title: L1MKG2203269-CON3

description: Library name: Sample1


title: CF_P56_Cre-_rep2 [ATAC-Seq]

status: Public on Jan 18 2026

type: SRA

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

library_source: genomic

data_processing:
Differentially expressed peaks were selected based on the following parameters: FDR ≤0.05, and Log Fold Change ≤ -0.5 for peaks downregulated and ≥ 0.5 for peaks upregulated
bigWig were generated with wigToBigWig command starting from Signal.Unique.str.out.wig file generated after STAR mapping.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Postnatal day P7

extract_protocol:
Cardiac fibroblasts (75000 sorted cells) were isolated using collagenase enzymatic reaction and FACS sorted based on the GFP fluorescence from  Col1a1-GFP allele and on the tdTomato fluorescence driven by the LepR-Cre. Purified Cardiac fibroblasts  were collected in Storing Buffer (10mM HEPES, 2mM MgCl2, 25mM KCl, 250mM Sucrose, 70% Glycerol) and stored at -80C.
Tagmentation, PCR-amplification and Libraries  were generated using the ATAC-seq kit (Active Motif# 53150) according to the manufacturer’s protocol and sequenced on Nextseq 550 System (Illumina)

tag: tissue

value: Postnatal day P7

tag: cell line

tag: cell type

value: primary cardiac fibroblasts

tag: genotype

tag: treatment


title: CF_P56_Cre-_rep1 [ATAC-Seq]


title: CF_P7_Cre+_rep1 [ATAC-Seq]


title: mouse brain H3K27ac histone modification, rep1

city: Beijing

first: Jiayu

last: Liu

address: Yiheyuan road

department: School of Life Sciences, Peking University

country: China

institute: Biomedical Pioneering Innovation Center (BIOPIC)

description:
Library name: mouse brain H3K27ac histone modification, mouse_R1
brain.h3k27ac.fragment.tsv.gz
charm_metadata_qcpass.tsv

library_source: other

data_processing:
Enrichment libraries and Hi-C libraries were processed using identical scripts. Initially, different read types were demultiplexed based on identification sequences in the R2 read.
For RNA data, we first removed reads containing no poly-A sequence following GAT5-RT primer sequence. We then aligned Read 1 to the GRCm38 reference genome using STAR. Duplicates were removed based on UMIs with UMI-tools. RNA count matrix was generated by FeatureCounts with parameters “-O -M --fraction”. We used RNAsnpSplit for phasing of allele- specific RNA counts.
For HiC data, reads were mapped to the GRCm38 reference genome with BWA-mem2 in “5SP” mode. Contacts and 3D genome structures were generated with Hickit software using default parameters. To remove potential contamination from RNA reads, we cleaned contacts between two exons from the same transcript, which accounted for ~0.04% of all contacts. For quality control of reconstructed 3D genome structures, five replicates were generated with random seeds, and median RMSD for each combination of 3 replicates was calculated. The first replicate in the combination with the minimum median RMSD value (if < 1.5) was used for downstream analysis. 3D proximity and 3D distance maps were generated as previously described with custom codes
For accessibility reads and histone modification reads, R2 reads, which represent Tn5 insertion sites, were aligned using BWA-mem2 with default parameters. Afterward, a custom Python script was employed to remove PCR duplicates, generating single-cell signal fragment files. For haplotype phasing, fragments were first assigned to a haplotype using SNP information from the R2 read. If the haplotype could not be determined from R2, SNP information from the R1 read was then utilized. All reads were mapped to the mm10 reference genome. All these processing steps were organized and implemented using Snakemake, and are available at https://github.com/skelviper/CHARM.
Assembly: mm10/GRCm38
Supplementary files format and content: The RNA modality comprises three gene-by-cell expression matrices for both mESC and brain samples: one phased with CAST/EiJ (cast), one with C57BL/6J (b6), and one representing the total genome (unphased).
Supplementary files format and content: Histone modification modality comprises fragments with H3K27me3 and H3K27ac for mESC and brain, respectively.
Supplementary files format and content: Accessibility modality comprises open chromatin fragments.
Supplementary files format and content: HiC modality comprises 5k/20k tdg files(reconstructed 3D structures) and pairs files.
Supplementary files format and content: For detailed file format description, see file_formate_README.txt.
Supplementary files format and content: charm_metadata_qcpass.tsv : cell-level information
Supplementary files format and content: feature_README.txt : CHARM-seq multi-omic descripitions
Supplementary files format and content: file_format_README.txt: format descriptions for processed data.

molecule: other

source_name: prefontal cortex(right)

extract_protocol:
Single-cell suspensions of mESC were obtained by TrypLE digestion and single-cell nuclei of cortieces were obtained by dounce homogenizer and filtration.
CHARM-seq

value: prefontal cortex(right)


title: CF_P7_Cre-_rep2 [ATAC-Seq]


title: mESC H3K27me3 histone modification

description:
Library name: mESC H3K27me3 histone modification
mesc.h3k27me3.fragment.tsv.gz
charm_metadata_qcpass.tsv

source_name: embryonic stem cell

value: embryonic stem cell


title: mouse brain H3K27ac histone modification, rep2

description:
Library name: mouse brain H3K27ac histone modification, mouse_R2
brain.h3k27ac.fragment.tsv.gz
charm_metadata_qcpass.tsv


title: mouse brain H3K27ac histone modification, rep3

description:
Library name: mouse brain H3K27ac histone modification, mouse_R3
brain.h3k27ac.fragment.tsv.gz
charm_metadata_qcpass.tsv


title: Replicate 1

city: Boston

first: Nezihi Murat

last: Karabacak

state: Massachusetts

address: 51 Blossom St

country: USA

institute: Massachusetts General Hospital

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
10x Genomics Cell Ranger 7.1.0 (via 10x Genomics Cloud Analysis) was used to perform sample de-multiplexing, barcode processing, and single-cell gene counting (alignment, barcoding, and unique molecular identifier [UMI] count).  Reads were aligned to the mm10-2020-A reference genome as appropriate for the input dataset. Downstream analysis steps were performed using Seurat v5. Cells identified as poor libraries or resulting from doublet cells were filtered by eliminating cells on both ends of the distribution, as well as cells with unusually high percent mitochondrial transcripts. Normalization, scaling, and dimensional reductions using principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) were performed using Seurat v5. Integrative analysis was performed using Harmony. Cell type labels were assigned based on characteristic relative marker gene expression levels between cell clusters using the FindAllMarkers function. Module scores were generated using the AddModuleScore function of Seurat to identify cell populations of interest. Module scores were calculated as the level of gene expression enrichment of a set gene list relative to a random control list, with higher module score values representing positive enrichment beyond background.
Assembly: mm10-2020-A
Supplementary files format and content: Gene expression matrix, barcodes and features in tab seperated files

molecule: total RNA

source_name: cMPCs and blood cells

extract_protocol:
Whole blood was sorted using microfluidic iChip. 10X was used to barcode single cells.
10x Genomics Chromium

value: cMPCs and blood cells

value: wild type

value: burn/tenotomy


title: CF_P56_Cre+_rep3

library_source: transcriptomic

data_processing:
The sequencing reads were processed to remove Illumina barcodes and aligned to the UCSC Mus musculus reference genome (build mm10) using STAR v.2.5.1b with default parameters.
ReadsPerGene.out.tab files were then processed with edgeR
RNA expression was calculated in reads per kilobase per million mapped reads (RPKM) considering the sum of exon length.
Differentially expressed coding genes were selected based on the following parameters: FDR ≤0.05, RPKM ≥1 in at least one biological condition, and Log Fold Change ≤ -0.5 for genes downregulated and ≥ 0.5 for genes upregulated
bigWig were generated with wigToBigWig command starting from Signal.Unique.str.out.wig file generated after STAR mapping.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: polyA RNA

source_name: Postnatal day P56

extract_protocol:
Cardiac fibroblasts were isolated using collagenase enzymatic reaction and FACS sorted based on the GFP fluorescence from  Col1a1-GFP allele and on the tdTomato fluorescence driven by the LepR-Cre. Purified Cardiac fibroblasts  were collected in Tryzol and RNA extracted using Direct-zol RNA Kits (Zymo Research #R2061)
Libraries  were generated using the TruSeq Stranded mRNA library Prep kit (Illumina# 20020594) and sequenced on Nextseq 2000 System (Illumina)

value: Postnatal day P56

value: sorted LepR-Cre positive population


title: CF_P56_Cre+_rep2


title: CF_P56_Cre+_rep1


title: CF_P56_Cre-_rep2

value: sorted LepR-Cre negative population


title: CF_P7_Cre+_rep3


title: mESC RNA modality

description:
Library name: mESC RNA modality
mesc.RNAcounts.gene.b6.format.tsv.gz
mesc.RNAcounts.gene.cast.format.tsv.gz
mesc.RNAcounts.gene.total.format.tsv.gz
charm_metadata_qcpass.tsv


title: CF_P7_Cre-_rep1 [ATAC-Seq]


title: CF_P7_Cre+_rep1


title: mouse brain HiC modality, rep1

description:
Library name: mouse brain HiC modality, mouse_R1
brain.20k.tdg.tar.gz
brain.5k.tdg.tar.gz
brain.pairs.tar.gz
charm_metadata_qcpass.tsv


title: mouse brain HiC modality, rep2

description:
Library name: mouse brain HiC modality, mouse_R2
brain.20k.tdg.tar.gz
brain.5k.tdg.tar.gz
brain.pairs.tar.gz
charm_metadata_qcpass.tsv


title: CF_P7_Cre+_rep2


title: mouse brain Accessibility modality, rep2

description:
Library name: mouse brain Accessibility modality, mouse_R2
brain.atac.fragment.tsv.gz
charm_metadata_qcpass.tsv


title: CF_P56_Cre-_rep1


title: CF_P56_Cre-_rep3


title: mESC Accessibility modality

description:
Library name: mESC Accessibility modality
mesc.atac.fragment.tsv.gz
charm_metadata_qcpass.tsv


title: mouse brain RNA modality, rep2

description:
Library name: mouse brain RNA modality, mouse_R2
brain.RNAcounts.gene.b6.format.tsv.gz
brain.RNAcounts.gene.cast.format.tsv.gz
brain.RNAcounts.gene.total.format.tsv.gz
charm_metadata_qcpass.tsv


title: mESC HiC modality

description:
Library name: mESC HiC modality
mesc.20k.tdg.tar.gz
mesc.5k.tdg.tar.gz
mesc.pairs.tar.gz
charm_metadata_qcpass.tsv


title: CF_P7_Cre-_rep3


title: mouse brain RNA modality, rep1

description:
Library name: mouse brain RNA modality, mouse_R1
brain.RNAcounts.gene.b6.format.tsv.gz
brain.RNAcounts.gene.cast.format.tsv.gz
brain.RNAcounts.gene.total.format.tsv.gz
charm_metadata_qcpass.tsv


title: HOpos_Patient_10

description:
Library name: HOpos_10
Flash-seq

data_processing:
Sequencing reads were aligned to the human genome (GRCh38) using the RNA-Seq Alignment App (v2.0.2) on Basespace (Illumina, CA).
Assembly: GRCh38
Supplementary files format and content: Comma separated value (csv) matrix of raw counts each sample.
Supplementary files format and content: Gene IDs

organism: Homo sapiens

source_name: Enriched blood

extract_protocol:
Whole blood was sorted using microfluidic iChip. RNA was purified from enriched blood sample using Qiagen micro kit.
Seqwell Rapid Kit was used according to manufacturer instructions

value: Enriched blood


title: CF_P7_Cre+_rep2 [ATAC-Seq]


title: Liver, SBR, WUSTL0717 5

city: Saint Louis

first: Gwendalyn

middle: J

last: Randolph

state: Missouri

address: 425 S. Euclid

institute: Washington University in St.Louis

description: Library name: Sample40

data_processing:
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: The TPM files were directly loaded into R for further analysis. Gene names were standardized, and duplicate entries were removed to retain unique gene features. Genes with zero TPM values across all samples were excluded. To reduce the impact of extreme values and facilitate comparisons, the TPM data were log2-transformed. Batch effects between experimental groups were corrected using the ComBat function from the sva R package. Normalized data were visualized with boxplots to confirm consistent sample distributions, ensuring comparability across datasets

source_name: Liver

extract_protocol:
Total RNA was extracted from the duodenum, the ileum, and the liver using Direct-zol RNA Miniprep Kits (Zymo Research). Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: The 8-week-old C57BL/6 male mice underwent either 50-60% small bowel resection or sham surgeries. Three weeks after the operation, the mice received daily treatments of WUSTL0717 (30 mg/kg) or vehicle for 7 weeks.

