title: control vs. lIFN

source_name: Interferon gamma treated cells, replicate 2

extract_protocol: On day 6 RNA was isolatated from the organoids with GeneJET RNA Purification Kit (Thermo Scientific)

value: 100ng/ml of recombinant Ifnγ was added to the medium on 2 and 5 day of organoid culture

value: Antral, gastric organoids from BL6 mice were grown for 2 days before treatment

source_name: Untreated control cells, replicate 2

value: untreated cells


title: Xindong23 wheat root_LP_rep2

status: Public on Nov 29 2021

type: RNA

city: Shihezi

first: Xiangchi

last: Zhang

address: Beisi Road, Shihezi, Xinjiang

country: China

institute: Shihezi University

description: Gene expression data fromXindong23 root under drought stress for 7 days by LP

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner with 7G upgrade.

data_processing: Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then Expression Console software (version 1.4.1, Affymetrix) offered RMA normalization. Then, a moderated t-test was performed to identify probe sets with differential expression between the different variants.

label: biotin

molecule: total RNA

organism: Triticum aestivum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The wheat plants were grown in growth cabinets (JNYQ, RXZ-300B-LED, China) with an 18 h day-length at 25°C under photosynthetically active light (250 µmole m-2 s-1) and a night temperature of 20°C.

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

treatment_protocol: The seedlings with each box contained the same capacity of Hoagland nutrient solution, which were divided into conventional phosphorus level (CP: 1.0 mmol /L) and low phosphorus level (LP: 0.05 mmol /L), respectively. KCl was used to replace part of KH2PO4 under low phosphorus condition. The nutrient solution was changed every 3 days. After 14d of culture, the Hoagland nutrient solution (both CP and LP) was configured with 15% (w/v) PEG-6000 to simulate drought stress on wheat seedlings for 7d.

tag: tissue

value: wheat seedlings root

tag: variety

tag: stress

value: under drought stress for 7 days by LP


title: Xindong23 wheat root_LP_rep1

source_name: Xindong23 root under drought stress for 7 days by LP


title: Xindong20 wheat root_LP_rep1

description: Gene expression data fromXindong20 root under drought stress for 7 days by LP


title: Xindong20 wheat root_LP_rep3

source_name: Xindong20 root under drought stress for 7 days by LP


title: Xindong23 wheat root_CP_rep2

description: Gene expression data fromXindong23 root under drought stress for 7 days by CP

value: under drought stress for 7 days by CP


title: Xindong20 wheat root_CP_rep2

description: Gene expression data fromXindong20 root under drought stress for 7 days by CP


title: B95

type: SRA

city: Harbin

first: Yingwei

last: Xue

address: 150, Haping St, Nangang District

department: Department of Gastrointestinal Oncology

institute: Harbin Medical University Cancer Hospital

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: gastric tumor

extract_protocol:
①RNA degradation and contamination was monitored on 1% agarose gels.② RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). ③ RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: tumor stage

value: ⅢB

tag: gender

value: male

tag: tissue type

value: gastric tumor


title: Xindong20 wheat root_CP_rep1

source_name: Xindong20 root under drought stress for 7 days by CP


title: Xindong23 wheat root_LP_rep3


title: Hpy vs. NI

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted dual-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Agilent FE software processed green and red signals were extracted and within-array normalized using method LOESS  was applied.

organism: Mus musculus

source_name: Non-infected controls, pooled RNA from 5 mice

label_protocol: RNA was labeled with the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

extract_protocol: RNA was isolated from snap-frozen antral tissue using RNeasy Mini Kit (Qiagen)

tag: treatment

value: Uninfected controls

tag: cell type

value: pooled tissue from stomach antrum from 5 mice

source_name: H.pylori infection, pooled RNA from 5 mice

value: Helicobacter pylori infection for 2 months


title: IFN vs. control

source_name: Untreated control cells, replicate 1

source_name: Interferon gamma treated cells, replicate 1


title: Xindong23 wheat root_CP_rep3

source_name: Xindong23 root under drought stress for 7 days by CP


title: Xindong20 wheat root_LP_rep2


title: B92

value: ⅠA

value: female


title: B90

value: ⅠB


title: B94

value: ⅡA


title: B93


title: B87


title: B89


title: B88


title: B84


title: B78


title: B85

value: ⅢA


title: B79

value: ⅢC


title: B82


title: B86


title: B555

source_name: paired normal gastric tissue

value: paired normal gastric tissue


title: B80

value: ⅡB


title: B554


title: B557

value: Ⅳ


title: B83


title: B77


title: B553


title: B552


title: B550


title: B549


title: B551


title: B547


title: B91


title: B546


title: B545


title: B543


title: B542


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title: B536


title: B541


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title: B153


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title: B116


title: B137


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title: B113


title: B129


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title: B109


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title: B112


title: B108


title: B106


title: B105


title: B103


title: B102


title: B121


title: B101


title: B100


title: CRC02_19_shKMT9_Vehicle_replicate3

city: Freiburg

first: Christopher

last: Berlin

address: Hugstetter Straße 55

institute: University Hospital Freiburg

description: processed data file: CountsTable_CRC02_19_shKMT9.txt

data_processing:
We aligned these reads to the mm10build of the mouse genome using STAR
The aligned reads were counted with the homer software (analyzeRNA) and edgeR
Genome_build: mm10, hg19
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

source_name: Patient-derived organoids - CMS3

extract_protocol: RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

tag: differentiation stage

value: Patient-derived organoids - CMS3


title: CRC02_19_shKMT9_Vehicle_replicate1


title: CRC02_19_shKMT9_Dox_replicate2


title: CRC02_19_shKMT9_Dox_replicate1


title: si-lncRNA-3

city: chengdu

first: huang

last: liang

address: No.24, South First Section, First Ring Road, Wuhou District, Chengdu City

institute: sicuan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by rsem. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: highly metastatic TNBC subline

growth_protocol: Cells were cultured according to the recommended protocols

extract_protocol:
Total RNA was extracted, and the quality of the RNA was assessed with the Agilent Bioanalyzer 2100. Transcriptome libraries from the mRNA fractions were generated following the RNA-Seq protocol (Illumina). Each sample was sequenced in a single lane with the Illumina PE150 Analyzer (Illumina) on a 150-bp paired-end run.   For strand-specific library construction, dUTP method of second-strand marking was employed as described. For the data processing, the raw sequencing reads were aligned to human reference genome (hg19) using the splice-aware aligner HISAT2. Read counts for each gene were normalized into FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values(66). The cutoff of differential gene expression was FDR <0.05, normalized by the respective control group.
Transcriptome libraries from the mRNA fractions were generated following the RNA-Seq protocol (Illumina).

treatment_protocol: Cells were transfected with specific siRNA duplexes targeting Uc003xsl.1 using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instruction.

tag: cell line

value: MDA-MB-231-P3 cells


title: CRC02_19_shKMT9_Dox_replicate3


title: si-lncRNA-2


title: si-NC-3

value: control


title: si-NC-2


title: B107

value: male


title: si-NC-1


title: MDA-MB-231-P3 cells-NKRF-siUc003xsl.1-treated_rep2

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
ChIP-seq reads were aligned to the NCBI: GRCh38.p11(huamn) genome with bowtie2
peaks were called using MASC2
bigwig files were generated using bedGraphToBigWig
Genome_build: NCBI: GRCh38.p11(huamn)
Supplementary_files_format_and_content: peak text  and bigwig files

molecule: genomic DNA

extract_protocol:
A total of 5×10e6 to 1 x 10e7 cells transfected with siRNAs or plasmids were collected and crosslinked in 1% formaldehyde solution for 10 min at room temperature, followed by the addition of 125 mM glycine for 5 min. ChIP assay was performed with a EZ-Magna ChIP Kit (Merck Millipore, USA) following the manufacturer′s instructions. The nuclear lysis was sheared to yield DNA fragments ranging from 100 to 500 bp by a sonication system-Bioruptor (Diagenode, Belgium). Two micrograms of normal IgG were used as the negative control, and anti-NKRF (ab168829, Abcam, USA) antibodies were used for each immunoprecipitation. The IPs were eluted and reverse crosslinked, after which the DNA fragments were purified. Immunoprecipitated and input DNAs were subjected to ChIP-seq analysis.
Libraries were prepared according to Illumina's instructions accompanying the Paired-EndDNA Sample PrepKit (PE-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the BGISEQ-500 following the manufacturer's protocols.

tag: chip antibody

value: NKRF(ab168829, Abcam, USA)


title: MDA-MB-231-P3 cells-NKRF-siUc003xsl.1-treated_rep1


title: MDA-MB-231-P3 cells-input DNA-siUc003xsl.1-treated_rep1


title: MDA-MB-231-P3 cells-NKRF_rep2


title: MDA-MB-231-P3 cells-input DNA-siUc003xsl.1-treated_rep2


title: MDA-MB-231-P3 cells-NKRF_rep1


title: MDA-MB-231-P3 cells-input DNA_rep2


title: si-lncRNA-1


title: MDA-MB-231-P3 cells-input DNA_rep1


title: CRC02_19_shKMT9_Vehicle_replicate2


title: B104

value: gastric tumor


title: Urine nonCOVID AKI 2

city: Birmingham

first: Matthew

middle: David

last: Cheung

state: AL

address: 1825 University Blvd

country: USA

institute: University of Alabama at Birmingham School of Medicine

data_processing:
10x Genomics Cell Ranger version 6.0
Genome_build: Human genome GRCh38 with SARS-CoV-2 genome (NC_045512.2)
Supplementary_files_format_and_content: mtx

molecule: polyA RNA

source_name: Urine

extract_protocol: All steps were performed on ice. Urine was collected as either a voided specimen or from a urinary catheter. Samples were immediately transferred to a biosafety level (BSL) 2+ laboratory for processing. Urine samples were transferred to a 50mL conical tube and centrifuged at 1000x g for 10 minutes at 4 degrees celsius. Cell pellets were washed with ice-cold PBS, filtered through a 40µm filter, and centrifuged again. Live cells were purified using the MACS Debris Removal Kit (Miltenyi Biotec) followed by the EasySep Annexin V Dead Cell Removal Kit (StemCell). Briefly, cells were resuspended in ice-cold PBS and mixed with debris removal solution. Cold PBS was overlaid on the mixture and centrifuged at 300x g for 10 minutes at 4 degrees celsius. The top two phases were aspirated and then remaining cells were washed with PBS. Cells were resuspended and mixed with Dead Cell Removal Cocktail, Biotin Selection Cocktail, then RapidSpheres before separation in an EasySep magnet. Cells were washed and resuspended in 52µL of PBS (no calcium or magnesium) + .04% BSA (Fisher Scientific) for scRNAseq processing. Purified cells were immediately processed using the Chromium 3’ Single Cell RNA sequencing kit (10X Genomics) according to the manufacturer’s instructions.

tag: disease state

value: non COVID AKI

tag: sediment

value: urine


title: Urine nonCOVID AKI 1


title: 18120pl2

city: Amsterdam

first: Vanessa

last: Donega

address: Boelelaan 1108

department: Anatomy and Neuroscience

country: Netherlands

institute: Amsterdam UMC

data_processing:
Raw reads were trimmed, aligned to the Ensembl release 75 Homo sapiens genome using RNA STAR version 2.53A
Data were filtered, normalized and scaled using Seurat 3.2.2
Genome_build: Ensembl release 75 Homo sapiens genome
Supplementary_files_format_and_content: tsv file containing matrix table with gene counts for every gene and every sample following trimming and alignment.

source_name: aged human SVZ

extract_protocol:
Briefly, cellular fraction was isolated from SVZ tissue by mechanical and enzymatic dissociation, followed by Percoll gradient centrifugation. Cell suspension was centrifuged at 1210 rpm for 10 min and incubated with the following fluorescently conjugated antibodies: donkey anti-rabbit (1:250; AF488 Invitrogen, Carlsbad, CA, USA), Fc-receptor (1:20; Myltenyi), anti-CD11b-PE (1:80; Invitrogen M1/70 clone) and anti-CD271 APC (1:11; Myltenyi) for 30 min at 4oC. Cells were passed through a 70 µm filter to remove any clumps or debris before sorting. 7-AAD is used as a marker to exclude dying cells (1:50; BD Pharmingen). FACS was performed immediately after antibody incubations.
Library was prepared according to the Cell-Seq2 protocol The primers used consisted of 24 bp polyT stretch, a 6 bp random molecular barcode (UMI), a cell-specific 8 bp barcode, the 5’ Illumina TruSeq small RNA kit adaptor and, a T7 promoter. TruSeq small RNA primers (Illumina, San Diego, CA, USA) were used for making the Illumina sequencing libraries. Sequencing was done on the Illumina NextSeq platform by sequencing paired-end at 75 bp read length (25 bp from R1 and 50 bp from R2) with a sequencing depth of 15M reads per 384-well plate.

