title: Inp 2

data_processing:
. Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover
reads were mapped to the Mus musculus genome assembly mm10 using Bowtie. Then, datasets were filtered by removing duplicated reads (Picard Markduplicates v.1.135) and false-positives regions identified by ENCODE (blacklisted regions v1) PMID: 31249361 or defined as repeatedly enriched in inputs and IgG ChIP-seq in our previous study (PMID: 28400425) (Intersectbed v 2.24.0). Replicates were finally merged and bigwig files were generated.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Liver biopsies were homogenized with a Dounce in 1 X cold PBS. Sample were then double cross-linked by incubating  30 min with 1 mM disuccinimidyl glutarate, followed by 10 min with 1% formaldehyde. After quenching, nuclei were inreched and Chromatin fragmentation was processed by 20 min incubation at 37°C with 20 gel units MNase. Reaction was stopped by addition of 50 mM EDTA and 2 min incubation on ice.  After 5 min centrifugation at 16,000g (4°C) pellet was resuspended in 50 mM Tris-HCl pH8, 10 mM EDTA, 1% SDS, 1 mM DTT and 1X protease inhibitor cocktail and sonicated for 5 min (30 sec ON, 30 sec OFF) with a Bioruptor Plus device.
Libraries were generated using MicroPlex Library Preparation kit V2


title: FFPE_DNA_507

status: Public on Jul 17 2025

type: genomic

city: Munich

first: Guokun

last: Zhang

address: Marchioninistr. 15

country: Germany

institute: IBE LMU

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing:
Sesame R package, normalization method = "db", background subtraction = "noobsb"
The Matrix_processed.txt contains Average Beta
The Matrix_signal_intensities.txt contains unmethylated and methylated signal intensities.
Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: breast cancer

label_protocol: Standard Illumina Protocol

extract_protocol: standard genomic DNA extraction from FFPE tissue

tag: age (years)

tag: gender

value: Female

tag: cohort

value: discovery

tag: treatment

value: 3 weeks endocrine therapy treated

tag: response

value: responder


title: FFPE_DNA_365

value: non-responder


title: FFPE_DNA_364


title: cd5rep1,cd5rep2

type: SRA

city: Shanghai

first: Qian

last: Wen

address: 320 Yueyang Road, Xuhui District

country: China

institute: Shanghai Institute of Nutrition and Health

description: Library name: Sample7

library_source: transcriptomic

data_processing:
fastp
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
The clear reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Collect the livers of mice from each treatment group and extract RNA using Trizol.
Total RNA was extracted and assessed for quality and quantity. mRNA was enriched using poly(A) selection with Oligo(dT) beads. The mRNA was then fragmented and reverse transcribed into cDNA using random primers. After second-strand synthesis, end repair and adapter ligation were performed. The resulting libraries were purified and amplified by PCR. Sequencing was carried out on the Illumina NovaSeq  platform.

tag: tissue

value: liver

tag: genotype

value: WT

value: Single cadmium treatment


title: J7_S961_CD [SAMPLE 29]

type: RNA

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 3.5 microgrammes of ssDNA were hybridized for 16 hr at 45C on MoGene 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on probeset level with NetAffx Annotation Release 36. Matrix values are Log2 RMA.
probe group file:MoGene-2_0-st.pgf and MoGene-2_0-st.clf
meta-probeset file:MoGene-2_0-st-v1.na36.mm10.probeset.csv

label: biotin

source_name: Liver

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

extract_protocol: rna extraction with trizol followed by 2 volume of 100% EtOH and rneasy column (macherey nagel) with Dnase treatment

tag: strain

tag: Sex

value: male

value: Liver

tag: diet

value: Chow Diet

tag: sacrifice day


title: FFPE_DNA_672


title: Ac-5

library_source: genomic

tag: antibody

tag: group

value: IR


title: Ac-4


title: cd2rep1,cd2rep2

description: Library name: Sample6


title: J20_Sas_CD [SAMPLE 28]

value: PBS


title: J85_S961_HFD [SAMPLE 26]

value: High Fat Diet


title: FFPE_DNA_673


title: cd1rep1,cd1rep2

description: Library name: Sample5


title: Ac-3

value: Ctrl


title: se39rep1,se39rep2

description: Library name: Sample9

value: Single selenium treatment


title: FFPE_DNA_425


title: FFPE_DNA_541


title: Ac-2


title: Inp 1


title: FFPE_DNA_540


title: CT29rep1,CT29rep2

description: Library name: Sample3

value: Control group


title: J85_Sas_CD [SAMPLE 25]


title: Ac-1


title: FFPE_DNA_573

value: Female


title: K27m-6


title: CT28rep1,CT28rep2

description: Library name: Sample2


title: K27m-5


title: J7_Sas_CD [SAMPLE 19]


title: CT27rep1,CT27rep2

description: Library name: Sample1


title: FFPE_DNA_754

value: discovery


title: FFPE_DNA_572

value: 3 weeks endocrine therapy treated


title: K27m-4


title: J85_Sas_CD [SAMPLE 18]


title: K27m-3


title: CT-seq of mESC

first: Zixin

last: Wang

address: Siping Road

institute: Tongji University

description: Library name: CT ES

data_processing:
Sequencing raw reads were trimmed using TrimGalore (v0.6.10) to remove adapters and low-quality bases.
Filtered reads were mapped to mm39 genome sequences using BASAL v1.8 (https://github.com/JiejunShi/BASAL).
Alignments deduplicated using sambamba (v1.0.1).
BASALkit (https://github.com/JiejunShi/BASAL) was used to call 5mC or 5hmC bases in CpG contexts. High-confidence 5mC or 5hmC sites (depth ≥ 5) were called using a binomial distribution with FDR < 0.05.
Assembly: mm39
Supplementary files format and content: BigWig CpG methylation or hydroxymethylation level files for each sample.

source_name: Mouse embryonic stem cell

extract_protocol:
Cells were harvested and washed with PBS.Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega) following the manufacturer’s instructions.
Library preparation was performed using the EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme), following the manufacturer's instructions.

tag: cell type

value: Mouse embryonic stem cell


title: J7_Sas_CD [SAMPLE 17]


title: CD-seq of mESC

description: Library name: CD ES


title: J20_S961_CD [SAMPLE 16]


title: FFPE_DNA_731

value: non-responder


title: CT30rep1,CT30rep2

description: Library name: Sample4

value: liver


title: K27m-2

value: WT


title: K27m-1


title: J85_S961_CD [SAMPLE 15]


title: FFPE_DNA_758


title: TAB-seq, hippocampus of AD mouse, rep1

description: Library name: TAB AD1

data_processing:
Sequencing raw reads were trimmed using TrimGalore (v0.6.10) to remove adapters and low-quality bases.
Filtered reads were mapped to mm39 genome sequences using BASAL v1.8 (https://github.com/JiejunShi/BASAL).
Alignments deduplicated using sambamba (v1.0.1).
BASALkit (https://github.com/JiejunShi/BASAL) was used to call 5mC or 5hmC bases in CpG contexts . High-confidence 5mC or 5hmC sites (depth ≥ 5) were called using a binomial distribution with FDR < 0.05.
Assembly: mm39
Supplementary files format and content: BigWig CpG methylation or hydroxymethylation level files for each sample.

source_name: Hippocampus

extract_protocol:
Tissue samples were homogenized and digested with proteinase K at 55°C for 1 hour.Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega) following the manufacturer’s instructions.
Library preparation was performed using the EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme), following the manufacturer's instructions.

value: Hippocampus


title: J20_Sas_CD [SAMPLE 23]

value: male


title: FFPE_DNA_730

value: responder


title: K4m-6

value: Liver


title: J85_Sas_HFD [SAMPLE 20]


title: J85_S961_CD [SAMPLE 14]

value: Chow Diet


title: J85_S961_CD [SAMPLE 13]


title: TAB-seq, hippocampus of WT mouse, rep2

description: Library name: TAB WT2


title: FFPE_DNA_828


title: K4m-4

value: IR


title: FFPE_DNA_418


title: TAB-seq, hippocampus of WT mouse, rep1

description: Library name: TAB WT1


title: ACE-seq, hippocampus of AD mouse, rep2

description: Library name: ACE AD2


title: FFPE_DNA_827


title: FFPE_DNA_419


title: TAB-seq, hippocampus of AD mouse, rep2

description: Library name: TAB AD2


title: K4m-3


title: J20_S961_CD [SAMPLE 11]

value: High Fat Diet


title: K4m-2

value: Ctrl


title: J85_Sas_HFD [SAMPLE 10]

value: PBS


title: ACE-seq, hippocampus of WT mouse, rep2

description: Library name: ACE WT2


title: J20_Sas_CD [SAMPLE 9]


title: K4m-1


title: ACE-seq, hippocampus of AD mouse, rep1

description: Library name: ACE AD1


title: ACE-seq, hippocampus of WT mouse, rep1

description: Library name: ACE WT1


title: K562-R cells, untreated, Biol rep 3

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.csv: K562-R_3

data_processing:
Adapter sequences were trimmed and low quality reads were deleted with Trimmomatic 0.38
Trimmed reads were mapped to the hg38 reference genome using HISAT2 v2.2.1.
Mapped SAM files were converted to BAM format and sorted using Samtools v1.19.2
Read quantification: Gene-level read counts were obtained using featureCounts v2.0.6 with the GENCODE v38.114 annotation
Assembly: hg38
Supplementary files format and content: csv file include raw counts for each Sample

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: K-562 cells were cultured and maintained in RPMI-1640 medium (Lonza, Basel, Switzerland) containing 1% antibiotics (streptomycin and penicillin), antimycotics (Lonza, Walkersville, MD, USA) and 10 % of heat-inactivated fetal bovine serum (FBS; Biowest, Riverside, MO, USA) at 37 °C in a humidified atmosphere with 5% CO₂. K562-R cells were cultured in the same medium as its parental cell lines, supplemented with 0.8 µM imatinib.

extract_protocol:
Total RNA was isolated using TRIzol™ reagent (Invitrogen) and assessed for quality using an Agilent 2100 Bioanalyzer. RNA quantification was performed using an ND-2000 Spectrophotometer (Thermo Inc.).
RNA libraries were prepared using the NEBNext Ultra II Directional RNA-Seq Kit (NEB). mRNA was isolated using the Poly(A) RNA Selection Kit (Lexogen).

treatment_protocol: No treatment

value: Bone marrow

tag: cell line

value: Myelogenous leukemia cell


title: CT-seq, hippocampus of AD mouse, rep2

description: Library name: CT AD2


title: K562-R cells, untreated, Biol rep 2

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.csv: K562-R_2


title: J7_S961_CD [SAMPLE 8]


title: CT-seq, hippocampus of AD mouse, rep1

description: Library name: CT AD1


title: J7_Sas_CD [SAMPLE 7]


title: J85_S961_CD [SAMPLE 12]


title: 06-T-DOXRV1001-A

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

country: USA

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 19.5h in an Eppendorf thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing: Data were analyzed with nSolver software version 4.0 and ROSALIND online software.

label: fluorescent probe

organism: Canis lupus familiaris

source_name: PBMCs

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from frozen PBMCs using Qiagen RNEasy kit per the manufacturer's instructions.