value: Liver

tag: strain

value: Wild type

tag: Sex

value: Male

value: Small bowel resection

tag: batch

value: Batch 2


title: mouse brain Accessibility modality, rep3

description:
Library name: mouse brain Accessibility modality, mouse_R3
brain.atac.fragment.tsv.gz
charm_metadata_qcpass.tsv


title: Liver, SBR, Vehicle 8

description: Library name: Sample39

value: Vehicle


title: mouse brain HiC modality, rep3

description:
Library name: mouse brain HiC modality, mouse_R3
brain.20k.tdg.tar.gz
brain.5k.tdg.tar.gz
brain.pairs.tar.gz
charm_metadata_qcpass.tsv


title: mouse brain Accessibility modality, rep1

description:
Library name: mouse brain Accessibility modality, mouse_R1
brain.atac.fragment.tsv.gz
charm_metadata_qcpass.tsv


title: CF_P7_Cre-_rep2

value: Postnatal day P7


title: Liver, SBR, Vehicle 6

description: Library name: Sample37


title: mouse brain RNA modality, rep3

description:
Library name: mouse brain RNA modality, mouse_R3
brain.RNAcounts.gene.b6.format.tsv.gz
brain.RNAcounts.gene.cast.format.tsv.gz
brain.RNAcounts.gene.total.format.tsv.gz
charm_metadata_qcpass.tsv


title: HOpos_Patient_6

description:
Library name: HOpos_6
Flash-seq


title: Liver, SBR, WUSTL0717 4

description: Library name: Sample35


title: Liver, SBR, Vehicle 7

description: Library name: Sample38


title: HOpos_Patient_1

description:
Library name: HOpos_1
Flash-seq


title: HOpos_Patient_2

description:
Library name: HOpos_2
Flash-seq


title: Liver, SBR, Vehicle 4

description: Library name: Sample31


title: Liver, SBR, WUSTL0717 3

description: Library name: Sample34


title: Liver, SBR, WUSTL0717 2

description: Library name: Sample33


title: HOneg_Patient_12

description:
Library name: HOneg_12
Flash-seq


title: Liver, SBR, Vehicle 3

description: Library name: Sample30


title: HOpos_Patient_9

description:
Library name: HOpos_9
Flash-seq


title: CF_P7_Cre-_rep1

value: primary cardiac fibroblasts


title: HOneg_Patient_11

description:
Library name: HOneg_11
Flash-seq


title: HOpos_Patient_8

description:
Library name: HOpos_8
Flash-seq


title: Liver, SBR, Vehicle 5

description: Library name: Sample36


title: HOpos_Patient_7

description:
Library name: HOpos_7
Flash-seq


title: HOpos_Patient_3

description:
Library name: HOpos_3
Flash-seq


title: Liver, SBR, Vehicle 1

description: Library name: Sample28


title: HOneg_Patient_8

description:
Library name: HOneg_8
Flash-seq


title: HOpos_Patient_4

description:
Library name: HOpos_4
Flash-seq


title: Liver, SBR, Vehicle 2

description: Library name: Sample29


title: HOneg_Patient_9

description:
Library name: HOneg_9
Flash-seq


title: Liver, Sham, Vehicle 5

description: Library name: Sample27

value: Sham


title: HOneg_Patient_7

description:
Library name: HOneg_7
Flash-seq


title: HOneg_Patient_6

description:
Library name: HOneg_6
Flash-seq


title: Liver, Sham, Vehicle 3

description: Library name: Sample25


title: HOneg_Patient_10

description:
Library name: HOneg_10
Flash-seq


title: Liver, Sham, Vehicle 4

description: Library name: Sample26


title: HOneg_Patient_4

description:
Library name: HOneg_4
Flash-seq


title: Liver, SBR, WUSTL0717 1

description: Library name: Sample32


title: HOneg_Patient_5

description:
Library name: HOneg_5
Flash-seq


title: Duodenum, SBR, WUSTL0717 3

description: Library name: Sample21

source_name: Duodenum

value: Duodenum

value: Batch 1


title: defenseless_ozone_3

city: Helsinki

first: Bikash

last: Baral

address: Pallaksentie 4C, 33

country: Finland

institute: University of Helsinki

description:
Library name: Sample12
defenseless_ozone

data_processing:
The computing platform (Puhti @ CSC) was used for preprocessing the files
RNA-Seq library was prepared using the Illumina Total RNA Library Prep Kit and was quality-checked using a Bioanalyzer
Sequence reads underwent pre-processing and quality assessment in adherence with established guidelines, employing FASTQC and SortmeRNA to remove RNA contaminants
STAR was utilized for read mapping using the atRTD3 transcriptome data as a reference, and the --quantMode GeneCounts to obtain the count number of reads per gene while mapping
Counts were imported into R using Bioconductor
Assembly: atRTD3 transcriptome data
Supplementary files format and content: .tab files contain GeneCounts

organism: Arabidopsis thaliana

source_name: Plant leaves

growth_protocol: Plants were grown in a 1:1 peat: vermiculite mixture under a 12-hour photoperiod with a 220-250 µmol/m2/s light intensity.

extract_protocol:
Post-exposure, samples were immediately flash-frozen in liquid nitrogen. The frozen samples were subjected to total RNA extraction using the Plant Spectrum RNA isolation kit. RNA quality was assessed using the bioanalyzer RNA 6000 Nano assay (Agilent Technologies) to determine RNA integrity values. High-quality RNA samples were then employed for complementary DNA synthesis and served as templates for quantitative polymerase chain reaction and transcriptome analysis.
RNA-Seq library was prepared using the Illumina Total RNA Library Prep Kit and was quality-checked using a Bioanalyzer (Agilent Technologies) at Novogene, Germany.

treatment_protocol: Control (without any treatment) and ozone treatment (350 nL·L-1; 2 hours)

value: Plant leaves

value: Leaves

value: defenseless mutant

value: Ozone


title: Liver, Sham, Vehicle 1

description: Library name: Sample23


title: HOneg_Patient_1

description:
Library name: HOneg_1
Flash-seq

value: cMPCs and blood cells


title: Duodenum, SBR, Vehicle 2

description: Library name: Sample18


title: defenseless_ozone_1

description:
Library name: Sample10
defenseless_ozone


title: Liver, Sham, Vehicle 2

description: Library name: Sample24


title: HOneg_Patient_3

description:
Library name: HOneg_3
Flash-seq

value: Enriched blood


title: HOneg_Patient_2

description:
Library name: HOneg_2
Flash-seq


title: Ileum, SBR, WUSTL0717 4

description: Library name: Sample17

source_name: Ileum

value: Ileum


title: Duodenum, SBR, WUSTL0717 4

description: Library name: Sample22

value: Wild type


title: defenseless_ozone_2

description:
Library name: Sample11
defenseless_ozone


title: Compound heterozygous Col4a3:G1332E, 3

type: RNA

city: Nicosia

first: Constantinos

last: Deltas

state: Aglantzia

address: Palaios dromos Lefkosias Lemesou No.215/6

department: Biology

country: Cyprus

institute: University of Cyprus

description: EKO

data_processing:
Differences in starting material were compensated for normalization to the endogenous reference genes b-actin.
Fold-Change (2^(- Delta Delta Ct)) is the normalized gene expression (2^(- Delta Ct)) in the Test Sample divided the normalized gene expression (2^(- Delta Ct)) in the Control Sample.
Fold Change worksheet reports test/control.

label: SYBR Green

source_name: Compound heterozygous Col4a3:G1332E

label_protocol: RT2 Profiler PCR Array (QIAGEN) is the method used for qPCR assay. This technique takes advantage of real-time PCR performance and combines it with the ability of microarrays to detect the expression of many genes related to UPR pathway simultaneously. Total RNA that was purified from glomeruli which were extracted from mutant and wild type kidneys was measured and then converted into first strand cDNA. qPCR was followed by using the instrument-specific and ready-to-use RT2 qPCR Master Mixes and gene specific primer sets. Determination of the relative expression was done by ddCt.

extract_protocol: Total RNA was extracted from glomeruli primaries cells using an RNA extraction kit (Macherey-Nagel, Düren,Germany).

value: Kidney glomeruli

tag: gender

value: Male

tag: age

value: 9 months


title: Col0_ozone_1

description:
Library name: Sample7
Col0_ozone

value: Wild-type (WT)


title: Ileum, SBR, WUSTL0717 3

description: Library name: Sample16

value: Small bowel resection


title: Duodenum, SBR, Vehicle 3

description: Library name: Sample19

value: Vehicle


title: defenseless_control_3

description:
Library name: Sample6
defenseless_control

value: Control


title: defenseless_control_2

description:
Library name: Sample5
defenseless_control


title: Duodenum, SBR, Vehicle 4

description: Library name: Sample20

value: Duodenum


title: Compound heterozygous Col4a3:G1332E, 1

description: EKO

value: Female


title: Ileum, SBR, Vehicle 4

description: Library name: Sample15

value: Batch 1


title: defenseless_control_1

description:
Library name: Sample4
defenseless_control

value: Plant leaves

value: Leaves


title: Duodenum, SBR, WUSTL0717 2

description: Library name: Sample14


title: Knockin mouse Col4a3:G1332E, 2

description: KI

source_name: Knockin mouse Col4a3:G1332E


title: HOpos_Patient_5

description:
Library name: HOpos_5
Flash-seq


title: Knockin mouse Col4a3:G1332E, 3

description: KI


title: Col0_control_2

description:
Library name: Sample2
Col0_control


title: Compound heterozygous Col4a3:G1332E, 2

description: EKO


title: Duodenum, SBR, WUSTL0717 1

description: Library name: Sample13


title: Knockin mouse Col4a3:G1332E, 1

description: KI


title: Col0_ozone_2

description:
Library name: Sample8
Col0_ozone

value: Ozone


title: Col0_control_3

description:
Library name: Sample3
Col0_control


title: Duodenum, Sham, Vehicle 2

description: Library name: Sample10

value: Sham


title: Col0_ozone_3

description:
Library name: Sample9
Col0_ozone


title: HEK293 DNA rep3

city: Rehovot

first: Simon

last: Fishilevich

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

description:
Library name: HEK293 DNA rep3
MPRA5_activity.txt

data_processing:
Each sample R1 and R3 reads (containing the barcode) were mapped with bowtie2 (--very-sensitive) to the barcode-oligo association list We applied several quality filters on the resulting alignments. We first filtered out read pairs that didn’t map as proper pairs, and then ensured the mapped sequence completely matched the known barcode sequence by requiring that both R1 and R3 reads have CIGAR stings = 15M, MD flags = 15 and a mapping quality of at least 20. We consolidated read abundance per barcode by selecting only reads with unique UMIs, the result being abundance counts for each barcode, across each replicate library of each cell type for both RNA and DNA.
Assembly: GRCh37
Supplementary files format and content: oligos_to_barcodes.txt file contains pairs of oligo-barcode associations. activity.txt file contains for each oligo the RNA read count, DNA read count, activity classification status and FDR.

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen).
For DNA/RNA barcode sequencing, mRNA was treated with Turbo DNase to remove contaminating DNA, and reverse transcribed with SuperScript IV (Invitrogen) using a primer containing unique molecular identifiers (UMIs). Resulting cDNA and genomic DNA was split into multiple reactions to reduce PCR jack-potting effects and barcode amplification performed with NEBNext high-fidelity polymerase for three cycles using a forward primer containing P5 adaptor and a sample index and a reverse primer containing P7 adaptor and UMIs. PCR products were purified with AMPure XP beads (Beckman Coulter) to remove primers and concentrate samples. These products underwent a second round of amplification using P5 and P7 primers. All reactions were pooled and run on agarose gels for size selection and submitted for sequencing. For DNA-barcode association, CRE-barcode fragment is amplified with a forward primer upstream from CRE and a reverse primer downstream from barcode, using a plasmid library as a template, followed by AMPure XP beads purification and sequencing.


title: Wild type 1

description: WT

source_name: Wild type


title: Osteoblasts RNA rep2

description:
Library name: Osteoblasts RNA rep2
MPRA4_activity.txt

source_name: Osteoblasts

value: Osteoblasts


title: HEK293 RNA rep3

description:
Library name: HEK293 RNA rep3
MPRA5_activity.txt


title: Osteoblasts DNA rep3

description:
Library name: Osteoblasts DNA rep3
MPRA4_activity.txt


title: HEK293 DNA rep2

description:
Library name: HEK293 DNA rep2
MPRA5_activity.txt


title: HUVEC SiYBX1 Replicate 1

city: Xiamen

first: Yuhong

last: Zhou

state: Fujian

address: No. 1999, Guankou Middle Road, Jimei District

department: Department of Basic Medicine

institute: Xiamen Medical College

description:
Library name: HUVEC_siYBX1_rep1
HUVEC with siYBX1; biological replicate 1. Paired-end 2x150 bp; PolyA selection. Reference: GRCh38 (Ensembl). Replace placeholders once sequencing details are finalized.

data_processing:
Quality control using FastQC to check read quality.
Alignment to the GRCh38 reference genome using STAR or HISAT2.
Quantification of gene expression using featureCounts or HTSeq.
Differential expression analysis using DESeq2 or edgeR.
Data visualization with ggplot2 and heatmap generation.
Assembly: GRCh38
Supplementary files format and content: Text files including read counts (counts_AllSample.xls).
Supplementary files format and content: normalized expression values (FPKM_AllSample.xls).

source_name: Endothelial cells (HUVEC)

growth_protocol: HUVECs were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO₂.

