl_27_5

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 27

tag: prr ligands

value: Ctrl


title: Ctrl_39_1

value: Donor 39


title: Ctrl_39_4


title: Ctrl_39_3


title: T101a_Ctrl_F_Blood_PND21


title: chp_33

value: lung tissue

value: yes

value: GG

tag: sample type

tag: psl

value: NO

tag: is

value: YES

tag: batch

tag: lane

tag: plate

tag: institution

value: LTRC


title: chp_32

tag: Sex

value: female

value: chp

value: no

value: explant


title: Ctrl_27_3


title: LANS-Set2_darkToLight_0min_RNA_Rep1

tag: strain

tag: genotype

tag: lans-set2 status

value: Dark to Light

tag: time after light change

value: 0 min

tag: chip antibody


title: Ctrl_27_2


title: Sfb Th17 replicate 2

city: New York

first: Dan

last: Littman

state: NY

address: 430 East 29th St Room 403

institute: New York University School of Medicine

data_processing:
Raw reads from bulk RNA-seq were aligned to the mm10 genome using STAR v 2.6.1d with the quantmode parameter to get read counts.
DESeq2 v 1.22.2 was used for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel of DEseq2 normalized counts

source_name: SILP

extract_protocol: 200ul of chloroform/1000ml total volume, incubate 3 min. RNA quality was assessed using Pico Bioanalyser chips (Agilent). RNASeq libraries were prepared using the Clontech Smart-Seq Ultra low RNA kit (Takara Bio) for cDNA preparation, starting with 550 pg of total RNA, and 13 cycles of PCR for cDNA amplification. The SMARTer Thruplex DNA-Seq kit (Takara Bio) was used for library prep, with 7 cycles of PCR amplification, following the manufacturer’s protocol. The amplified library was purified using AMPure beads, quantified by Qubit and QPCR, and visualized in an Agilent Bioanalyzer. The libraries were pooled equimolarly, and run on a HiSeq 4000, as paired end reads, 50 nucleotides in length. Precipitate with one volume of 100% isopropanol. Leave @ -20 for > 1 hr.  Spin down @ full speed, 30min, 4oC. Gently aspirate with a pipet tip and resuspend in freshly prepared 75% ETOH. Mix by inverting the tube.  Spin down @ full speed, 5min, 4oC. Gently aspirate with a pipet tip and resuspend thoroughly in up to 87.5ul of prewarmed H2O. Add 10ul of buffer RDD and 2.5ul of resuspended DNAse solution. Incubate for 10minutes @ RTemp.  Add b-ME to buffer RLT à [3.5ul per 350ul of RLT]. Then, add 350ul of buffer RLT and mix very well.  Add 250ul of 100% ETOH and mix very well by pipetting.  Add 700ul to RNeasy minElute column. Pipette out the flow through rather than decanting to avoid salt accumulation around the sides of the collection tube. Reuse the collection tube for the next step. Pipet 500 μl Buffer RPE onto the RNeasy MinElute spin column. Close the lid gently and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm) to wash the column. Discard the flow-through and reuse the collection tube in the next step. Pipet 500 μl of freshly prepared 80% ethanol onto the RNeasy MinElute spin column. Close the lid gently and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the collection tube with the flow-through. After centrifugation, carefully remove the RNeasy MinElute spin column from the collection tube to avoid the carryover of ethanol.   Place the RNeasy MinElute spin column into a new 2 ml collection tube (supplied). Open the lid of the spin column, and centrifuge at full speed for 5 min to dry the membrane. Discard the collection tube with the flow-through. Place the RNeasy MinElute spin column in a new 1.5 ml collection tube (supplied). Add 14 μl RNase-free water directly to the center of the spin column membrane. Close the lid gently, and centrifuge for 1 min at full speed to elute the RNA.