tag: time

value: Baseline

tag: ost (overall survival time)

tag: ost >400 days (long-term survivor)

value: N


title: 06-T-DOXRV1001-B

value: 7d post-tx


title: K562-R cells, untreated, Biol rep 1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.csv: K562-R_1


title: 05-T-DOXRV1001-D

value: Relapse


title: CT-seq, hippocampus of WT mouse, rep2

description: Library name: CT WT2


title: J85_Sas_HFD [SAMPLE 6]


title: J85_S961_CD [SAMPLE 5]


title: K562 cells, untreated, biol rep 2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.csv: K562_2


title: CT-seq, hippocampus of WT mouse, rep1

description: Library name: CT WT1


title: CD-seq, hippocampus of AD mouse, rep2

description: Library name: CD AD2


title: 05-T-DOXRV1001-C

value: 28d post-tx


title: J20_Sas_CD [SAMPLE 4]


title: J7_Sas_CD [SAMPLE 3]


title: CD-seq, hippocampus of AD mouse, rep1

description: Library name: CD AD1


title: K562 cells, untreated, biol rep 1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.csv: K562_1


title: 05-T-DOXRV1001-A


title: microglia_SPF_8w_F_4

city: Freiburg im Breisgau

first: Omar

last: Mossad

address: Breisacher str 64

department: Institute of Neuropathology

institute: University Hospital Freiburg

data_processing:
Illumina CASAVA1.8.2  software used for basecalling.
Quality of sequencing reads stored in FASTQ files was assessed using FastQC (0.67) and trimmed using Trim Galore! (0.4.3). Strandedness of the library preparations was estimated for each sample using RSeQC (2.6.4)
Reads were mapped on the mouse genome version mm10 (UCSC) using STAR aligner (2.5.2) with RefGene annotation and index with 100 bp splice junction overhang. The number of reads mapped to each gene (counts) was extracted from the BAM files using Feature-Count (1.5.3) with the annotation version mm10 from UCSC and the following parameters: exon feature file, unstranded, a minimum mapping quality per read of 12, a minimum overlap of 1bp and other parameters set to default. A quality report of each step was generated using MultiQC (1.5.0). The process to extract the gene counts from FASTQ files was run on Galaxy. Two samples with a low mapping rate (< 75%) were removed.
A differential expression analysis was performed with DESeq2 (1.32.0) with a design model integrating the different factors (microbiota and age) and their interactions. The addition of each factor and interactions were tested beforehand and the number of genes with significant adjusted p-values for the LRT (Likelihood Ratio Test) was reported as the percentage of vari-ables' effect on transcriptomic profile. An exploratory analysis and visualization of variance stabilizing transformation (VST) calculated by the DESeq2 model were performed. After that, normalized counts generated by DESeq2 were assessed for artifacts or contamination by other cell types. The list of genes used was based on single-cell RNA-sequencing data previ-ously obtained by our group. 30 marker genes of non-microglial cell types were removed. R version 4.1.0 was used to perform the Ward error sum of squares hierarchical clustering method and principal components analyses (PCA). Using the DESeq2 model, the differen-tially expressed genes (DEGs) showing adjusted p-values (Wald test) of less than 0.05 and absolute fold change greater than 1.5 were identified.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with normalized gene counts for every gene and every sample

source_name: whole brain

extract_protocol:
Total RNA was extracted from FACS sorted CD11b+CD45lowLin- microglia cells using The ARCTURUS PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. The SMARTer v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) was used to generate first strand cDNA from 500 to 750 pg total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up.
Library preparation was carried out as described in the Illumina Nextera XT Sample Prepara-tion Guide (Illumina). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposase. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illu-mina TruSeq SR Cluster Kit v3.

value: Microglia

tag: age

value: 6-10 weeks

value: Female


title: CD-seq, hippocampus of WT mouse, rep2

description: Library name: CD WT2

value: Hippocampus


title: J20_Sas_CD [SAMPLE 2]

value: male

value: Liver


title: J85_S961_HFD [SAMPLE 1]


title: microglia_SPF_8w_F_3


title: 05-T-DOXRV1001-B


title: 04-T-DOXRV1001-C

value: Y


title: K562 cells, untreated, biol rep 3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.csv: K562_3


title: microglia_SPF_8w_F_1


title: 03-T-DOXRV1001-D


title: Retinal organoids at day 170 of differentiation, 12h light (flickering 40 Hz) and 12h dark for 7 days, bulk seq 1

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

country: Czech Republic

institute: Masaryk University

description: Library name: Bulk_seq_40 Hz 1

data_processing:
Bulk RNA sequencing: The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v0.39 with settings CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35.  Single-cell RNA analysis: All data analysis and visualizations were conducted using R. We performed quality control checks for each sample in R for each sample and removed any cells with <1000 reads or 500 genes or >10% mitochondrial reads. Doublets were predicted using DoubletFinder and filtered from the data. The Seurat R package (version 5.1.0) was then used to process the data.
Assembly: Bulk RNA sequencing: human reference genome (Ensembl GRCh38 annotation) using STAR v2.7.3a with default settings, except for --outFilterMismatchNoverLmax 0.66 and --twopassMode Basic.  Single-cell RNA sequencing: human reference genome refdata-gex-GRCh38-2020-A
Supplementary files format and content: Bulk RNA sequencing: Mapped sequencing reads were assigned to specified genomic features using featureCounts (Rsubread library). Normalized (VST-transformed) reads are in bulk_normalized_counts_vst.csv file  Single-cell RNA sequencing: RDS files for dark and photostimulated at 40 Hz, respectively

source_name: Retinal organoid

extract_protocol:
Bulk RNA sequencing: Retinal organoids were washed twice with PBS and dissociated in RNA Blue Reagent (Top-Bio). Samples were either stored at −80 °C or processed immediately. Organoids were homogenized using an insulin syringe, and total RNA was extracted using the Direct-zol™ RNA MicroPrep Kit (ZYMO RESEARCH, Cat. No.: R2062), following the manufacturer’s protocol.  Single-cell RNA sequencing: Organoid dissociation was carried out using the Neurosphere Dissociation Kit (#130-095-943, Miltenyi Biotec) according to the manufacturer’s instructions. Briefly, organoids were washed twice with cold HBSS (#14025092, Gibco) and transferred into Eppendorf tubes containing 960 μL of preheated Buffer X (each set of 15 organoids was dissociated in a separate tube). Then, 25 μL of Enzyme P, 10 μL of Buffer Y, and 5 μL of Enzyme A were added and mixed gently. The tubes were placed on a thermal mixer with a block (Eppendorf) for 10 minutes at 37°C and 800 rpm. The organoids were dissociated using a fire-polished Pasteur pipette by pipetting up and down 10 times slowly. They were then incubated again under the same conditions for 5 minutes in the thermal mixer and pipetted up and down 10 times with the Pasteur pipette. After adding cold HBSS containing 5% FBS to the single-cell suspension, the mixture was passed through a 40 μm cell strainer placed on a 15 mL tube. Cells were counted, and the tubes were centrifuged at 300×g for 10 minutes at room temperature. The supernatant was aspirated completely, and the cells were resuspended in cold HBSS containing 5% FBS at a concentration of 1000 cells/μL and kept on ice. (Total single cell number 1.500.000/sample)
Bulk RNA sequencing: RNA integrity was checked on the Fragment Analyzer using RNA Kit 15 nt (Agilent Technologies). 500ng of total RNA was used as input for library preparation using QuantSeq 3′ mRNA-Seq FWD with UDI 12 nt Kit (v.2) (Lexogen) in combination with UMI Second Strand Synthesis Module for QuantSeq FWD. Quality control for library quantity and size distribution was done using QuantiFluor dsDNA System (Promega) and High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies). Final library pool was sequenced on NextSeq using High Output Kit v2.5 75 cycles (Illumina) in single-end mode.  Single-cell RNA sequencing: Library preparation was conducted using the same protocol. The quality and quantity of the prepared libraries were assessed using the High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies) and the QuantiFluor dsDNA System (Promega). The libraries were then sequenced using the AVITI sequencing platform (Element Biosciences), employing the AVITI 2×75 Sequencing Kit Cloudbreak FS High Output (150 Gb). Sequencing reads were processed using Cell Ranger software version 8.0.1 (10x Genomics), with FASTQ files aligned to the human reference genome refdata-gex-GRCh38-2020-A, also provided by 10x Genomics, to generate gene expression matrices for downstream analyses.

value: Retinal organoid

value: hESC H9

value: wt

value: photostimulation - 40 Hz


title: microglia_SPF_52w_F_6

value: 50-54 weeks


title: K4m-5

value: IR

value: WT


title: Retinal organoids at day 170 of differentiation, 12h light (flickering 40 Hz) and 12h dark for 7 days, bulk seq 2

description: Library name: Bulk_seq_40 Hz 2


title: CD-seq, hippocampus of WT mouse, rep1

description: Library name: CD WT1


title: microglia_SPF_52w_F_5


title: 03-T-DOXRV1001-C


title: Retinal organoids at day 170 of differentiation, 12h light (1-100 Hz flickering) and 12h dark for 7 days, bulk seq 2

description: Library name: Bulk_seq_Random 2

value: photostimulation - random frequency


title: Hippocampus of AD mouse, rep2

description: Library name: AD2

data_processing:
RNA-seq data raw reads were trimmed using TrimGalore (v0.6.10) to remove adapters and low-quality bases.
Filtered reads were mapped to mm39 genome sequences using STAR v2.7.10b with default parameters.
Mapped reads were quantified using featureCounts5 v2.0.6.
Assembly: mm39
Supplementary files format and content: tsv file containing raw counts s for each sample.

extract_protocol:
Total RNA from the hippocampus was extracted using Trizol reagent (Sangon) according to the manufacturer’s instructions.
RNA-seq transcriptome libraries were prepared following the Illumina® Stranded mRNA Prep, Ligation protocol using 1 μg of total RNA.


title: 04-T-DOXRV1001-D

value: Relapse


title: 04-T-DOXRV1001-A

value: Baseline


title: Hippocampus of AD mouse, rep1

description: Library name: AD1


title: Retinal organoids at day 170 of differentiation, 12h light (1-100 Hz flickering) and 12h dark for 7 days, bulk seq 1

description: Library name: Bulk_seq_Random 1


title: microglia_SPF_52w_F_4

value: Microglia


title: Hippocampus of WT mouse, rep3

description: Library name: WT3


title: Hippocampus of WT mouse, rep2

description: Library name: WT2


title: Retinal organoids at day 170 of differentiation, 12h light (constant light) and 12h dark for 7 days, bulk seq 2

description: Library name: Bulk-seq_Constant 2

value: photostimulation - constant light


title: 03-T-DOXRV1001-B

value: 7d post-tx


title: Hippocampus of AD mouse, rep3

description: Library name: AD3

value: Hippocampus


title: 02-T-DOXRV1001-D


title: 03-T-DOXRV1001-A


title: microglia_SPF_52w_F_2

value: Female


title: 02-T-DOXRV1001-C

value: 28d post-tx


title: Hippocampus of WT mouse, rep1

description: Library name: WT1


title: 02-T-DOXRV1001-B

value: Y


title: microglia_SPF_104w_M_4

value: Male


title: Input ChIP-seq in TKO rep2

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

description: Library name: Input_TKO_rep2_1

data_processing:
Trim adapter and low quality reads using Trim_galore
Map reads on mouse genome by Bowtie2
Remove PCR duplicates by Picard
Assembly: mm10
Supplementary files format and content: bigWig

source_name: TKO

growth_protocol: We used previously established Setdb1, Suv39h1/2, Ehmt1, Ehmt2 KO iMEFs to analysis the role of uH2A in heterochromatin maintenance (Fukuda et al., 2023). Mouse embryonic fibroblasts were maintained in Dulbecco's modified Eagle's medium (Nacalai tesque, 08458-16) containing 10% fetal bovine serum (Biosera, FB1061), MEM Non-Essential medium and 2-Mercaptoethanol (Nacalai tesque, 21417-52).

extract_protocol:
ChIP DNA was extracted by Native ChIP protocol
5 × 10⁵ iMEFs were crosslinked in 1 mL PBS supplemented with 0.1 mL Crosslinking Buffer (100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES [pH 8.0], 11% PFA) at 25°C for 20 min. The reaction was quenched by adding 0.125 M glycine. After washing with PBS, the pellet was resuspended in 300 µL SDS lysis buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% SDS, protease inhibitor). Chromatin was sonicated using a Picoruptor (Diagenode) with a cycle of 30 sec on/30 sec off for a total of five cycles. The lysate was then centrifuged at 15,000 rpm for 10 min at 4°C. The supernatant was diluted with 1.2 mL Chromatin Dilution Buffer (10% Tris-HCl [pH 7.5], 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1× cOmplete EDTA-free protease inhibitor ( Roche, 11836170001), 1 mM PMSF). From the diluted chromatin solution, 100 µL was set aside for input control, and the remaining portion was incubated with 8 µg of anti-CTCF antibody (Active Motif #61311) and 10 l of Protein A/G agarose beads (Santa Cruz, sc-2003). The mixture was rotated at 4°C overnight. After rotating the solution, the beads were sequentially washed by low salt buffer (150 mM NaCl, Tris-HCl pH8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (500 mM NaCl, Tris-HCl pH8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (25 mM LiCl, 10 mM Tris-HCl pH8.0, 1 mM EDTA, 1% NP40, 1% DOC), TE, and were suspended in Salting method buffer (20 mM Tris pH8.0, 10mM EDTA, 400 mM NaCl). Input and ChIP samples were de-crosslinked by RNaseA, SDS and Protease K treatment, and purified by QIAquick PCR purification kit (Qiagen).

treatment_protocol: To inhibit EZH1/2 catalytic activity, iMEFs were cultured for seven days with 1 uM DS3201.