extract_protocol:
RNA extraction using Trizol reagent (Thermo Fisher) for total RNA isolation.
Library construction using standard RNA-seq protocols involving RNA fragmentation, reverse transcription, and adapter ligation

treatment_protocol: Cells treated with siYBX1, incubated for 48 hours.

value: Endothelial cells (HUVEC)

value: HUVEC

value: Endothelial cell

value: Wildtype


title: Col0_control_1

description:
Library name: Sample1
Col0_control


title: HEK293 RNA rep2

description:
Library name: HEK293 RNA rep2
MPRA5_activity.txt


title: Wild type 3

description: WT

value: Kidney glomeruli

value: Male

value: 9 months


title: Wild type 2

description: WT


title: Ileum, SBR, WUSTL0717 2

description: Library name: Sample8

value: Ileum

value: Wild type

value: Small bowel resection


title: HEK293 RNA rep1

description:
Library name: HEK293 RNA rep1
MPRA5_activity.txt


title: Chondrocytes RNA rep3

description:
Library name: Chondrocytes RNA rep3
MPRA2_activity.txt

source_name: Fetal Chondrocytes

value: Fetal Chondrocytes

value: Chondrocytes


title: Osteoblasts DNA rep1

description:
Library name: Osteoblasts DNA rep1
MPRA4_activity.txt


title: HEK293 DNA rep1

description:
Library name: HEK293 DNA rep1
MPRA5_activity.txt


title: Osteoblasts RNA rep3

description:
Library name: Osteoblasts RNA rep3
MPRA4_activity.txt


title: HUVEC SiYBX1 Replicate 2

description:
Library name: HUVEC_siYBX1_rep2
HUVEC with siYBX1; biological replicate 2. Paired-end 2x150 bp; PolyA selection. Reference: GRCh38 (Ensembl). Replace placeholders once sequencing details are finalized.


title: Chondrocytes DNA rep3

description:
Library name: Chondrocytes DNA rep3
MPRA2_activity.txt


title: Ileum, SBR, WUSTL0717 1

description: Library name: Sample7

value: Batch 1


title: Duodenum, Sham, Vehicle 3

description: Library name: Sample11

value: Duodenum

value: Vehicle


title: HUVEC SiNC Replicate 1

description:
Library name: HUVEC_siNC_rep1
HUVEC with siNC; biological replicate 1. Paired-end 2x150 bp; PolyA selection. Reference: GRCh38 (Ensembl). Replace placeholders once sequencing details are finalized.

value: siNC


title: Osteoblasts DNA rep2

description:
Library name: Osteoblasts DNA rep2
MPRA4_activity.txt

value: Osteoblasts


title: Chondrocytes RNA rep2

description:
Library name: Chondrocytes RNA rep2
MPRA2_activity.txt


title: Ileum, SBR, Vehicle 2

description: Library name: Sample5


title: HUVEC SiNC Replicate 2

description:
Library name: HUVEC_siNC_rep2
HUVEC with siNC; biological replicate 2. Paired-end 2x150 bp; PolyA selection. Reference: GRCh38 (Ensembl). Replace placeholders once sequencing details are finalized.

value: Endothelial cells (HUVEC)


title: Young keratinocytes siS100A7-1

city: Bunkyo-Ku

first: Ge

last: Peng

state: Tokyo

address: 2-1-1 Hongo

country: Japan

institute: Juntendo University Graduate School of Medicine

description:
Library name: SAMPLE-7
Column name in All_samples_raw_counts.txt

data_processing:
The process includes poly(A) mRNA enrichment and fragmentation followed by cDNA synthesis, end repair, adaptor ligations, and PCR amplification.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Primary keratinocyte

extract_protocol:
Total RNA was isolated from cultured keratinocytes using an Rneasy Plus Micro Kit according to the manufacturer's instructions
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

value: Primary keratinocyte

value: S100A7 knockdown

value: Keratinocyte differentiation


title: Chondrocytes DNA rep2

description:
Library name: Chondrocytes DNA rep2
MPRA2_activity.txt


title: Ileum, SBR, Vehicle 1

description: Library name: Sample4


title: Chondrocytes DNA rep1

description:
Library name: Chondrocytes DNA rep1
MPRA2_activity.txt


title: Young keratinocytes siS100A7-2

description:
Library name: SAMPLE-8
Column name in All_samples_raw_counts.txt


title: Young keratinocytes siCtrl-2

description:
Library name: SAMPLE-6
Column name in All_samples_raw_counts.txt

value: WT


title: Chondrocytes RNA rep1

description:
Library name: Chondrocytes RNA rep1
MPRA2_activity.txt


title: Young keratinocytes siCtrl-1

description:
Library name: SAMPLE-5
Column name in All_samples_raw_counts.txt


title: Neurons RNA rep3

description:
Library name: Neurons RNA rep3
MPRA1_activity.txt

source_name: NGN2-induced neurons

value: NGN2-induced neurons

value: Neurons


title: Neurons DNA rep3

description:
Library name: Neurons DNA rep3
MPRA1_activity.txt


title: Osteoblasts RNA rep1

description:
Library name: Osteoblasts RNA rep1
MPRA4_activity.txt


title: MPRA3 Barcode-oligonucleotide

description:
Library name: MPRA3 Barcode-oligonucleotide
MPRA3_oligos_to_barcodes.txt

organism: synthetic construct

source_name: plasmid library

value: plasmid library


title: Neurons RNA rep2

description:
Library name: Neurons RNA rep2
MPRA1_activity.txt


title: JHT-3

city: Mainz

first: Xinyuan

address: Langenbeckstraße 1

department: Institute for Molecular Medicine

country: Germany

institute: University Medical Center, Johannes Gutenberg University Mainz

description:
Library name: SAMPLE-6
6_EKDL230004708

data_processing:
The sequence reads were trimmed for adaptor sequences before being analyzed with Qiagen's CLC Genomics Workbench (v23.0.2 with CLC's default settings for RNA- Seq analysis). Raw RNA sequencing reads were mapped to the reference genome GRCm38.
Assembly: GRCm38
Supplementary files format and content: XLSX file containing differential gene expression analysis results comparing WT and JHT samples. The table includes gene identifiers, log2 fold changes, and statistical significance values (p-values and adjusted p-values). Differentially expressed genes were defined using thresholds of fold change ≥ 2 and adjusted p-value < 0.05.

source_name: Spleen

extract_protocol:
RNA was purified from MCMV-M45 tetramer+ CD8+ T cells with the RNeasy Plus Micro Kit according to the manufacturer’s protocol (Qiagen). RNA was quantified with a Qubit flex fluorometer (Invitrogen) and the quality was assessed on a Bioanalyzer 2100 (Agilent) using a RNA 6000 Pico chip (Agilent). Samples with an RNA integrity number (RIN) of > 8 were used for cDNA amplification using Smart-Seq V4 Ultra Low Input RNA Kit (Takara).
Libraries were made from 1ng of full-length cDNA using the Nextera-XT DNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. The quantity of the cDNA libraries was assessed with Qubit flex fluorometer (Invitrogen) and the average library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay

value: Spleen

value: CD8+ T cells

value: B cell-deficient JHT

value: MCMV-infected


title: Young keratinocyte-2

description:
Library name: SAMPLE-2
Column name in All_samples_raw_counts.txt


title: Aged keratinocyte-2

description:
Library name: SAMPLE-4
Column name in All_samples_raw_counts.txt


title: Ileum, Sham, Vehicle 2

description: Library name: Sample2

value: Ileum

value: Wild type

value: Male

value: Sham

value: Batch 1


title: MPRA4 Barcode-oligonucleotide

description:
Library name: MPRA4 Barcode-oligonucleotide
MPRA4_oligos_to_barcodes.txt


title: Aged keratinocyte-1

description:
Library name: SAMPLE-3
Column name in All_samples_raw_counts.txt


title: Neurons DNA rep2

description:
Library name: Neurons DNA rep2
MPRA1_activity.txt


title: Neurons RNA rep1

description:
Library name: Neurons RNA rep1
MPRA1_activity.txt


title: Ileum, SBR, Vehicle 3

description: Library name: Sample6

value: Small bowel resection

value: Vehicle


title: Ileum, Sham, Vehicle 1

description: Library name: Sample1


title: MPRA5 Barcode-oligonucleotide

description:
Library name: MPRA5 Barcode-oligonucleotide
MPRA5_oligos_to_barcodes.txt


title: MPRA1 Barcode-oligonucleotide

description:
Library name: MPRA1 Barcode-oligonucleotide
MPRA1_oligos_to_barcodes.txt


title: JHT-1

description:
Library name: SAMPLE-4
4_EKDL230004706


title: MPRA2 Barcode-oligonucleotide

description:
Library name: MPRA2 Barcode-oligonucleotide
MPRA2_oligos_to_barcodes.txt


title: JHT-2

description:
Library name: SAMPLE-5
5_EKDL230004707


title: Ileum, Sham, Vehicle 3

description: Library name: Sample3


title: Neurons DNA rep1

description:
Library name: Neurons DNA rep1
MPRA1_activity.txt


title: Young keratinocyte-1

description:
Library name: SAMPLE-1
Column name in All_samples_raw_counts.txt

value: Primary keratinocyte


title: Proximal organization 2

city: Urumqi

first: Ayiheng

last: Qukuerhan

state: Xinjiang

address: No.137, Liyuoshan South Road, Xincheng District, Urumqi

institute: Xinjiang Medical University Affiliated First Hospital

data_processing:
Sample storage and handling
RNA-seq library preparation and sequencing
Analysis of sequencing data
Identification and screening of DEGs using FPKM
Assembly: human genome GRCh38
Supplementary files format and content: tab-delimited text include reads counts for each Sample
Supplementary files format and content: tab-delimited text include FPKM counts for each Sample

extract_protocol:
Total RNA was extracted from JORRP tumor tissue and adjacent non-tumor tissues by using the method of Chomczynski et al.  with Trizol reagent (Invitrogen, cat.NO15596026). The quality and quantity of RNA were determined with a Nanodrop one (A260/A280). The integrity of RNA was confirmed using 1.5% agarose gel electrophoresis.
Qualified RNA was quantified using the QubitTM RNA Broad Spectrum Analysis Kit (Life Technologies, Q10210). According to the manufacturer's instructions, total RNA was used for stranded RNA sequencing library preparation with KCTM Stranded mRNA Library Preparation Kit (catalog number: DR08402, Wuhan Saike Health, China).PCR products of 200-500 bps in length were enriched, quantified, and double-ended sequenced on the PE150 model Novaseq6000 sequencer (Illumina).

value: Laryngeal tissue


title: WT-3

description:
Library name: SAMPLE-3
3_EKDL230004705

value: wild type


title: Duodenum, Sham, Vehicle 1

description: Library name: Sample9

value: Duodenum


title: Proximal organization 1


title: HCF_#4_GDF10_rep3

data_processing:
ReadsPerGene.out.tab files were then processed with edgeR
RNA expression was calculated in reads per kilobase per million mapped reads (RPKM) considering the sum of exon length.
Differentially expressed coding genes were selected based on the following parameters: FDR ≤0.05, RPKM ≥1 in at least one biological condition, and Log Fold Change ≤ -0.5 for genes downregulated and ≥ 0.5 for genes upregulated
Read count extraction and normalization were performed using ....
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Adult Heart

growth_protocol: Human cardiac fibroblasts (HCFs) were purchased from Promocell. HCFs were cultured at 37 °C in 5% CO2 using Fibroblast Growth Medium 3 (PromoCell) for up to 10 passages following the manufacturer’s instructions.

extract_protocol:
Human cardiac fibroblasts were collected in Tryzol and RNA extracted using Direct-zol RNA Kits (Zymo Research #R2061)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: In preparation for GDF10 treatment, cells were starved overnight in Basal Medium 3 (PromoCell) and then stimulated with vehicle (4mMHCl) or 0.5 μg/mL GDF10 (R&D Systems) for 24 hrs.

value: Adult Heart

value: primary human cardiac fibroblasts


title: WT-2

description:
Library name: SAMPLE-2
2_EKDL230004704

value: Spleen


title: After treatment in case 2

city: changsha

first: Muqi

state: Hunan

address: No.138 Tongzipo Road, Yuelu District, Changsha

department: Institute for Cell Transplantation and Gene Therapy

institute: the 3rd Xiangya Hospital of Central South University

description: Library name: simple5

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: hepatocellular carcinoma

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: hepatocellular carcinoma

value: male

value: 34 years old

tag: time point

value: After treatment


title: After treatment in case 3

description: Library name: simple6

value: 60 years old


title: HCF_#3_GDF10_rep2


title: HCF_#4_CTL_rep3

value: vehicle


title: Papilloma tissue 3


title: Before treatment in case 3

description: Library name: simple3

value: Before treatment


title: WT2

description: Library name: Sample 2

data_processing:
The generated raw data was preprocessed according to the Illumina standard protocol, and transcript alignment,counting, and demultiplexing were carried out utilizing the BD Rhapsody WTA analytic pipeline. Output matrices RSEC_MolsPerCell were further read into R (version 4.2.3) separately and converted to Seurat object using Seurat R package(version 4.3.0.1).
Assembly: GRCm38
Supplementary files format and content: csv file includes processed molecular counts per cell

source_name: spleen

extract_protocol:
Splenic CD11c+ cells were enriched with CD11c-MACS beads (Miltenyi Biotec), and then cells were labeled with the Mouse Immune Single-Cell Multiplexing Kit (BD Biosciences). Labeled cells have been counted and captured using the BD Rhapsody Single-Cell Analysis System Instrument (BD Biosciences) according to the provided instructions.
Whole transcriptome analysis (WTA) library preparation and Sample Tag library preparation were produced following the BD Rhapsody System mRNA WTA and Sample Tag Library Preparation Protocol. The quality and quantity of cDNA libraries were checked using the Agilent Bioanalyzer 2100 (Agilent), and sequencing (150 PE reads aiming for 50.000 raw reads/cell) was done at Novogene (Cambridge, UK) using the Illumina NovaSeq 6000 (Illumina).