treatment_protocol: For SILP cell preparation: the small intestine was removed immediately after euthanasia, carefully stripped of mesenteric fat and Peyer’s patches/cecal patch, sliced longitudinally and vigorously washed in cold HEPES buffered (25mM), divalent cation-free HBSS to remove all fecal traces. The tissue was cut into 1-inch fragments and placed in a 50ml conical containing 10ml of HEPES buffered (25mM), divalent cation-free HBSS and 1 mM of fresh DTT. The conical was placed in a bacterial shaker set to 37 °C and 200rpm for 10 minutes. After 45 seconds of vigorously shaking the conical by hand, the tissue was moved to a fresh conical containing 10ml of HEPES buffered (25mM), divalent cation-free HBSS and 5 mM of EDTA. The conical was placed in a bacterial shaker set to 37 °C and 200rpm for 10 minutes. After 45 seconds of vigorously shaking the conical by hand, the EDTA wash was repeated once more in order to completely remove epithelial cells. The tissue was minced and digested in 5-7ml of 10% FBS-supplemented RPMI containing collagenase (1 mg/ml collagenaseD; Roche), DNase I (100 µg/ml; Sigma), dispase (0.05 U/ml; Worthington) and subjected to constant shaking at 155rpm, 37 °C for 35 min (small intestine) or 55 min (large intestine). Digested tissue was vigorously shaken by hand for 2 min before adding 2 volumes of media and subsequently passed through a 70 µm cell strainer. The tissue was spun down and resuspended in 40% buffered percoll solution, which was then aliquoted into a 15ml conical. An equal volume of 80% buffered percoll solution was underlaid to create a sharp interface. The tube was spun at 2200rpm for 22 min at 22 °C to enrich for live mononuclear cells. Lamina propria (LP) lymphocytes were collected from the interface and washed once prior to staining in MACS buffer (dPBS+2% FCS+2mM EDTA) containing a mixture of antibodies (CD11b, CD4, TCRb, Klrc1). Cells were washed twice before sorted into Trizol LS with Aria II. Spin @ full speed for 30 seconds. Repeat the previous step; i.e Pipet 500 μl Buffer RPE onto the RNeasy MinElute spin column. Close the lid gently and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm) to wash the column. Discard the flow-through and reuse the collection tube in the next step.