tag: nbb donor number

tag: age

value: subventricular zone (SVZ)


title: Urine nonCOVID AKI 4


title: Urine nonCOVID AKI 3


title: Urine no AKI 3

value: CTL


title: 18119pl1

value: female


title: 18112pl1


title: B318

value: ⅠB


title: NoPre_M1_A4_A9_S269

city: New York

first: Kevin Andrew

middle: Uy

last: Gonzales

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Sequencing reads for scRNA-seq libraries were aligned to the mouse reference genome, combined with sequences for ERCC spike-ins as artificial chromosomes, using STAR (version 2.5.2a) with default parameters for paired-end reads.
Transcript expressions were calculated using the Salmon quantification software (version 0.14.1)
Gene expression levels as TPMs and counts were obtained using Tximport (version 1.12.3). TPMs were transformed to log2(TPM + 1).
Count and TPM matrices were filtered by removing cells with <1500 genes detected per cell and genes expressed in <5% of the cell population.
Genome_build: mouse release M23 (GRCm38.p6)
Supplementary_files_format_and_content: Count matrix file
Supplementary_files_format_and_content: TPM matrix file

source_name: keratinocytes

extract_protocol:
Skin were trypsinized to extract basal stem cells, which were then FACS-sorted with a 100-μm nozzle into 96 well PCR plates (Bio-Rad) containing 2μl of lysis buffer [0.2% Triton X-100, 2U/μl RNaseOUT (Thermo Scientific), 0.25μM oligo-dT30VN primer and 1:8,000,000 diluted ERCC spike-in RNAs (Ambion)].
Briefly, after sorting, plates were briefly centrifuged, snap-frozen in liquid nitrogen and stored at −80°C. Plates were then thawed on ice and incubated for 3 min at 72°C to lyse cells. Reverse transcription (4U/μl Maxima H- transcriptase), template switching reaction and PCR pre-amplification (15 cycles) were performed according to the protocol. PCR product was cleaned up using 0.8X AMPure XP beads (Beckman Coulter) and the quality and quantity of cDNA libraries were measured by Agilent 2200 TapeStation and Qubit Florometer (Thermal Fisher Scientific). To exclude empty wells and low-quality libraries, the cDNA libraries were assessed by qPCR with a primer pair for the housekeeping gene Gapdh (Table S2). Samples showing high Ct value (> 35 cycles) or no PCR amplification were discarded. 50-100pg of each cDNA library was used for generating Illumina sequencing library using a Nextera XT DNA library preparation kits (Illumina). After the final PCR amplification, samples were pooled and cleaned by 0.9X AMPure XP beads.

value: skin

tag: strain

value: CD1 x C57BL/6J cross

tag: genotype

value: full-thickness wounded

tag: timepoint (days post-wound)


title: NoPre_M1_A4_B1_S272

tag: tissue


title: NoPre_M1_A4_B3_S274


title: NoPre_M1_A4_A8_S268


title: NoPre_M1_A4_A7_S267


title: NoPre_M1_A4_A4_S265


title: NoPre_M1_A4_B12_S2


title: NoPre_M1_A4_B11_S1


title: NoPre_M1_A4_A1_S263


title: NoPre_M1_A4_A3_S264


title: 18120pl1


title: NoPre_M1_A4_A11_S270


title: NoPre_M1_A3_H7_S258


title: NoPre_M1_A3_H5_S257


title: Urine AKI 3

value: COVID AKI


title: NoPre_M1_A3_H4_S256


title: 18112pl2


title: NoPre_M1_A3_H2_S255


title: NoPre_M1_A3_G9_S250


title: NoPre_M1_A3_H11_S261


title: NoPre_M1_A3_H1_S254


title: NoPre_M1_A3_G5_S247


title: NoPre_M1_A3_H10_S260


title: NoPre_M1_A4_A6_S266


title: NoPre_M1_A4_A12_S271


title: NoPre_M1_A3_H9_S259


title: NoPre_M1_A3_G4_S246


title: NoPre_M1_A3_G3_S245


title: NoPre_M1_A3_G1_S243


title: NoPre_M1_A3_G2_S244


title: NoPre_M1_A3_G12_S253


title: NoPre_M1_A3_G11_S252


title: NoPre_M1_A3_G8_S249


title: NoPre_M1_A3_F2_S234


title: DremelD80_F4_B4_G8_S68

source_name: YFP+ keratinocytes

value: partial-thickness wounded


title: NoPre_M1_A3_H12_S262


title: NoPre_F1_A3_F1_S233


title: NoPre_M1_A3_F8_S239


title: NoPre_M1_A3_F4_S236


title: NoPre_M1_A3_F5_S237


title: NoPre_M1_A3_F9_S240


title: DremelD80_F4_B4_F11_S59


title: NoPre_M1_A3_F7_S238


title: DremelD80_F4_B4_A8_S3


title: NoPre_M1_A3_G6_S248


title: DremelD80_F4_B4_A3_S2


title: DremelD80_F4_B4_A2_S1


title: CtrlD80_F4_B3_A9_S301

value: unwounded

value: 80dpw (unwounded control)


title: CtrlD80_F4_B3_A8_S300


title: DremelD80_F4_B4_A1_S381


title: CtrlD80_F4_B3_A6_S298


title: NoPre_M1_A3_G10_S251


title: CtrlD80_F4_B3_A4_S296


title: NoPre_M1_A3_F3_S235


title: CtrlD80_F4_B3_A5_S297


title: B143

value: ⅡA

value: paired normal gastric tissue


title: CtrlD80_F4_B2_H12_S292


title: D80_Punch_2

data_processing:
75bp paired-end reads were aligned to mm10 using Bowtie with the parameters –X 2000 and –m 1.
Duplicates were removed using Picard.
Peaks were called using MACS2 (2.1.1.20160309) with the parameter –keep-dup all to let MACS skip the filtering and keep all the sequencing tags.
Peaks with a score per million (SPM) < 9 were considered insignificant and removed
Reads were normalized based on the total number of reads in significant peaks in each sample using the genomecov function in bedtools (v2.29.2)
Genome_build: mm10
Supplementary_files_format_and_content: peak bed files
Supplementary_files_format_and_content: bigwig files

source_name: wound-responsive epidermal stem cell progeny

extract_protocol:
Skin were trypsinized to extract basal stem cells, which were then FACS-sorted to isolate populations of interest.
Freshly sorted cells (15K-100K) were pelleted and incubated with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer, samples were immediately subjected to a transposition reaction at 37°C for 30 min with 2-10μl TnD transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10-15 cycles.


title: D80_Punch_1


title: D7_Punch_2


title: CtrlD80_F4_B3_A12_S303


title: D7_Punch_1


title: unw_M2_YFPp_F1_S58

value: 0dpw (unwounded)