value: TKO

value: MEF

value: No treatment

tag: batch


title: microglia_SPF_104w_M_2

tag: treatment


title: Retinal organoids at day 170 of differentiation, cultured in the dark, bulk seq 1

description: Library name: Bulk-seq_Dark 1

value: Retinal organoid

value: hESC H9

value: wt

value: dark


title: microglia_SPF_104w_M_1


title: Input ChIP-seq in Setdb1KO rep2

description: Library name: Input_Setdb1KO_rep2_1


title: Input, Hypoxia, MiaPaCa-MYB KO-HIF1αOE, replicate 3

city: Jackson

first: Shashi

last: Anand

state: MS

address: 2500 N State St

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

description: Library name: MiaPaCa-2 MYB KO-HIF1αOE, Hypoxia, Input, replicate 3

data_processing:
Briefly, the sequencing reads were evaluated for the quality control based on base quality, GC content, presence of sequencing adaptors and overrepresented sequences using FastQC tool. Sequencing reads were then aligned to the Human Reference Genome (assembly hg19) using bowtie and BWA. Quality check was performed for the aligned reads and duplicate reads were removed using Picard tool and uniquely mapped reads were then subjected to peak calling using MACS2 software.
Assembly: GRCh37 or hg19 (February 2009 genome version)
Supplementary files format and content: BigWig

source_name: Pancrease

growth_protocol: Pancreatic cancer cells were cultured in RPMI supplemented with 10% FBS and allowed them to grow in a CO2 incubator at 37°C and 5% CO2.

extract_protocol:
MYB and HIF1α ChIP were carried out using ChIP-IT Express Enzymatic Kit (Active Motif, CA, USA) as per manufacturers instruction manual.
ChIP-seq libraries were prepared using NEB Next Ultra II DNA library prep kit. Briefly, 10-15 ng of DNA was used as starting material for input and IP samples. DNA libraries were sequenced using illumina NextSeq 500 plateform.

treatment_protocol: Cells were subjected to either normxoxia (20% O2) or hypoxia (1% O2) treatment. Hypoxia treatment was given in a hypoxia chamber equipped with an oxygen controller (BioSpherix, Parish, NY) for 6h.

value: Pancrease

value: Human Pancreatic Cancer Cells

value: MYB KO-HIF1αOE (Hypoxia)


title: Input ChIP-seq in TKO rep1

description: Library name: Input_TKO_rep1_1


title: Input ChIP-seq in Setdb1KO rep1

description: Library name: Input_Setdb1KO_rep1_1


title: 02-T-DOXRV1001-A

value: Baseline


title: 01-T-DOXRV1001-A


title: microglia_SPF_104w_F_3

value: Microglia


title: 01-T-DOXRV1001-B

value: 7d post-tx


title: microglia_SPF_52w_F_3

value: 50-54 weeks

value: Female


title: Input, Hypoxia, MiaPaCa-MYB KO-HIF1αOE, replicate 2

description: Library name: MiaPaCa-2 MYB KO-HIF1αOE, Hypoxia, Input, replicate 2


title: 07-T-TAK-C

value: 28d post-tx

value: N


title: Input ChIP-seq in 5KOcln55 rep2

description: Library name: Input_5KOclone55_rep2_1


title: Input, Hypoxia, MiaPaCa-MYB KO-HIF1αOE, replicate 1

description: Library name: MiaPaCa-2 MYB KO-HIF1αOE, Hypoxia, Input, replicate 1


title: microglia_SPF_104w_F_2


title: Retinal organoids at day 170 of differentiation, 12h light (constant light) and 12h dark for 7 days, bulk seq 1

description: Library name: Bulk-seq_Constant 1

value: photostimulation - constant light


title: microglia_SPF_104w_F_1


title: ChIP-seq, HIF1α, Hypoxia, MiaPaCa-MYB KO-HIF1αOE, replicate 3

description: Library name: MiaPaCa-2 MYB KO-HIF1αOE, Hypoxia, ChIP-seq HIF1α, replicate 3


title: 07-T-TAK-B


title: Retinal organoids at day 170 of differentiation, cultured in the dark, bulk seq 2

description: Library name: Bulk-seq_Dark 2


title: Input ChIP-seq in 5KOcln14 rep2

description: Library name: Input_5KOclone14_rep2_1

value: MEF


title: 07-T-TAK-A


title: microglia_SPF_8w_M_4

value: 6-10 weeks

value: Male


title: ChIP-seq, HIF1α, Hypoxia, MiaPaCa-MYB KO-HIF1αOE, replicate 2

description: Library name: MiaPaCa-2 MYB KO-HIF1αOE, Hypoxia, ChIP-seq HIF1α, replicate 2


title: microglia_SPF_8w_M_3


title: 05-T-TAK-C

value: Y


title: Input ChIP-seq in 5KOcln14 rep1

description: Library name: Input_5KOclone14_rep1_1

value: No treatment


title: Input ChIP-seq in WT rep2

description: Library name: Input_3-12_rep2_1

source_name: WT iMEFs

value: WT iMEFs

value: WT


title: ChIP-seq, HIF1α, Hypoxia, MiaPaCa-MYB KO-HIF1αOE, replicate 1

description: Library name: MiaPaCa-2 MYB KO-HIF1αOE, Hypoxia, ChIP-seq HIF1α, replicate 1

value: Pancrease

value: Human Pancreatic Cancer Cells


title: ChIP-seq, HIF1α, Hypoxia, MiaPaCa-2 cells, replicate 3

description: Library name: MiaPaCa-2 Control, Hypoxia, ChIP-seq HIF1α, replicate 3

value: Control (Hypoxia)


title: 05-T-TAK-B


title: Input ChIP-seq in WT rep1

description: Library name: Input_3-12_rep1_1


title: microglia_SPF_52w_M_5

value: Microglia


title: 05-T-TAK-A

value: Baseline


title: microglia_SPF_52w_M_4

value: 50-54 weeks


title: CTCF ChIP-seq in TKO rep2

description: Library name: ChIP_TKO_rep2_1

value: TKO


title: ChIP-seq, HIF1α, Hypoxia, MiaPaCa-2 cells, replicate 1

description: Library name: MiaPaCa-2 Control, Hypoxia, ChIP-seq HIF1α, replicate 1


title: Input ChIP-seq in 5KOcln55 rep1

description: Library name: Input_5KOclone55_rep1_1


title: microglia_SPF_52w_M_3


title: CTCF ChIP-seq in TKO rep1

description: Library name: ChIP_TKO_rep1_1


title: Input, Hypoxia, MiaPaCa-HIF1α KO, replicate 3

description: Library name: MiaPaCa-2 HIF1α KO, Hypoxia, Input, replicate 3

value: HIF1α KO (Hypoxia)


title: 03-T-TAK-C

value: 28d post-tx


title: Input, Hypoxia, MiaPaCa-HIF1α KO, replicate 2

description: Library name: MiaPaCa-2 HIF1α KO, Hypoxia, Input, replicate 2


title: 03-T-TAK-D

value: Relapse


title: CTCF ChIP-seq in Setdb1KO rep2

description: Library name: ChIP_Setdb1KO_rep2_1

value: MEF


title: microglia_SPF_52w_M_2


title: CTCF ChIP-seq in Setdb1KO rep1

description: Library name: ChIP_Setdb1KO_rep1_1


title: microglia_SPF_52w_M_1


title: microglia_SPF_8w_M_2

value: 6-10 weeks


title: CTCF ChIP-seq in 5KOcln55 rep2

description: Library name: ChIP_5KOclone55_rep2_1


title: 03-T-TAK-A


title: 03-T-TAK-B

value: 7d post-tx


title: ChIP-seq, HIF1α, Hypoxia, MiaPaCa-2 cells, replicate 2

description: Library name: MiaPaCa-2 Control, Hypoxia, ChIP-seq HIF1α, replicate 2


title: Input, Hypoxia, MiaPaCa-HIF1α KO, replicate 1

description: Library name: MiaPaCa-2 HIF1α KO, Hypoxia, Input, replicate 1


title: 02-T-TAK-D

value: N


title: CTCF ChIP-seq in 5KOcln55 rep1

description: Library name: ChIP_5KOclone55_rep1_1

value: No treatment


title: ChIP-seq, MYB, Hypoxia, MiaPaCa-HIF1α KO, replicate 2

description: Library name: MiaPaCa-2 HIF1α KO, Hypoxia, ChIP-seq MYB, replicate 2


title: KO6_eWAT

city: Kowloon

first: Thashma

middle: Pemmanda

last: Ganapathy

address: 11 Yuk Choi Road

department: Health Technology and Information

country: Hong Kong

institute: The Hong Kong Polytechnic University

description: Library name: F2K6

data_processing:
The raw data from the DNBSEQ-G400 sequencers were processed through several key steps. First, sequencing reads were demultiplexed based on unique barcodes. Adapter sequences were then removed using SOAPnuke to minimize biases, followed by quality control to filter out low-quality reads and those with excessive "N" bases. The cleaned reads were aligned to a reference genome (mm39) using HISAT2, facilitating the identification of gene expression patterns. These cleaned reads were subsequently used for further analysis.
Assembly: mm39
Supplementary files format and content: Raw counts data in .csv format

source_name: Epididymal adipose tissue

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Catalogue# 74104, Qiagen) following the manufacturer’s instructions. The procedure involved homogenizing tissue samples in the provided lysis buffer to release RNA, followed by applying the lysate to RNeasy spin columns, where RNA binds to the column membrane. After several washing steps to eliminate contaminants, high-purity RNA was eluted in RNase-free water.
RNA libraries for sequencing in DNBSEQ-G400 were prepared using the MGIEasy RNA Library Prep Set according to the manufacturer’s protocol. This process involved extracting and enriching total RNA, followed by fragmentation, cDNA synthesis, and ligation of specialized adapters to prepare the samples for sequencing.

value: Epididymal adipose tissue

value: 105-week old animal model of ageing


title: CTCF ChIP-seq in 5KOcln14 rep2

description: Library name: ChIP_5KOclone14_rep2_1


title: KO5_eWAT

description: Library name: F2K5


title: KO4-eWAT

description: Library name: F2K4


title: 02-T-TAK-C


title: KO3-eWAT

description: Library name: F2K3


title: 02-T-TAK-B


title: ChIP-seq, MYB, Hypoxia, MiaPaCa-HIF1α KO, replicate 1

description: Library name: MiaPaCa-2 HIF1α KO, Hypoxia, ChIP-seq MYB, replicate 1

value: Pancrease


title: 02-T-TAK-A


title: ChIP-seq, MYB, Hypoxia, MiaPaCa-HIF1α KO, replicate 3

description: Library name: MiaPaCa-2 HIF1α KO, Hypoxia, ChIP-seq MYB, replicate 3

value: Human Pancreatic Cancer Cells


title: Input, Hypoxia, MiaPaCa-2 cells, replicate 3

description: Library name: MiaPaCa-2 Control, Hypoxia, Input, replicate 3

value: Control (Hypoxia)


title: CTCF ChIP-seq in 5KOcln14 rep1

description: Library name: ChIP_5KOclone14_rep1_1


title: 01-T-TAK-D


title: CTCF ChIP-seq in WT rep2

description: Library name: ChIP_3-12_rep2_1

value: WT iMEFs

value: WT


title: WT5_eWAT

description: Library name: F2W5

value: Wild-type


title: 01-T-TAK-C


title: WT6_eWAT

description: Library name: F2W6


title: Input, Hypoxia, MiaPaCa-2 cells, replicate 2

description: Library name: MiaPaCa-2 Control, Hypoxia, Input, replicate 2


title: WT2_eWAT

description: Library name: F2W2


title: 01-T-TAK-A

value: Baseline


title: Input ChIP-seq in TKO+DS rep2

description: Library name: Input_TKO+DS_2_1

value: TKO

value: DS3201 treatment


title: Input ChIP-seq in TKO+DS rep1

description: Library name: Input_TKO+DS_1_1


title: WT3_eWAT

description: Library name: F2W3


title: 01-T-TAK-B


title: ChIP-seq, MYB, Hypoxia, MiaPaCa-2 cells, replicate 3

description: Library name: MiaPaCa-2 Control, Hypoxia, ChIP-seq MYB, replicate 3


title: CTCF ChIP-seq in WT rep1

description: Library name: ChIP_3-12_rep1_1


title: 07-T-KPT9274-C

value: 28d post-tx


title: ChIP-seq, MYB, Hypoxia, MiaPaCa-2 cells, replicate 2

description: Library name: MiaPaCa-2 Control, Hypoxia, ChIP-seq MYB, replicate 2


title: DMSO_T24 to T30 Rep3

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke software developed by BGI
SOAPnuke software filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --polyX 50 -- minReadLen 100", steps of filtering
1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), remove the entire read; 2. Filter read length: if the length of the sequencing read is less than 100 bp, discard the entire read; 3. Remove N: if the N content in the sequencing read accounts for 0.1% or more of the entire read, discard the entire read; 4. Remove polyX: if the length of polyX (X can be A, T, G or C) in the sequencing read exceeds 50bp, discard the entire read; 5. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing Figure 2 Bioinformatic analysis workflow 15 / 18 read account for 40.0% or more of the entire read, discard the entire read; 6. Obtain Clean reads: the output read quality value system is set to Phred+33
Images generated by sequencers are converted by base calling into nucleotide sequences, which are called raw data or raw reads and are stored in FASTQ format. FASTQ files are text files that store both reads sequences and their corresponding quality scores. Each read is described in four lines as follows: The first line is the sequence identifier and related description information, starting with'@'; the second line is the base sequence information; the third line starts with'+', followed by the sequence identifier, description information, or nothing; The four lines are quality information, which corresponds to the sequence in the second line. Each base has a quality score. Depending on the scoring system, each character represents a different quality value
Assembly: The reference transcriptome have been download on ensembl version 110 : https://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/cdna/
Supplementary files format and content: Tab-delimited files include normalized count for each set of sample