value: Treg

tag: mouse population

value: SFB


title: LANS-Set2_darkToLight_20min_RNA_Rep1

value: 20 min

tag: genome build


title: chp_31

tag: tissue

value: male

tag: age

tag: diagnosis

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

value: biopsy


title: Sfb Treg replicate 2

tag: cell type


title: chp_35

value: lung tissue

tag: sample type

tag: psl

tag: is

tag: batch


title: T101a_Ctrl_F_Liver_PND21

tag: Sex

value: Female

tag: treatment

value: Ctrl

tag: time


title: LANS-Set2_lightToDark_90min_RNA_Rep3

tag: strain

tag: genotype

tag: lans-set2 status

value: Light to Dark

value: 90 min


title: Ctrl_27_6

value: Monocyte derived dendritic cells

tag: donor

value: Donor 27

tag: prr ligands


title: cG_45_3

value: Donor 45


title: Sfb Th17 replicate 1

tag: mouse population


title: LANS-Set2_lightToDark_60min_RNA_Rep3

tag: time after light change

value: 60 min

tag: chip antibody

tag: genome build


title: chp_30

tag: tissue

value: female

tag: age

tag: diagnosis

value: chp

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: explant

value: YES

tag: lane

tag: plate

tag: institution

value: LTRC


title: Ctrl_27_4

tag: cell type


title: chp_29

tag: Sex

value: male

value: GG

tag: sample type

tag: psl

tag: is

value: NO

tag: batch


title: Sfb Treg replicate 1

tag: mouse population

value: SFB


title: cG_45_2

tag: donor

tag: prr ligands


title: chp_28

value: lung tissue

value: yes


title: LANS-Set2_lightToDark_0min_RNA_Rep3

tag: strain

tag: genotype

tag: lans-set2 status

value: Light to Dark

tag: time after light change

value: 0 min

tag: chip antibody

tag: genome build


title: cG_45_1

value: Monocyte derived dendritic cells


title: LANS-Set2_lightToDark_30min_RNA_Rep3

value: 30 min


title: EAE Th1* replicate 2

source_name: spinal cord

value: Treg

value: EAE


title: LANS-Set2_lightToDark_90min_RNA_Rep2

value: 90 min


title: cG_39_3

value: Donor 39


title: chp_27

tag: tissue

tag: age

tag: diagnosis

value: chp

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: explant

tag: lane

tag: plate


title: chp_26

tag: Sex

value: male

tag: sample type

value: biopsy

tag: psl

tag: is

value: YES

tag: institution

value: LTRC


title: cG_39_2

tag: cell type

tag: donor

tag: prr ligands


title: EAE Th1* replicate 1

tag: mouse population


title: EAE Th17 replicate 1


title: LANS-Set2_lightToDark_60min_RNA_Rep2

tag: strain

tag: genotype

tag: lans-set2 status

tag: time after light change

value: 60 min

tag: chip antibody


title: cG_39_1


title: chp_25

tag: tissue

value: lung tissue

value: female

tag: age

tag: diagnosis

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: TT

value: NO

tag: batch


title: LANS-Set2_lightToDark_30min_RNA_Rep2

value: Light to Dark

value: 30 min

tag: genome build


title: EAE Treg replicate 2

value: EAE


title: LANS-Set2_darkToLight_60min_RNA_Rep1

value: Dark to Light


title: chp_23

tag: Sex

value: chp

value: GT

tag: sample type

tag: psl

tag: is

tag: lane

tag: plate


title: LANS-Set2_lightToDark_0min_RNA_Rep2

tag: strain

value: 0 min


title: LANS-Set2_lightToDark_60min_RNA_Rep1

tag: genotype


title: cG_27_3

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 27

tag: prr ligands


title: 8F3_RNA: Foot regeneration RNA-seq, 8 hours post amputation, replicate 3

city: Davis

first: Jack

last: Cazet

state: CA

address: 1 Shields Ave.

department: MCB

institute: University of California, Davis

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: SE -threads 16  -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were then mapped to the Hydra vulgaris 2.0 genome and read counts were calculated using rsem (V. 1.2.31) using the following settings: --no-bam-output --bowtie2.
processed data files format and content: Read count matrix for gene models from the Hydra vulgaris 2.0 genome for all RNA-seq samples. Generated using rsem.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

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:
Total RNA was extracted from 30 regenerating tissue pieces using a standard trizol extraction. DNA was then removed using a DNaseI digest. A final purification step was then performed using a Zymogen RNA Clean & Concentrator kit.
Illumina TruSeq Stranded mRNA.

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: tissue

value: Mid-Body Column

tag: timepoint

value: 8 hours post amputation

tag: regeneration type

value: Foot Regeneration

tag: treatment

value: Untreated


title: chp_24

value: lung tissue

value: female

tag: age

tag: diagnosis

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

value: biopsy

value: YES

tag: batch

tag: institution

value: LTRC


title: chp_20

tag: Sex

value: male

value: yes

tag: sample type

tag: psl

value: NO

tag: is


title: 8F2_RNA: Foot regeneration RNA-seq, 8 hours post amputation, replicate 2

tag: strain


title: LANS-Set2_lightToDark_0min_RNA_Rep1

tag: genotype

tag: lans-set2 status

value: Light to Dark

tag: time after light change

tag: chip antibody

tag: genome build


title: chp_19

tag: tissue

value: chp

tag: lane

tag: plate


title: 8F1_RNA: Foot regeneration RNA-seq, 8 hours post amputation, replicate 1

tag: timepoint

tag: regeneration type

tag: treatment


title: 8H3_RNA: Head regeneration RNA-seq, 8 hours post amputation, replicate 3

value: Head Regeneration


title: rph1d_RNA_Rep3


title: E10.5cKO 3 [WTCHG_230271_281_1KO_3]

city: London

first: Albert

last: Basson

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

department: Craniofacial Development and Stem Cell Biology

country: United Kingdom

institute: King's College London

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

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

source_name: sox1-Cre; Chd8f/f_E10.5_cortex

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

tag: developmental stage

value: Embryonic day 10.5

tag: genotype/variation

value: sox1-Cre; Chd8f/f

value: Cortex


title: LANS-Set2_lightToDark_30min_RNA_Rep1

value: 30 min


title: LANS-Set2_lightToDark_90min_RNA_Rep1

value: 90 min


title: Eae Treg Replicate 1

tag: cell type

tag: mouse population

value: EAE


title: chp_18

value: lung tissue

tag: Sex

value: female

tag: age

tag: diagnosis

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: explant

tag: psl

tag: is

tag: batch

tag: institution


title: MG-treated + PD0325901 5h - replicate 3

city: Leuven

first: Frederic

last: Lluis

state: Leuven

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
50 bp single-end reads were generated. An average of 20 million reads were obtained from all samples. Quality control of raw reads was performed with the FastQC v0.11.5. The adapters were filtered with ea-utils v1.2.2.18. The splice-aware alignment was performed with TopHat v2.0.13 against the mouse genome mm10. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded.  The minimal score of alignment quality to be included in count analysis was 10. Resulting SAM and BAM alignment files were handled with Samtools v0.1.19.24. Quantification of reads per gene was performed with HT-Seq count v0.5.3p3. Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq. Reported p-values were adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: csv with normalized counts