value: spleen

value: CD11c+ cells

value: Wild-Type


title: Papilloma tissue 1


title: HCF_#3_CTL_rep2


title: WT-1

description:
Library name: SAMPLE-1
1_EKDL230004703

value: CD8+ T cells

value: MCMV-infected


title: After treatment in case 1

description: Library name: simple4

value: 50 years old


title: HCF_#1_CTL_rep1


title: Papilloma tissue 2

value: Laryngeal tissue


title: Before treatment in case 1

description: Library name: simple1


title: hCMEC/D3 cells, EV-Epinephrine-1, 12h

status: Public on Jan 17 2026

city: Manhasset

first: Betty

last: Diamond

state: NY

address: 350 Community Drive

institute: Feinstein Institutes for Medical Research

description: Library name: EV_E1_Epi

data_processing:
R 4.4.1
Quality control was performed using FastQC
Reads were aligned using STAR aligner to the hg38 reference genome downloaded from Ensembl (database version 112.38/GENCODE 46)
Differential expression analysis was performed using R statistical software (v4.4.1; R Core Team 2024) with the DESeq2 package and log fold changes shrunk using “ashr
Assembly: hg38
Supplementary files format and content: csv files include counts per gene labeled with Ensembl ID (Column A), Gene Symbol (Column B), and merged Gene Symbol and Ensembl ID (Column C, geneName) with columns D-AG representing counts for each sample.

extract_protocol:
Cells were homogenized using QIAshredder kits (Qiagen) and RNA was extracted using the RNeasy kit (Qiagen). 1 ng of total RNA was used for construction of sequencing libraries.
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.

value: Brain Microvascular Endothelial Cell


title: WT1

description: Library name: Sample 1


title: hCMEC/D3 cells, EV-Epinephrine-2, 12h

description: Library name: EV_E2_Epi


title: HCF_#1_GDF10_rep1

value: Adult Heart

value: primary human cardiac fibroblasts


title: hCMEC/D3 cells, EV-C5a-2, 12h

description: Library name: EV_D2_C5a


title: hCMEC/D3 cells, EV-Epinephrine-3, 12h

description: Library name: EV_E3_Epi


title: hCMEC/D3 cells, EV-IL-1β-3, 12h

description: Library name: EV_C3_IL1b


title: hCMEC/D3 cells, EV-C5a-3, 12h

description: Library name: EV_D3_C5a


title: Before treatment in case 2

description: Library name: simple2

value: hepatocellular carcinoma


title: hCMEC/D3 cells, EV-C5a-1, 12h

description: Library name: EV_D1_C5a


title: hCMEC/D3 cells, EV-IL-1β-2, 12h

description: Library name: EV_C2_IL1b


title: hCMEC/D3 cells, EV-IL-1β-1, 12h

description: Library name: EV_C1_IL1b


title: hCMEC/D3 cells, Epinephrine-3, 12h

description: Library name: E3_Epi


title: hCMEC/D3 cells, EV-Control-2, 12h

description: Library name: EV_A2_Ctl


title: hCMEC/D3 cells, Epinephrine-2, 12h

description: Library name: E2_Epi


title: hCMEC/D3 cells, EV-Control-1, 12h

description: Library name: EV_A1_Ctl


title: 8_8_M93_047_tet_EV_Dox_rep_2

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 8_8_M93_047_tet_EV_Dox_rep_2_S8

data_processing:
Using Hg19 genome and gtf file with RSEM and bowtie2 as aligner obtained the raw counts and FPKM values.
Assembly: Hg19
Supplementary files format and content: Text file with RSEM raw counts and FPKM values

growth_protocol: RPMI media, 10% tet-free FBS, 1%Penn/Strep

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Libraries for 3’ mRNA-seq were generated from 100ng of DNase treated total RNA using the QuantSeq FWD Library Preparation kit (Lexogen, Vienna, Austria), according to manufacturer’s directions.  Overall library size was determined using the Agilent Tapestation and the DNA 5000 Screentape (Agilent, Santa Clara, CA).  Libraries were quantitated using real-time PCR (Kapa Biosystems, Wilmington, MA)

treatment_protocol: Vehicle (DMSO), nutlin, doxycycline, or nutlin+doxycycline (24 hours)

value: Human melanoma cell line

value: Doxycycline


title: hCMEC/D3 cells, EV-Control-3, 12h

description: Library name: EV_A3_Ctl


title: 6_6_M93_047_tet_EV_Nutl_rep_3

description: Library name: 6_6_M93_047_tet_EV_Nutl_rep_3_S6

value: Nutlin


title: hCMEC/D3 cells, EV-TNF⍺-1, 12h

description: Library name: EV_B1_TNF


title: hCMEC/D3 cells, C5a-2, 12h

description: Library name: D2_C5a


title: 5_5_M93_047_tet_EV_Nutl_rep_2

description: Library name: 5_5_M93_047_tet_EV_Nutl_rep_2_S5


title: 9_9_M93_047_tet_EV_Dox_rep_3

description: Library name: 9_9_M93_047_tet_EV_Dox_rep_3_S9


title: 7_7_M93_047_tet_EV_Dox_rep_1

description: Library name: 7_7_M93_047_tet_EV_Dox_rep_1_S7


title: hCMEC/D3 cells, EV-TNF⍺-3, 12h

description: Library name: EV_B3_TNF


title: hCMEC/D3 cells, C5a-3, 12h

description: Library name: D3_C5a


title: hCMEC/D3 cells, EV-TNF⍺-2, 12h

description: Library name: EV_B2_TNF


title: hCMEC/D3 cells, Epinephrine-1, 12h

description: Library name: E1_Epi


description: Library name: 48_48_M93_047_tet_PADI4KO_Nutl_and_Dox_rep_3_S48

value: Nutlin+Doxycycline


title: hCMEC/D3 cells, C5a-1, 12h

description: Library name: D1_C5a


title: hCMEC/D3 cells, TNF⍺-3, 12h

description: Library name: B3_TNF


description: Library name: 46_46_M93_047_tet_PADI4KO_Nutl_and_Dox_rep_1_S46


title: hCMEC/D3 cells, IL-1β-1, 12h

description: Library name: C1_IL1b


title: hCMEC/D3 cells, IL-1β-2, 12h

description: Library name: C2_IL1b


title: hCMEC/D3 cells, TNF⍺-2, 12h

description: Library name: B2_TNF


title: 4_4_M93_047_tet_EV_Nutl_rep_1

description: Library name: 4_4_M93_047_tet_EV_Nutl_rep_1_S4


title: 44_44_M93_047_tet_PADI4KO_Dox_rep_2

description: Library name: 44_44_M93_047_tet_PADI4KO_Dox_rep_2_S44


title: hCMEC/D3 cells, Control-3, 12h

description: Library name: A3_Ctl


title: hCMEC/D3 cells, Control-2, 12h

description: Library name: A2_Ctl


title: 43_43_M93_047_tet_PADI4KO_Dox_rep_1

description: Library name: 43_43_M93_047_tet_PADI4KO_Dox_rep_1_S43


description: Library name: 47_47_M93_047_tet_PADI4KO_Nutl_and_Dox_rep_2_S47


title: hCMEC/D3 cells, TNF⍺-1, 12h

description: Library name: B1_TNF


title: 42_42_M93_047_tet_PADI4KO_Nutl_rep_3

description: Library name: 42_42_M93_047_tet_PADI4KO_Nutl_rep_3_S42


title: hCMEC/D3 cells, Control-1, 12h

description: Library name: A1_Ctl


title: 40_40_M93_047_tet_PADI4KO_Nutl_rep_1

description: Library name: 40_40_M93_047_tet_PADI4KO_Nutl_rep_1_S40


title: 3_3_M93_047_tet_EV_Untrt_rep_3

description: Library name: 3_3_M93_047_tet_EV_Untrt_rep_3_S3

value: Vehicle


title: ASO-PURPL

city: Guangzhou

first: xiaojuan

last: teng

address: 2 Lujing Road, Yuexiu District, Guangzhou City

institute: Dermatology Hospital, Southern Medical University

description: ASO-PURPL.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using AdapterRemoval
Trimmed sequence reads were mapped to hg38 using STAR.
FPKM values for each Sample were performed using cufflinks.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BJ cells

growth_protocol: cells were cultured in Dulbecco’s modified Eagle medium (DMEM, SIGMA) supplemented with 10% fetal bovine serum (BIOLOGICAL INDUSTRIES) and maintained at 37 °C with 5% CO2 in a humidified atmosphere.

extract_protocol:
RNA was harvested using TriZol reagent (Invitrogen) and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue source

value: skin

value: BJ cells

value: fibroblast

value: PURPL knockdown


description: Library name: 36_36_M93_047_tet_D350A_Nutl_and_Dox_rep_3_S36


title: ASO-NC_2

description:
01ASO_NC_1
OE2_ASO2.xlsx

source_name: skin

value: ASO-NC


title: ASO-PURPL_2

description:
03ASO_2_1
OE2_ASO2.xlsx


title: 41_41_M93_047_tet_PADI4KO_Nutl_rep_2

description: Library name: 41_41_M93_047_tet_PADI4KO_Nutl_rep_2_S41


title: OE-PURPL_2

description:
04over_purpl1
OE2_ASO2.xlsx

value: PURPL overexpression


title: PCDNA_2

description:
03controlPCDNA
OE2_ASO2.xlsx

value: PCDNA


title: OE-PURPL

description: OE-PURPL.txt


title: 37_37_M93_047_tet_PADI4KO_Untrt_rep_1

description: Library name: 37_37_M93_047_tet_PADI4KO_Untrt_rep_1_S37


title: PCDNA

description: OE-PURPL.txt


description: Library name: 35_35_M93_047_tet_D350A_Nutl_and_Dox_rep_2_S35


description: Library name: 34_34_M93_047_tet_D350A_Nutl_and_Dox_rep_1_S34


title: ASO-NC

description: ASO-PURPL.txt


title: hCMEC/D3 cells, IL-1β-3, 12h

description: Library name: C3_IL1b


title: Hanafy CMSRU | 024 | TMEM119+

city: Camden

first: Khalid

last: Hanafy

state: NJ

address: 401 Broadway,

department: Biomedical Sciences

institute: Cooper Medical School of Rowan Univ

description: Library name: DSP-1001660023496-A-D12_S48

data_processing:
FASTQ fileswere processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2. Briefly, reads were trimmed to remove low quality bases and adapter sequences. Paired end reads were stitched and aligned, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum one mismatch allowed. Reads matching the same barcode were deduplicated by UMI. The number of raw reads was highly linearly correlated with the number of unique UMIs at all AOI sizes, suggesting largely uniform library amplification. However, to correct for any PCR amplification bias, all analyses in this study use UMI deduplicated counts. Data were exported to Excel for further analysis.
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Frozen sections of 4%PFA perfused prefixed mouse brains were sent to the University of Minnesota Genomics Center for probe hybridization, immunofluorescence staining, and selection of ROIs for analysis. 1x Tris-EDTA (pH9.0) solution and steaming the solution to 95⁰C method were used for antigen retrieval followed by Proteinase K digestion at 37⁰C for 5 minutes (1 µg/mL) to expose RNA targets.
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep manual. The DSP aspirate was dried and resuspended in 10 μL DEPC-treated water, and 4 μL was used in a PCR reaction. NanoString SeqCode primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled either in equal volumes or in proportion relative to AOI size, depending on the experiment, and purified with two rounds of AMPure XP beads (Beckman Coulter).Libraries were sequenced on an Illumina NextSeq 2000, according to the manufacturer’s instructions, with at least 27 × 27 paired end reads.