title: unw_M2_YFPp_G8_S64


title: unw_M2_YFPp_G6_S63


title: unw_M2_YFPp_G4_S61


title: unw_M2_YFPp_G11_S67


title: unw_M2_YFPp_E9_S54


title: unw_M2_YFPp_G5_S74


title: unw_M2_YFPp_G9_S65


title: unw_M2_YFPp_F6_S60


title: unw_M2_YFPp_H6_S69


title: unw_M2_YFPp_F3_S59


title: unw_M2_YFPp_G10_S66


title: unw_M2_YFPp_H5_S68


title: unw_M2_YFPp_H9_S71


title: unw_M2_YFPp_E11_S56


title: unw_M2_YFPp_H7_S70


title: unw_M2_YFPp_E12_S57


title: unw_M2_YFPp_E10_S55


title: unw_M2_YFPp_D7_S49


title: D7_Punch_3


title: unw_M2_YFPp_E7_S53


title: unw_M2_YFPp_D6_S48


title: unw_M2_YFPp_D2_S47


title: unw_M2_YFPp_D12_S52


title: unw_M2_YFPp_C9_S45


title: unw_M2_YFPp_C8_S44


title: unw_M2_YFPp_D9_S50


title: unw_M2_YFPp_D10_S51


title: unw_M2_YFPp_C7_S43


title: unw_M2_YFPp_C3_S42


title: unw_M2_YFPp_B9_S41


title: unw_M2_YFPp_B5_S39


title: unw_M2_YFPp_B7_S40


title: unw_M2_YFPp_A8_S37


title: unw_M2_YFPp_A6_S36


title: unw_M2_YFPp_A9_S38


title: unw_M2_YFPn_H12_S16


title: unw_M2_YFPn_G4_S14


title: unw_M2_YFPp_A5_S35


title: unw_M2_YFPn_E4_S10


title: unw_M2_YFPn_G12_S15


title: unw_M2_YFPn_E3_S9


title: unw_M2_YFPn_F12_S13


title: unw_M2_YFPn_D8_S7


title: unw_M2_YFPn_F3_S11


title: unw_M2_YFPn_F9_S12


title: unw_M2_YFPn_D7_S6


title: unw_M2_YFPn_D3_S5


title: unw_M2_YFPn_D11_S8


title: unw_M2_YFPn_C10_S3


title: unw_M2_YFPn_C11_S4


title: unw_M2_YFPn_B8_S1


title: unw_M2_YFPn_2_G5_S101


title: unw_M2_YFPn_2_F6_S98


title: unw_M2_YFPn_2_G11_S103


title: unw_M2_YFPn_2_F5_S97


title: unw_M2_YFPn_2_E9_S94


title: unw_M2_YFPn_2_F10_S99


title: unw_M2_YFPn_2_D7_S91


title: unw_M2_YFPn_2_F11_S100


title: unw_M2_YFPn_2_D9_S92


title: unw_M2_YFPn_C4_S2


title: unw_M2_YFPn_2_D1_S87


title: unw_M2_YFPn_2_D5_S90


title: unw_M2_YFPn_2_D3_S88


title: unw_M2_YFPn_2_H5_S104


title: unw_M2_YFPn_2_C7_S84


title: unw_M2_YFPn_2_C12_S86


title: unw_M2_YFPn_2_D4_S89


title: unw_M2_YFPn_2_C9_S85


title: unw_M2_YFPn_2_G9_S102


title: unw_M2_YFPn_2_C6_S83


title: unw_M2_YFPn_2_B1_S81


title: unw_M2_YFPp_C10_S46


title: unw_M2_YFPn_2_A4_S76


title: unw_M2_YFPn_2_B10_S78


title: unw_M2_YFPn_2_B9_S80


title: unw_M2_F3_S23


title: unw_M2_YFPn_2_A8_S77


title: unw_M2_YFPn_2_B3_S79


title: unw_M2_F7_S24


title: unw_M2_F1_S22


title: unw_M2_YFPn_2_F2_S96


title: unw_M2_YFPn_2_E11_S95


title: unw_M2_YFPn_2_C2_S82


title: unw_M2_E1_S21


title: unw_M2_D1_S20


title: unw_M2_C8_S19


title: unw_M2_C2_S17


title: unw_M2_C5_S18


title: unw_H7_S85


title: unw_H3_S82


title: unw_G8_S76


title: unw_FX_YFPp_F5_S33


title: unw_FX_YFPp_G4_S39


title: unw_FX_YFPp_H2_S96


title: unw_FX_YFPp_H10_S44


title: unw_FX_YFPp_G6_S40


title: unw_FX_YFPp_F9_S35


title: unw_FX_YFPp_F10_S36


title: unw_FX_YFPp_E8_S29


title: unw_FX_YFPp_E5_S27


title: unw_FX_YFPp_G8_S41


title: unw_M2_YFPn_2_E7_S93


title: unw_FX_YFPp_F12_S38


title: unw_G5_S73


title: unw_FX_YFPp_G10_S42


title: unw_FX_YFPp_E7_S28


title: unw_FX_YFPp_F6_S34


title: unw_FX_YFPp_E3_S91


title: unw_FX_YFPp_F11_S37


title: unw_FX_YFPp_E4_S26


title: unw_FX_YFPp_E12_S31


title: unw_FX_YFPp_E2_S25


title: unw_FX_YFPp_G9_S95


title: unw_FX_YFPp_D6_S21


title: unw_FX_YFPp_H4_S43


title: unw_FX_YFPp_D5_S20


title: unw_FX_YFPp_E10_S30


title: unw_FX_YFPp_D8_S22


title: unw_FX_YFPp_D3_S19


title: unw_G7_S75


title: unw_FX_YFPp_F4_S32


title: unw_FX_YFPp_C7_S81


title: unw_FX_YFPp_D1_S83


title: unw_FX_YFPp_D2_S18


title: unw_FX_YFPp_C9_S16


title: unw_FX_YFPp_C2_S78


title: unw_FX_YFPp_B8_S10


title: unw_FX_YFPp_C1_S77


title: unw_FX_YFPp_B6_S9


title: unw_FX_YFPp_C4_S13


title: unw_FX_YFPp_D10_S23


title: unw_FX_YFPp_C6_S15


title: unw_FX_YFPp_D12_S24


title: unw_FX_YFPp_C12_S17


title: unw_FX_YFPp_C3_S12


title: unw_FX_YFPp_C5_S14


title: unw_FX_YFPp_A8_S4


title: unw_FX_YFPn_G4_S95


title: unw_FX_YFPp_B10_S11


title: unw_FX_YFPn_G11_S96


title: unw_FX_YFPp_B4_S62


title: unw_FX_YFPp_B2_S5


title: unw_FX_YFPp_C10_S82


title: unw_FX_YFPp_A6_S3


title: unw_FX_YFPn_G3_S94


title: unw_FX_YFPp_A5_S2


title: unw_FX_YFPp_A3_S1


title: unw_FX_YFPp_B5_S75


title: unw_FX_YFPp_B3_S6


title: unw_FX_YFPn_F9_S91


title: unw_FX_YFPn_F6_S90


title: unw_FX_YFPn_F5_S89


title: unw_FX_YFPn_F11_S92


title: unw_FX_YFPn_E1_S87


title: unw_FX_YFPn_D7_S86


title: unw_FX_YFPn_C8_S82


title: unw_FX_YFPn_D5_S85


title: unw_FX_YFPn_F12_S93


title: unw_FX_YFPn_F3_S88


title: unw_FX_YFPn_B6_S77


title: unw_FX_YFPn_C3_S79


title: unw_FX_YFPn_D3_S84


title: unw_FX_YFPn_C6_S81


title: unw_FX_YFPn_B2_S74


title: unw_FX_YFPn_A3_S70


title: unw_FX_YFPn_A2_S69


title: unw_FX_YFPn_A6_S71


title: unw_FX_YFPn_C12_S83


title: unw_FX_YFPn_B10_S78


title: unw_FX_YFPn_B4_S75


title: unw_FX_YFPn_A10_S73


title: unw_F6_YFPp2_G6_S34


title: unw_FX_YFPn_B5_S76


title: unw_F6_YFPp2_G3_S33


title: unw_F6_YFPp2_F8_S30


title: unw_F6_YFPp2_F7_S29


title: unw_FX_YFPn_A8_S72


title: unw_F6_YFPp2_F6_S28


title: unw_F6_YFPp2_F3_S26


title: unw_F6_YFPp2_F5_S27


title: unw_F6_YFPp2_F9_S31


title: unw_F6_YFPp2_F1_S25


title: unw_F6_YFPp2_E3_S19


title: unw_F6_YFPp2_E7_S21


title: unw_F6_YFPp2_E2_S18


title: unw_F6_YFPp2_D9_S16


title: unw_F6_YFPp2_F12_S32


title: unw_F6_YFPp2_D8_S15


title: unw_F6_YFPp2_E10_S24


title: unw_F6_YFPp2_E4_S20


title: unw_F6_YFPp2_E8_S22


title: unw_F6_YFPp2_D3_S12


title: unw_F6_YFPp2_D4_S13


title: unw_F6_YFPp2_C7_S9


title: unw_FX_YFPn_C5_S80


title: unw_F6_YFPp2_D2_S11


title: unw_F6_YFPp2_E9_S23


title: unw_F6_YFPp2_D7_S14


title: unw_F6_YFPp2_C5_S8


title: unw_F6_YFPp2_C3_S7


title: unw_F6_YFPp2_C10_S10


title: unw_F6_YFPp2_B7_S4


title: unw_F6_YFPp2_B9_S6


title: unw_F6_YFPp2_B4_S3


title: unw_F6_YFPp2_B8_S5


title: unw_F6_YFPp2_A5_S1


title: unw_F6_YFPn_H12_S68


title: unw_F6_YFPn_H9_S67


title: unw_F6_YFPn_G9_S64


title: unw_F6_YFPn_G10_S65


title: unw_F6_YFPp2_D11_S17


title: unw_F6_YFPn_G8_S63


title: unw_F6_YFPn_F9_S60


title: unw_F6_YFPn_F5_S57


title: unw_F6_YFPn_F10_S61


title: unw_F6_YFPn_E8_S52


title: unw_F6_YFPn_F4_S56


title: unw_F6_YFPn_E7_S51


title: unw_F6_YFPn_E9_S53


title: unw_F6_YFPn_F8_S59


title: unw_F6_YFPn_F6_S58


title: unw_F6_YFPn_E5_S49


title: unw_F6_YFPn_E12_S55


title: unw_F6_YFPn_E6_S50


title: unw_F6_YFPn_E3_S47


title: unw_F6_YFPn_D9_S45


title: unw_F6_YFPp2_B3_S2


title: unw_F6_YFPn_D6_S43


title: unw_F6_YFPn_D5_S42


title: unw_F6_YFPn_E4_S48


title: unw_F6_YFPn_D3_S40


title: unw_F6_YFPn_E10_S54


title: unw_F6_YFPn_C9_S38


title: unw_F6_YFPn_D10_S46


title: unw_F6_YFPn_G11_S66


title: unw_F6_YFPn_C7_S36


title: unw_F6_YFPn_C6_S35


title: unw_F6_YFPn_C11_S39


title: unw_F6_YFPn_C4_S34


title: unw_F6_YFPn_B8_S32


title: unw_F6_YFPn_G4_S62


title: unw_F6_YFPn_B4_S28


title: unw_F6_YFPn_B6_S30


title: unw_F6_YFPn_B2_S26


title: unw_F6_YFPn_D7_S44


title: unw_F6_YFPn_B3_S27


title: unw_F6_YFPn_A6_S25


title: unw_F6_YFPn_2_H4_S176


title: unw_F6_YFPn_D4_S41


title: unw_F6_YFPn_2_G8_S172


title: unw_F6_YFPn_2_G7_S171


title: unw_F6_YFPn_2_G6_S170


title: unw_F6_YFPn_2_G9_S173


title: unw_F6_YFPn_2_G4_S168


title: unw_F6_YFPn_2_G2_S166


title: unw_F6_YFPn_2_G5_S169


title: unw_F6_YFPn_B7_S31


title: unw_F6_YFPn_C8_S37


title: unw_F6_YFPn_C3_S33


title: unw_F6_YFPn_2_G12_S175


title: unw_F6_YFPn_B5_S29


title: unw_F6_YFPn_2_G1_S165


title: unw_F6_YFPn_2_H5_S177


title: unw_F6_YFPn_2_F4_S160


title: unw_F6_YFPn_2_H6_S178


title: unw_F6_YFPn_2_F3_S159


title: unw_F6_YFPn_2_H12_S179


title: unw_F6_YFPn_2_F2_S158


title: unw_F6_YFPn_2_G11_S174


title: unw_F6_YFPn_2_F12_S164


title: unw_F6_YFPn_2_F11_S163


title: unw_F6_YFPn_2_F1_S157


title: unw_F6_YFPn_2_F10_S162


title: unw_F6_YFPn_2_E8_S152


title: unw_F6_YFPn_2_G3_S167


title: unw_F6_YFPn_2_E3_S147


title: unw_F6_YFPn_2_E4_S148


title: unw_F6_YFPn_2_E2_S146


title: unw_F6_YFPn_2_E12_S156


title: unw_F6_YFPn_2_E10_S154


title: unw_F6_YFPn_2_E11_S155


title: unw_F6_YFPn_2_D8_S142


title: unw_F6_YFPn_2_D7_S141


title: unw_F6_YFPn_2_D6_S140


title: unw_F6_YFPn_2_D5_S139


title: unw_F6_YFPn_2_F6_S161


title: unw_F6_YFPn_2_D4_S138


title: unw_F6_YFPn_2_D3_S137


title: unw_F6_YFPn_2_E9_S153


title: unw_F6_YFPn_2_D10_S143


title: unw_F6_YFPn_2_C8_S130


title: unw_F6_YFPn_2_E7_S151


title: unw_F6_YFPn_2_D11_S144


title: unw_F6_YFPn_2_D1_S135


title: unw_F6_YFPn_2_E5_S149


title: unw_F6_YFPn_2_C7_S129


title: unw_F6_YFPn_2_C5_S127


title: unw_F6_YFPn_2_D2_S136


title: unw_F6_YFPn_2_C3_S125


title: unw_F6_YFPn_2_C10_S132


title: unw_F6_YFPn_2_C2_S124


title: unw_F6_YFPn_2_C11_S133


title: unw_F6_YFPn_2_C1_S123


title: unw_F6_YFPn_2_B9_S119


title: unw_F6_YFPn_2_E1_S145


title: unw_F6_YFPn_2_B8_S118


title: unw_F6_YFPn_2_C12_S134


title: unw_F6_YFPn_2_B6_S116


title: unw_F6_YFPn_2_B7_S117


title: unw_F6_YFPn_2_B2_S113


title: unw_F6_YFPn_2_C9_S131