source_name: Primary fibroblasts

growth_protocol: Mouse primary fibroblasts were isolated from the end of the tail (0,5 cm) of C57BL/6 mouse model under anesthesia (isoflurane). Tails were disaggregated by collagenase IV digestion for 40 minutes at 37°C in agitation. The obtained cells were cultured in DMEM GlutaMax (Ca No. 61965-026, Gibco Life Science, Grand island) supplemented with 10% of fetal bovine serum, 1% of penicillin-streptomycin, 1% of L-glutamine, 1% of sodium pyruvate and 1% of nonessential amino acids at 37°C in a humidified incubator with 5% of CO2

extract_protocol:
Micrografts (MG) were obtained from skin murine biopsies (1 cm2) using a sterile tissue destroyer (Rigeneracons®). Tissues were re-suspended in 1 mL PBS, disrupted, and filtered through 70 microm filter membranes.
Library preparation was performed with the Illumina TruSeq Stranded mRNA Sample Preparation Kit, according to the manufacturers protocol (48 samples, Cat No. 20020594). Denaturation of RNA was performed at 65°C in a thermocycler and cooled down to 4°C. Samples were indexed to allow for multiplexing. Sequencing libraries were quantified using the Qubit fluorometer (Thermo Fisher Scientific, Massachusetts, USA). Library quality and size range was assessed using the Bioanalyzer (Agilent Technologies) with the DNA 1000 kit (Agilent Technologies, California, USA) according to the manufacturer’s instructions. Libraries were diluted to a final concentration of 2nM and sequenced on Illumina HiSeq4000 sequencing system, according to the manufacturer’s recommendations.

treatment_protocol: The extracted MG were then diluted 1:10 in growth media and applied on murine primary fibroblasts on an in vitro model of wound healing (cell scratch assay)

value: MG-treated and PD0325901

tag: time

value: 5h hours

value: Primary fibroblasts


title: chp_22

tag: tissue

value: male

value: yes

value: GT

value: biopsy

value: YES

tag: lane

tag: plate

value: LTRC


title: cG_27_1

value: Monocyte derived dendritic cells

tag: donor

value: Donor 27

tag: prr ligands


title: chp_21

value: chp

value: no

value: GG

value: NO


title: MG-treated + PD0325901 5h - replicate 1

tag: treatment

tag: cell type


title: E10.5cKO 1 [WTCHG_232859_279_1KO_1]

tag: strain

tag: developmental stage

value: Embryonic day 10.5

tag: genotype/variation

value: sox1-Cre; Chd8f/f

value: Cortex


title: chp_104

value: lung tissue

tag: Sex

tag: age

tag: diagnosis

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: explant

value: UCSF


title: EAE Th17 replicate 2

tag: mouse population

value: EAE


title: E10.5cKO 3 [WTCHG_232859_281_1KO_3]


title: chp_15

value: female

tag: sample type

tag: psl

tag: is

tag: batch

tag: institution


title: cG_27_2

tag: donor


title: rph1d_RNA_Rep2

tag: genotype

tag: lans-set2 status

tag: time after light change

tag: chip antibody

tag: genome build


title: E10.5cKO 1 [WTCHG_230271_279_1KO_1]

tag: strain

tag: developmental stage

tag: genotype/variation

tag: tissue


title: MG-treated + PD0325901 5h - replicate 2

tag: treatment

value: MG-treated and PD0325901

tag: time

value: 5h hours

tag: cell type

value: Primary fibroblasts


title: 3F2_RNA: Foot regeneration RNA-seq, 3 hours post amputation, replicate 2

value: Mid-Body Column

tag: timepoint

value: 3 hours post amputation

tag: regeneration type

value: Foot Regeneration

value: Untreated


title: WT_RNA_Rep3

value: WT


title: rph1d_RNA_Rep1


title: 8H2_RNA: Head regeneration RNA-seq, 8 hours post amputation, replicate 2

value: 8 hours post amputation

value: Head Regeneration


title: chp_17

tag: Sex

value: male

tag: age

tag: diagnosis

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

tag: sample type

tag: psl

value: NO

tag: is

tag: batch

tag: lane

tag: plate

value: LTRC


title: E10.5cKO 2 [WTCHG_230271_280_1KO_2]