value: Brain

value: Glial cells


title: 33_33_M93_047_tet_D350A_Dox_rep_3

description: Library name: 33_33_M93_047_tet_D350A_Dox_rep_3_S33


title: 31_31_M93_047_tet_D350A_Dox_rep_1

description: Library name: 31_31_M93_047_tet_D350A_Dox_rep_1_S31


title: Hanafy CMSRU | 023 | TMEM119+

description: Library name: DSP-1001660023496-A-D10_S46


title: Hanafy CMSRU | 023 | GFAP+

description: Library name: DSP-1001660023496-A-D09_S45


title: 30_30_M93_047_tet_D350A_Nutl_rep_3

description: Library name: 30_30_M93_047_tet_D350A_Nutl_rep_3_S30


title: 32_32_M93_047_tet_D350A_Dox_rep_2

description: Library name: 32_32_M93_047_tet_D350A_Dox_rep_2_S32


title: 2_2_M93_047_tet_EV_Untrt_rep_2

description: Library name: 2_2_M93_047_tet_EV_Untrt_rep_2_S2


title: Hanafy CMSRU | 021 | TMEM119+

description: Library name: DSP-1001660023496-A-D06_S42


title: 39_39_M93_047_tet_PADI4KO_Untrt_rep_3

description: Library name: 39_39_M93_047_tet_PADI4KO_Untrt_rep_3_S39


title: 38_38_M93_047_tet_PADI4KO_Untrt_rep_2

description: Library name: 38_38_M93_047_tet_PADI4KO_Untrt_rep_2_S38


title: Hanafy CMSRU | 022 | GFAP+

description: Library name: DSP-1001660023496-A-D07_S43


title: Hanafy CMSRU | 022 | TMEM119+

description: Library name: DSP-1001660023496-A-D08_S44


title: Hanafy CMSRU | 021 | GFAP+

description: Library name: DSP-1001660023496-A-D05_S41


title: 27_27_M93_047_tet_D350A_Untrt_rep_3

description: Library name: 27_27_M93_047_tet_D350A_Untrt_rep_3_S27


title: 29_29_M93_047_tet_D350A_Nutl_rep_2

description: Library name: 29_29_M93_047_tet_D350A_Nutl_rep_2_S29


title: 26_26_M93_047_tet_D350A_Untrt_rep_2

description: Library name: 26_26_M93_047_tet_D350A_Untrt_rep_2_S26


title: Hanafy CMSRU | 024 | GFAP+

description: Library name: DSP-1001660023496-A-D11_S47


title: Hanafy CMSRU | 019 | GFAP+

description: Library name: DSP-1001660023496-A-D01_S37


title: Hanafy CMSRU | 020 | TMEM119+

description: Library name: DSP-1001660023496-A-D04_S40


title: Hanafy CMSRU | 019 | TMEM119+

description: Library name: DSP-1001660023496-A-D02_S38


description: Library name: 23_23_M93_047_tet_WT_PADI4_Nutl_and_Dox_rep_2_S23


title: Hanafy CMSRU | 018 | TMEM119+

description: Library name: DSP-1001660023496-A-C12_S36


title: Hanafy CMSRU | 017 | TMEM119+

description: Library name: DSP-1001660023496-A-C10_S34


description: Library name: 22_22_M93_047_tet_WT_PADI4_Nutl_and_Dox_rep_1_S22


title: Hanafy CMSRU | 018 | GFAP+

description: Library name: DSP-1001660023496-A-C11_S35


title: 20_20_M93_047_tet_WT_PADI4_Dox_rep_2

description: Library name: 20_20_M93_047_tet_WT_PADI4_Dox_rep_2_S20


description: Library name: 24_24_M93_047_tet_WT_PADI4_Nutl_and_Dox_rep_3_S24


title: 1_1_M93_047_tet_EV_Untrt_rep_1

description: Library name: 1_1_M93_047_tet_EV_Untrt_rep_1_S1


title: 28_28_M93_047_tet_D350A_Nutl_rep_1

description: Library name: 28_28_M93_047_tet_D350A_Nutl_rep_1_S28


title: Hanafy CMSRU | 016 | TMEM119+

description: Library name: DSP-1001660023496-A-C08_S32


title: Hanafy CMSRU | 017 | GFAP+

description: Library name: DSP-1001660023496-A-C09_S33


title: 21_21_M93_047_tet_WT_PADI4_Dox_rep_3

description: Library name: 21_21_M93_047_tet_WT_PADI4_Dox_rep_3_S21


title: Hanafy CMSRU | 020 | GFAP+

description: Library name: DSP-1001660023496-A-D03_S39


title: 19_19_M93_047_tet_WT_PADI4_Dox_rep_1

description: Library name: 19_19_M93_047_tet_WT_PADI4_Dox_rep_1_S19


title: 17_17_M93_047_tet_WT_PADI4_Nutl_rep_2

description: Library name: 17_17_M93_047_tet_WT_PADI4_Nutl_rep_2_S17


title: Hanafy CMSRU | 016 | GFAP+

description: Library name: DSP-1001660023496-A-C07_S31


title: Hanafy CMSRU | 015 | TMEM119+

description: Library name: DSP-1001660023496-A-C06_S30


title: 25_25_M93_047_tet_D350A_Untrt_rep_1

description: Library name: 25_25_M93_047_tet_D350A_Untrt_rep_1_S25


title: Hanafy CMSRU | 015 | GFAP+

description: Library name: DSP-1001660023496-A-C05_S29


title: Hanafy CMSRU | 014 | TMEM119+

description: Library name: DSP-1001660023496-A-C04_S28


title: 16_16_M93_047_tet_WT_PADI4_Nutl_rep_1

description: Library name: 16_16_M93_047_tet_WT_PADI4_Nutl_rep_1_S16


title: 12_12_M93_047_tet_EV_Nutl_and_Dox_rep_3

description: Library name: 12_12_M93_047_tet_EV_Nutl_and_Dox_rep_3_S12


title: Hanafy CMSRU | 014 | GFAP+

description: Library name: DSP-1001660023496-A-C03_S27


title: 14_14_M93_047_tet_WT_PADI4_Untrt_rep_2

description: Library name: 14_14_M93_047_tet_WT_PADI4_Untrt_rep_2_S14


title: Hanafy CMSRU | 013 | TMEM119+

description: Library name: DSP-1001660023496-A-C02_S26


title: 13_13_M93_047_tet_WT_PADI4_Untrt_rep_1

description: Library name: 13_13_M93_047_tet_WT_PADI4_Untrt_rep_1_S13


title: 11_11_M93_047_tet_EV_Nutl_and_Dox_rep_2

description: Library name: 11_11_M93_047_tet_EV_Nutl_and_Dox_rep_2_S11


title: Hanafy CMSRU | 012 | GFAP+

description: Library name: DSP-1001660023496-A-B11_S23


title: 10_10_M93_047_tet_EV_Nutl_and_Dox_rep_1

description: Library name: 10_10_M93_047_tet_EV_Nutl_and_Dox_rep_1_S10


title: Hanafy CMSRU | 012 | TMEM119+

description: Library name: DSP-1001660023496-A-B12_S24


title: Hanafy CMSRU | 011 | TMEM119+

description: Library name: DSP-1001660023496-A-B10_S22


description: Library name: 46_46-HCT116-tet-PADI4KO-Nutlin-and-Doxycycline-replicate-1_S106

growth_protocol: McCoy's 5A media, 10% tet-free FBS, 1%Penn/Strep

value: colorectal cancer cell line


description: Library name: 47_47-HCT116-tet-PADI4KO-Nutlin-and-Doxycycline-replicate-2_S107


title: Hanafy CMSRU | 010 | GFAP+

description: Library name: DSP-1001660023496-A-B07_S19


title: Hanafy CMSRU | 009 | TMEM119+

description: Library name: DSP-1001660023496-A-B06_S18


title: 15_15_M93_047_tet_WT_PADI4_Untrt_rep_3

description: Library name: 15_15_M93_047_tet_WT_PADI4_Untrt_rep_3_S15


description: Library name: 44_44-HCT116-tet-PADI4KO-Doxycyline-replicate-2_S104


description: Library name: 45_45-HCT116-tet-PADI4KO-Doxycyline-replicate-3_S105


title: Hanafy CMSRU | 009 | GFAP+

description: Library name: DSP-1001660023496-A-B05_S17


title: Hanafy CMSRU | 008 | GFAP+

description: Library name: DSP-1001660023496-A-B03_S15


title: Hanafy CMSRU | 010 | TMEM119+

description: Library name: DSP-1001660023496-A-B08_S20


description: Library name: 48_48-HCT116-tet-PADI4KO-Nutlin-and-Doxycycline-replicate-3_S108


title: Hanafy CMSRU | 008 | TMEM119+

description: Library name: DSP-1001660023496-A-B04_S16


title: Hanafy CMSRU | 007 | TMEM119+

description: Library name: DSP-1001660023496-A-B02_S14


description: Library name: 41_41-HCT116-tet-PADI4KO-Nutlin-replicate-2_S101


description: Library name: 43_43-HCT116-tet-PADI4KO-Doxycyline-replicate-1_S103


title: Hanafy CMSRU | 007 | GFAP+

description: Library name: DSP-1001660023496-A-B01_S13


title: Hanafy CMSRU | 013 | GFAP+

description: Library name: DSP-1001660023496-A-C01_S25


description: Library name: 40_40-HCT116-tet-PADI4KO-Nutlin-replicate-1_S100


title: Hanafy CMSRU | 006 | TMEM119+

description: Library name: DSP-1001660023496-A-A12_S12


title: Hanafy CMSRU | 011 | GFAP+

description: Library name: DSP-1001660023496-A-B09_S21


title: Hanafy CMSRU | 006 | GFAP+

description: Library name: DSP-1001660023496-A-A11_S11


description: Library name: 38_38-HCT116-tet-PADI4KO-untreated-replicate-2_S98


description: Library name: 37_37-HCT116-tet-PADI4KO-untreated-replicate-1_S97


description: Library name: 39_39-HCT116-tet-PADI4KO-untreated-replicate-3_S99


title: Hanafy CMSRU | 005 | GFAP+

description: Library name: DSP-1001660023496-A-A09_S9


title: Hanafy CMSRU | 005 | TMEM119+

description: Library name: DSP-1001660023496-A-A10_S10


description: Library name: 35_35-HCT116-tet-D350A-Nutlin-and-Doxycycline-replicate-2_S95


title: Hanafy CMSRU | 004 | GFAP+

description: Library name: DSP-1001660023496-A-A07_S7


title: Hanafy CMSRU | 003 | TMEM119+

description: Library name: DSP-1001660023496-A-A06_S6


title: Hanafy CMSRU | 004 | TMEM119+

description: Library name: DSP-1001660023496-A-A08_S8


description: Library name: 33_33-HCT116-tet-D350A-Doxycyline-replicate-3_S93


description: Library name: 31_31-HCT116-tet-D350A-Doxycyline-replicate-1_S91


description: Library name: 34_34-HCT116-tet-D350A-Nutlin-and-Doxycycline-replicate-1_S94


description: Library name: 42_42-HCT116-tet-PADI4KO-Nutlin-replicate-3_S102


description: Library name: 32_32-HCT116-tet-D350A-Doxycyline-replicate-2_S92


description: Library name: 36_36-HCT116-tet-D350A-Nutlin-and-Doxycycline-replicate-3_S96


title: Hanafy CMSRU | 002 | TMEM119+

description: Library name: DSP-1001660023496-A-A04_S4


title: Hanafy CMSRU | 002 | GFAP+

description: Library name: DSP-1001660023496-A-A03_S3


description: Library name: 30_30-HCT116-tet-D350A-Nutlin-replicate-3_S90


title: Hanafy CMSRU | 001 | GFAP+

description: Library name: DSP-1001660023496-A-A01_S1


description: Library name: 27_27-HCT116-tet-D350A-untreated-replicate-3_S87


description: Library name: 29_29-HCT116-tet-D350A-Nutlin-replicate-2_S89


title: Hanafy CMSRU | 001 | TMEM119+

description: Library name: DSP-1001660023496-A-A02_S2


title: Experiment34

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
Adapter and low-quality reads were discarded using Python script AfterQC (Chen et al., 2017). Paired-end reads were aligned to the mouse reference genome mm10 using STAR (v2.5.3a) with default parameters, except for the use of setting output type (–out-SAMtype) (Dobin et al., 2013). Reads were then counted with FeatureCounts (v1.5.3) (Liao et al., 2014). Cells with nGene > 3 000, percentage of mitochondrial genes < 10%, and percentage of ERCC < 5% were included. Genes with expression in at least one cell were included.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each cell

source_name: substantia nigra

extract_protocol:
The RNA collected from neurons by patch-seq were converted to DNA using the Smart-seq2 protocol
RNA libaries were prepared with the HyperPlus kit following manufacturer's instruction

value: substantia nigra

value: dopaminergic neuron


description: Library name: 28_28-HCT116-tet-D350A-Nutlin-replicate-1_S88


description: Library name: 25_25-HCT116-tet-D350A-untreated-replicate-1_S85


description: Library name: 26_26-HCT116-tet-D350A-untreated-replicate-2_S86


description: Library name: 24_24-HCT116-tet-PADI4-Nutlin-and-Doxycycline-replicate-3_S84


description: Library name: 23_23-HCT116-tet-PADI4-Nutlin-and-Doxycycline-replicate-2_S83


title: Control36


title: Hanafy CMSRU | 003 | GFAP+

description: Library name: DSP-1001660023496-A-A05_S5


title: Control37


description: Library name: 22_22-HCT116-tet-PADI4-Nutlin-and-Doxycycline-replicate-1_S82


title: SH_1

city: Fuzhou

first: xiandong

last: lin

state: fujian

address: No. 420 Fuma Road, Jinan District

institute: Fujian Cancer Hospital and Fujian Medical University Cancer Hospital

description: Library name: SAMPLE4

data_processing:
Basecalls performed using Illumina CASAVA1.7 software
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
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
featureCounts v1.5.0-p3 was used to count the reads numbers mapped toeach gene
Differential expression analysis oftwo conditions/groups (two biological replicates per condition) was performedusing the DESeq2 R package (1.20.0)
Assembly: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/280/675/GCF_000280675.1_ASM28067v1/GCF_000280675.1_ASM28067v1_genomic.fna.gz
Supplementary files format and content: FPKM of each detected genes

source_name: lung

growth_protocol: Calu-SR mesenchymal cells were maintained in DMEM supplemented with 10% fetaloovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 370