extract_protocol:
RNA has been extracted using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer recommendations
Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB)

value: Hepatocyte


title: Pema_T24 to t30 Rep3


title: Input ChIP-seq in Setdb1KO+DS rep1

description: Library name: Input_Setdb1KO+DS_1_1

value: MEF


title: Input ChIP-seq in Setdb1KO+DS rep2

description: Library name: Input_Setdb1KO+DS_2_1


title: 07-T-KPT9274-B

value: 7d post-tx


title: Pema T14 to T20 Rep 3


title: Input ChIP-seq in 5KOcln55+DS rep2

description: Library name: Input_5KO55+DS_2_1


title: 07-T-KPT9274-A

value: N


title: Input, Normoxia, MiaPaCa-2 cells, replicate 2

description: Library name: MiaPaCa-2 Control, Normoxia, Input, replicate 2

value: Control (Normoxia)


title: Input, Hypoxia, MiaPaCa-2 cells, replicate 1

description: Library name: MiaPaCa-2 Control, Hypoxia, Input, replicate 1


title: DMSO_T14 to T20 Rep3


title: Input ChIP-seq in 5KOcln55+DS rep1

description: Library name: Input_5KO55+DS_1_1


title: 06-T-KPT9274-D

value: Relapse

value: Y


title: Input, Normoxia, MiaPaCa-2 cells, replicate 1

description: Library name: MiaPaCa-2 Control, Normoxia, Input, replicate 1

value: Pancrease


title: Input ChIP-seq in 5KOcln14+DS rep2

description: Library name: Input_5KO14+DS_2_1


title: Pema T0 to T24 Rep 3


title: ChIP-seq, MYB, Normoxia, MiaPaCa-2 cells, replicate 3

description: Library name: MiaPaCa-2 Control, Normoxia, ChIP-seq MYB, replicate 3

value: Human Pancreatic Cancer Cells


title: DMSO_T0 to T24 Rep3


title: Input ChIP-seq in 5KOcln14+DS rep1

description: Library name: Input_5KO14+DS_1_1


title: 06-T-KPT9274-B


title: 06-T-KPT9274-C


title: ChIP-seq, MYB, Normoxia, MiaPaCa-2 cells, replicate 1

description: Library name: MiaPaCa-2 Control, Normoxia, ChIP-seq MYB, replicate 1


title: ChIP-seq, MYB, Hypoxia, MiaPaCa-2 cells, replicate 1

description: Library name: MiaPaCa-2 Control, Hypoxia, ChIP-seq MYB, replicate 1

value: Control (Hypoxia)


title: Input, Normoxia, MiaPaCa-2 cells, replicate 3

description: Library name: MiaPaCa-2 Control, Normoxia, Input, replicate 3


title: Input ChIP-seq in WT+DS rep2

description: Library name: Input_3-12+DS_2_1

value: WT iMEFs


title: Pema_T24 to t30 Rep2


title: 06-T-KPT9274-A


title: DMSO_T24 to T30 Rep2


title: Input ChIP-seq in WT+DS rep1

description: Library name: Input_3-12+DS_1_1

value: WT


title: Control, time 48h, Individual 01, replicate 3

city: Olsztyn

first: Carsten

last: carlberg

address: Tuwima 10

country: Poland

institute: institute of animal reproduction and food sciences of polish academy of sciences

description: Library name: 48h_R3

data_processing:
Read alignment using STAR v2.7.10b using default parameters
Quantification using FastQC v0.12.1 and featureCounts v2.0.3 using default parameters for reverse strand
Filtering for protein coding genes and read counts normalization (normalized CPM)
Assembly: GRCh38.p13,  Aligned to GENCODE version 42
Supplementary files format and content: Excel table of CPM normalized read counts

source_name: peripheral blood mononuclear cells

growth_protocol: no in vitro culture

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: Before and after intake of 80000 IU of vitamin D3 at 04h, 24h and 48h

value: peripheral blood mononuclear cells

tag: subject status

value: Healthy Individual

value: PBMC

value: 80000 IU vitamin D3

tag: time point

value: After 48 hours of vitamin D bolus intake


title: 05-T-KPT9274-C

value: 28d post-tx


title: 05-T-KPT9274-B


title: Pema T14 to T20 Rep 2

value: Hepatocyte


title: DMSO_T14 to T20 Rep2


title: CTCF ChIP-seq in TKO+DS rep1

description: Library name: ChIP_TKO+DS_1_1

value: TKO

value: MEF

tag: genotype

value: DS3201 treatment


title: CTCF ChIP-seq in TKO+DS rep2

description: Library name: ChIP_TKO+DS_2_1


title: 05-T-KPT9274-A

value: Baseline

value: N


title: Control, time 48h, Individual 01, replicate 1

description: Library name: 48h_R1

tag: tissue


title: 04-T-KPT9274-C


title: Pema T0 to T24 Rep 2


title: ChIP-seq, MYB, Normoxia, MiaPaCa-2 cells, replicate 2

description: Library name: MiaPaCa-2 Control, Normoxia, ChIP-seq MYB, replicate 2

value: Pancrease

value: Control (Normoxia)


title: DMSO_T0 to T24 Rep2


title: 04-T-KPT9274-B

value: 7d post-tx


title: Control, time 24h, Individual 01, replicate 3

description: Library name: 24h_R3

value: After 24 hours of vitamin D bolus intake


title: CTCF ChIP-seq in 5KOcln55+DS rep2

description: Library name: ChIP_5KO55+DS_2_1


title: Control, time 24h, Individual 01, replicate 2

description: Library name: 24h_R2


title: 04-T-KPT9274-A


title: DMSO_T24 to T30 Rep1


title: 03-T-KPT9274-D

value: Relapse

value: Y


title: CTCF ChIP-seq in Setdb1KO+DS rep1

description: Library name: ChIP_Setdb1KO+DS_1_1


title: CTCF ChIP-seq in 5KOcln55+DS rep1

description: Library name: ChIP_5KO55+DS_1_1


title: Pema_T24 to t30 Rep1


title: 03-T-KPT9274-C


title: CTCF ChIP-seq in 5KOcln14+DS rep2

description: Library name: ChIP_5KO14+DS_2_1


title: Pema T14 to T20 Rep 1


title: CTCF ChIP-seq in 5KOcln14+DS rep1

description: Library name: ChIP_5KO14+DS_1_1


title: Control, time 04h, Individual 01, replicate 1

description: Library name: 04h_R1

value: peripheral blood mononuclear cells

value: Healthy Individual

value: After 04 hours of vitamin D bolus intake


title: Control, time 24h, Individual 01, replicate 1

description: Library name: 24h_R1

value: PBMC

value: 80000 IU vitamin D3


title: Control, time 04h, Individual 01, replicate 3

description: Library name: 04h_R3


title: CTCF ChIP-seq in Setdb1KO+DS rep2

description: Library name: ChIP_Setdb1KO+DS_2_1


title: CTCF ChIP-seq in WT+DS rep2

description: Library name: ChIP_3-12+DS_2_1

value: WT iMEFs

value: WT


title: 03-T-KPT9274-B


title: DMSO_T14 to T20 Rep1

value: Hepatocyte


title: Control, time 48h, Individual 01, replicate 2

description: Library name: 48h_R2

value: After 48 hours of vitamin D bolus intake


title: Control, time 0h, Individual 01, replicate 3

description: Library name: 0h_R3

value: control

value: Before vitamin D bolus intake


title: 02-T-KPT9274-D


title: DMSO_T0 to T24 Rep1


title: Pema T0 to T24 Rep 1


title: Control, time 0h, Individual 01, replicate 2

description: Library name: 0h_R2


title: 03-T-KPT9274-A

value: Baseline


title: RNA-Seq of C. auris strain 20-1498 at 42C Rep3 R1

city: Ciudad de México

first: Daniel

last: Clark-Flores

state: Ciudad de México

address: Prol. de Carpio y Plan de Ayala. Col. Sto. Tomás

department: Microbiología

country: Mexico

institute: Instituto Politécnico Nacional

description:
Library name: Candidozyma_auris_42C_Rep3_R1
Sample D3 corresponds to 42°C, replicate 3

data_processing:
Raw reads were processed with Trimmomatic v0.39. The quality of filtered reads was evaluated using FastQC v0.12.1. The reference genome of C. auris clade IV B11243 (GCA_003014415.1) was downloaded from FungiDB (https://fungidb.org/fungidb/app/). Clean reads were mapped with STAR v2.7.11b and read counts per gene were obtained using FeatureCounts v2.1.1. Differential expression analysis was performed in R v4.2.2 using DESeq2 v1.44.0. Genes with log2FoldChange ≥0.585 or ≤−0.585 and padj <0.05 were considered differentially expressed.
Results were processed in Python v3.13.2. Three-dimensional principal component analysis was performed with scikit-learn v1.2.2 and visualized using plotly v5.15.0. The sample distance matrix was generated by calculating Euclidean distances and represented as a heatmap with seaborn v0.12.0. The volcano plot was constructed from the differential expression analysis using matplotlib v3.7.1. Differentially expressed genes were anno-tated in FungiDB (https://fungidb.org/fungidb/app/) and assigned putative functions by identifying orthologs in CandidaDB (http://www.candidagenome.org) using the pBLAST tool.
Based on functional annotation, Gene Ontology terms associated with biological processes were retrieved, and over-represented terms were visualized in enrichment plots. Finally, differentially expressed orthologous genes were depicted in a lollipop plot using matplotlib v3.7.1.
Assembly: C. auris clade IV B11243 (GCA_003014415.1
Supplementary files format and content: Tab-delimited count matrix with raw gene counts across all samples (file: all.counts42C)
Supplementary files format and content: CSV file containing DESeq2 differential expression results including log2 fold changes, p-values, and adjusted p-values (file: Deseq2_42C).

organism: Candidozyma auris

source_name: whole organism

growth_protocol: Stationary-phase cultures of Candidozyma auris clade IV strain 20-1498 in YPD at 37°C were incubated for six hours at 37°C and 42°C in YNB medium with 2% dextrose and 0.5% (NH4)2SO4.

extract_protocol:
Total RNA was extracted using the GeneJET RNA Purification Kit (Thermo Scientific; Waltham, MA, USA) following the manufacturer’s instructions. RNA quality was as-sessed by RNA integrity number (RIN). Library preparation, based on poly-A enrich-ment, and sequencing on an Illumina NovaSeq X Plus 150 platform were performed by NOVOGENE (CA, USA). Three biological replicates were sequenced per condition.
Libraries prepared with NEBNext Ultra RNA Library Prep Kit (polyA selection) and sequenced on Illumina NovaSeq (2×150 bp).

value: whole organism

value: wild type

value: Stationary-phase cells grown in YPD medium at 37°C were subsequently cultured for six hours in YNB medium supplemented with 2% dextrose and 0.5% (NH4)2SO4 at 42°C.