tag: strain

tag: developmental stage

value: Embryonic day 10.5

tag: genotype/variation

value: sox1-Cre; Chd8f/f

value: Cortex


title: E10.5CTRL 2 [WTCHG_232859_277_1WT_2]

source_name: Chd8f/f / Chd8 f/+_E10.5_cortex

value: Combination of Chd8f/f / Chd8 f/+

tag: tissue


title: 8H1_RNA: Head regeneration RNA-seq, 8 hours post amputation, replicate 1

tag: treatment


title: 3H2_RNA: Head regeneration RNA-seq, 3 hours post amputation, replicate 2

tag: timepoint


title: chp_10

value: lung tissue

value: female

value: no

value: GG

value: biopsy

value: YES

tag: institution


title: WT_RNA_Rep1

tag: genotype

value: WT

tag: lans-set2 status

tag: time after light change

tag: chip antibody

tag: genome build


title: 3F3_RNA: Foot regeneration RNA-seq, 3 hours post amputation, replicate 3

value: Mid-Body Column

value: 3 hours post amputation

tag: regeneration type

value: Foot Regeneration

value: Untreated


title: EMD differentiation T=0 rep3

city: Bethlehem

first: Ashvin

last: Iyer

state: Pennsylvania

address: 1325B Johnston Drive

department: Pharmaceutical Sciences

institute: University of the Sciences

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

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.

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: chp_16

tag: Sex

value: male

tag: age

tag: diagnosis

value: chp

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: explant

tag: psl

value: NO

tag: is

tag: batch

value: LTRC


title: chp_14

tag: tissue

value: lung tissue

value: female

tag: lane

tag: plate


title: WT_RNA_Rep2

tag: strain

tag: genotype

tag: lans-set2 status


title: E10.5cKO 2 [WTCHG_232859_280_1KO_2]

tag: developmental stage

value: Embryonic day 10.5

tag: genotype/variation

value: sox1-Cre; Chd8f/f

value: Cortex


title: E10.5CTRL 3 [WTCHG_232859_278_1WT_3]

value: Combination of Chd8f/f / Chd8 f/+


title: Q133H differentiation T=24 rep3

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

tag: cell type


title: EMD differentiation T=48 rep3

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


title: chp_13

tag: Sex

value: GG

value: biopsy

value: YES

tag: institution


title: 3F1_RNA: Foot regeneration RNA-seq, 3 hours post amputation, replicate 1

value: Mid-Body Column

tag: timepoint

value: 3 hours post amputation

tag: regeneration type

value: Foot Regeneration

tag: treatment

value: Untreated


title: E10.5CTRL 3 [WTCHG_230271_278_1WT_3]


title: EMD differentiation T=24 rep3

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

value: H2K myogenic precursor cells


title: 3H3_RNA: Head regeneration RNA-seq, 3 hours post amputation, replicate 3

value: Head Regeneration


title: S54F differentiation T=48 rep3

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


title: chp_40

value: unknown

tag: age

tag: diagnosis

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: UNKNOWN

tag: sample type

value: explant

tag: psl

value: NO

value: UCSF


title: chp_7

tag: tissue

value: lung tissue

value: female

value: no

tag: is

tag: batch

tag: lane

tag: plate

value: LTRC


title: chp_11

value: male

value: yes

value: GG

value: YES


title: LANS-Set2_darkToLight_60min_RNA_Rep2

tag: strain

tag: genotype

tag: lans-set2 status

value: Dark to Light

tag: time after light change

value: 60 min

tag: chip antibody

tag: genome build


title: 0H3_RNA: Head regeneration RNA-seq, 0 hours post amputation, replicate 3

value: Mid-Body Column

tag: timepoint

value: 0 hours post amputation

tag: regeneration type

value: Head Regeneration

tag: treatment

value: Untreated


title: E10.5CTRL 2 [WTCHG_230271_277_1WT_2]

tag: developmental stage

value: Embryonic day 10.5

tag: genotype/variation

value: Combination of Chd8f/f / Chd8 f/+

value: Cortex


title: neo/-3 [WTCHG_282157_281_1NEOMINUS_3]