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The integrity of total RNA from each sample was assessed by agarose gel electrophoresis, and RNA concentration and quality were further evaluated using a NanoDrop ND-1000 spectrophotometer. For each sample, 1–2 μg of total RNA was used for RNA sequencing library construction. mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, or alternatively, rRNA was removed using the Ribo-Zero Magnetic Gold Kit. The resulting RNA was then used for library preparation with the KAPA Stranded RNA-Seq Library Prep Kit (Roche). This kit employs a dUTP-based strand-specific library construction strategy, which includes the following steps: (1) fragmentation of mRNA-enriched or rRNA-depleted RNA; (2) reverse transcription to synthesize first-strand cDNA; (3) incorporation of dUTP during second-strand cDNA synthesis; (4) end repair and A-tailing of double-stranded cDNA; (5) ligation of Illumina-specific adapters; and (6) PCR amplification and purification to obtain the final RNA-seq libraries. The constructed libraries were quality-controlled using an Agilent 2100 Bioanalyzer to assess library concentration, fragment size distribution (400–600 bp), and adapter contamination, and were quantified by qPCR. Based on the quantification results and the required sequencing depth, libraries from different samples were pooled and subjected to sequencing.

treatment_protocol: No specific treatment for each strain

value: lung

value: lung cancer cells

value: AURKA-KD

value: Cultivated in cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton, followed by shaking at 150 rpm for 5 days at 25 degree centigrade

value: Day 5


description: Library name: 21_21-HCT116-tet-PADI4-Doxycyline-replicate-3_S81

value: Doxycycline


title: Control33


title: SH_2

description: Library name: SAMPLE5


description: Library name: 20_20-HCT116-tet-PADI4-Doxycyline-replicate-2_S80


title: SH_3

description: Library name: SAMPLE6


title: Experiment35


title: Control35


description: Library name: 19_19-HCT116-tet-PADI4-Doxycyline-replicate-1_S79


title: NC_2

description: Library name: SAMPLE2

value: WT


title: Control32


title: Control31


title: Control34


description: Library name: 17_17-HCT116-tet-PADI4-Nutlin-replicate-2_S77

value: Nutlin


title: HDF cells, Osteogenic medium with recombinat protein, Treated group

city: Chuncheon-si

first: Manho

last: Kim

address: Kangwondaehakgil 1

department: Biomedical science

country: South Korea

institute: Kangwon National University

description: Library name: Protein

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19(UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Primary cells

growth_protocol: HDF cells were matintained in DMEM containing 10% fetal bovine serum (FBS). Osteoblasts were maintained in Osteoblasts Growth medium (Promocell).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: To induce direct conversion of HDF cells, HDFs cells were treated with osteogenic medium containing 10 mM β-glycerol phosphate , 50 μg/ml ascorbic acid and 100 nM dexamethasone for 24 days. The Protein treatment group was treated with 80 μg/mL of Oct4-30Kc19 and 300 μg/mL of Cbfβ-30Kc19 daily for the first 8 days. Osteoblasts were cultured in Promocell's Osteoblasts Growth Medium to maintain the gene expression pattern of osteoblasts. All cells were incubated in humidified atmosphere withb 5% CO2 at 37 °C.

value: Human dermal fibroblats

value: Osteogenic medium with Oct4-30Kc19, Cbfβ-30Kc19


title: HDF cells, Osteogenic medium, Control

description: Library name: HDF_OM

value: Osteogenic medium only


description: Library name: 16_16-HCT116-tet-PADI4-Nutlin-replicate-1_S76


description: Library name: 15_15-HCT116-tet-PADI4-untreated-replicate-3_S75

value: Vehicle


title: Experiment31

city: Beijing


title: 9-HCT116_D350Atet_Nutlin_ChIP_H3K27ac

description: Library name: 9-HCT116_D350Atet_Nutlin_ChIP_H3K27ac_S42

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a). Homer and macs2 were used for peak call and diffbind for diffrential bind. Deeptool used for bigwigfiles.
Assembly: Hg19
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.

extract_protocol:
Non-histone samples were first crosslinked with EGS for 25 minutes. All cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, cells were sonicated with a Cavaris S220 Ultrasonicator.
Barcoded libraries were made using NEB Ultra II DNA Library Prep Kit for Illumina following manufacturer's instructions and quantified by Agilent 4200 Tapestation System.

value: Human melanoma cell line


title: Experiment30


title: NC_1

description: Library name: SAMPLE1


description: Library name: 18_18-HCT116-tet-PADI4-Nutlin-replicate-3_S78


title: Experiment27


title: Osteoblasts, Osteoblast growth medium, Positive control

description: Library name: OB

value: Human osteoblasts

value: Osteoblats growth medium


title: 6-HCT116_D350Atet_Nutlin_ChIP_PADI4

description: Library name: 6-HCT116_D350Atet_Nutlin_ChIP_PADI4_S39


description: Library name: 13_13-HCT116-tet-PADI4-untreated-replicate-1_S73

value: colorectal cancer cell line


title: NC_3

description: Library name: SAMPLE3


description: Library name: 4-HCT116_D350Atet_untreated_ChIP_H3K27ac_S37


title: Experiment29

value: substantia nigra

value: dopaminergic neuron


description: Library name: 14_14-HCT116-tet-PADI4-untreated-replicate-2_S74


title: 3-HCT116_D350Atet_untreated_ChIP_citH3

description: Library name: 3-HCT116_D350Atet_untreated_ChIP_citH3_S36


title: 8-HCT116_D350Atet_Nutlin_ChIP_citH3

description: Library name: 8-HCT116_D350Atet_Nutlin_ChIP_citH3_S41


title: 7-HCT116_D350Atet_Nutlin_ChIP_p53

description: Library name: 7-HCT116_D350Atet_Nutlin_ChIP_p53_S40


title: Experiment26


title: 23-HCT116_D350Atet_Doxy_input

description: Library name: 23-HCT116_D350Atet_Doxy_input_S56


description: Library name: 12_12-HCT116-tet-EV-Nutlin-and-Doxycycline-replicate-3_S72

value: Nutlin+Doxycycline


title: 24-HCT116_D350Atet_NutlinandDoxy_input

description: Library name: 24-HCT116_D350Atet_NutlinandDoxy_input_S57


title: Experiment25


title: Experiment24


description: Library name: 11_11-HCT116-tet-EV-Nutlin-and-Doxycycline-replicate-2_S71


title: Experiment23


description: Library name: 5-HCT116_D350Atet_untreated_ChIP_H3R17me2_S38


title: 21-HCT116_D350Atet_untreated_input

description: Library name: 21-HCT116_D350Atet_untreated_input_S54


title: 45_45_M93_047_tet_PADI4KO_Dox_rep_3

description: Library name: 45_45_M93_047_tet_PADI4KO_Dox_rep_3_S45


title: 2-HCT116_D350Atet_untreated_ChIP_p53

description: Library name: 2-HCT116_D350Atet_untreated_ChIP_p53_S35


description: Library name: 20-HCT116_D350Atet_NutlinandDoxy_ChIP_H3KR17me2_S53


description: Library name: 18-HCT116_D350Atet_NutlinandDoxy_ChIP_citH3_S51


description: Library name: 9_9-HCT116-tet-EV-Doxycyline-replicate-3_S69


description: Library name: 10_10-HCT116-tet-EV-Nutlin-and-Doxycycline-replicate-1_S70


description: Library name: 19-HCT116_D350Atet_NutlinandDoxy_ChIP_H3K27ac_S52


title: 22-HCT116_D350Atet_Nutlin_input

description: Library name: 22-HCT116_D350Atet_Nutlin_input_S55


description: Library name: 7_7-HCT116-tet-EV-Doxycyline-replicate-1_S67


description: Library name: 17-HCT116_D350Atet_NutlinandDoxy_ChIP_p53_S50


title: Experiment21


title: Experiment20


description: Library name: 8_8-HCT116-tet-EV-Doxycyline-replicate-2_S68


title: Control30


description: Library name: 16-HCT116_D350Atet_NutlinandDoxy_ChIP_PADI4_S49


title: 15-HCT116_D350Atet_Doxy_ChIP_H3R17me2

description: Library name: 15-HCT116_D350Atet_Doxy_ChIP_H3R17me2_S48


title: 13-HCT116_D350Atet_Doxy_ChIP_citH3

description: Library name: 13-HCT116_D350Atet_Doxy_ChIP_citH3_S46


title: 14-HCT116_D350Atet_Doxy_ChIP_H3K27ac

description: Library name: 14-HCT116_D350Atet_Doxy_ChIP_H3K27ac_S47


title: Control29


title: 12-HCT116_D350Atet_Doxy_ChIP_p53

description: Library name: 12-HCT116_D350Atet_Doxy_ChIP_p53_S45


title: 11-HCT116_D350Atet_Doxy_ChIP_PADI4

description: Library name: 11-HCT116_D350Atet_Doxy_ChIP_PADI4_S44


title: 5_5-HCT116-tet-EV-Nutlin-replicate-2

description: Library name: 5_5-HCT116-tet-EV-Nutlin-replicate-2_S65


title: 10-HCT116_D350Atet_Nutlin_ChIP_H3R17me2

description: Library name: 10-HCT116_D350Atet_Nutlin_ChIP_H3R17me2_S43


title: 4_4-HCT116-tet-EV-Nutlin-replicate-1

description: Library name: 4_4-HCT116-tet-EV-Nutlin-replicate-1_S64


title: 8-M93-047_tetPADI4_Nutlin_ChIP_citH3

description: Library name: 8-M93-047_tetPADI4_Nutlin_ChIP_citH3_S8


title: 6_6-HCT116-tet-EV-Nutlin-replicate-3

description: Library name: 6_6-HCT116-tet-EV-Nutlin-replicate-3_S66


title: 3_3-HCT116-tet-EV-untreated-replicate-3

description: Library name: 3_3-HCT116-tet-EV-untreated-replicate-3_S63


title: 18_18_M93_047_tet_WT_PADI4_Nutl_rep_3

description: Library name: 18_18_M93_047_tet_WT_PADI4_Nutl_rep_3_S18


title: Control28


title: Control27


title: Control26


title: 1-HCT116_D350Atet_untreated_ChIP_PADI4

description: Library name: 1-HCT116_D350Atet_untreated_ChIP_PADI4_S34


title: 2_2-HCT116-tet-EV-untreated-replicate-2

description: Library name: 2_2-HCT116-tet-EV-untreated-replicate-2_S62


title: 7-M93-047_tetPADI4_Nutlin_ChIP_p53

description: Library name: 7-M93-047_tetPADI4_Nutlin_ChIP_p53_S7


title: Control24


title: 6-M93-047_tetPADI4_Nutlin_ChIP_PADI4

description: Library name: 6-M93-047_tetPADI4_Nutlin_ChIP_PADI4_S6


description: Library name: 31-M93-047_tetKO_NutlinandDoxy_ChIP_PADI4_S31

value: Nutlin+Doxycyline


title: 9-M93-047_tetPADI4_Nutlin_ChIP_H3K27ac

description: Library name: 9-M93-047_tetPADI4_Nutlin_ChIP_H3K27ac_S9


title: Control25


description: Library name: 5-M93-047_tetPADI4_untreated_ChIP_H3R17me2_S5


title: 1_1-HCT116-tet-EV-untreated-replicate-1

description: Library name: 1_1-HCT116-tet-EV-untreated-replicate-1_S61


title: 32-M93-047_tetKO_NutlinandDoxy_ChIP_p53

description: Library name: 32-M93-047_tetKO_NutlinandDoxy_ChIP_p53_S32


description: Library name: 4-M93-047_tetPADI4_untreated_ChIP_H3K27ac_S4


title: 28-M93-047_tetKO_Nutlin_ChIP_p53

description: Library name: 28-M93-047_tetKO_Nutlin_ChIP_p53_S28


title: 33-M93-047_tetKO_NutlinandDoxy_input

description: Library name: 33-M93-047_tetKO_NutlinandDoxy_input_S33


title: Control23


title: 30-M93-047_tetKO_Doxy_ChIP_p53

description: Library name: 30-M93-047_tetKO_Doxy_ChIP_p53_S30


title: Control21


title: 27-M93-047_tetKO_Nutlin_ChIP_PADI4

description: Library name: 27-M93-047_tetKO_Nutlin_ChIP_PADI4_S27


title: P56-FUP2, F, LTR

type: genomic

city: Birtinya

first: Nathan

last: Wellington

state: QLD

address: 12 Innovation Pkwy,

department: Thompson Institute

country: Australia

institute: University of the Sunshine Coast

hyb_protocol: All DNA samples were bisulphite converted with the Zymo EZ-96 DNA Methylation kit.