title: unw_F6_YFPn_2_B4_S115


title: unw_F6_YFPn_2_B12_S122


title: unw_F6_YFPn_2_C4_S126


title: unw_F6_YFPn_2_C6_S128


title: unw_F6_YFPn_2_B11_S121


title: unw_F6_YFPn_2_B10_S120


title: unw_F6_YFPn_2_A9_S111


title: unw_F6_YFPn_2_B3_S114


title: unw_F6_YFPn_2_A7_S109


title: unw_F6_YFPn_2_A6_S108


title: unw_F6_YFPn_2_A4_S107


title: unw_F6_YFPn_2_A8_S110


title: unw_F6_YFPn_2_A2_S105


title: unw_F6_YFPn_2_A3_S106


title: unw_F11_S68


title: unw_F6_YFPn_2_B1_S112


title: unw_F_Epd_D1_S286


title: unw_F_Epd_D6_S287


title: unw_F_Epd_C6_S283


title: unw_F_Epd_C8_S285


title: unw_F_Epd_C7_S284


title: unw_F_Epd_C5_S282


title: unw_F_Epd_C3_S280


title: unw_F_Epd_B8_S277


title: unw_F_Epd_C1_S279


title: unw_F_Epd_C4_S281


title: unw_F_Epd_B7_S276


title: unw_F_Epd_B5_S275


title: unw_F_Epd_B2_S274


title: unw_F_Epd_B10_S278


title: unw_F_Epd_A5_S272


title: unw_F_Epd_A1_S271


title: unw_B8_S18


title: unw_B3_S13


title: homeo_ctrl_2mo_F_H9_S228


title: unw_F_Epd_B1_S273


title: unw_C2_S24


title: unw_F_Epd_E2_S288


title: homeo_ctrl_2mo_F_H10_S229


title: homeo_ctrl_2mo_F_H1_S227


title: homeo_ctrl_2mo_F_F9_S222


title: homeo_ctrl_2mo_F_G1_S225


title: homeo_ctrl_2mo_F_G11_S226


title: homeo_ctrl_2mo_F_F8_S221


title: homeo_ctrl_2mo_F_F7_S220


title: homeo_ctrl_2mo_F_E6_S213


title: homeo_ctrl_2mo_F_E5_S212


title: homeo_ctrl_2mo_F_F5_S219


title: homeo_ctrl_2mo_F_F2_S217


title: homeo_ctrl_2mo_F_E4_S211


title: homeo_ctrl_2mo_F_F12_S224


title: homeo_ctrl_2mo_F_F3_S218


title: homeo_ctrl_2mo_F_E2_S209


title: homeo_ctrl_2mo_F_E11_S215


title: homeo_ctrl_2mo_F_E12_S216


title: homeo_ctrl_2mo_F_E10_S214


title: homeo_ctrl_2mo_F_E1_S208


title: homeo_ctrl_2mo_F_D9_S204


title: homeo_ctrl_2mo_F_E3_S210


title: homeo_ctrl_2mo_F_D8_S203


title: homeo_ctrl_2mo_F_D5_S200


title: homeo_ctrl_2mo_F_D6_S201


title: homeo_ctrl_2mo_F_D4_S199


title: homeo_ctrl_2mo_F_D3_S198


title: homeo_ctrl_2mo_F_D2_S197


title: homeo_ctrl_2mo_F_D11_S206


title: homeo_ctrl_2mo_F_C8_S192


title: homeo_ctrl_2mo_F_C7_S191


title: homeo_ctrl_2mo_F_F11_S223


title: homeo_ctrl_2mo_F_C9_S193


title: homeo_ctrl_2mo_F_D12_S207


title: homeo_ctrl_2mo_F_C4_S189


title: homeo_ctrl_2mo_F_C11_S195


title: homeo_ctrl_2mo_F_C10_S194


title: homeo_ctrl_2mo_F_C12_S196


title: homeo_ctrl_2mo_F_B5_S183


title: unw_F6_YFPn_2_E6_S150


title: homeo_ctrl_2mo_F_B12_S187


title: homeo_ctrl_2mo_F_D7_S202


title: homeo_ctrl_2mo_F_A9_S181


title: homeo_ctrl_2mo_F_B6_S184


title: homeo_ctrl_2mo_F_A11_S182


title: homeo_ctrl_2mo_F_B11_S186


title: homeo_ctrl_2mo_F_A3_S180


title: D7_F2_H9_S192


title: D7_F2_G9_S190


title: homeo_ctrl_2mo_F_D10_S205


title: homeo_ctrl_2mo_F_C6_S190


title: D7_F2_G8_S189


title: D7_F2_G7_S188


title: D7_F2_G4_S186


title: D7_F2_G12_S191


title: D7_F2_F6_S182


title: D7_F2_G6_S187


title: D7_F2_F5_S181


title: homeo_ctrl_2mo_F_C3_S188


title: D7_F2_F8_S184


title: D7_F2_F9_S185


title: homeo_ctrl_2mo_F_B8_S185


title: D7_F2_F3_S180


title: D7_F2_E6_S176


title: D7_F2_E8_S178


title: D7_F2_E3_S175


title: D7_F2_E11_S179


title: D7_F2_E1_S173


title: D7_F2_D8_S169


title: D7_F2_D9_S170


title: D7_F2_D5_S167


title: D7_F2_D3_S165


title: D7_F2_F7_S183


title: D7_F2_D7_S168


title: D7_F2_D2_S164


title: D7_F2_C6_S160


title: D7_F2_C8_S161


title: D7_F2_D1_S163


title: D7_F2_D11_S172


title: D7_F2_D10_S171


title: D7_F2_C3_S157


title: D7_F2_C5_S159


title: D7_F2_D4_S166


title: D7_F2_C4_S158


title: D7_F2_C2_S156


title: D7_F2_B5_S153


title: D7_F2_B6_S154


title: D7_F2_C10_S162


title: D7_F2_C1_S155


title: D7_F2_E2_S174


title: D7_F2_B3_S151


title: D7_F2_B4_S152


title: D7_F1_CD200p_H9_S302


title: D7_F1_CD200p_G11_S300


title: D7_F1_CD200p_G10_S299


title: D7_F1_CD200p_G12_S301


title: D7_F1_CD200p_F8_S292


title: D7_F2_A5_S150


title: D7_F1_CD200p_G5_S297


title: D7_F1_CD200p_G9_S298


title: D7_F1_CD200p_F5_S290


title: D7_F1_CD200p_F6_S291


title: D7_F1_CD200p_F9_S293


title: D7_F1_CD200p_F3_S384


title: D7_F1_CD200p_E7_S378


title: D7_F1_CD200p_E6_S377


title: D7_F1_CD200p_F11_S295


title: D7_F1_CD200p_E8_S379


title: D7_F1_CD200p_E9_S380


title: D7_F1_CD200p_F12_S296


title: D7_F1_CD200p_F10_S294


title: D7_F1_CD200p_F4_S289


title: D7_F1_CD200p_E4_S375


title: D7_F1_CD200p_E5_S376


title: D7_F1_CD200p_E12_S383


title: D7_F1_CD200p_E3_S374


title: D7_F1_CD200p_E2_S373


title: D7_F1_CD200p_E11_S382


title: D7_F1_CD200p_E10_S381


title: D7_F1_CD200p_D9_S371


title: D7_F1_CD200p_D8_S370


title: D7_F1_CD200p_D7_S369


title: D7_F1_CD200p_D4_S366


title: D7_F1_CD200p_D6_S368


title: D7_F1_CD200p_D3_S365


title: D7_F1_CD200p_D5_S367


title: D7_F1_CD200p_D10_S372


title: D7_F1_CD200p_D1_S364


title: D7_F1_CD200p_C9_S362


title: D7_F1_CD200p_C6_S359


title: D7_F1_CD200p_C3_S356


title: D7_F1_CD200p_C5_S358


title: D7_F1_CD200p_C4_S357


title: D7_F1_CD200p_B9_S352


title: D7_F1_CD200p_B4_S348


title: D7_F1_CD200p_B5_S349


title: D7_F1_CD200p_B6_S350


title: D7_F1_CD200p_B7_S351


title: D7_F1_CD200p_C8_S361


title: D7_F1_CD200p_B3_S347


title: D7_F1_CD200p_C1_S354


title: D7_F1_CD200p_C7_S360


title: D7_F1_CD200p_B2_S346


title: D7_F1_CD200p_B11_S353


title: D7_F1_CD200p_A9_S344


title: D7_F1_CD200p_A8_S343


title: D7_F1_CD200p_C2_S355


title: D7_F1_CD200p_C10_S363


title: D7_F1_CD200p_A3_S340


title: D7_F1_CD200p_A5_S342


title: D7_F1_CD200p_A4_S341


title: D7_F1_CD200p_A2_S339


title: D6_M1_D9_S369


title: D7_F1_CD200p_A10_S345


title: D6_M1_CD200p_D7_S275


title: D6_M1_CD200p_D5_S273


title: D6_M1_CD200p_D9_S277


title: D6_M1_CD200p_D8_S276


title: D6_M1_D1_S363


title: D6_M1_CD200p_D3_S272


title: D6_M1_CD200p_D11_S279


title: D6_M1_CD200p_C9_S271


title: D6_M1_CD200p_D6_S274


title: D6_M1_CD200p_C5_S267


title: D6_M1_CD200p_C3_S265


title: D6_M1_CD200p_C7_S269


title: D6_M1_CD200p_D10_S278


title: D6_M1_CD200p_C6_S268


title: D6_M1_CD200p_C4_S266


title: D6_M1_CD200p_C8_S270


title: D6_M1_CD200p_B3_S258


title: D6_M1_CD200p_C2_S264


title: D6_M1_CD200p_B2_S257


title: D6_M1_CD200p_B5_S260


title: D6_M1_CD200p_B4_S259


title: D6_M1_CD200p_B10_S261


title: D6_M1_E1_S373


title: D6_M1_CD200p_B12_S263


title: D6_M1_CD200p_B11_S262


title: D6_M1_CD200p_B1_S256


title: D6_M1_CD200p_A3_S252


title: D6_M1_CD200p_A6_S253


title: D6_M1_CD200p_A11_S254


title: D7_F2_E7_S177


title: D6_M1_C10_S361


title: D6_F3_H9_S338


title: D6_F3_H5_S336


title: D6_F3_H8_S337


title: D6_M1_C11_S362


title: D6_M1_CD200p_A1_S251


title: D6_F3_H4_S335


title: D6_F3_G4_S328


title: D6_F3_G5_S329


title: D6_F3_G2_S326


title: D6_F3_H3_S334


title: D6_F3_G7_S330


title: D6_F3_F8_S322


title: D6_F3_G11_S333


title: D6_F3_F5_S321


title: D6_F3_F4_S320


title: D6_F3_F3_S319


title: D6_F3_F11_S325


title: D6_F3_F9_S323


title: D6_F3_F1_S317


title: D6_F3_F2_S318


title: D6_F3_E5_S313


title: D6_F3_F10_S324


title: D6_F3_E9_S314


title: D6_F3_E11_S316


title: D6_M1_CD200p_A12_S255


title: D6_F3_G9_S331


title: D6_F3_E10_S315


title: D6_F3_G3_S327


title: D6_F3_D11_S312


title: D6_F3_D6_S307


title: D6_F3_D4_S306


title: D6_F3_D9_S310


title: D6_F3_CD200p_G7_S384


title: D6_F3_CD200p_G3_S381


title: D6_F3_CD200p_G5_S383


title: D6_F3_CD200p_G4_S382


title: D6_F3_D10_S311


title: D6_F3_CD200p_F12_S380


title: D6_F3_CD200p_F3_S378


title: D6_F3_CD200p_E8_S374


title: D6_F3_CD200p_E3_S371


title: D6_F3_CD200p_E2_S370


title: D6_F3_CD200p_E4_S372


title: D6_F3_CD200p_E12_S377


title: D6_F3_CD200p_E6_S373


title: D6_F3_CD200p_E10_S376


title: D6_F3_G10_S332


title: D6_F3_D3_S305


title: D6_F3_CD200p_D9_S367


title: D6_F3_CD200p_D8_S366


title: D6_F3_D8_S309


title: D6_F3_D7_S308


title: D6_F3_CD200p_E1_S369


title: D6_F3_D1_S304


title: D6_F3_CD200p_D6_S365


title: D6_F3_CD200p_D4_S363


title: D6_F3_CD200p_D2_S361


title: D6_F3_CD200p_D5_S364


title: D6_F3_CD200p_C9_S357


title: D6_F3_CD200p_F5_S379


title: D6_F3_CD200p_C8_S356


title: D6_F3_CD200p_E9_S375


title: D6_F3_CD200p_C5_S354


title: D6_F3_CD200p_C4_S353


title: D6_F3_CD200p_C3_S352


title: D6_F3_CD200p_C11_S359


title: D6_F3_CD200p_C12_S360


title: D6_F3_CD200p_C1_S350


title: D6_F3_CD200p_B7_S344


title: D6_F3_CD200p_B6_S343


title: D6_F3_CD200p_D11_S368


title: D6_F3_CD200p_D3_S362


title: D6_F3_CD200p_B12_S349


title: D6_F3_CD200p_A6_S337


title: D6_F3_CD200p_A8_S338


title: D6_F3_CD200p_B11_S348


title: D6_F3_CD200p_B2_S341


title: D6_F3_CD200p_B10_S347


title: D6_F3_CD200p_A11_S339


title: D6_F3_CD200p_C7_S355


title: D6_F3_C8_S303


title: D6_F3_C7_S302


title: D6_F3_CD200p_B4_S342


title: D6_F3_CD200p_C2_S351


title: D6_F3_CD200p_C10_S358


title: D6_F3_CD200p_B9_S346


title: D6_F3_CD200p_B8_S345


title: PreD_M2_A3_E4_S224

value: 3dpw (80dpw partial-thickness wounded)