source_name: Chd8 neo/-_E12.5_cortex

value: Embryonic day 12.5

value: Chd8 neo/-


title: Q133H differentiation T=48 rep3

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

tag: cell type

value: H2K myogenic precursor cells


title: 3H1_RNA: Head regeneration RNA-seq, 3 hours post amputation, replicate 1

tag: tissue

value: 3 hours post amputation


title: 0H2_RNA: Head regeneration RNA-seq, 0 hours post amputation, replicate 2


title: E10.5CTRL 1 [WTCHG_232859_276_1WT_1]


title: neo/-2 [WTCHG_282157_280_1NEOMINUS_2]


title: chp_9

value: lung tissue

tag: Sex

value: female

tag: age

tag: diagnosis

value: chp

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: biopsy

tag: psl

value: NO

tag: is

tag: institution

value: LTRC


title: chp_12

value: yes

value: GG

value: YES

tag: batch

tag: lane

tag: plate


title: 0H1_RNA: Head regeneration RNA-seq, 0 hours post amputation, replicate 1

tag: strain

value: Mid-Body Column

tag: timepoint

value: 0 hours post amputation

tag: regeneration type

value: Head Regeneration

value: Untreated


title: chp_4


title: 0F3_RNA: Foot regeneration RNA-seq, 0 hours post amputation, replicate 3

value: Foot Regeneration

tag: treatment


title: neo/-1 [WTCHG_281991_279_1NEOMINUS_1]

tag: developmental stage

value: Embryonic day 12.5

tag: genotype/variation

value: Chd8 neo/-

value: Cortex


title: Q133H differentiation T=0  rep3

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

tag: cell type

value: H2K myogenic precursor cells


title: S54F differentiation T=24 rep3

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


title: chp_3

tag: tissue

value: lung tissue

tag: Sex

value: male

tag: age

value: chp

value: GT


title: 12iF5: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 5, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iF5_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. (12iF_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/)

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)

value: 12 hours post amputation

value: treated with  5uM iCRT14 for 14 hours


title: 0F2_RNA: Foot regeneration RNA-seq, 0 hours post amputation, replicate 2


title: Del9599 differentiation T=24 rep3

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: chp_8

value: female

tag: diagnosis

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: biopsy

value: NO

value: LTRC


title: Del9599 differentiation T=0 rep3

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: E10.5CTRL 1 [WTCHG_230271_276_1WT_1]

value: Embryonic day 10.5

value: Combination of Chd8f/f / Chd8 f/+


title: chp_2

tag: psl

value: YES

tag: is

tag: institution


title: neo/-3 [WTCHG_281991_281_1NEOMINUS_3]

value: Embryonic day 12.5

value: Chd8 neo/-


title: 12iF4: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iF4_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. (12iF_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: neo/neo3 [WTCHG_281991_284_1NEONEO_3]

source_name: Chd8 neo/neo_E12.5_cortex

value: Chd8 neo/neo

value: Cortex


title: Wild type differentiation T=48 rep3

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

source_name: Wildtype H2K myogenic precursor cells

value: H2K myogenic precursor cells


title: 0F1_RNA: Foot regeneration RNA-seq, 0 hours post amputation, replicate 1

value: 0 hours post amputation

value: Untreated


title: chp_6

value: lung tissue

value: male

value: chp

value: GG

tag: batch

tag: lane

tag: plate


title: neo/-2 [WTCHG_281991_280_1NEOMINUS_2]

tag: strain


title: S54F differentiation T=0 rep3

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


title: Wild type differentiation T=24 rep3

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


title: neo/neo2 [WTCHG_281991_302_1NEONEO_2]


title: chp_5

value: female

value: yes

value: GT

value: biopsy

value: NO

value: LTRC


title: TCF21 KD - TCF21 KD 3 [C2_siT1]

city: Stanford

first: Juyong

middle: Brian

last: Kim

address: 300 Pasteur Dr.