title: 02-T-KPT9274-C

value: 28d post-tx


title: RNA-Seq of C. auris strain 20-1498 at 42C Rep2 R1

description:
Library name: Candidozyma_auris_42C_Rep2_R1
Sample D2 corresponds to 42°C, replicate 2


title: Control, time 04h, Individual 01, replicate 2

description: Library name: 04h_R2


title: RNA-Seq of C. auris strain 20-1498 at 42C Rep1 R1

description:
Library name: Candidozyma_auris_42C_Rep1_R1
Sample D1 corresponds to 42°C, replicate 1


title: ICP1 preadipocytes, transfected with pCMV-myc-KLF2, 48 h, rep 2

city: Shihezi

first: Zhiwei

state: Xinjiang

address: A101-3,Xing 3 Building

department: Histology and Embryology

institute: Shihezi University

description: Library name: KLF2_2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step,  clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et  al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts  representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: ftp://ftp.ensembl.org/pub/release-109/fasta/gallus_gallus/dna/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.toplevel.fa.gz
Supplementary files format and content: xls file contained FPKM values for each sample

organism: Gallus gallus

growth_protocol: chicken IPC1 cells were cultured in DMEM/F12 (Gibco, Grand Island, NY) supplemented with 10% FBS (#C04001, Viva Cell Biosciences, Shanghai, China) at 37 °C and 5% CO2

extract_protocol:
After the transfection for 48 h, the ICP1 cells were harvested using TRIzol™ Reagent (#15596026, Invitrogen, Carlsbad, CA) for subsequent RNA sequencing. The RNA-seq library preparation, sequencing and data analysis were conducted by Novogene Corporation (Beijing, China). The cellular constituents within an individual well of the cell culture plate were considered a biological replicate. Each experimental outcome comprises three biological replicates.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The ICP1 cells were inoculated into 6-well plates, and when the cells reached 60%-80% confluence, the given plasmids were transfected into the cells using ExFect® Transfection Reagent (#T101-02, Vazyme, Nanjing, China).

value: preadipocytes

value: KLF2 overexpression


title: ICP1 preadipocytes, transfected with pCMV-myc-KLF2, 48 h, rep 3

description: Library name: KLF2_3


title: ICP1 preadipocytes, transfected with pCMV-myc-KLF2, 48 h, rep 1

description: Library name: KLF2_1


title: RNA-Seq of C. auris strain 20-1498 at 37C Rep3 R1

description:
Library name: Candidozyma_auris_37C_Rep3_R1
Sample A3 corresponds to 37°C, replicate 3

value: Stationary-phase cells grown in YPD medium at 37°C were subsequently cultured for six hours in YNB medium supplemented with 2% dextrose and 0.5% (NH4)2SO4 at 37°C.


title: 01-T-KPT9274-D

value: Relapse

value: Y


title: RNA-Seq of C. auris strain 20-1498 at 37C Rep2 R1

description:
Library name: Candidozyma_auris_37C_Rep2_R1
Sample A2 corresponds to 37°C, replicate 2


title: Electrode implanted cochlea,  scRNAseq

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description:
Library name: EL
10X Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced on a Nextseq2000 instrument (Illumina, San Diego, CA, United States) reads were subsequently processed using 10x Genomics CellRanger analytical pipeline using default settings and 10x Genomics downloadable mm10 genome.
Quality control was conducted using the following parameters: nFeature_RNA >900 & nFeature_RNA <5000 & percent.mt <15. Doublet detection was conducted with scDblFinder using the default parameters without clustering information. The raw gene expression matrix was normalized using the scTransform function in Seurat, and the P1 and P30 datasets were integrated after batch correction using the reciprocal principal component analysis (RPCA) method.
Assembly: GRCm38
Supplementary files format and content: Tab-separated tables and matrix files

source_name: cochlea; Cd11b+ cells

extract_protocol:
Inner ears from a total of four P1 mice and four P30 mice were collected. The SV was micro-dissected from the spiral ligament and lysed in either 0.5 mg/ml trypsin at 37°C for 7 min for P1 tissue, or 400-600 units/mL accutase at 37°C for 25 min for P30 tissue. Media was gently replaced with 5% FBS in DMEM to stop lysis, and the tissue was triturated and then filtered using a 20 µm filter (pluriSelect Life Science, El Cajon, CA, United States), and the cells were kept on ice for 35 min. The cell pellet was then suspended in 50 µL of the filtered media and cell counts were performed using a Luna automated cell counter (Logos Biosystems, Annandale, VA, United States). A cell density of 1 x 106 cells/ml was used to load onto the 10X genomics chip.
Library preparation was performed according to the instructions in the 10x Genomics Chromium Single Cell 3’ Chip Kit V2.

value: cochlea; Cd11b+ cells

tag: strain

tag: Sex

value: pooled male and female

value: CX3CR1+/GFP Thy1+/YFP

value: Electrode implanted


title: Nuclei_MaizeLeaves_IsolatedUsingFACS_SingleFilter_Startegy_Run2

city: Gainesville

first: Kelly

last: Balmant

state: FL

address: 1253 Fifield Hall, Room 2204

department: Horticultural Sciences

institute: University of Florida

description:
Library name: Leaf_FACS_SingleFilter_Run2
Samples Leaf_FACS_SingleFIlter_Run1 and Samples Leaf_FACS_SingleFIlter_Run2 are the exctly same samples, sequenced twice

data_processing:
Demultiplexing, genome alignment, and generation of the cont matrices were performed using  CellRanger pipeline (v7, 10X Genomics)
Assembly: Zea mays genome (B73 RefGen_v5). For our analysis, we downloaded the mitochondria and chloroplast reference genomes and annotation files from Ensembl (ftp://ftp.ensemblgenomes.org/pub/plants/release-42) and concatenated both to the B73v5 genome.
Supplementary files format and content: h5

organism: Zea mays

source_name: 4th fully extended leaf from V5 stage plants

extract_protocol:
After nuclei isolation following Conde et al (2021), we used a FACS strategy for clean-up and enrichment of the nuclei using a BD FACSAriaTM IIU/III upgraded cell sorter. We used a double-filter strategy to negatively select autofluorescent chloroplast and positively select DAPI-stained nuclei (Fig 1). The Peridinin-Chlorophyll-Protein (PerCP) filter, excited by the 488 nm blue laser and captured with a 670/30 nm bandpass filter, was used to remove the events that emitted in this range. After this, the DAPI-positive population was selected according to emission in the 450/50 nm bandpass filter and then based on size and granularity using the forward versus side scatter (FSC vs SSC) plot. Finally, the selected population corresponding to nuclei was sorted, aiming for 40,000 nuclei for library preparation using 10X Genomics sc-RNAseq kit.
We followed the Single Cell v3.1 Dual Index Gene Expression protocol from 10x Genomics. A total of 20,000 sorted nuclei were used for cDNA synthesis and sample amplification following the manufacturer’s instructions.


title: ICP1 preadipocytes, transfected with pCMV-myc, 48 h, rep 3

description: Library name: EV_3

value: EV

value: transfected with pCMV-myc


title: CTCF ChIP-seq in WT+DS rep1

description: Library name: ChIP_3-12+DS_1_1

value: WT iMEFs

value: MEF

value: WT

value: DS3201 treatment


title: Nuclei_MaizeLeaves_IsolatedUsingFACS_SingleFilter_Startegy_Run1

description:
Library name: Leaf_FACS_SingleFilter_Run1
Samples Leaf_FACS_SingleFIlter_Run1 and Samples Leaf_FACS_SingleFIlter_Run2 are the exctly same samples, sequenced twice

value: 4th fully extended leaf from V5 stage plants


title: RNA-Seq of C. auris strain 20-1498 at 37C Rep1 R1

description:
Library name: Candidozyma_auris_37C_Rep1_R1
Sample A1 corresponds to 37°C, replicate 1

value: whole organism

value: wild type


title: Nuclei_MaizeLeaves_IsolatedUsingFACS_DoubleFilter_Startegy

description: Library name: Leaf_FACS_DoubleFilter


title: pREC8-SCC1 rec8 chip rep 2

status: Public on Jul 16 2025

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
GSM1695735
pREC8-SCC1-99-101-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009).Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) (for single-end data) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Axis sites (Red1 summits in wild type conditions) were identified using MACS2 narrow and -log10 qvalue of 20.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph
Supplementary_files_format_and_content: bed

organism: Saccharomyces cerevisiae

source_name: pREC8-SCC1 rec8 chip rep 2

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles.
Library preparation was performed using Illumina TruSeq DNA Sample Prep Kits v1 but adaptors were used at 1:20 dilution. Amplified ChIP DNA between 300 and 500bp was gel purified on 1.8% agarose gel. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 51 bp single-end or paired-end reads.

tag: meiotic time point

value: 3 hour


title: Control, time 0h, Individual 01, replicate 1

description: Library name: 0h_R1

value: peripheral blood mononuclear cells

value: Healthy Individual

value: PBMC

value: control

value: Before vitamin D bolus intake


title: pREC8-SCC1 rec8 input rep 2

description:
GSM1695733
pREC8-SCC1-99-101-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: pREC8-SCC1 rec8 input rep 2


title: 01-T-KPT9274-A

value: Baseline

value: Y


title: ICP1 preadipocytes, transfected with pCMV-myc, 48 h, rep 2

description: Library name: EV_2

value: preadipocytes

value: EV


title: Non-implanted cochlea,  sRNAseq

description:
Library name: NE
10X Genomics

value: cochlea; Cd11b+ cells

value: pooled male and female

value: CX3CR1+/GFP Thy1+/YFP

value: Non-implanted


title: pREC8-SCC1 rec8 chip rep 1

description:
GSM1695734
pREC8-SCC1-99-101-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: pREC8-SCC1 rec8 chip rep 1

tag: antibody


title: ICP1 preadipocytes, transfected with pCMV-myc, 48 h, rep 1

description: Library name: EV_1

value: transfected with pCMV-myc


title: REC8-HA3 input rep 2

description:
GSM1695723
Rec8-wildtype-50-75-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: REC8-HA3 input rep 2


title: 02-T-KPT9274-B

value: 7d post-tx


title: REC8-HA3 chip rep 1

description:
GSM1695724
Rec8-wildtype-50-75-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: REC8-HA3 chip rep 1

value: anti-HA


title: pREC8-SCC1 rec8 input rep 1

description:
GSM1695732
pREC8-SCC1-99-101-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: pREC8-SCC1 rec8 input rep 1

value: 3 hour


title: rec8D anti-Red1 rep4

description: Red1-rec8D-39-62-193-90-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D anti-Red1 rep5


title: rec8D input for Red1 rep4

source_name: rec8D input for Red1 rep5


title: rec8D anti-Red1 rep3

description:
GSM2320255
Red1-rec8D-39-62-193-90-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D anti-Red1 rep4


title: REC8-HA3 input rep 1

description:
GSM1695722
Rec8-wildtype-50-75-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: REC8-HA3 input rep 1


title: 02-T-KPT9274-A

source_name: PBMCs


title: rec8D input for Red1 rep3

description:
GSM2320253
Red1-rec8D-39-62-193-90-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D input for Red1 rep4


title: rec8D anti-Red1 rep2

description:
GSM1695731
Red1-rec8D-39-62-193-90-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D anti-Red1 rep3


title: rec8D input for Red1 rep1

description:
GSM1695728
Red1-rec8D-39-62-193-90-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D input for Red1 rep2


title: rec8D input for Red1 rep2

description:
GSM1695729
Red1-rec8D-39-62-193-90-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D input for Red1 rep3


title: wild type anti-Red1 rep4

description:
GSM1695719
Red1-wildtype-71-34-199-29-Reps-SK1Yue-PM_B3W3_MACS2_over20_summits.bed

source_name: wild type anti-Red1 rep4


title: wild type input for Red1 rep4

description:
GSM1695717
Red1-wildtype-71-34-199-29-Reps-SK1Yue-PM_B3W3_MACS2_over20_summits.bed

source_name: wild type input for Red1 rep4


title: wild type anti-Red1 rep3

description:
Red1-wildtype-29-34-199-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph
Red1-wildtype-71-34-199-29-Reps-SK1Yue-PM_B3W3_MACS2_over20_summits.bed

source_name: wild type anti-Red1 rep3


title: wild type anti-Red1 replicate 2

source_name: wild type anti-Red1 rep2


title: wild type input for Red1 rep3

source_name: wild type input for Red1 rep3


title: wild type anti-Red1 replicate 1

description:
GSM1695718
Red1-wildtype-29-34-199-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph
Red1-wildtype-71-34-199-29-Reps-SK1Yue-PM_B3W3_MACS2_over20_summits.bed

source_name: wild type anti-Red1 rep1


title: REC8-HA3 chip rep 2

description:
GSM1695725
Rec8-wildtype-50-75-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: REC8-HA3 chip rep 2


title: wild type input for Red1 rep1

description:
GSM1695716
Red1-wildtype-29-34-199-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph
Red1-wildtype-71-34-199-29-Reps-SK1Yue-PM_B3W3_MACS2_over20_summits.bed

source_name: wild type input for Red1 rep1


title: no tag control spo11D resonicated input

description: AH9041I-031517-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: no tag control spo11D resonicated input