title: PreD_M2_A3_F11_S242


title: PreD_M2_A3_E3_S223


title: PreD_M2_A3_F10_S241


title: PreD_M2_A3_E7_S227


title: PreD_M2_A3_E9_S229


title: PreD_M2_A3_E5_S225


title: D6_F3_CD200p_A4_S336


title: PreD_M2_A3_E6_S226


title: PreD_M2_A3_E8_S228


title: PreD_M2_A3_E11_S231


title: PreD_M2_A3_E12_S232


title: PreD_M2_A3_E1_S221


title: PreD_M2_A3_D8_S216


title: PreD_M2_A3_E10_S230


title: PreD_M2_A3_D6_S214


title: PreD_M2_A3_D9_S217


title: PreD_M2_A3_D2_S211


title: PreD_M2_A3_D1_S210


title: PreD_M2_A3_D3_S212


title: PreD_M2_A3_D11_S219


title: PreD_M2_A3_D10_S218


title: D6_F3_CD200p_B1_S340


title: PreD_M2_A3_D7_S215


title: PreD_M2_A3_C9_S206


title: PreD_M2_A3_C8_S205


title: PreD_M2_A3_D12_S220


title: PreD_M2_A3_C7_S204


title: PreD_M2_A3_C4_S201


title: PreD_M2_A3_C6_S203


title: PreD_M2_A3_C3_S200


title: PreD_M2_A3_C12_S209


title: PreD_M2_A3_C1_S198


title: PreD_M2_A3_C5_S202


title: PreD_M2_A3_C10_S207


title: PreD_M2_A3_B9_S194


title: PreD_M2_A3_B8_S193


title: PreD_M2_A3_B7_S192


title: PreD_M2_A3_B6_S191


title: PreD_M2_A3_B5_S190


title: PreD_M2_A3_E2_S222


title: PreD_M2_A3_B4_S189


title: PreD_M2_A3_C11_S208


title: PreD_M2_A3_B2_S187


title: PreD_M2_A3_B11_S196


title: PreD_M2_A3_B12_S197


title: PreD_M2_A3_D5_S213


title: PreD_M2_A3_B3_S188


title: PreD_M2_A3_A7_S181


title: PreD_M2_A3_A9_S183


title: PreD_M2_A3_A6_S180


title: PreD_M2_A3_A8_S182


title: PreD_M2_A3_A4_S179


title: PreD_M2_A3_A2_S177


title: PreD_M2_A3_C2_S199


title: PreD_M2_A3_A3_S178


title: PreD_M2_A3_A1_S176


title: PreD_M2_A3_A10_S184


title: PreD_M2_A3_A12_S186


title: PreD_M2_A2_H8_S171


title: PreD_M2_A2_H7_S170


title: PreD_M2_A2_H6_S169


title: PreD_M2_A2_H9_S172


title: PreD_M2_A2_H4_S167


title: PreD_M2_A2_H5_S168


title: PreD_M2_A2_H3_S166


title: PreD_M2_A3_B10_S195


title: PreD_M2_A2_H2_S165


title: PreD_M2_A2_H10_S173


title: PreD_M2_A2_G8_S160


title: PreD_M2_A2_G9_S161


title: PreD_M2_A2_H11_S174


title: PreD_M2_A2_G5_S157


title: PreD_M2_A2_G2_S154


title: PreD_M2_A2_G4_S156


title: PreD_M2_A2_G7_S159


title: PreD_M2_A2_G6_S158


title: PreD_M2_A2_G10_S162


title: PreD_M2_A2_G12_S164


title: PreD_M2_A2_G11_S163


title: PreD_M2_A2_G1_S153


title: PreD_M2_A3_A11_S185


title: PreD_M2_A2_F8_S148


title: PreD_M2_A2_G3_S155


title: PreD_M2_A2_F3_S143


title: PreD_M2_A2_F7_S147


title: PreD_M2_A2_F2_S142


title: PreD_M2_A2_F6_S146


title: PreD_M2_A2_F12_S152


title: PreD_M2_A2_F11_S151


title: PreD_M2_A2_F10_S150


title: PreD_M2_A2_E7_S135


title: PreD_M2_A2_E9_S137


title: PreD_M2_A2_E8_S136


title: PreD_M2_A2_E5_S133


title: PreD_M2_A2_F9_S149


title: PreD_M2_A2_E4_S132


title: PreD_M2_A2_E3_S131


title: PreD_M2_A2_E2_S130


title: PreD_M2_A2_E1_S129


title: PreD_M2_A2_E10_S138


title: PreD_M2_A2_D8_S125


title: PreD_M2_A2_D7_S124


title: PreD_M2_A2_F5_S145


title: PreD_M2_A2_D6_S123


title: PreD_M2_A2_E12_S140


title: PreD_M2_A2_F4_S144


title: PreD_M2_A2_D5_S122


title: PreD_M2_A2_D2_S119


title: PreD_M2_A2_F1_S141


title: PreD_M2_A2_D1_S118


title: PreD_M2_A2_D3_S120


title: PreD_M2_A2_D11_S127


title: PreD_M2_A2_D12_S128


title: PreD_M2_A2_D9_S126


title: PreD_M2_A2_E11_S139


title: PreD_M2_A2_D4_S121


title: PreD_M2_A2_C9_S114


title: PreD_M2_A2_E6_S134


title: PreD_M2_A2_C8_S113


title: PreD_M2_A2_C11_S116


title: PreD_M2_A2_C10_S115


title: PreD_M2_A2_C4_S109


title: PreD_M2_A2_B6_S99


title: PreD_M2_A2_C6_S111


title: PreD_M2_A2_C5_S110


title: PreD_M2_A2_C3_S108


title: PreD_M2_A2_C2_S107


title: PreD_M2_A2_B2_S95


title: PreD_M2_A2_C12_S117


title: PreD_M2_A2_C1_S106


title: PreD_M2_A2_B9_S102


title: PreD_M2_A2_A7_S89


title: PreD_M2_A2_A8_S90


title: PreD_M2_A2_B8_S101


title: PreD_M2_A2_A4_S86


title: PreD_M2_A2_A5_S87


title: PreD_M2_A2_B5_S98


title: PreD_M2_A2_B4_S97


title: PreD_M2_A2_B7_S100


title: PreD_M2_A2_B3_S96


title: PreD_M2_A2_A12_S94


title: PreD_M2_A2_A10_S92


title: PreD_M2_A2_B10_S103


title: PreD_M2_A2_B12_S105


title: PreD_M2_A2_A9_S91


title: PreD_M2_A2_B11_S104


title: PreD_M1_A1_H7_S79


title: PreD_M2_A2_A6_S88


title: PreD_M1_A1_H11_S82


title: PreD_M2_A2_C7_S112


title: PreD_M2_A2_A11_S93


title: PreD_M2_A2_A1_S84


title: PreD_M1_A1_H9_S80


title: PreD_M1_A1_H12_S83


title: PreD_M2_A2_A3_S85


title: PreD_M1_A1_G12_S75


title: PreD_M1_A1_G11_S74


title: PreD_M1_A1_G5_S69


title: PreD_M1_A1_F2_S56


title: PreD_M1_A1_F9_S62


title: PreD_M1_A1_F12_S65


title: PreD_M1_A1_F11_S64


title: PreD_M1_A1_E8_S51


title: PreD_M1_A1_F10_S63


title: PreD_M1_A1_H10_S81


title: PreD_M1_A1_G10_S73


title: PreD_M1_A1_E9_S52


title: PreD_M1_A1_H3_S78


title: PreD_M1_A1_G8_S71


title: PreD_M1_A1_E1_S45


title: PreD_M1_A1_E5_S48


title: PreD_M1_A1_E12_S54


title: PreD_M1_A1_E7_S50


title: PreD_M1_A1_E10_S53


title: PreD_M1_A1_D8_S40


title: PreD_M1_A1_D7_S39


title: PreD_M1_A1_D6_S38


title: PreD_M1_A1_D12_S44


title: PreD_M1_A1_D9_S41


title: PreD_M1_A1_D11_S43


title: PreD_M1_A1_D3_S35


title: PreD_M1_A1_D4_S36


title: PreD_M1_A1_C9_S29


title: PreD_M1_A1_D1_S33


title: PreD_M1_A1_D10_S42


title: PreD_M1_A1_C6_S26


title: PreD_M1_A1_C5_S25


title: PreD_M1_A1_C7_S27


title: PreD_M1_A1_C2_S22


title: PreD_M1_A1_C1_S21


title: PreD_M1_A1_C4_S24


title: PreD_M1_A1_B9_S17


title: PreD_M1_A1_C10_S30


title: PreD_M1_A1_C8_S28


title: PreD_M1_A1_C3_S23


title: PreD_M1_A1_C11_S31


title: PreD_M1_A1_B7_S15


title: PreD_M1_A1_C12_S32


title: PreD_M1_A1_B8_S16


title: PreD_M1_A1_B5_S13


title: PreD_M1_A1_B6_S14


title: PreD_M1_A1_B4_S12


title: PreD_M1_A1_B2_S10


title: PreD_M1_A1_B3_S11


title: PreD_M1_A1_B11_S19


title: PreD_M1_A1_B12_S20


title: PreD_M1_A1_B1_S9


title: PreD_F1_A1_A6_S5


title: PreD_M1_A1_B10_S18


title: PreD_F1_A1_A4_S4


title: PreD_F1_A1_A2_S2


title: PreD_F1_A1_A3_S3


title: PreD_F1_A1_A12_S8


title: NoPre_M2_B2_H8_S290


title: NoPre_M2_B2_H5_S288


title: NoPre_M2_B2_H7_S289


title: NoPre_M2_B2_H3_S286


title: NoPre_M2_B2_H2_S285


title: PreD_F1_A1_A11_S7


title: NoPre_M2_B2_G9_S280


title: NoPre_M2_B2_G6_S277


title: NoPre_M2_B2_H10_S291


title: NoPre_M2_B2_H1_S284


title: NoPre_M2_B2_G7_S278


title: NoPre_M2_B2_G2_S275


title: NoPre_M2_B2_G3_S276


title: NoPre_M2_B2_G11_S282


title: NoPre_M2_B2_G8_S279


title: NoPre_M2_B2_G1_S274


title: NoPre_M2_B2_F8_S272


title: NoPre_M2_B2_G12_S283


title: NoPre_M2_B2_G10_S281


title: PreD_F1_A1_A1_S1


title: NoPre_M2_B2_F5_S269


title: NoPre_M2_B2_F7_S271


title: NoPre_M2_B2_F4_S268


title: NoPre_M2_B2_F6_S270


title: NoPre_M2_B2_F3_S267


title: NoPre_M2_B2_F2_S266


title: NoPre_M2_B2_F11_S273


title: NoPre_M2_B2_F1_S265


title: NoPre_M2_B2_H4_S287


title: NoPre_M2_B2_E9_S262


title: NoPre_M2_B2_E8_S261


title: NoPre_M2_B2_E6_S259


title: NoPre_M2_B2_E5_S258


title: NoPre_M2_B2_E3_S257


title: NoPre_M2_B2_E2_S256


title: NoPre_M2_B2_D6_S250


title: NoPre_M2_B2_D2_S246


title: NoPre_M2_B2_D5_S249


title: NoPre_M2_B2_D7_S251


title: NoPre_M2_B2_D1_S245


title: NoPre_M2_B2_D9_S252


title: NoPre_M2_B2_D11_S254


title: NoPre_M2_B2_D4_S248


title: NoPre_M2_B2_C8_S242


title: NoPre_M2_B2_C6_S241


title: NoPre_M2_B2_D3_S247


title: NoPre_M2_B2_D10_S253


title: NoPre_M2_B2_C5_S240


title: NoPre_M2_B2_C11_S244


title: NoPre_M2_B2_B8_S234


title: NoPre_M2_B2_B7_S233


title: NoPre_M2_B2_C10_S243


title: NoPre_M2_B2_B6_S232


title: NoPre_M2_B2_C3_S239


title: NoPre_M2_B2_B5_S231


title: NoPre_M2_B2_B3_S230


title: NoPre_M2_B2_C2_S238


title: NoPre_M2_B2_E7_S260


title: NoPre_M2_B2_E1_S255


title: NoPre_M2_B2_B10_S235


title: NoPre_M2_B2_B12_S236


title: NoPre_M2_B2_A9_S224


title: NoPre_M2_B2_A8_S223


title: NoPre_M2_B2_A7_S222


title: NoPre_M2_B2_A2_S218


title: NoPre_M2_B2_A3_S219


title: NoPre_M2_B2_C1_S237


title: NoPre_M2_B2_A11_S226


title: NoPre_M2_B2_A12_S227


title: NoPre_M2_B2_A6_S221


title: NoPre_M2_B1_H1_S209


title: NoPre_M2_B1_H2_S210


title: NoPre_M2_B1_G5_S204


title: NoPre_M2_B1_G9_S206


title: NoPre_M2_B1_H10_S214


title: NoPre_M2_B1_H12_S216


title: NoPre_M2_B1_G4_S203


title: NoPre_M2_B2_B2_S229


title: NoPre_M2_B1_G2_S201


title: NoPre_M2_B2_B1_S228


title: NoPre_M2_B1_H3_S211


title: NoPre_M2_B1_F9_S199


title: NoPre_M2_B2_A4_S220


title: NoPre_M2_B1_F8_S198


title: NoPre_M2_B1_G10_S207


title: NoPre_M2_B1_F11_S200


title: NoPre_M2_B1_H7_S212


title: NoPre_M2_B1_H9_S213


title: NoPre_M2_B1_E8_S189


title: NoPre_M2_B1_E9_S190


title: NoPre_M2_B2_A1_S217


title: NoPre_M2_B1_E5_S187


title: NoPre_M2_B1_E4_S186


title: NoPre_M2_B1_G12_S208


title: NoPre_M2_B1_E2_S184


title: NoPre_M2_B1_D8_S179


title: NoPre_M2_B1_C9_S172


title: NoPre_M2_B1_C6_S171


title: NoPre_M2_B1_D5_S177


title: NoPre_M2_B1_E10_S191


title: NoPre_M2_B1_D1_S176


title: NoPre_M2_B1_F6_S196


title: NoPre_M2_B1_F5_S195


title: NoPre_M2_B1_F7_S197


title: NoPre_M2_B1_D7_S178


title: NoPre_M2_B1_E3_S185


title: NoPre_M2_B1_E11_S192


