title: RGF_organoid3_P10

city: Jinan

first: liqiang

last: guo

state: Shandong

address: No. 107, Wenhua West Road

department: Shandong University

institute: Qilu Hospital

description: Library name: RGF_org3_P10

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then 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: GRCh38
Supplementary files format and content: HISAT2 v2.0.5
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
RNA libaries were prepared for sequencing using standard Illumina protocols
RNA libraries for scRNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: kidney

value: kidney organoid

tag: genotype

value: WT


title: Cisplatin, Muscle, 11

status: Public on May 15 2025

type: SRA

city: Inashiki-gun

first: Hitomi

last: Sekine

state: Ibaraki

address: 3586, Yoshiwara, Ami-machi

department: TSUMURA Kampo Research Laboratories Kampo Research & Development Division

country: Japan

institute: TSUMURA & CO.

description:
Library name: Sample 21
cisplatin_C.28

library_source: transcriptomic

data_processing:
miRNA-seq libraries were sequenced using single reads on a NextSeq 500 system (Illumina).
Raw sequencing reads were trimmed and quality-filtered using cutadapt (version 3.7).
The trimmed reads were aligned to the mouse reference genome GRCm39 (mm39) using STAR (version 2.7.9a), and the resulting BAM files were processed using Samtools (version 1.12).
Gene-level counts were obtained by assigning reads to annotated genes using featureCounts (version 2.0.1).
FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm39 (mm39)
Supplementary files format and content: The tab-delimited text file contains either read count or FPKM data for each sample.

molecule: total RNA

organism: Mus musculus

source_name: the red regions of the gastrocnemius muscle

extract_protocol:
The miRNeasy Mini Kit (217004; Qiagen, Valencia, CA, United States) was used for miRNA extraction from red muscle of gastrocnemius muslce.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Qualities of total RNA were assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0. For library preparation, the QIAseq miRNA Library Kit (QIAGEN, 331502) was used according to the manufacturer’s instructions.

tag: tissue

tag: strain

tag: Sex

value: male

tag: treatment

value: Cisplatin


title: PSCD_PB_14

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

country: USA

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

data_processing:
Adapter and quality read trimming was performed using Skewer (version 0.2.1) and alignments were performed using SALMON (version 1.3.0) against the human primary assembly transcriptome (GRCh38 v42).
Assembly: GRCh38 v42
Supplementary files format and content: Tab-delimited text file includes raw counts.
Supplementary files format and content: Tab-delimited text file includes abundance (TPM).

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
QIAamp® RNA Blood kit (Qiagen #52304) and RNase-Free DNase Sets (Qiagen catalog 79254) were used for RNA extraction from peripheral blood samples.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq6000 at PE150. Each library was sequenced to 6G (20 million paired-end reads).

value: Whole Blood

value: Female

tag: age

tag: group

value: PSCD

tag: disease

value: Pediatric sickle cell disease

tag: scd

value: Hemoglobin SS


title: PCON_PB_1

value: Male

value: PCON

value: Healthy

value: Normal


title: Cisplatin, Muscle, 04

description:
Library name: Sample 14
cisplatin_C.09

value: the red regions of the gastrocnemius muscle


title: RGF_organoid2_P6

country: China

description: Library name: RGF_org2_P6

library_source: transcriptomic single cell

tag: cell line

tag: cell type


title: RGF_organoid1_P3

description: Library name: RGF_org1_P3


title: breast tumor P408T

type: RNA

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

hyb_protocol: protocol for miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1, Agilent Technologies)

scan_protocol: scanning protocol: AgilentG3_miRNA high-sensitivity

data_processing:
data extraction: Feature Extraction version software (v11.5.1.1, Agilent) with default parameters for miRNA (Grid: 046064_D_F_20141006)
Total gene signal for all miRNA genes on the microarrays was extracted from the Feature extraction reports, quantile normalized, and log2 transformed with the help of AgiMicroRna and Linear Models for Microarray Data (limma) R/Bioconductor software packages (v3.17). The genes detected in less than 75% of samples or having intensities less than 20 percentile were excluded from further analysis.

source_name: breast tumor

extract_protocol: Total RNA was extracted from fresh frozen tumor tissue using the TRIzol reagent (Thermo Fisher Scientific) following the manufacturer’s protocol.

value: primary tumor tissue

tag: gender

value: female


title: Cisplatin, Muscle, 03

description:
Library name: Sample 13
cisplatin_C.08


title: ISOGK treated 3

city: Hefei City

first: ZHIDAN

last: ZHANG

state: Anhui Province

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

description: Library name: ISOGK3

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HUVEC

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qisagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: HUVEC

value: ISOGK


title: breast tumor P400T

label_protocol: protocol for miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1, Agilent Technologies)