title: no tag control spo11D resonicated anti-PK9


title: SMC4-PK9 spo11D resonicated input

description: AH8920I-031517-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SMC4-PK9 spo11D resonicated input


title: SMC4-PK9 spo11-Y135F resonicated anti-PK9 rep1

description: AH8630I-168-763-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph


title: SMC4-PK9 spo11-Y135F resonicated input rep1


title: rec8D resonicated anti-PK9 rep2

description: AH8428I-166-324-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D resonicated anti-PK9 rep2


title: SMC4-PK9 spo11D resonicated anti-PK9

source_name: SMC4-PK9 spo11D resonicated anti-PK9


title: 01-T-KPT9274-C

source_name: PBMCs

value: 28d post-tx


title: rec8D resonicated anti-PK9 rep1

source_name: rec8D resonicated anti-PK9 rep1


title: spo11-Y135F resonicated anti-PK9 rep1

description: AH8643I-170-765-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: spo11-Y135F resonicated anti-PK9 rep1


title: rec8D resonicated input rep1

source_name: rec8D resonicated input rep1


title: SMC4-PK9 rec8D resonicated anti-PK9 rep2

description: AH7660I-164-330-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph


title: spo11-Y135F resonicated input rep1

source_name: spo11-Y135F resonicated input rep1


title: SMC4-PK9 rec8D resonicated input rep2

source_name: SMC4-PK9 rec8D resonicated input rep2


title: rec8D resonicated input rep2

source_name: rec8D resonicated input rep2


title: SMC4-PK9 rec8D resonicated anti-PK9 rep1


title: SMC4-PK9 rec8D resonicated input rep1

source_name: SMC4-PK9 rec8D resonicated input rep1


title: rec8D anti-Red1 rep1

description:
GSM1695730
Red1-rec8D-39-62-193-90-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D anti-Red1 rep2


title: wild type resonication anti-PK9 rep1

description: AH7797I-148-185-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: wild type resonication anti-PK9 rep1


title: wild type resonication input rep1

source_name: wild type resonication input rep1


title: 01-T-KPT9274-B


title: SMC4-PK9 resonication anti-PK9 rep2

description: AH6408I-144-183-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SMC4-PK9 resonication anti-PK9 rep2


title: SMC4-PK9 resonication input rep2

source_name: SMC4-PK9 resonication input rep2


title: SMC4-PK9 resonication anti-PK9 rep1

source_name: SMC4-PK9 resonication anti-PK9 rep1


title: SMC4-PK9 anti-PK9 no resonication rep3

description: AH6408-3h-notreson-PK9-28-37-77-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SMC4-PK9 anti-PK9 no resonication rep3


title: no tag control anti-PK9 no resonication

description: AH7797B-v5-140401-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: no tag control anti-PK9 no resonication


title: no tag control input no resonication

source_name: no tag control input no resonication


title: SMC4-PK9 resonication input rep1

source_name: SMC4-PK9 resonication input rep1


title: SMC4-PK9 input no resonication rep3

source_name: SMC4-PK9 input no resonication rep3


title: SMC4-PK9 input no resonication rep1

description:
AH6408-3h-notreson-PK9-28-37-77-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph
Red1-wildtype-71-34-199-29-Reps-SK1Yue-PM_B3W3_MACS2_over20_summits.bed
Red1-wildtype-29-34-199-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SMC4-PK9 input no resonication rep1


title: SMC4-PK9 input no resonication rep2

source_name: SMC4-PK9 input no resonication rep2


title: rec8D SCC2-HA anti-Red1 rep1

description: AH8869B-381-771-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D SCC2-HA anti-Red1 rep1


title: SMC4-PK9 anti-PK9 no resonication rep2

source_name: SMC4-PK9 anti-PK9 no resonication rep2


title: SMC4-PK9 anti-PK9 no resonication rep1

source_name: SMC4-PK9 anti-PK9 no resonication rep1


title: SCC2-3HA spo11-Y135F input rep1

description: AH8868B-397-769-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SCC2-3HA spo11-Y135F input rep1


title: SCC2-3HA spo11-Y135F anti-HA rep1

source_name: SCC2-3HA spo11-Y135F anti-HA rep1


title: PANC-1, C16_400nM, rep3, Run2

city: Toon

first: Mitsuhito

last: Koizumi

state: Ehime

address: Shitsukawa

institute: Ehime University Graduate School

description: Library name: Sample 15

data_processing:
Paired end reads (75 bp) were sequenced using the MiSeq Reagent Kit V3 150 cycles on a MiSeq system (Illumina).
Mapping to the human genome data hg38 was performed using TopHat (https://ccb.jhu.edu/software/tophat/index.shtml) and sequence reads were assigned to genomic features using feature counts.
The differential expression analysis tool, TCC (Bioconductor. org), was used to normalize each sample before determining the differences in expression using the tmm package in R (https://www.r-project.org/).
Assembly: hg38
Supplementary files format and content: CSV files include TMM values for each sample

source_name: cell line

growth_protocol: PANC-1 and MIA PaCa-2 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin. Cells were incubated in a 37 ℃ humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from PANC-1 cells using TRIzol reagent (Thermo Fisher Scientific).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit from Illumina, the NEBNext Poly(A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos from Illumina (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: RNA was collected from PANC-1 cells 72 hours after transfection with control, PKR siRNA 1, or PKR siRNA 2, and 72 hours after treatment with DMSO or C16.

value: cell line

value: epithelial


title: wild type resonication anti-PK9 rep2

source_name: wild type resonication anti-PK9 rep2


title: PANC-1, C16_800nM, rep2, Run2

description: Library name: Sample 17


title: PANC-1, C16_800nM, rep3, Run2

description: Library name: Sample 18


title: SCC2-3HA input rep1

description: AH8867B-379-767-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SCC2-3HA input rep1


title: PANC-1, C16_800nM, rep1, Run2

description: Library name: Sample 16


title: wild type resonication input rep2

source_name: wild type resonication input rep2


title: PANC-1, C16_400nM, rep2, Run2

description: Library name: Sample 14


title: PANC-1, DMSO, rep3, Run2

description: Library name: Sample 12


title: PANC-1, DMSO, rep1, Run2

description: Library name: Sample 10


title: PANC-1, C16_400nM, rep1, Run2

description: Library name: Sample 13


title: PANC-1, PKR siRNA 2, rep3, Run1

description: Library name: Sample 9


title: PANC-1, PKR siRNA 2, rep2, Run1

description: Library name: Sample 8


title: PANC-1, DMSO, rep2, Run2

description: Library name: Sample 11


title: PANC-1, PKR siRNA 1, rep2, Run1

description: Library name: Sample 5


title: PANC-1, PKR siRNA 2, rep1, Run1

description: Library name: Sample 7


title: PANC-1, PKR siRNA 1, rep3, Run1

description: Library name: Sample 6


title: rec8D SCC2-HA input rep1

source_name: rec8D SCC2-HA input rep1


title: PANC-1, PKR siRNA 1, rep1, Run1

description: Library name: Sample 4


title: PANC-1, Control siRNA, rep1, Run1

description: Library name: Sample 1


title: SCC2-3HA anti-HA rep1

source_name: SCC2-3HA anti-HA rep1


title: PANC-1, Control siRNA, rep3, Run1

description: Library name: Sample 3


title: Mediastinal Liposarcoma, WDLPS, sample 03

city: Kobe

first: Suguru

last: Mitsui

state: Hyogoken

institute: Kobe University Graduate School of Medicine School of Medicine: Kobe Daigaku Daigakuin Igakukei Kenkyuka Igakubu

description: Library name: MLPS_03

data_processing:
Transcript-level quantification data (TPM) and gene-level raw counts were generated and provided as processed data files.
Assembly: GRCh38
Supplementary files format and content: Two CSV files are included: one with TPM values, and one with raw gene-level counts. Each file contains five samples (columns) and gene rows.

source_name: mediastinal tumor tissue

growth_protocol: Not applicable.

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor tissue using a standard protocol. Specific kit information was not specified in the manuscript.
RNA-seq libraries were constructed following the standard protocol and sequenced using the Illumina NovaSeq 6000 platform.

treatment_protocol: All samples were obtained from patients who underwent surgical resection without preoperative therapy.

value: mediastinal tumor tissue

tag: disease

value: liposarcoma

tag: histology

value: WDLPS

value: male

value: surgery


title: Mediastinal Liposarcoma, WDLPS, sample 04

description: Library name: MLPS_04


title: Mediastinal Liposarcoma, DDLPS, sample 02

description: Library name: MLPS_02

value: DDLPS

value: female


title: Mediastinal Liposarcoma, DDLPS, sample 01

description: Library name: MLPS_01


title: Mediastinal Liposarcoma, WDLPS, sample 05

description: Library name: MLPS_05


title: E7803019-Visit 8-AZD2423 20 mg

city: Piscataway

first: Lei Yu

last: Lei Yu

state: New Jersey

address: 145 Bevier Rd

department: Genetics

institute: Rutgers University, New Brunswick: School of Arts and Sciences

description:
Library name: AA776535-17
AA776535-17,E7803019,Visit 8,AZD2423 20 mg,56,F,56,155,23.31,WHITE,AA776535_17,CKRO220004015-1A,28,Average Pain NRS Last 12 Hours,5.4,Worst Pain NRS Last 12 Hours,6.8,30,Burning Pain,6,Burning Superfic. Spont. Pain Sub Score,6,Electric Shock Pain,6,Evoked Pain Sub Score,6,NPSI Total Score,65,Pain Attacks,3,Pain Brushing,7,Pain Pins and Needle,6,Pain Present,3,Pain Pressure,6,Pain Something Cold,5,Paresthesia/Dysesthesia Sub Score,6.5,Paroxysmal Pain Sub Score,6.5,Pressing Deep Spont. Pain Sub Score,7.5,Pressure Pain,8,Squeezing Pain,7,Stabbing Pain,7,Tingling,7,

data_processing:
Combined raw data was delivered via FTP in fast q format.
Assembly: GRCh38
Supplementary files format and content: Tab delimited files (tsv) of merged salmon quantification

source_name: blood

extract_protocol:
RNA Extraction from Paxgene tube.
GlobinClear with NEBNext Ultra II RNA (directional) with PolyA selection.

value: blood

value: painful diabetic neuropathy


title: E7805017-Visit 8-Placebo

description:
Library name: AA811766-17
AA811766-17,E7805017,Visit 8,Placebo,59,F,63,158,25.24,OTHER,AA811766_17,CKRO220002271-1A,28,Average Pain NRS Last 12 Hours,8,Worst Pain NRS Last 12 Hours,8,29,Burning Pain,9,Burning Superfic. Spont. Pain Sub Score,9,Electric Shock Pain,9,Evoked Pain Sub Score,8,NPSI Total Score,87,Pain Attacks,1,Pain Brushing,8,Pain Pins and Needle,9,Pain Present,1,Pain Pressure,8,Pain Something Cold,8,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,9,Pressing Deep Spont. Pain Sub Score,9,Pressure Pain,9,Squeezing Pain,9,Stabbing Pain,9,Tingling,9,


title: E7802013-Visit 8-Placebo

description:
Library name: AA718843-17
AA718843-17,E7802013,Visit 8,Placebo,61,M,102,169,35.71,WHITE,AA718843_17,CKRO220003968-1A,28,Average Pain NRS Last 12 Hours,5.7,Worst Pain NRS Last 12 Hours,5.7,29,Burning Pain,6,Burning Superfic. Spont. Pain Sub Score,6,Electric Shock Pain,5,Evoked Pain Sub Score,5.33,NPSI Total Score,51,Pain Attacks,2,Pain Brushing,5,Pain Pins and Needle,4,Pain Present,2,Pain Pressure,5,Pain Something Cold,6,Paresthesia/Dysesthesia Sub Score,4.5,Paroxysmal Pain Sub Score,5,Pressing Deep Spont. Pain Sub Score,5,Pressure Pain,5,Squeezing Pain,5,Stabbing Pain,5,Tingling,5,


title: E7805022-Visit 8-AZD2423 20 mg

description:
Library name: AA811764-17
AA811764-17,E7805022,Visit 8,AZD2423 20 mg,60,M,138,183,41.21,WHITE,AA811764_17,CKRO220003906-1A,28,Average Pain NRS Last 12 Hours,4.5,Worst Pain NRS Last 12 Hours,6.1,29,Burning Pain,5,Burning Superfic. Spont. Pain Sub Score,5,Electric Shock Pain,8,Evoked Pain Sub Score,4.67,NPSI Total Score,39,Pain Attacks,4,Pain Brushing,6,Pain Pins and Needle,5,Pain Present,3,Pain Pressure,4,Pain Something Cold,4,Paresthesia/Dysesthesia Sub Score,5,Paroxysmal Pain Sub Score,5,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,2,Tingling,5,