title: NoPre_M2_B1_F3_S194


title: NoPre_M2_B1_F1_S193


title: NoPre_M2_B1_E7_S188


title: NoPre_M2_B1_C2_S169


title: NoPre_M2_B1_C1_S168


title: NoPre_M2_B1_C3_S170


title: NoPre_M2_B1_C10_S173


title: NoPre_M2_B1_B8_S165


title: NoPre_M2_B1_B7_S164


title: NoPre_M2_B1_B4_S162


title: NoPre_M2_B1_B6_S163


title: NoPre_M2_B1_E1_S183


title: NoPre_M2_B1_C11_S174


title: NoPre_M2_B1_B12_S167


title: NoPre_M2_B1_B2_S160


title: NoPre_M2_B1_B3_S161


title: NoPre_M2_B1_B10_S166


title: NoPre_M2_B1_A8_S157


title: NoPre_M2_B1_A3_S153


title: NoPre_M2_B1_A7_S156


title: NoPre_M2_B1_A12_S159


title: NoPre_M2_B1_A6_S155


title: NoPre_M2_B1_A2_S152


title: NoPre_M2_B1_C12_S175


title: NoPre_M1_A5_G7_S141


title: NoPre_M1_A5_G8_S142


title: NoPre_M1_A5_H7_S146


title: NoPre_M1_A5_G9_S143


title: NoPre_M1_A5_G4_S138


title: NoPre_M1_A5_G3_S137


title: NoPre_M1_A5_F8_S130


title: NoPre_M1_A5_G11_S145


title: NoPre_M2_B1_A10_S158


title: NoPre_M1_A5_F5_S128


title: NoPre_M1_A5_F1_S124


title: NoPre_M1_A5_G6_S140


title: NoPre_M1_A5_F10_S132


title: NoPre_M1_A5_G2_S136


title: NoPre_M1_A5_G1_S135


title: NoPre_M1_A5_E8_S120


title: NoPre_M1_A5_G10_S144


title: NoPre_M1_A5_F9_S131


title: NoPre_M1_A5_F7_S129


title: NoPre_M1_A5_F3_S126


title: NoPre_M1_A5_F2_S125


title: NoPre_M1_A5_F11_S133


title: NoPre_M1_A5_F12_S134


title: NoPre_M1_A5_E7_S119


title: NoPre_M1_A5_E6_S118


title: NoPre_M1_A5_E10_S122


title: NoPre_M1_A5_E9_S121


title: NoPre_M1_A5_E5_S117


title: NoPre_M1_A5_D6_S107


title: NoPre_M1_A5_E4_S116


title: NoPre_M1_A5_D2_S104


title: NoPre_M1_A5_E1_S114


title: NoPre_M1_A5_D8_S109


title: NoPre_M1_A5_D10_S111


title: NoPre_M1_A5_D11_S112


title: NoPre_M1_A5_E2_S115


title: NoPre_M1_A5_F4_S127


title: NoPre_M1_A5_C7_S98


title: NoPre_M1_A5_E11_S123


title: NoPre_M1_A5_D7_S108


title: NoPre_M1_A5_D9_S110


title: NoPre_M1_A5_D5_S106


title: NoPre_M1_A5_D4_S105


title: NoPre_M1_A5_D12_S113


title: NoPre_M1_A5_C9_S100


title: NoPre_M1_A5_C6_S97


title: NoPre_M1_A5_C2_S93


title: NoPre_M1_A5_C11_S102


title: NoPre_M1_A5_B5_S84


title: NoPre_M1_A5_B6_S85


title: NoPre_M1_A5_C5_S96


title: NoPre_M1_A5_C3_S94


title: NoPre_M1_A5_B12_S91


title: NoPre_M1_A5_B11_S90


title: NoPre_M1_A5_B7_S86


title: NoPre_M1_A5_C10_S101


title: NoPre_M1_A5_C1_S92


title: NoPre_M1_A5_B9_S88


title: NoPre_M1_A5_A7_S75


title: NoPre_M1_A5_B4_S83


title: NoPre_M1_A5_A9_S77


title: NoPre_M1_A5_B2_S81


title: NoPre_M1_A5_C12_S103


title: NoPre_M1_A5_A12_S80


title: NoPre_M1_A5_A5_S73


title: NoPre_M1_A5_A6_S74


title: NoPre_M1_A5_A4_S72


title: NoPre_M1_A5_A3_S71


title: NoPre_M1_A5_A1_S69


title: NoPre_M1_A5_A11_S79


title: NoPre_M1_A5_A2_S70


title: NoPre_M1_A5_A8_S76


title: NoPre_M1_A4_H5_S65


title: NoPre_M1_A4_H4_S64


title: NoPre_M1_A4_H3_S63


title: NoPre_M1_A4_H1_S61


title: NoPre_M1_A4_H2_S62


title: NoPre_M1_A5_A10_S78


title: NoPre_M1_A4_G8_S56


title: NoPre_M1_A4_H9_S66


title: NoPre_M1_A5_B10_S89


title: NoPre_M1_A4_G9_S57


title: NoPre_M1_A4_H10_S67


title: NoPre_M1_A4_H12_S68


title: NoPre_M1_A4_G7_S55


title: NoPre_M1_A4_G4_S52


title: NoPre_M1_A4_G5_S53


title: NoPre_M1_A4_G12_S60


title: NoPre_M1_A4_F9_S46


title: NoPre_M1_A4_G10_S58


title: NoPre_M1_A4_G11_S59


title: NoPre_M1_A4_F7_S44


title: NoPre_M1_A4_F4_S41


title: NoPre_M1_A4_F1_S38


title: NoPre_M1_A4_F12_S49


title: NoPre_M1_A4_F3_S40


title: NoPre_M1_A4_F10_S47


title: NoPre_M1_A4_F11_S48


title: NoPre_M1_A4_E8_S33


title: NoPre_M1_A4_E4_S29


title: NoPre_M1_A4_E9_S34


title: NoPre_M1_A4_E5_S30


title: NoPre_M1_A4_G6_S54


title: NoPre_M1_A4_E7_S32


title: NoPre_M1_A4_E2_S27


title: NoPre_M1_A4_E1_S26


title: NoPre_M1_A4_G2_S51


title: NoPre_M1_A4_E12_S37


title: NoPre_M1_A4_G1_S50


title: NoPre_M1_A4_E10_S35


title: NoPre_M1_A4_E3_S28


title: NoPre_M1_A4_D9_S22


title: NoPre_M1_A4_D8_S21


title: NoPre_M1_A4_D7_S20


title: NoPre_M1_A4_D6_S19


title: NoPre_M1_A4_F2_S39


title: NoPre_M1_A4_D3_S16


title: NoPre_M1_A4_D2_S15


title: NoPre_M1_A4_D4_S17


title: NoPre_M1_A4_D1_S14


title: NoPre_M1_A4_D12_S25


title: NoPre_M1_A4_C9_S10


title: NoPre_M1_A4_D11_S24


title: NoPre_M1_A4_D10_S23


title: NoPre_M1_A4_C8_S9


title: NoPre_M1_A4_C7_S8


title: NoPre_M1_A4_C6_S7


title: NoPre_M1_A4_E11_S36


title: NoPre_M1_A4_C5_S6


title: NoPre_M1_A4_C4_S5


title: NoPre_M1_A4_C1_S3


title: NoPre_M1_A4_B9_S280


title: NoPre_M1_A4_C12_S13


title: NoPre_M1_A4_B6_S277


title: NoPre_M1_A4_C10_S11


title: NoPre_M1_A4_C2_S4


title: D6_F3_C6_S301


title: NoPre_M1_A4_B4_S275


title: D6_F3_C5_S300


title: D6_F3_C3_S298


title: D6_F3_C4_S299


title: D6_F3_C2_S297


title: D6_F3_B8_S295


title: D6_F3_B7_S294


title: D6_F3_B4_S292


title: D6_F3_B2_S290


title: D6_F3_B6_S293


title: D6_F3_B3_S291


title: D6_F3_B11_S296


title: D5_F5_G4_S282


title: D6_F3_A4_S289


title: D5_F5_E10_S274


title: D5_F5_E3_S270


title: D5_F5_F1_S276


title: D5_F5_D5_S264


title: D5_F5_D1_S262


title: D5_F5_B8_S253


title: NoPre_M1_A4_C11_S12


title: D5_F4_CD200p_H5_S245


title: D5_F4_CD200p_H3_S243


title: D5_F4_CD200p_H10_S249


title: D5_F4_CD200p_H9_S248


title: D5_F4_CD200p_H11_S250


title: D5_F4_CD200p_H8_S247


title: D5_F4_CD200p_G7_S238


title: D5_F4_CD200p_H7_S246


title: D5_F4_CD200p_G8_S239


title: D5_F4_CD200p_G11_S242


title: D5_F4_CD200p_G3_S234


title: D5_F4_CD200p_H4_S244


title: D5_F4_CD200p_G9_S240


title: D5_F4_CD200p_G6_S237


title: D5_F4_CD200p_G5_S236


title: D5_F4_CD200p_G10_S241


title: D5_F4_CD200p_F9_S233


title: D5_F4_CD200p_F8_S232


title: D5_F4_CD200p_G4_S235


title: D5_F4_CD200p_E9_S226


title: D5_F4_CD200p_F6_S231


title: D5_F4_CD200p_F2_S228


title: D5_F4_CD200p_F5_S230


title: D5_F4_CD200p_F4_S229


title: D5_F4_CD200p_E7_S224


title: D5_F4_CD200p_E8_S225


title: D5_F4_CD200p_E3_S220


title: D5_F4_CD200p_E4_S221


title: D5_F4_CD200p_E10_S227


title: D5_F4_CD200p_E2_S219


title: D5_F4_CD200p_D9_S216


title: D5_F4_CD200p_D8_S215


title: D5_F4_CD200p_E1_S218


title: D5_F4_CD200p_D6_S214


title: D5_F4_CD200p_D3_S212


title: D5_F4_CD200p_E5_S222


title: D5_F4_CD200p_D5_S213


title: D5_F4_CD200p_D11_S217


title: D5_F4_CD200p_D2_S211


title: D5_F4_CD200p_C8_S208


title: D5_F4_CD200p_C7_S207


title: D5_F4_CD200p_D1_S210


title: D5_F4_CD200p_C5_S206


title: D5_F4_CD200p_C9_S209


title: D5_F4_CD200p_E6_S223


title: D5_F4_CD200p_C1_S204


title: D5_F4_CD200p_C2_S205


title: D5_F4_CD200p_B6_S203


title: D5_F4_CD200p_B4_S201


title: D5_F4_CD200p_A8_S197


title: D5_F4_CD200p_B2_S199


title: D5_F4_CD200p_B1_S198


title: D5_F4_CD200p_B3_S200


title: D5_F4_CD200p_A6_S196


title: D5_F4_CD200p_A1_S193


title: D5_F4_CD200p_A3_S194


title: D5_F4_C10_S327


title: D4_M2_H9_S190


title: D4_M2_H7_S189


title: D5_F4_B1_S311


title: D5_F4_CD200p_A4_S195


title: D4_M2_H5_S188


title: D4_M2_H11_S192


title: D4_M2_G9_S184


title: D4_M2_H1_S187


title: D4_M2_H10_S191


title: D4_M2_G8_S183


title: D4_M2_G7_S182


title: D4_M2_G5_S181


title: D4_M2_G11_S186


title: D4_M2_G10_S185


title: D4_M2_F6_S175


title: D4_M2_F7_S176


title: D4_M2_F8_S177


title: D5_F4_CD200p_B5_S202


title: D4_M2_G4_S180


title: D4_M2_F11_S179


title: D4_M2_F10_S178


title: D4_M2_E8_S171


title: D4_M2_E7_S170


title: D4_M2_E9_S172


title: D4_M2_E5_S168


title: D4_M2_E6_S169


title: D4_M2_E2_S165


title: D4_M2_D6_S158


title: D4_M2_D8_S160


title: D4_M2_D2_S156


title: D4_M2_D10_S162


title: D4_M2_F4_S174


title: D4_M2_D1_S155


title: D4_M2_C6_S153


title: D4_M2_D11_S163


title: D4_M2_D4_S157


title: D4_M2_E4_S167


title: D4_M2_D9_S161


title: D4_M2_B9_S150


title: D4_M2_B7_S149


title: D4_M2_E3_S166


title: D4_M2_C10_S154


title: D4_M2_B5_S148


title: D4_M2_C1_S151


title: D4_M2_B3_S146


title: D4_M2_A9_S143


title: D4_M2_A5_S141


title: D4_M2_E10_S173


title: D4_M2_E1_S164


title: D4_M2_D7_S159


title: D4_M2_C4_S152


title: D4_M2_A4_S140


title: D4_M2_A3_S139


title: D4_F6_G9_S201


title: D4_M2_B4_S147


title: D4_F6_H11_S204


title: D4_F6_H10_S203


title: D4_M2_A2_S138


title: D4_F6_H6_S202


title: D4_F6_G8_S200


title: D4_M2_A11_S144


title: D4_F6_F5_S193


title: D4_F6_F4_S288


title: D4_F6_E9_S284


title: D4_F6_E7_S282


title: D4_F6_F11_S196


title: D4_F6_F2_S287


title: D4_F6_G5_S199


title: D4_F6_E4_S281


title: D4_F6_F6_S194


title: D4_M2_B2_S145


title: D4_M2_A8_S142


title: D4_F6_E1_S280


title: D4_F6_E11_S285


title: D3_F1_H7_S149


title: D3_F1_H5_S148


title: D4_F6_G4_S198


title: D3_F1_H1_S147


title: D3_F1_G9_S144


title: D3_F1_G11_S146


title: D4_F6_E8_S283


title: D4_F6_F10_S195


title: D4_F6_G1_S197


title: D3_F1_F6_S140


title: D3_F1_G3_S143


title: D3_F1_E2_S131


title: D3_F1_E3_S132


title: D3_F1_E7_S135


title: D3_F1_E4_S133


title: D3_F1_F10_S142


title: D3_F1_E5_S134


title: D4_F6_E12_S286


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title: K562_KRAB_5kb_5d_dox_H3K9me3