scan_protocol: Samples were processed on an Illumina Human Methylation EPIC v2.0 Bead Chip utilising the Illumina Infinium HD Methylation assay protocol

data_processing:
Methylation package V1.9.0 in Illumina GenomeStudio V2011.1
Average Beta

label: Cy3 and Cy5

source_name: PBMC

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen) RNA was extracted via the RNeasy mini kit (Qiagen) as per manufacturer’s instructions for cells

value: PBMC

value: female

tag: disease

value: Post Traumatic Stress Disorder

value: Ketamine

tag: response

value: Long Term Responder

tag: timepoint

value: 4 Weeks Post Treatment (FUP2)


title: 3-M93-047_tetPADI4_untreated_ChIP_citH3

description: Library name: 3-M93-047_tetPADI4_untreated_ChIP_citH3_S3


title: 29-M93-047_tetKO_Doxy_ChIP_PADI4

description: Library name: 29-M93-047_tetKO_Doxy_ChIP_PADI4_S29

value: Doxycycline


title: P56-FUP1, F, LTR

value: 1 Week Post Treatment (FUP1)


title: P53-BAS, F, LTR

value: Baseline


title: Control22


title: 23-M93-047_tetPADI4_Doxy_input

description: Library name: 23-M93-047_tetPADI4_Doxy_input_S23

value: Human melanoma cell line


title: 22-M93-047_tetPADI4_Nutlin_input

description: Library name: 22-M93-047_tetPADI4_Nutlin_input_S22

value: Nutlin


title: P52-FUP2, M, LTR

value: male


title: 26-M93-047_tetKO_untreated_ChIP_p53

description: Library name: 26-M93-047_tetKO_untreated_ChIP_p53_S26

value: Vehicle


title: P56-BAS, F, LTR


title: 21-M93-047_tetPADI4_untreated_input

description: Library name: 21-M93-047_tetPADI4_untreated_input_S21


title: Control20

value: substantia nigra


title: Control15

value: dopaminergic neuron


title: Experiment13


title: 25-M93-047_tetKO_untreated_ChIP_PADI4

description: Library name: 25-M93-047_tetKO_untreated_ChIP_PADI4_S25


title: 2-M93-047_tetPADI4_untreated_ChIP_p53

description: Library name: 2-M93-047_tetPADI4_untreated_ChIP_p53_S2


title: P52-FUP1, M, LTR


title: P53-FUP2, F, LTR


title: P53-FUP1, F, LTR


title: 24-M93-047_tetPADI4_NutlinandDoxy_input

description: Library name: 24-M93-047_tetPADI4_NutlinandDoxy_input_S24


title: Control19


description: Library name: 17-M93-047_tetPADI4_NutlinandDoxy_ChIP_p53_S17


description: Library name: 18-M93-047_tetPADI4_NutlinandDoxy_ChIP_citH3_S18


description: Library name: 20-M93-047_tetPADI4_NutlinandDoxy_ChIP_H3KR17me2_S20


description: Library name: 19-M93-047_tetPADI4_NutlinandDoxy_ChIP_H3K27ac_S19


title: P52-BAS, M, LTR


title: Control08


title: Control07


title: P50-FUP2, F, LTR


title: Control10


title: 15-M93-047_tetPADI4_Doxy_ChIP_H3R17me2

description: Library name: 15-M93-047_tetPADI4_Doxy_ChIP_H3R17me2_S15


title: 1-M93-047_tetPADI4_untreated_ChIP_PADI4

description: Library name: 1-M93-047_tetPADI4_untreated_ChIP_PADI4_S1


title: 9-HCT116_tetPADI4_Nutlin_ChIP_H3K27ac

description: Library name: 9-HCT116_tetPADI4_Nutlin_ChIP_H3K27ac_S9

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a). Homer and macs2 were used for peak call and diffbind for diffrential bind. Deeptool used for bigwigfiles.
Assembly: Hg19 or mm10
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.

growth_protocol: Various

value: human colon cancer cell line


title: Control09


title: Control05


title: P51-FUP1, M, NR

value: Non responder


title: P51-FUP2, M, NR

value: PBMC


title: 6-HCT116_tetPADI4_Nutlin_ChIP_PADI4

description: Library name: 6-HCT116_tetPADI4_Nutlin_ChIP_PADI4_S6


title: 14-M93-047_tetPADI4_Doxy_ChIP_H3K27ac

description: Library name: 14-M93-047_tetPADI4_Doxy_ChIP_H3K27ac_S14


title: 12-M93-047_tetPADI4_Doxy_ChIP_p53

description: Library name: 12-M93-047_tetPADI4_Doxy_ChIP_p53_S12


title: 13-M93-047_tetPADI4_Doxy_ChIP_citH3

description: Library name: 13-M93-047_tetPADI4_Doxy_ChIP_citH3_S13


description: Library name: 4-HCT116_tetPADI4_untreated_ChIP_H3K27ac_S4


description: Library name: 5-HCT116_tetPADI4_untreated_ChIP_H3R17me2_S5


description: Library name: 10-M93-047_tetPADI4_Nutlin_ChIP_H3R17me2_S10


title: Control06


title: 11-M93-047_tetPADI4_Doxy_ChIP_PADI4

description: Library name: 11-M93-047_tetPADI4_Doxy_ChIP_PADI4_S11


description: Library name: 16-M93-047_tetPADI4_NutlinandDoxy_ChIP_PADI4_S16

value: Nutlin+Doxycyline


title: Control16


title: P50-FUP1, F, LTR

value: female

value: Post Traumatic Stress Disorder


title: P49-FUP1, F, NR

value: Ketamine


title: 32-HCT116_tetKO_NutlinandDoxy_ChIP_p53

description: Library name: 32-HCT116_tetKO_NutlinandDoxy_ChIP_p53_S32

value: Nutlin+Doxycycline


title: 7-HCT116_tetPADI4_Nutlin_ChIP_p53

description: Library name: 7-HCT116_tetPADI4_Nutlin_ChIP_p53_S7


title: Control02


title: Control04


description: Library name: 31-HCT116_tetKO_NutlinandDoxy_ChIP_PADI4_S31


title: 3-HCT116_tetPADI4_untreated_ChIP_citH3

description: Library name: 3-HCT116_tetPADI4_untreated_ChIP_citH3_S3


title: 30-HCT116_tetKO_Doxy_ChIP_p53

description: Library name: 30-HCT116_tetKO_Doxy_ChIP_p53_S30

value: Doxycycline


title: Control01


title: P51-BAS, M, NR


title: P46-FUP2, M, NR

value: 4 Weeks Post Treatment (FUP2)


title: 29-HCT116_tetKO_Doxy_ChIP_PADI4

description: Library name: 29-HCT116_tetKO_Doxy_ChIP_PADI4_S29


title: 8-HCT116_tetPADI4_Nutlin_ChIP_citH3

description: Library name: 8-HCT116_tetPADI4_Nutlin_ChIP_citH3_S8


title: Experiment07


title: P50-BAS, F, LTR

value: Long Term Responder

value: Baseline


title: 27-HCT116_tetKO_Nutlin_ChIP_PADI4

description: Library name: 27-HCT116_tetKO_Nutlin_ChIP_PADI4_S27

value: Nutlin


title: P49-FUP2, F, NR


title: Control03


title: P49-BAS, F, NR


title: P46-FUP1, M, NR

value: male

value: 1 Week Post Treatment (FUP1)


title: Experiment06

value: substantia nigra


title: 26-HCT116_tetKO_untreated_ChIP_p53

description: Library name: 26-HCT116_tetKO_untreated_ChIP_p53_S26

value: Vehicle


title: Experiment04

value: dopaminergic neuron


title: 22-HCT116_tetPADI4_Nutlin_input

description: Library name: 22-HCT116_tetPADI4_Nutlin_input_S22

value: human colon cancer cell line


title: P40-FUP1, F, STR, WB

source_name: Whole Blood

value: Whole Blood

value: Short Term Responder


description: Library name: 20-HCT116_tetPADI4_NutlinandDoxy_ChIP_H3KR17me2_S20


title: Experiment03


title: P46-BAS, M, NR

value: PBMC

value: Non responder


title: 33-HCT116_tetKO_NutlinandDoxy_input

description: Library name: 33-HCT116_tetKO_NutlinandDoxy_input_S33


title: Experiment05


title: 21-HCT116_tetPADI4_untreated_input

description: Library name: 21-HCT116_tetPADI4_untreated_input_S21


title: 24-HCT116_tetPADI4_NutlinandDoxy_input

description: Library name: 24-HCT116_tetPADI4_NutlinandDoxy_input_S24


title: 25-HCT116_tetKO_untreated_ChIP_PADI4

description: Library name: 25-HCT116_tetKO_untreated_ChIP_PADI4_S25


title: 23-HCT116_tetPADI4_Doxy_input

description: Library name: 23-HCT116_tetPADI4_Doxy_input_S23


description: Library name: 18-HCT116_tetPADI4_NutlinandDoxy_ChIP_citH3_S18


title: P40-BAS, F, STR, WB

value: female

value: Post Traumatic Stress Disorder

value: Ketamine


title: P40-FUP2, F, STR, WB

value: 4 Weeks Post Treatment (FUP2)


title: 2-HCT116_tetPADI4_untreated_ChIP_p53

description: Library name: 2-HCT116_tetPADI4_untreated_ChIP_p53_S2


title: Experiment02


title: Experiment01


title: 28-HCT116_tetKO_Nutlin_ChIP_p53

description: Library name: 28-HCT116_tetKO_Nutlin_ChIP_p53_S28


description: Library name: 19-HCT116_tetPADI4_NutlinandDoxy_ChIP_H3K27ac_S19

value: Nutlin+Doxycycline


description: Library name: 17-HCT116_tetPADI4_NutlinandDoxy_ChIP_p53_S17


title: P40-BAS, F, STR

value: Baseline


title: control72


description: Library name: 16-HCT116_tetPADI4_NutlinandDoxy_ChIP_PADI4_S16


title: Experiment33


title: 15-HCT116_tetPADI4_Doxy_ChIP_H3R17me2

description: Library name: 15-HCT116_tetPADI4_Doxy_ChIP_H3R17me2_S15

value: Doxycycline


title: control71


title: 14-HCT116_tetPADI4_Doxy_ChIP_H3K27ac

description: Library name: 14-HCT116_tetPADI4_Doxy_ChIP_H3K27ac_S14


title: P39-FUP2, F, NR


title: P39-BAS, F, NR


title: control70


title: P37-FUP2, F, LTR

value: Long Term Responder


title: 12-HCT116_tetPADI4_Doxy_ChIP_p53

description: Library name: 12-HCT116_tetPADI4_Doxy_ChIP_p53_S12


title: 10-HCT116_tetPADI4_Nutlin_ChIP_H3R17me2

description: Library name: 10-HCT116_tetPADI4_Nutlin_ChIP_H3R17me2_S10

value: Nutlin


title: 7-M93-047_D350Atet_Nutlin_ChIP_p53

description: Library name: 7-M93-047_D350Atet_Nutlin_ChIP_p53_S40

value: human melanoma cell line


title: P37-FUP1, F, LTR

value: 1 Week Post Treatment (FUP1)


title: control69

value: substantia nigra

value: dopaminergic neuron


title: 8-M93-047_D350Atet_Nutlin_ChIP_citH3

description: Library name: 8-M93-047_D350Atet_Nutlin_ChIP_citH3_S41


title: 6-M93-047_D350Atet_Nutlin_ChIP_PADI4

description: Library name: 6-M93-047_D350Atet_Nutlin_ChIP_PADI4_S39


title: control68


title: 1-HCT116_tetPADI4_untreated_ChIP_PADI4

description: Library name: 1-HCT116_tetPADI4_untreated_ChIP_PADI4_S1

value: human colon cancer cell line

value: Vehicle


description: Library name: 5-M93-047_D350Atet_untreated_ChIP_H3R17me2_S38


title: P36-FUP2, F, NR

value: PBMC


title: 11-HCT116_tetPADI4_Doxy_ChIP_PADI4

description: Library name: 11-HCT116_tetPADI4_Doxy_ChIP_PADI4_S11


title: P36-FUP1, F, NR

value: Non responder


title: 9-M93-047_D350Atet_Nutlin_ChIP_H3K27ac

description: Library name: 9-M93-047_D350Atet_Nutlin_ChIP_H3K27ac_S42


title: P37-BAS, F, LTR

value: female


title: control66


title: 13-HCT116_tetPADI4_Doxy_ChIP_citH3

description: Library name: 13-HCT116_tetPADI4_Doxy_ChIP_citH3_S13


description: Library name: 4-M93-047_D350Atet_untreated_ChIP_H3K27ac_S37


title: control65


title: control67


title: control64


title: 3-M93-047_D350Atet_untreated_ChIP_citH3

description: Library name: 3-M93-047_D350Atet_untreated_ChIP_citH3_S36


title: 22-M93-047_D350Atet_Nutlin_input

description: Library name: 22-M93-047_D350Atet_Nutlin_input_S55


title: P36-BAS, F, NR

value: Post Traumatic Stress Disorder


title: P35-FUP2, M, LTR

value: male

value: Ketamine


title: 23-M93-047_D350Atet_Doxy_input

description: Library name: 23-M93-047_D350Atet_Doxy_input_S56

value: Doxycyline


title: control63


description: Library name: 20-M93-047_D350Atet_NutlinandDoxy_ChIP_H3KR17me2_S53

value: Nutlin+Doxycycline


title: P35-FUP1, M, LTR


title: 21-M93-047_D350Atet_untreated_input

description: Library name: 21-M93-047_D350Atet_untreated_input_S54


title: P35-BAS, M, LTR

value: Baseline


description: Library name: 19-M93-047_D350Atet_NutlinandDoxy_ChIP_H3K27ac_S52


description: Library name: 18-M93-047_D350Atet_NutlinandDoxy_ChIP_citH3_S51


title: 24-M93-047_D350Atet_NutlinandDoxy_input

description: Library name: 24-M93-047_D350Atet_NutlinandDoxy_input_S57


title: P31-FUP2, F, LTR

value: Long Term Responder

value: 4 Weeks Post Treatment (FUP2)