title: E7803021-Visit 8-Placebo

description:
Library name: AA776534-20
AA776534-20,E7803021,Visit 8,Placebo,56,F,97,175,31.67,BLACK OR AFRICAN AMERICAN  ,AA776534_20,CKRO220002273-1A,28,Average Pain NRS Last 12 Hours,5.5,Worst Pain NRS Last 12 Hours,6,29,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,7,Evoked Pain Sub Score,6.67,NPSI Total Score,66,Pain Attacks,2,Pain Brushing,7,Pain Pins and Needle,7,Pain Present,3,Pain Pressure,6,Pain Something Cold,7,Paresthesia/Dysesthesia Sub Score,6.5,Paroxysmal Pain Sub Score,6.5,Pressing Deep Spont. Pain Sub Score,6.5,Pressure Pain,7,Squeezing Pain,6,Stabbing Pain,6,Tingling,6,


title: E7805019-Visit 8-Placebo

description:
Library name: AA811765-20
AA811765-20,E7805019,Visit 8,Placebo,50,M,90,187,25.74,WHITE,AA811765_20,CKRO220004011-1A,28,Average Pain NRS Last 12 Hours,1.8,Worst Pain NRS Last 12 Hours,3.1,29,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,7,Evoked Pain Sub Score,3.67,NPSI Total Score,28,Pain Attacks,2,Pain Brushing,0,Pain Pins and Needle,2,Pain Present,4,Pain Pressure,5,Pain Something Cold,6,Paresthesia/Dysesthesia Sub Score,2.5,Paroxysmal Pain Sub Score,5,Pressing Deep Spont. Pain Sub Score,1,Pressure Pain,2,Squeezing Pain,0,Stabbing Pain,3,Tingling,3,


title: E7812015-Visit 8-AZD2423 20 mg

description:
Library name: AA718553-17
AA718553-17,E7812015,Visit 8,AZD2423 20 mg,34,F,111,162,42.3,WHITE,AA718553_17,CKRO220003925-1A,28,Average Pain NRS Last 12 Hours,8.1,Worst Pain NRS Last 12 Hours,8.1,30,Burning Pain,10,Burning Superfic. Spont. Pain Sub Score,10,Electric Shock Pain,7,Evoked Pain Sub Score,9,NPSI Total Score,87,Pain Attacks,3,Pain Brushing,9,Pain Pins and Needle,10,Pain Present,0,Pain Pressure,9,Pain Something Cold,9,Paresthesia/Dysesthesia Sub Score,9.5,Paroxysmal Pain Sub Score,7,Pressing Deep Spont. Pain Sub Score,8.5,Pressure Pain,9,Squeezing Pain,8,Stabbing Pain,7,Tingling,9,


title: E7812010-Visit 8-AZD2423 20 mg

description:
Library name: AA718554-17
AA718554-17,E7812010,Visit 8,AZD2423 20 mg,54,M,160,184,47.26,WHITE,AA718554_17,CKRO220004018-1A,28,Average Pain NRS Last 12 Hours,0.6,Worst Pain NRS Last 12 Hours,0.6,31,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,2,Evoked Pain Sub Score,1,NPSI Total Score,7,Pain Attacks,3,Pain Brushing,1,Pain Pins and Needle,0,Pain Present,4,Pain Pressure,1,Pain Something Cold,1,Paresthesia/Dysesthesia Sub Score,1,Paroxysmal Pain Sub Score,1,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,0,Tingling,2,


title: E7802012-Visit 8-AZD2423 150 mg

description:
Library name: AA712136-13
AA712136-13,E7802012,Visit 8,AZD2423 150 mg,49,F,80,153,34.17,OTHER,AA712136_13,CKRO220002261-1A,28,Average Pain NRS Last 12 Hours,3.7,Worst Pain NRS Last 12 Hours,4.7,29,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,5,Evoked Pain Sub Score,6.33,NPSI Total Score,63,Pain Attacks,0,Pain Brushing,9,Pain Pins and Needle,10,Pain Present,1,Pain Pressure,10,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,10,Paroxysmal Pain Sub Score,5,Pressing Deep Spont. Pain Sub Score,3.5,Pressure Pain,7,Squeezing Pain,0,Stabbing Pain,5,Tingling,10,


title: E7803021-Visit 3-Placebo

description:
Library name: AA631918-17
AA631918-17,E7803021,Visit 3,Placebo,56,F,97,175,31.67,BLACK OR AFRICAN AMERICAN  ,AA631918_17,CKRO220003887-1A,-1,Average Pain NRS Last 12 Hours,6.4,Worst Pain NRS Last 12 Hours,6.6,1,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,7,Evoked Pain Sub Score,7.67,NPSI Total Score,76,Pain Attacks,0,Pain Brushing,8,Pain Pins and Needle,7,Pain Present,1,Pain Pressure,7,Pain Something Cold,8,Paresthesia/Dysesthesia Sub Score,7.5,Paroxysmal Pain Sub Score,7.5,Pressing Deep Spont. Pain Sub Score,8,Pressure Pain,8,Squeezing Pain,8,Stabbing Pain,8,Tingling,8,


title: E7806045-Visit 8-AZD2423 20 mg

description:
Library name: AA615856-20
AA615856-20,E7806045,Visit 8,AZD2423 20 mg,72,M,94,183,28.07,WHITE,AA615856_20,CKRO220003909-1A,28,Average Pain NRS Last 12 Hours,6.2,Worst Pain NRS Last 12 Hours,8.4,29,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,6,Evoked Pain Sub Score,0,NPSI Total Score,28,Pain Attacks,3,Pain Brushing,0,Pain Pins and Needle,8,Pain Present,3,Pain Pressure,0,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,8,Paroxysmal Pain Sub Score,4.5,Pressing Deep Spont. Pain Sub Score,1.5,Pressure Pain,3,Squeezing Pain,0,Stabbing Pain,3,Tingling,8,


title: E7810013-Visit 8-Placebo

description:
Library name: AA628800-20
AA628800-20,E7810013,Visit 8,Placebo,67,M,106,165,38.93,WHITE,AA628800_20,CKRO220003950-1A,28,Average Pain NRS Last 12 Hours,8.1,Worst Pain NRS Last 12 Hours,8.8,31,Burning Pain,10,Burning Superfic. Spont. Pain Sub Score,10,Electric Shock Pain,3,Evoked Pain Sub Score,7.67,NPSI Total Score,78,Pain Attacks,1,Pain Brushing,9,Pain Pins and Needle,9,Pain Present,2,Pain Pressure,8,Pain Something Cold,6,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,5.5,Pressing Deep Spont. Pain Sub Score,8,Pressure Pain,8,Squeezing Pain,8,Stabbing Pain,8,Tingling,9,


title: E7806048-Visit 8-AZD2423 20 mg

description:
Library name: AA615855-17
AA615855-17,E7806048,Visit 8,AZD2423 20 mg,53,M,106,174,35.01,WHITE,AA615855_17,CKRO220004053-1A,28,Average Pain NRS Last 12 Hours,7,Worst Pain NRS Last 12 Hours,7,29,Burning Pain,8,Burning Superfic. Spont. Pain Sub Score,8,Electric Shock Pain,6,Evoked Pain Sub Score,7.67,NPSI Total Score,75,Pain Attacks,1,Pain Brushing,8,Pain Pins and Needle,8,Pain Present,1,Pain Pressure,8,Pain Something Cold,7,Paresthesia/Dysesthesia Sub Score,8,Paroxysmal Pain Sub Score,6.5,Pressing Deep Spont. Pain Sub Score,7.5,Pressure Pain,8,Squeezing Pain,7,Stabbing Pain,7,Tingling,8,


title: PANC-1, Control siRNA, rep2, Run1

description: Library name: Sample 2

tag: cell line

tag: cell type


title: E7806040-Visit 8-AZD2423 20 mg

description:
Library name: AA615854-20
AA615854-20,E7806040,Visit 8,AZD2423 20 mg,62,F,124,170,42.91,WHITE,AA615854_20,CKRO220003886-1A,28,Average Pain NRS Last 12 Hours,9,Worst Pain NRS Last 12 Hours,9,29,Burning Pain,9,Burning Superfic. Spont. Pain Sub Score,9,Electric Shock Pain,9,Evoked Pain Sub Score,9,NPSI Total Score,90,Pain Attacks,3,Pain Brushing,9,Pain Pins and Needle,9,Pain Present,0,Pain Pressure,9,Pain Something Cold,9,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,9,Pressing Deep Spont. Pain Sub Score,9,Pressure Pain,9,Squeezing Pain,9,Stabbing Pain,9,Tingling,9,


title: E7806059-Visit 3-Placebo

description:
Library name: AA615837-17
AA615837-17,E7806059,Visit 3,Placebo,68,F,62,152,26.84,WHITE,AA615837_17,CKRO220003913-1A,-1,Average Pain NRS Last 12 Hours,5.2,Worst Pain NRS Last 12 Hours,5.9,1,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,7,Evoked Pain Sub Score,4,NPSI Total Score,57,Pain Attacks,3,Pain Brushing,5,Pain Pins and Needle,4,Pain Present,2,Pain Pressure,4,Pain Something Cold,3,Paresthesia/Dysesthesia Sub Score,4.5,Paroxysmal Pain Sub Score,7,Pressing Deep Spont. Pain Sub Score,7.5,Pressure Pain,7,Squeezing Pain,8,Stabbing Pain,7,Tingling,5,


title: E7812010-Visit 3-AZD2423 20 mg

description:
Library name: AA566067-20
AA566067-20,E7812010,Visit 3,AZD2423 20 mg,54,M,160,184,47.26,WHITE,AA566067_20,CKRO220004006-1A,-1,Average Pain NRS Last 12 Hours,6,Worst Pain NRS Last 12 Hours,6.2,1,Burning Pain,4,Burning Superfic. Spont. Pain Sub Score,4,Electric Shock Pain,7,Evoked Pain Sub Score,6,NPSI Total Score,50,Pain Attacks,1,Pain Brushing,6,Pain Pins and Needle,6,Pain Present,0,Pain Pressure,8,Pain Something Cold,4,Paresthesia/Dysesthesia Sub Score,6,Paroxysmal Pain Sub Score,6.5,Pressing Deep Spont. Pain Sub Score,1.5,Pressure Pain,3,Squeezing Pain,0,Stabbing Pain,6,Tingling,6,


title: E7806042-Visit 8-Placebo

description:
Library name: AA615852-20
AA615852-20,E7806042,Visit 8,Placebo,52,F,123,156,50.54,OTHER,AA615852_20,CKRO220002255-1A,28,Average Pain NRS Last 12 Hours,6.7,Worst Pain NRS Last 12 Hours,6.8,28,Burning Pain,5,Burning Superfic. Spont. Pain Sub Score,5,Electric Shock Pain,8,Evoked Pain Sub Score,6.33,NPSI Total Score,70,Pain Attacks,0,Pain Brushing,6,Pain Pins and Needle,8,Pain Present,1,Pain Pressure,6,Pain Something Cold,7,Paresthesia/Dysesthesia Sub Score,8,Paroxysmal Pain Sub Score,8,Pressing Deep Spont. Pain Sub Score,7,Pressure Pain,7,Squeezing Pain,7,Stabbing Pain,8,Tingling,8,


title: E7812015-Visit 3-AZD2423 20 mg

description:
Library name: AA566066-17
AA566066-17,E7812015,Visit 3,AZD2423 20 mg,34,F,111,162,42.3,WHITE,AA566066_17,CKRO220003897-1A,-1,Average Pain NRS Last 12 Hours,7.1,Worst Pain NRS Last 12 Hours,8,1,Burning Pain,9,Burning Superfic. Spont. Pain Sub Score,9,Electric Shock Pain,10,Evoked Pain Sub Score,8.33,NPSI Total Score,79,Pain Attacks,1,Pain Brushing,9,Pain Pins and Needle,9,Pain Present,3,Pain Pressure,9,Pain Something Cold,7,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,9.5,Pressing Deep Spont. Pain Sub Score,4,Pressure Pain,8,Squeezing Pain,0,Stabbing Pain,9,Tingling,9,