city: Stanford

first: Sarah

last: Lensch

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

data_processing:
library strategy: CUT&RUN
Make genome file with appropriate reporter appended to end of genome file
Align reads to genome with Bowtie 2 version 2.3.4.1 with command 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x {reference genome} -p 8 -1 {first mate of pair} -2 {second mate of pair} -S {output SAM file name}'
Convert SAM files to BAM files and subsequently sort and index BAM files with Samtools version 1.7
Quantify and mark duplicates with Picard version 11.0.7 with command 'java -jar {picard tool} MarkDuplicates -I {input sorted BAM file} -O {output deduplicated BAM file} -M {output metrics file} --REMOVE_DUPLICATES true'
Subtract duplicate reads and remove reads from regions where alignment is ambigous (ie non-unique reporter element sequences)
Normalize by reads per million with bamCoverage version 3.3.1 with command 'bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file} --outFileFormat bedgraph --extendReads --centerReads --binSize 10 --normalizeUsing CPM'
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files

source_name: immortalised myelogenous leukemia cell line

growth_protocol: Cells were cultured at 37°C in a humidified incubator (Panasonic MCO-230AICUVL) with 5% CO2. CHO-K1 cells were grown in Alpha MEM Earle’s Salts media with 10% Tet Approved FBS (Takara Bio 631367, Lots # A16039 & #17033) and 1X Penicillin/Streptomycin/L-glutamine (Gibco 10378016). CHO-K1 cells were passaged by rinsing with Dulbecco's Phosphate-Buffered Saline (DPBS, Gibco 14190250), and incubating at room temperature with 0.25% Trypsin (Gibco, 25200056). K562 cells were grown in RPMI 1640 medium (Gibco, 11875119) with 10% Tet Approved FBS (Takara Bio 631367, Lot #17033) and 1X Penicillin/Streptomycin/L-glutamine (Gibco 10378016).

extract_protocol:
CUT&RUN for the K562 KRAB and CHO-K1 KRAB cell lines was performed according to the third version of the published protocol on protocols.io. For each antibody condition, 250,000 K562 or CHO-K1 cells were harvested and incubated with 10uL of activated Concanavalin A beads. Cells were permeabilized with 0.05% digitonin and incubated at room temperature for two hours with a 1:100 dilution of one of the following antibodies: guinea pig anti-rabbit IgG H&L chain (Antibodies-Online; Cat. No.: ABIN101961); rabbit anti-H3ac (Active Motif; Cat. No.: 39139); rabbit anti-H3K4me3 (Active Motif; Cat. No.: 39159); rabbit anti-H3K9me3 (Abcam; Cat. No.: ab8898). Unbound antibody was washed out, and cells were incubated with 140ng/mL of a protein A and micrococcal nuclease fusion (pA-MNase; generously provided by the Henikoff lab). Unbound pA-MNase was washed out, and cells were resuspended in a low-salt buffer. Tubes were placed in a thermal block chilled to 0°C, and 10mM CaCl2 was added to trigger DNA cleavage by pA-MNase. After 5 minutes, the reaction was stopped by chelating calcium ions with the addition of 20mM EGTA, and tubes were incubated at 37°C for 30 minutes under physiological salt conditions to promote diffusion of fragmented chromatin into the supernatant. Fragmented chromatin in the supernatant was collected and purified using the DNA Clean & Concentrator-5 kit (Zymo; Cat. No.: D4004). CUT&RUN for the CHO-K1 HDAC4 cell lines was performed using the EpiCypher CUTANA ChIC/CUT&RUN Kit (Cat. No.: 14-1048) according to the User Manual Version 2.0 with the following conditions: an input of 500,000 CHO-K1 cells per antibody condition; a final digitonin concentration of 0.01%; an overnight antibody incubation at 4°C with 1:100 dilutions of the anti-H3Kac and anti-H3K9me3 antibodies described above along with a 1:50 dilution of rabbit anti-H3K27me3 (Cell Signaling Technologies, Cat. No: 9733S); and DNA purification with the provided spin columns.
Dual-indexed sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs; Cat. No.: E7645L) with 12-14 cycles of PCR, and size selection was performed with either Agencourt AMPure XP (Beckman Coulter; Cat. No.: A63880) or SPRIselect (Beckman Coulter; Cat. No.: B23318) magnetic beads. Library concentrations were quantified with the Qubit 1X dsDNA HS Assay Kit (Invitrogen; Cat. No.: Q33231), and library fragment sizes were assessed with the High Sensitivity D1000 ScreenTape (Agilent; Cat. No.: 5067-5584) and High Sensitivity D1000 Reagent (Agilent; Cat. No.: 5067-5585) on an Agilent 4200 TapeStation System. Libraries were pooled for genome-wide sequencing.

treatment_protocol: Cells were treated with 1000 ng/mL doxycyline (dox) (Tocris Bioscience, 4090) for 5 days during which fresh dox diluted from frozen aliquots was added to the media before each cell passage every 2-3 days.

tag: reporter

value: 5kb spacer

tag: chromatin regulator

value: KRAB

value: dox (1000 ng/mL)

tag: timepoint

value: 5 days

tag: antibody

value: H3K9me3 (Abcam; Cat. No.:ab8898)


title: K562_KRAB_5kb_5d_nodox_H3K9me3

tag: treatment

value: no dox


title: K562_KRAB_5kb_5d_dox_H3K4me3

value: H3K4me3 (Active Motif; Cat. No.:39159)


title: K562_KRAB_5kb_5d_dox_H3Kac

value: H3Kac (Active Motif; Cat. No.:39139)


title: K562_KRAB_5kb_5d_dox_IgG

value: IgG (Antibodies-Online; Cat. No.:ABIN101961)


title: 3dpwP3_D5_S312

value: skin

value: CD1 x C57BL/6J cross


title: 3dpwP3_D7_S314

value: partial-thickness wounded


title: K562_KRAB_5kb_5d_nodox_H3K4me3


title: 3dpwP3_D6_S313


title: K562_KRAB_NS_5d_dox_H3K9me3

value: no spacer


title: 3dpwP3_D4_S311


title: 3dpwP3_D2_S310


title: K562_KRAB_5kb_5d_nodox_IgG


title: 3dpwP3_E8_S324


title: 3dpwP3_D11_S318


title: 3dpwP3_E3_S319


title: sample_96 - PCNSL - ABC

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

hyb_protocol: Approximately 100 ng of total RNA from each sample was analyzed using the Human v3 miRNA expression assay kit, following manufacturer’s instructions (NanoString Technologies, Inc., Seattle, USA).

scan_protocol: Raw data were pulled from digital analyzer and imported into nSolver4.0 (NanoStringtm) for data quality check. Data sets that passed all QC checks (including imaging quality, binding density, positive control linearity and limit of detection) were exported as a .csv file for downstream statistical analysis.

data_processing: Raw NanoString read counts and clinical information was imported into the R statistical environment (version 3.5.1). We discarded miRNAs with low expression (read count <= 1 in more than 60 samples) from all analysis. Data normalization was done with the NanoStringNorm package (version 1.2.1) using the following options: CodeCount = “geo.mean”, Background = “mean.2sd”, SampleContent = “housekeeping.geo.mean”, OtherNorm = “quantile”. We used the ath, cel, osa and NEG miRNA classes as negative controls, the POS class as positive controls, the ACTB, B2M, GAPDH, RPL19 and RPLP0 genes as housekeeping genes, and everything else as endogenous miRNAs.

label: not provided

source_name: CNS lymphoma brain tissue biopsy FFPE sample

extract_protocol: RNA isolation from 64 PCNSL and 9 SCNSL samples was performed using the RecoverAll™ kit (Life Technologies/Ambion, Inc, Foster City USA) according to the manufacturer’s instructions.

value: PCNSL

value: ABC

value: h

tag: institute

value: C

tag: event

value: exit

value: yes

value: no


title: K562_KRAB_5kb_5d_nodox_H3Kac

tag: cell line

value: 5kb spacer

value: KRAB

value: 5 days


title: sample_95 - PCNSL - GC

label_protocol: Approximately 100 ng of total RNA from each sample was analyzed using the Human v3 miRNA expression assay kit, following manufacturer’s instructions (NanoString Technologies, Inc., Seattle, USA).

value: GC

value: g


title: sample_99 - SCNSL - GC

value: SCNSL


title: 3dpwP3_D10_S317

value: skin


title: sample_91 - PCNSL - ABC

value: alive


title: K562_KRAB_NS_5d_nodox_H3K4me3

value: no dox

value: H3K4me3 (Active Motif; Cat. No.:39159)


title: K562_KRAB_NS_5d_dox_H3K4me3

value: no spacer

value: dox (1000 ng/mL)


title: K562_KRAB_NS_5d_dox_H3Kac

value: H3Kac (Active Motif; Cat. No.:39139)


title: sample_90 - PCNSL - ABC

value: PCNSL

value: ABC

value: h

value: C


title: sample_9 - PCNSL - ABC

value: a

value: A

value: exit

value: yes

value: no


title: sample_89 - PCNSL - ABC

value: g


title: K562_KRAB_NS_5d_nodox_H3Kac

value: KRAB

value: 5 days


title: 3dpwP3_C7_S305

value: skin

value: CD1 x C57BL/6J cross

value: partial-thickness wounded


title: K562_KRAB_NS_5d_nodox_H3K9me3

value: no spacer

value: no dox

value: H3K9me3 (Abcam; Cat. No.:ab8898)


title: 3dpwP3_C9_S307


title: sample_88 - PCNSL - GC

value: PCNSL

value: GC


title: 3dpwP3_C8_S306


title: K562_KRAB_NS_5d_dox_IgG

value: dox (1000 ng/mL)

value: IgG (Antibodies-Online; Cat. No.:ABIN101961)


title: sample_87 - PCNSL - ABC

value: ABC

value: h

value: C


title: sample_86 - PCNSL - ABC

value: yes

value: no


title: 3dpwP3_C6_S304


title: sample_85 - PCNSL - ABC

value: g


title: 3dpwP3_C5_S303


title: healthy_hiPSCCM_2 [miRNA-seq]

city: Munich

first: Dena

last: Esfandyari

state: Bavaria

address: Haus 607, Biedersteiner Str. 29, IPT

department: Institute of Pharmacology and Toxicology

institute: Technical University of Munich

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
Trim Galore! (v0.4.2) for adapter trimming
MiRDeep2 (v2.0.0) for alignment of forward or reverse reads against miRBase21 mature and hairpin sequences and quantification.
Genome_build: miRBase21 mature and hairpin sequences
Supplementary_files_format_and_content: csv of raw and normalized read counts generated by MiRDeep2 quatifier

growth_protocol: the hiPSCs were maintained in Geltrex-coated plates (1 ml per 35 mm plate, 1 hour incubation at 37 °C) in E8-flex medium (2 ml per 35 mm plate, medium exchange every other day) and passaged with Versene (1 ml per 35 mm plate, incubation for 5-10 min at room temperature) when confluent. For cardiac differentiation, the cells were passaged into 12 well plates and cultured in cardio differentiation medium to reach 85-90% of confluency, the optimal cell density for starting the differentiation (d0). The differentiation carried out using Wnt signaling modulators, CHIR99021 and IWP2 (both from Merck Millipore). The yielded hiPSC-CMs were maintained in cardio culture medium and one round of metabolic selection was performed between d20-30 in order to enrich cardiomyocytes. After selection hiPSC-CMs were enzymatically dissociated (using Collagenase I and Trypsin), replated in lower densities and maintained in cardio culture medium for approximately 60 days for further maturation.

extract_protocol:
Total RNA from healthy hiPSC-CMs (2 replicates) was extracted using TriFast (peqLab). The integrity and quantity of RNA was measured using Agilent Bioanalyzer 2100.
700 ng RNA with RIN>9 was used for library construction using NEBNext small RNA library prep kit according to manufacturer’s instructions with an AMPure XP bead-based size selection step.

treatment_protocol: the cells were untreated.