title: control60


title: control61


title: control59


title: 14-M93-047_D350Atet_Doxy_ChIP_H3K27ac

description: Library name: 14-M93-047_D350Atet_Doxy_ChIP_H3K27ac_S47

value: human melanoma cell line


title: 15-M93-047_D350Atet_Doxy_ChIP_H3R17me2

description: Library name: 15-M93-047_D350Atet_Doxy_ChIP_H3R17me2_S48


title: control58


title: 2-M93-047_D350Atet_untreated_ChIP_p53

description: Library name: 2-M93-047_D350Atet_untreated_ChIP_p53_S35


title: 11-M93-047_D350Atet_Doxy_ChIP_PADI4

description: Library name: 11-M93-047_D350Atet_Doxy_ChIP_PADI4_S44


title: P31-FUP1, F, LTR

value: 1 Week Post Treatment (FUP1)


title: control57

value: substantia nigra


title: 23_HCT116_PADI4tet_Doxy_input

description: Library name: 23_HCT116_PADI4tet_Doxy_input_S23

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a). Homer and macs2 were used for peak call. Deeptool used for bigwigfiles.
Assembly: Hg19
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.

value: colorectal cancer cell line

value: Doxycycline


title: 12-M93-047_D350Atet_Doxy_ChIP_p53

description: Library name: 12-M93-047_D350Atet_Doxy_ChIP_p53_S45


title: P31-BAS, F, LTR


title: 22_HCT116_PADI4tet_Nutlin_input

description: Library name: 22_HCT116_PADI4tet_Nutlin_input_S22

value: Nutlin


title: P30-FUP1, M, LTR, WB

value: Whole Blood


title: 24_HCT116_PADI4tet_NutlinandDoxy_input

description: Library name: 24_HCT116_PADI4tet_NutlinandDoxy_input_S24

value: Nutlin + Doxycycline


title: 13-M93-047_D350Atet_Doxy_ChIP_citH3

description: Library name: 13-M93-047_D350Atet_Doxy_ChIP_citH3_S46


title: control62

value: dopaminergic neuron


title: control56


title: 21_HCT116_PADI4tet_untreated_input

description: Library name: 21_HCT116_PADI4tet_untreated_input_S21

value: untreated


title: P30-FUP2, M, LTR, WB

value: male

value: Post Traumatic Stress Disorder


title: 1-M93-047_D350Atet_untreated_ChIP_PADI4

description: Library name: 1-M93-047_D350Atet_untreated_ChIP_PADI4_S34

value: Vehicle


title: P30-FUP2, M, LTR, P

source_name: Pellet

value: Pellet

value: Ketamine


description: Library name: 17-M93-047_D350Atet_NutlinandDoxy_ChIP_p53_S50

value: Nutlin+Doxycycline


title: P40-FUP2, F, STR

value: PBMC

value: female

value: Short Term Responder

value: 4 Weeks Post Treatment (FUP2)


description: Library name: 16-M93-047_D350Atet_NutlinandDoxy_ChIP_PADI4_S49

value: human melanoma cell line


title: Experiment56

value: substantia nigra


description: Library name: 10-M93-047_D350Atet_Nutlin_ChIP_H3R17me2_S43

value: Nutlin


description: Library name: 19_HCT116_PADI4tet_Doxy_ChIP_PADI4abonline_S19

value: colorectal cancer cell line

value: Doxycycline


title: P30-BAS, M, LTR, WB

value: Whole Blood

value: Long Term Responder

value: Baseline


description: Library name: 20_HCT116_PADI4tet_NutlinandDoxy_ChIP_PADI4abonline_S20

value: Nutlin + Doxycycline


title: P30-BAS, M, LTR

value: male

value: Post Traumatic Stress Disorder


title: Experiment52

value: dopaminergic neuron


title: Experiment55


title: Experiment53


title: P30-BAS, M, LTR, P

value: Pellet

value: Ketamine


title: 15_HCT116_PADI4tet_Doxy_ChIP_PADI4pt

description: Library name: 15_HCT116_PADI4tet_Doxy_ChIP_PADI4pt_S15


description: Library name: 18_HCT116_PADI4tet_Nutlin_ChIP_PADI4abonline_S18


description: Library name: 16_HCT116_PADI4tet_NutlinandDoxy_ChIP_PADI4pt_S16


title: P29-FUP2, M, NR

value: PBMC

value: Non responder


description: Library name: 17_HCT116_PADI4tet_untreated_ChIP_PADI4abonline_S17

value: untreated


title: P29-FUP1, M, NR

value: 1 Week Post Treatment (FUP1)


title: 14_HCT116_PADI4tet_Nutlin_ChIP_PADI4pt

description: Library name: 14_HCT116_PADI4tet_Nutlin_ChIP_PADI4pt_S14


title: 13_HCT116_PADI4tet_untreated_ChIP_p53

description: Library name: 13_HCT116_PADI4tet_untreated_ChIP_p53_S13


title: 10_HCT116_PADI4tet_Nutlin_ChIP_p53

description: Library name: 10_HCT116_PADI4tet_Nutlin_ChIP_p53_S10


title: Experiment49

value: substantia nigra


title: 11_HCT116_PADI4tet_Doxy_ChIP_p53

description: Library name: 11_HCT116_PADI4tet_Doxy_ChIP_p53_S11


title: P28-FUP1, M, STR

value: Short Term Responder


title: control54


title: P29-BAS, M, NR


description: Library name: 9_HCT116_PADI4tet_untreated_ChIP_PADI4pt_S9

value: colorectal cancer cell line


description: Library name: 12_HCT116_PADI4tet_NutlinandDoxy_ChIP_p53_S12


title: control55


description: Library name: 8_HCT116_PADI4tet_NutlinandDoxy_ChIP_citH3_S8


title: P28-BAS, M, STR


title: 7_HCT116_PADI4tet_Doxy_ChIP_citH3

description: Library name: 7_HCT116_PADI4tet_Doxy_ChIP_citH3_S7

value: Doxycycline


title: control53


description: Library name: 5_HCT116_PADI4tet_untreated_ChIP_H3K27ac_S5


title: 6_HCT116_PADI4tet_Nutlin_ChIP_citH3

description: Library name: 6_HCT116_PADI4tet_Nutlin_ChIP_citH3_S6

value: Nutlin


title: control52


description: Library name: 4_HCT116_PADI4tet_NutlinandDoxy_ChIP_H3K27ac_S4


title: control50


title: P27-FUP2, F, STR

value: female

value: 4 Weeks Post Treatment (FUP2)


title: control51


title: P27-FUP1, F, STR, WB

value: Whole Blood


title: control49


title: 2_HCT116_PADI4tet_Nutlin_ChIP_H3K27ac

description: Library name: 2_HCT116_PADI4tet_Nutlin_ChIP_H3K27ac_S2


title: 8-Yumm17_copEV_Nutlin_ChIP_citH3

description: Library name: 8-Yumm17_copEV_Nutlin_ChIP_citH3_S41

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a). Homer and macs2 were used for peak call and diffbind for diffrential bind. Deeptool used for bigwigfiles.
Assembly: mm10
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.

growth_protocol: DMEM/F12 media, 10% FBS, 1%Penn/Strep, 1%NEAA

value: Mouse melanoma


title: P27-BAS, F, STR, WB

value: Post Traumatic Stress Disorder

value: Baseline


title: 7-Yumm17_copEV_Nutlin_ChIP_p53

description: Library name: 7-Yumm17_copEV_Nutlin_ChIP_p53_S40


title: 6-Yumm17_copEV_Nutlin_ChIP_PADI4

description: Library name: 6-Yumm17_copEV_Nutlin_ChIP_PADI4_S39


title: 9-Yumm17_copEV_Nutlin_ChIP_H3K27ac

description: Library name: 9-Yumm17_copEV_Nutlin_ChIP_H3K27ac_S42


title: P27-FUP2, F, STR, WB


title: control47

value: dopaminergic neuron


title: 3-Yumm17_copEV_untreated_ChIP_citH3

description: Library name: 3-Yumm17_copEV_untreated_ChIP_citH3_S36

value: Vehicle


title: control46


title: 3_HCT116_PADI4tet_Doxy_ChIP_H3K27ac

description: Library name: 3_HCT116_PADI4tet_Doxy_ChIP_H3K27ac_S3


title: 5-Yumm17_copEV_untreated_ChIP_H3R17me2

description: Library name: 5-Yumm17_copEV_untreated_ChIP_H3R17me2_S38


title: P21-FUP2, F, NR

value: PBMC

value: Ketamine


title: 4-Yumm17_copEV_untreated_ChIP_H3K27ac

description: Library name: 4-Yumm17_copEV_untreated_ChIP_H3K27ac_S37


title: control48


title: 23-Yumm17_A2_5H_untreated_input

description: Library name: 23-Yumm17_A2_5H_untreated_input_S56


title: P21-BAS, F, NR

value: Non responder


title: 24-Yumm17_A2_5H_Nutlin_input

description: Library name: 24-Yumm17_A2_5H_Nutlin_input_S57


title: 21-Yumm17_copEV_untreated_input

description: Library name: 21-Yumm17_copEV_untreated_input_S54


title: 1_HCT116_PADI4tet_untreated_ChIP_citH3

description: Library name: 1_HCT116_PADI4tet_untreated_ChIP_citH3_S1

value: untreated


title: control44

value: substantia nigra


title: 2-Yumm17_copEV_untreated_ChIP_p53

description: Library name: 2-Yumm17_copEV_untreated_ChIP_p53_S35


title: P27-FUP1, F, STR

value: Short Term Responder

value: 1 Week Post Treatment (FUP1)


title: control42


title: 22-Yumm17_copEV_Nutlin_input

description: Library name: 22-Yumm17_copEV_Nutlin_input_S55


title: control45


title: P18-FUP1, M, LTR, WB

value: male

value: Long Term Responder


title: control43


title: 16-Yumm17_A2_5H_Nutlin_ChIP_PADI4

description: Library name: 16-Yumm17_A2_5H_Nutlin_ChIP_PADI4_S49

value: Nutlin


title: 19-Yumm17_A2_5H_Nutlin_ChIP_H3K27ac

description: Library name: 19-Yumm17_A2_5H_Nutlin_ChIP_H3K27ac_S52


title: 17-Yumm17_A2_5H_Nutlin_ChIP_p53

description: Library name: 17-Yumm17_A2_5H_Nutlin_ChIP_p53_S50


title: 11-Yumm17_A2_5H_untreated_ChIP_PADI4

description: Library name: 11-Yumm17_A2_5H_untreated_ChIP_PADI4_S44


title: 15-Yumm17_A2_5H_untreated_ChIP_H3R17me2

description: Library name: 15-Yumm17_A2_5H_untreated_ChIP_H3R17me2_S48


title: Experiment46


title: 18-Yumm17_A2_5H_Nutlin_ChIP_citH3

description: Library name: 18-Yumm17_A2_5H_Nutlin_ChIP_citH3_S51


title: P19-FUP1, M, STR


title: 12-Yumm17_A2_5H_untreated_ChIP_p53

description: Library name: 12-Yumm17_A2_5H_untreated_ChIP_p53_S45


title: P21-FUP1, F, NR

value: female


title: Experiment47


title: P19-BAS, M, STR


title: 20-Yumm17_A2_5H_Nutlin_ChIP_H3KR17me2

description: Library name: 20-Yumm17_A2_5H_Nutlin_ChIP_H3KR17me2_S53


title: Experiment48


title: 1-Yumm17_copEV_untreated_ChIP_PADI4

description: Library name: 1-Yumm17_copEV_untreated_ChIP_PADI4_S34


title: Experiment45


title: P18-BAS, M, LTR


title: P18-FUP2, M, LTR, WB

value: Whole Blood

value: 4 Weeks Post Treatment (FUP2)


title: P18-BAS, M, LTR, WB

value: Post Traumatic Stress Disorder


title: P18-FUP1, M, LTR,