title: E7805022-Visit 3-AZD2423 20 mg

description:
Library name: AA519071-20
AA519071-20,E7805022,Visit 3,AZD2423 20 mg,60,M,138,183,41.21,WHITE,AA519071_20,CKRO220004022-1A,-1,Average Pain NRS Last 12 Hours,5.6,Worst Pain NRS Last 12 Hours,7.1,1,Burning Pain,6,Burning Superfic. Spont. Pain Sub Score,6,Electric Shock Pain,7,Evoked Pain Sub Score,4.33,NPSI Total Score,39,Pain Attacks,2,Pain Brushing,4,Pain Pins and Needle,6,Pain Present,2,Pain Pressure,7,Pain Something Cold,2,Paresthesia/Dysesthesia Sub Score,5,Paroxysmal Pain Sub Score,5,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,3,Tingling,4,


title: E7813012-Visit 3-AZD2423 20 mg

description:
Library name: AA505072-17
AA505072-17,E7813012,Visit 3,AZD2423 20 mg,65,F,109,149,49.1,WHITE,AA505072_17,CKRO220003999-1A,-1,Average Pain NRS Last 12 Hours,7.6,Worst Pain NRS Last 12 Hours,7.6,1,Burning Pain,10,Burning Superfic. Spont. Pain Sub Score,10,Electric Shock Pain,10,Evoked Pain Sub Score,5.67,NPSI Total Score,73,Pain Attacks,3,Pain Brushing,6,Pain Pins and Needle,10,Pain Present,2,Pain Pressure,5,Pain Something Cold,6,Paresthesia/Dysesthesia Sub Score,10,Paroxysmal Pain Sub Score,8,Pressing Deep Spont. Pain Sub Score,5,Pressure Pain,10,Squeezing Pain,0,Stabbing Pain,6,Tingling,10,


title: E7802016-Visit 8-AZD2423 150 mg

description:
Library name: AA718842-17
AA718842-17,E7802016,Visit 8,AZD2423 150 mg,69,F,103,157,41.79,WHITE,AA718842_17,CKRO220004049-1A,28,Average Pain NRS Last 12 Hours,8.6,Worst Pain NRS Last 12 Hours,9.3,29,Burning Pain,6,Burning Superfic. Spont. Pain Sub Score,6,Electric Shock Pain,5,Evoked Pain Sub Score,1.67,NPSI Total Score,32,Pain Attacks,4,Pain Brushing,3,Pain Pins and Needle,0,Pain Present,4,Pain Pressure,1,Pain Something Cold,1,Paresthesia/Dysesthesia Sub Score,1.5,Paroxysmal Pain Sub Score,5,Pressing Deep Spont. Pain Sub Score,4,Pressure Pain,4,Squeezing Pain,4,Stabbing Pain,5,Tingling,3,


title: E7805019-Visit 3-Placebo

description:
Library name: AA519070-20
AA519070-20,E7805019,Visit 3,Placebo,50,M,90,187,25.74,WHITE,AA519070_20,CKRO220003912-1A,-1,Average Pain NRS Last 12 Hours,6.1,Worst Pain NRS Last 12 Hours,7.8,1,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,8,Evoked Pain Sub Score,2,NPSI Total Score,36,Pain Attacks,3,Pain Brushing,0,Pain Pins and Needle,7,Pain Present,4,Pain Pressure,0,Pain Something Cold,6,Paresthesia/Dysesthesia Sub Score,7,Paroxysmal Pain Sub Score,8,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,8,Tingling,7,


title: E7806035-Visit 8-AZD2423 20 mg

description:
Library name: AA468805-17
AA468805-17,E7806035,Visit 8,AZD2423 20 mg,68,M,106,178,33.46,WHITE,AA468805_17,CKRO220003880-1A,28,Average Pain NRS Last 12 Hours,4.8,Worst Pain NRS Last 12 Hours,4.8,29,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,0,Evoked Pain Sub Score,3.33,NPSI Total Score,30,Pain Attacks,4,Pain Brushing,5,Pain Pins and Needle,5,Pain Present,0,Pain Pressure,5,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,5,Paroxysmal Pain Sub Score,0,Pressing Deep Spont. Pain Sub Score,5,Pressure Pain,5,Squeezing Pain,5,Stabbing Pain,0,Tingling,5,


title: E7806055-Visit 8-Placebo

description:
Library name: AA468804-20
AA468804-20,E7806055,Visit 8,Placebo,52,M,107,178,33.77,BLACK OR AFRICAN AMERICAN  ,AA468804_20,CKRO220002257-1A,28,Average Pain NRS Last 12 Hours,3.9,Worst Pain NRS Last 12 Hours,3.9,29,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,0,Evoked Pain Sub Score,3,NPSI Total Score,21,Pain Attacks,3,Pain Brushing,4,Pain Pins and Needle,6,Pain Present,0,Pain Pressure,5,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,6,Paroxysmal Pain Sub Score,0,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,0,Tingling,6,


title: E7806029-Visit 8-AZD2423 150 mg

description:
Library name: AA468801-20
AA468801-20,E7806029,Visit 8,AZD2423 150 mg,59,M,95,178,29.98,WHITE,AA468801_20,CKRO220003974-1A,28,Average Pain NRS Last 12 Hours,5.7,Worst Pain NRS Last 12 Hours,5.8,29,Burning Pain,5,Burning Superfic. Spont. Pain Sub Score,5,Electric Shock Pain,0,Evoked Pain Sub Score,0,NPSI Total Score,25,Pain Attacks,4,Pain Brushing,0,Pain Pins and Needle,5,Pain Present,3,Pain Pressure,0,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,5,Paroxysmal Pain Sub Score,0,Pressing Deep Spont. Pain Sub Score,5,Pressure Pain,5,Squeezing Pain,5,Stabbing Pain,0,Tingling,5,


title: E7806042-Visit 3-Placebo

description:
Library name: AA468720-17
AA468720-17,E7806042,Visit 3,Placebo,52,F,123,156,50.54,OTHER,AA468720_17,CKRO220004005-1A,-1,Average Pain NRS Last 12 Hours,6.9,Worst Pain NRS Last 12 Hours,7.1,1,Burning Pain,8,Burning Superfic. Spont. Pain Sub Score,8,Electric Shock Pain,8,Evoked Pain Sub Score,8,NPSI Total Score,80,Pain Attacks,1,Pain Brushing,8,Pain Pins and Needle,8,Pain Present,1,Pain Pressure,8,Pain Something Cold,8,Paresthesia/Dysesthesia Sub Score,8,Paroxysmal Pain Sub Score,8,Pressing Deep Spont. Pain Sub Score,8,Pressure Pain,8,Squeezing Pain,8,Stabbing Pain,8,Tingling,8,


title: E7806040-Visit 3-AZD2423 20 mg

description:
Library name: AA468719-20
AA468719-20,E7806040,Visit 3,AZD2423 20 mg,62,F,124,170,42.91,WHITE,AA468719_20,CKRO220003990-1A,-1,Average Pain NRS Last 12 Hours,9,Worst Pain NRS Last 12 Hours,9,1,Burning Pain,9,Burning Superfic. Spont. Pain Sub Score,9,Electric Shock Pain,9,Evoked Pain Sub Score,9,NPSI Total Score,90,Pain Attacks,0,Pain Brushing,9,Pain Pins and Needle,9,Pain Present,0,Pain Pressure,9,Pain Something Cold,9,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,9,Pressing Deep Spont. Pain Sub Score,9,Pressure Pain,9,Squeezing Pain,9,Stabbing Pain,9,Tingling,9,


title: E7809012-Visit 8-AZD2423 20 mg

description:
Library name: AA340686-20
AA340686-20,E7809012,Visit 8,AZD2423 20 mg,56,F,115,157,46.66,BLACK OR AFRICAN AMERICAN  ,AA340686_20,CKRO220004057-1A,28,Average Pain NRS Last 12 Hours,7.9,Worst Pain NRS Last 12 Hours,8.3,31,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,4,Evoked Pain Sub Score,1.67,NPSI Total Score,29,Pain Attacks,3,Pain Brushing,0,Pain Pins and Needle,6,Pain Present,0,Pain Pressure,5,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,5.5,Paroxysmal Pain Sub Score,2,Pressing Deep Spont. Pain Sub Score,4.5,Pressure Pain,5,Squeezing Pain,4,Stabbing Pain,0,Tingling,5,


title: E7806048-Visit 3-AZD2423 20 mg

description:
Library name: AA468716-17
AA468716-17,E7806048,Visit 3,AZD2423 20 mg,53,M,106,174,35.01,WHITE,AA468716_17,CKRO220003949-1A,-1,Average Pain NRS Last 12 Hours,7,Worst Pain NRS Last 12 Hours,7,1,Burning Pain,6,Burning Superfic. Spont. Pain Sub Score,6,Electric Shock Pain,6,Evoked Pain Sub Score,3.67,NPSI Total Score,43,Pain Attacks,2,Pain Brushing,4,Pain Pins and Needle,5,Pain Present,1,Pain Pressure,2,Pain Something Cold,5,Paresthesia/Dysesthesia Sub Score,5.5,Paroxysmal Pain Sub Score,4,Pressing Deep Spont. Pain Sub Score,3.5,Pressure Pain,2,Squeezing Pain,5,Stabbing Pain,2,Tingling,6,


title: E7806050-Visit 3-AZD2423 150 mg

description:
Library name: AA468717-17
AA468717-17,E7806050,Visit 3,AZD2423 150 mg,62,F,128,165,47.02,WHITE,AA468717_17,CKRO220003948-1A,-1,Average Pain NRS Last 12 Hours,6.1,Worst Pain NRS Last 12 Hours,6.9,1,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,7,Evoked Pain Sub Score,5.33,NPSI Total Score,65,Pain Attacks,1,Pain Brushing,5,Pain Pins and Needle,7,Pain Present,0,Pain Pressure,6,Pain Something Cold,5,Paresthesia/Dysesthesia Sub Score,7,Paroxysmal Pain Sub Score,6.5,Pressing Deep Spont. Pain Sub Score,7.5,Pressure Pain,7,Squeezing Pain,8,Stabbing Pain,6,Tingling,7,


title: E7808019-Visit 3-AZD2423 150 mg

description:
Library name: AA466258-17
AA466258-17,E7808019,Visit 3,AZD2423 150 mg,55,M,105,180,32.41,WHITE,AA466258_17,CKRO220003890-1A,-1,Average Pain NRS Last 12 Hours,4.2,Worst Pain NRS Last 12 Hours,4.9,1,Burning Pain,1,Burning Superfic. Spont. Pain Sub Score,1,Electric Shock Pain,2,Evoked Pain Sub Score,1,NPSI Total Score,14,Pain Attacks,2,Pain Brushing,1,Pain Pins and Needle,2,Pain Present,2,Pain Pressure,2,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,3,Paroxysmal Pain Sub Score,1.5,Pressing Deep Spont. Pain Sub Score,0.5,Pressure Pain,1,Squeezing Pain,0,Stabbing Pain,1,Tingling,4,


title: E7808015-Visit 3-AZD2423 150 mg

description:
Library name: AA466255-20
AA466255-20,E7808015,Visit 3,AZD2423 150 mg,53,M,104,180,32.1,WHITE,AA466255_20,CKRO220004023-1A,-1,Average Pain NRS Last 12 Hours,7,Worst Pain NRS Last 12 Hours,7.3,1,Burning Pain,8,Burning Superfic. Spont. Pain Sub Score,8,Electric Shock Pain,8,Evoked Pain Sub Score,6.33,NPSI Total Score,75,Pain Attacks,1,Pain Brushing,7,Pain Pins and Needle,8,Pain Present,1,Pain Pressure,6,Pain Something Cold,6,Paresthesia/Dysesthesia Sub Score,8,Paroxysmal Pain Sub Score,8,Pressing Deep Spont. Pain Sub Score,8,Pressure Pain,8,Squeezing Pain,8,Stabbing Pain,8,Tingling,8,


title: E7802016-Visit 3-AZD2423 150 mg

description:
Library name: AA442571-17
AA442571-17,E7802016,Visit 3,AZD2423 150 mg,69,F,103,157,41.79,WHITE,AA442571_17,CKRO220003922-1A,-1,Average Pain NRS Last 12 Hours,7.9,Worst Pain NRS Last 12 Hours,8,1,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,7,Evoked Pain Sub Score,7.33,NPSI Total Score,76,Pain Attacks,2,Pain Brushing,7,Pain Pins and Needle,8,Pain Present,2,Pain Pressure,8,Pain Something Cold,7,Paresthesia/Dysesthesia Sub Score,8.5,Paroxysmal Pain Sub Score,7,Pressing Deep Spont. Pain Sub Score,8,Pressure Pain,8,Squeezing Pain,8,Stabbing Pain,7,Tingling,9,