tag: cell type

value: iPSC-derived cardiomyocyte

value: untreated

value: healthy

tag: molecule type

value: small RNA


title: sample_92 - PCNSL - ABC

value: exit


title: sample_84 - PCNSL - ABC

value: alive


title: sample_83 - PCNSL - ABC


title: sample_8 - PCNSL - ABC

value: a

value: A


title: 3dpwP3_C4_S302

value: skin

value: CD1 x C57BL/6J cross

value: partial-thickness wounded


title: sample_78 - PCNSL - GC

value: PCNSL

value: GC


title: healthy_hiPSCCM_1 [miRNA-seq]

tag: disease state


title: 3dpwP3_C3_S301


title: sample_74 - PCNSL - ABC

value: ABC

value: h

value: C


title: healthy_hiPSCCM_mimic365 [scRNA-seq]

description: single cell 3' mRNA library (10x Genomics)

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
cellranger v6.0.1 for LQT1 and v2.1.0 healthy cells for alignment, filtering, barcode counting, UMI counting, demultiplexing of HTOs
Genome_build: GRCh38, Gencode annotation v33 for LQT1 and v28 for healthy cells
Supplementary_files_format_and_content: Feature-Barcode Matrices and HTOs from cellranger (10x Genomics)

source_name: iPSC-derived cardiomyocyte

extract_protocol:
After transfection of hiPSC-CMs with mimics or antimiRs for 48 hours, the cells were washed and dissociated to single cells with collagenase II and trypsine and proceeded for single cell capture, barcoding and library preparation (10x genomics). For LQT1 hiPSC-CMs, the cells from different treatment conditions were stained with TotalSeq-A cell hashing antibodies (according to Biolegend's instructions) and were pooled together prior to single cell capture with Chromium.
Barcoding and library preparation from healthy hiPSC-CMs was done using Chromium single cell 3’ (v2, 10x Genomics). For LQT1 cells Chromium Next GEM single cell 3’ (v3.1, 10x Genomics) was used for preparation of gene expression library. The libraries from the TotalSeq-A hashtag oligonucleotides (HTO) for cell multiplexing was prepared according to Biolegend's cell hashing manual.

treatment_protocol: To elevate the intracellular level of miR-365, the cells were transfected with synthetic mimic-365. Inhibition of endogenous miR-365 was achieved by transfection of LNA-antimiR-365 (Exiqon-Qiagen). Negative control oligonucleotides with the same chemistry were used in each case (mimic-Ctrl and antimir-Ctrl, respectively). Transfection was performed using Lipofectamine RNAiMAX to  reach final concentration of 25 nM oligonucleotides. The medium was exchanged 15-24 hours after transfection and the cells were processed 48 hours post-transfection.

tag: cell/sample type


title: healthy_hiPSCCM_antimiR365 [scRNA-seq]


title: K562_KRAB_NS_5d_nodox_IgG

value: no spacer

value: KRAB

value: no dox

value: 5 days

value: IgG (Antibodies-Online; Cat. No.:ABIN101961)


title: sample_73 - PCNSL - ABC

value: yes

value: no


title: 3dpwP3_C11_S309


title: sample_72 - PCNSL - ABC

value: g


title: 3dpwP3_C10_S308


title: sample_70 - PCNSL - ABC

value: exit


title: sample_69 - PCNSL - GC

value: alive


title: healthy_hiPSCCM_antimiR365_3

data_processing:
bcl2fastq (v2.20) for basecalling, fastq conversion, adapter trimming (only for SQT1 samples) and demultiplexing
Trim Galore! (v0.4.2 in Galaxy) for adapter trimming in healthy hiPSC-CMs
RNA STAR (v2.6.0 in Galaxy) with default parameters for alignment
StringTie (v1.3.6 in Galaxy) was used for transcript assembly and quantification
DESeq2 (v2.11.40.2 in Galaxy) for differential expression analysis and normalizing the counts
Genome_build: GRCh38, Gencode annotation v34 for SQT1 and v28 for healthy cells
Supplementary_files_format_and_content: tabular raw gene counts; excel file of the normalized count generated by DESeq2, TPM and FPKM

extract_protocol:
After transfection of hiPSC-CMs with mimics or antimiRs for 48 h, the cells were washed with PBS 3 times and total RNA was isolated using peqGOLD RNAPure (VWR). The integrity and quantity of RNA was determined using Agilent Bioanalyzer 2100 or Agilent TapeStation 4200.
For healthy hiPSC-CMs, libraries were prepared from 1 µg RNA using Illumina TruSeq Stranded mRNA kit and for SQT1 hiPSC-CMs Illumina mRNA ligation kit was used for library preparation.

treatment_protocol: To elevate the intracellular level of miR-365, the cells were transfected with synthetic mimic-365. Inhibition of endogenous miR-365 was achieved by transfection of LNA-antimiR-365 (Exiqon-Qiagen). Negative control oligonucleotides with the same chemistry were used in each case (mimic-Ctrl and antimir-Ctrl, respectively). Transfection was performed using Lipofectamine RNAiMAX to  reach a final concentration of 25 nM oligonucleotides. The medium was exchanged 15-24 hours after transfection and the cells were processed 48 hours post-transfection.

value: iPSC-derived cardiomyocyte

value: healthy


title: sample_68 - PCNSL - ABC

value: PCNSL

value: f

value: A


title: 3dpwP3_B9_S299

value: skin

value: CD1 x C57BL/6J cross

value: partial-thickness wounded


title: sample_67 - PCNSL - ABC

value: ABC


title: sample_66 - PCNSL - ABC


title: sample_65 - PCNSL - ABC


title: healthy_hiPSCCM_antimiR365_2


title: healthy_hiPSCCM_antimiRCtrl_3

value: antimiR-Ctrl


title: healthy_hiPSCCM_antimiR365_1


title: 3dpwP3_B7_S297


title: sample_75 - PCNSL - ABC

value: C


title: 3dpwP3_B8_S298


title: sample_64 - PCNSL - ABC


title: healthy_hiPSCCM_antimiRCtrl_2


title: 3dpwP3_B6_S296


title: sample_71 - PCNSL - ABC


title: 3dpwP3_B5_S295


title: sample_62 - PCNSL - GC

value: GC


title: sample_60 - PCNSL - UC

value: UC

value: yes


title: sample_58 - PCNSL - ABC

value: no


title: sample_61 - PCNSL - UC

value: exit


title: healthy_hiPSCCM_mimic365_3


title: 3dpwP3_B4_S294


title: sample_56 - PCNSL - ABC

value: alive


title: sample_6 - PCNSL - ABC

value: a


title: sample_57 - PCNSL - UC


title: healthy_hiPSCCM_antimiRCtrl_1

value: iPSC-derived cardiomyocyte

value: healthy


title: 3dpwP3_B3_S293


title: sample_5 - PCNSL - ABC

value: PCNSL

value: b


title: healthy_hiPSCCM_mimic365_2


title: healthy_hiPSCCM_mimic365_1


title: sample_51 - PCNSL - GC

value: c

value: A


title: 3dpwP3_B10_S300

value: skin

value: CD1 x C57BL/6J cross

value: partial-thickness wounded


title: healthy_hiPSCCM_mimicCtrl_3

value: mimic-Ctrl


title: sample_53 - PCNSL - GC

value: GC


title: 3dpwP3_A9_S291


title: sample_49 - PCNSL - ABC

value: ABC

value: e

value: B


title: sample_45 - PCNSL - ABC

value: exit


title: sample_46 - SCNSL - ABC

value: SCNSL

value: yes

value: no


title: 3dpwP3_A7_S290


title: 3dpwP3_A6_S289


title: sample_47 - PCNSL - ABC


title: sample_43 - PCNSL - GC

value: d


title: sample_42 - SCNSL - GC

value: alive


title: healthy_hiPSCCM_untreated_3

value: iPSC-derived cardiomyocyte

value: untreated

value: healthy


title: healthy_hiPSCCM_mimicCtrl_1


title: healthy_hiPSCCM_mimicCtrl_2


title: healthy_hiPSCCM_untreated_2


title: 3dpwP3_A4_S287

value: skin


title: healthy_hiPSCCM_untreated_1


title: 3dpwP3_A3_S286

value: CD1 x C57BL/6J cross


title: sample_48 - SCNSL - GC


title: H1H1b-2

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

description: diploid-and-auto-tetraploid_gene_counts.txt

data_processing:
Sequencing reads were trimmed for adapter sequences using cutadapt v1.8.1 and read quality was confirmed using fastqc v0.11.9.
Reads were aligned using STAR v2.7.1a with two-pass mapping to a concatenated human-chimpanzee genome (hg38 and pt6).
The number of uniquely-mapped reads (MAPQ = 255) that overlap each gene was counted with featurecounts from the subread v1.6.0 package using a curated annotation (hg38.pt6.gtf). To generate the annotations, GRCh38.94 human exon annotations from Ensembl were mapped from hg38 to pt6 using pslMap. After removing mappings where the number of bases that map is less than half of the query exon size, we retained only exons that uniquely mapped from humans to chimpanzees. We then removed genes for which exons map to opposite DNA strands, different scaffolded chromosomes, or where consecutive exons map more than 800kb apart. We further filtered out exons where more than 10% of reads from diploid or auto-tetraploid lines map to the incorrect species when mapped to the composite genome.
Genome_build: hg38 and pt6
Supplementary_files_format_and_content: Gene counts for each species are represented with the human ensembl ID in the processed files. For allo-tetraploid lines, each sample is represented twice in the associated processed file, once as human allele counts ("Hs" prefix) and once as chimpanzee allele counts ("Pt" prefix).

source_name: induced pluripotent stem cells

growth_protocol: iPSC lines were grown in mTeSR1 or mTeSR Plus (StemCell Technologies).

extract_protocol:
RNA was isolated using the Direct-Zol RNA Miniprep kit (Zymo Research, cat #R2051) or by Genewiz.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep (Illumina) or by Genewiz and sequenced on a HiSeq 4000 (2x150bp).

treatment_protocol: iPSCs were collected using accutase and flash frozen for storage at -80C.

value: induced pluripotent stem cells


title: sample_44 - PCNSL - ABC

value: PCNSL


title: sample_40 - PCNSL - ABC


title: sample_41 - PCNSL - ABC


title: sample_39 - PCNSL - ABC


title: 3dpwP3_A2_S285

value: partial-thickness wounded


title: sample_37 - PCNSL - ABC

value: ABC


title: sample_35 - PCNSL - UC

value: UC


title: sample_36 - PCNSL - ABC

value: B


title: sample_34 - PCNSL - ABC


title: H1H1b-1


title: sample_38 - PCNSL - ABC

value: exit


title: 3dpwP3_A12_S292


title: sample_31 - PCNSL - ABC

value: b

value: A


title: sample_33 - PCNSL - GC

value: GC


title: 3dpwP3_A5_S288


title: H1H1a-2


title: sample_30 - PCNSL - ABC

value: yes

value: no


title: sample_29 - PCNSL - ABC

value: a


title: H2-2


title: 3dpwP2_H9_S284


title: H2-3


title: 3dpwP2_H7_S282


title: H1H1a-1


title: 3dpwP2_H4_S279


title: 3dpwP2_H8_S283


title: H2-1


title: sample_27 - PCNSL - ABC


title: sample_28 - PCNSL - ABC

value: alive


title: 3dpwP2_H5_S280


title: sample_20 - PCNSL - ABC

value: c


title: sample_25 - PCNSL - ABC


title: sample_26 - PCNSL - GC


title: sample_21 - PCNSL - ABC


title: H1-2


title: 3dpwP2_H6_S281

value: skin


title: H1-3


title: sample_12 - PCNSL - ABC


title: sample_105 - PCNSL - ABC

value: g

value: C


title: sample_14 - PCNSL - ABC

value: PCNSL


title: sample_104 - SCNSL - GC

value: SCNSL


title: H1-1

value: induced pluripotent stem cells


title: sample_16 - SCNSL - ABC

value: ABC


title: sample_11 - PCNSL - ABC


title: sample_2 - SCNSL - ABC


title: sample_103 - SCNSL - GC


title: sample_102 - SCNSL - ABC


title: 3dpwP2_G8_S275

value: CD1 x C57BL/6J cross

value: partial-thickness wounded


title: B75

value: paired normal gastric tissue

tag: tumor stage

value: IIIB

tag: age

tag: gender

value: female


title: B76

value: male


title: 3dpwP2_G9_S276

tag: strain

tag: genotype

tag: timepoint (days post-wound)


title: 3dpwP2_G7_S274

tag: tissue


title: 3dpwP2_G6_S273


title: B74


title: B73

value: IIIC


title: 3dpwP2_G2_S269


title: 3dpwP2_G3_S270


title: 3dpwP2_G4_S271


title: 3dpwP2_G11_S278


title: B71


title: 3dpwP2_G10_S277


title: B70


title: 3dpwP2_F9_S266


title: 3dpwP2_G5_S272


title: B68


title: B67


title: B69


title: 3dpwP2_F8_S265


title: B66


title: B72


title: 3dpwP2_F7_S264


title: 3dpwP2_F6_S263


title: B64


title: 3dpwP2_F5_S262


title: B63


title: B62