institute: Stanford University

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

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

source_name: HCASMC_TCF21 KD - TCF21 KD

growth_protocol: HCASMC media, passages 5-8

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

tag: cell line

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: coronary artery

tag: genotype/treatment

value: TCF21 knockdown


title: neo/-1 [WTCHG_282157_279_1NEOMINUS_1]

tag: developmental stage

value: Embryonic day 12.5

tag: genotype/variation

value: Chd8 neo/-

value: Cortex


title: neo/neo2 [WTCHG_282157_302_1NEONEO_2]

value: Chd8 neo/neo

tag: tissue


title: Del9599 differentiation T=48 rep3

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

tag: cell type

value: H2K myogenic precursor cells


title: 12iF1: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iF1_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. (12iF_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

tag: timepoint

value: 12 hours post amputation

tag: regeneration type

value: Foot Regeneration

tag: treatment

value: treated with  5uM iCRT14 for 14 hours


title: neo/neo1 [WTCHG_282157_282_1NEONEO_1]


title: TCF21 KD - TCF21 KD 1 [C1_siT1]


title: 12iH2: Head regeneration ATAC-seq, 12 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iH2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Head Regeneration


title: Emerin null differentiation T=0 rep3

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


title: neo/neo3 [WTCHG_282157_284_1NEONEO_3]

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


title: 12iF3: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iF3_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. (12iF_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: HET 3 [WTCHG_282157_278_1HET_3]

source_name: Chd8 +/-_E12.5_cortex


title: chp_1

source_name: Human lung

value: lung tissue

tag: Sex

value: female

tag: age

tag: diagnosis

value: chp

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type


title: AHR OE - AHR OE 2 [AHROE2]

description: processed data file: all_genes_exp.txt

source_name: HCASMC_AHR OE - AHR OE

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: coronary artery

value: AHR overexpression


title: AHR OE - AHR OE 1 [AHROE1]

description: processed data file: all_genes_exp.txt


title: 12iF2: Foot regeneration ATAC-seq, 12 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iF2_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. (12iF_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 rep3

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


title: HET 2 [WTCHG_281991_277_1HET_2]

value: Embryonic day 12.5


title: EMD differentiation T=0 rep2

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


title: Emerin null differentiation T=48 rep3

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: TCF21 KD - TCF21 KD 2 [C1_siT2]

value: TCF21 knockdown


title: HET 1 [WTCHG_281991_276_1HET_1]

value: Cortex


title: 8iF1: Foot regeneration ATAC-seq, 8 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iF1_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. (8iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: 8 hours post amputation

value: treated with  5uM iCRT14 for 10 hours


title: Emerin null differentiation T=24 rep3

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

value: H2K myogenic precursor cells


title: HET 3 [WTCHG_281991_278_1HET_3]


title: AHR OE - AHR OE 4 [AHR4]

description: processed data file: all_genes_exp.txt


title: 8iH5: Head regeneration ATAC-seq, 8 hours post amputation, replicate 5, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iH5_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (8iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Mid-Body Column


title: CTRL 3 [WTCHG_281991_275_1CTRL_3]

source_name: Chd8 +/+_E12.5_cortex


title: 12iH1: Head regeneration ATAC-seq, 12 hours post amputation, replicate 1, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iH1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: 12 hours post amputation

value: treated with  5uM iCRT14 for 14 hours


title: S54F differentiation T=48 rep2

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


title: EMD differentiation T=48 rep2

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


title: 8iF4: Foot regeneration ATAC-seq, 8 hours post amputation, replicate 4, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iF4_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. (8iF_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Foot Regeneration


title: HET 2 [WTCHG_282157_277_1HET_2]


title: 8iF3: Foot regeneration ATAC-seq, 8 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iF3_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. (8iF_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: Q133H differentiation T=48 rep2

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


title: 8iF2: Foot regeneration ATAC-seq, 8 hours post amputation, replicate 2, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (8iF2_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. (8iF_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: CTRL 3 [WTCHG_282157_275_1CTRL_3]


title: S54F differentiation T=24 rep2

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


title: AHR OE - Control 4 [C4]

description: processed data file: all_genes_exp.txt

source_name: HCASMC_AHR OE - control

value: Control


title: AHR OE - AHR OE 3 [AHROE3]

description: processed data file: all_genes_exp.txt


title: Q133H differentiation T=24 rep2

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


title: neo/neo1 [WTCHG_281991_282_1NEONEO_1]

value: Chd8 neo/neo


title: EMD differentiation T=24 rep2

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


title: AHR OE - Control 3 [C3]

description: processed data file: all_genes_exp.txt


title: 12iH3: Head regeneration ATAC-seq, 12 hours post amputation, replicate 3, iCRT14 treated

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. (12iH3_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (12iH_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Head Regeneration


title: CTRL 2 [WTCHG_282157_274_1CTRL_2]

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


title: HET 1 [WTCHG_282157_276_1HET_1]