title: Cisplatin, Muscle, 02

description:
Library name: Sample 12
cisplatin_C.07


title: breast tumor P377T


title: PSCD_PB_13


title: PCON_PB_3


title: ISOGK treated 2

description: Library name: ISOGK2


title: Cisplatin, Muscle, 01

description:
Library name: Sample 11
cisplatin_C.06


title: breast tumor P611T


title: ISOGK treated 1

description: Library name: ISOGK1


title: PSCD_PB_10


title: PSCD_PB_12


title: breast tumor P421T


title: Vehicle, Muscle, 09

description:
Library name: Sample 9
vehicle_V.24

value: Vehicle


title: Vehicle, Muscle, 10

description:
Library name: Sample 10
vehicle_V.25

value: male


title: PSCD_PB_8


title: Vehicle control 2

description: Library name: DMSO2

value: DMSO


title: breast tumor P596T


title: breast tumor P539T


title: Vehicle, Muscle, 08

description:
Library name: Sample 8
vehicle_V.23


title: breast tumor P535T


title: breast tumor P420T


title: Vehicle control 3

description: Library name: DMSO3


title: PSCD_PB_9

value: Whole Blood


title: Vehicle control 1

description: Library name: DMSO1


title: PSCD_PB_11


title: PSCD_PB_6


title: Vehicle, Muscle, 07

description:
Library name: Sample 7
vehicle_V.22


title: Vehicle, Muscle, 06

description:
Library name: Sample 6
vehicle_V.21


title: PSCD_PB_5

value: Hemoglobin S ? 0 thalassemia


title: LNCaP-R1881-Vanetoclax-1

city: New York

first: Nabila

last: Zaman

state: New York

address: 1425 Madison Ave, 15-52

institute: Mount Sinai

description: 40X read

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Assembly: hg19
Supplementary files format and content: tab-delimited file containing normalized counts

source_name: Prostate

growth_protocol: Cells Cultures 10% Charcoal Stripped Serum in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Trizol and Direct-zol RNA Miniprep Kits; according to manufacturer's instruction
Illumina Stranded Total RNA Prep with Ribo-Zero Plus according to manufacturer's instruction

treatment_protocol: Venetoclax in presence or absence of R1881 TREATED  for 24 hrs in 60-70% confluent cells

value: Prostate

value: LNCaP

value: Prostate cancer Cell

value: parental LNCaP

value: 1nM R1881 + 7.7 um Venetoclax in 10% CSS  24 Hr


title: PSCD_PB_4

value: Female

value: PSCD

value: Pediatric sickle cell disease

value: Hemoglobin SS


title: Vehicle, Muscle, 05

description:
Library name: Sample 5
vehicle_V.05

value: the red regions of the gastrocnemius muscle


title: breast tumor P525T

value: primary tumor tissue

value: female


title: LNCaP-R1881-2

description: 40X read

value: 1nM R1881 + DMSO in 10% CSS  24 Hr


title: breast tumor P489T


title: PSCD_PB_2


title: Vehicle, Muscle, 04

description:
Library name: Sample 4
vehicle_V.04

value: male

value: Vehicle


title: LNCaP-R1881-1

description: 40X read


title: breast tumor Z163T


title: PSCD_PB_1

value: Whole Blood


title: PSCD_PB_7

value: Male


title: breast tumor Z161T


title: LNCaP-Venetoclax-2

description: 40X read

value: Prostate

value: 7.7 mm Venetoclax 10% CSS  24 Hr


title: Vehicle, Muscle, 02

description:
Library name: Sample 2
vehicle_V.02


title: breast tumor Z160T


title: Vehicle, Muscle, 01

description:
Library name: Sample 1
vehicle_V.01


title: hEC and hNSPC co-culture

city: Irvine

first: Lisa

middle: A

last: Flanagan

state: CA

address: 845 Health Sciences Rd

institute: University of California, Irvine

description: 10x Genomics

data_processing:
Reads were aligned to reference genome using 10x Genomics pipeline Cell Ranger count v6.0.1
Assembly: GRCh38 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: EPCs AD & SC27s

growth_protocol: Cells were plated on laminin-coated plates and cultured for 5 days before collection for scRNA-seq

extract_protocol:
Cells for single-cell RNA sequencing were prepared on the same day using the same cell sources for each condition to reduce batch effects. Cells were dissociated, resuspended in 0.4% BSA and a cell strainer was used to ensure single cells.
Library was constructed per manufacturer's protocol (10x Genomics Chromium Single Cell 3' Reagent Kit (v3.1 chemistry)

value: EPCs AD & SC27s

value: endothelial cells & neural stem/progenitor cells

value: co-culture (5hEC:1hNSPC)


title: breast tumor Z159T


title: LNCaP-Venetoclax-1

description: 40X read

value: LNCaP

value: Prostate cancer Cell

value: parental LNCaP

value: 7.7 mm Venetoclax   in 10% CSS  24 Hr


title: hNSPCs in hEC CM

description: 10x Genomics

value: neural stem/progenitor cells

value: 50% hEC CM


title: LNCaP-DMSO-2

description: 40X read

value: DMSO in 10% CSS  24 Hr


title: breast tumor P534T

value: primary tumor tissue

value: female


title: 4T1 tumors, day 28

city: Baltimore

first: Jose

last: Adrover

state: Maryland

address: 855 N Wolfe St

department: Cell Biology

institute: Johns Hopkins University

data_processing:
Single Cell sequencing data were pre-processed by cellranger 7.1.0 from 10X Genomics.
Assembly: mm10
Supplementary files format and content: "filtered_feature_bc_matrix" folder contents from cellranger outputs

source_name: Tumor

growth_protocol: Orthotopic 4T1 tumors, day 28

extract_protocol:
The tumors were digested both mechanically and enzymatically (Collagenase/Hyaluronidase, and DNaseI) and single cell suspensions of viable cells were prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.
Barcoded cDNA library was prepared as per manufacturer's instructions, 10X Genomics.

value: Tumor


title: hNSPCs media control

description: 10x Genomics

value: media control


title: LNCaP-R1881-Vanetoclax-2

description: 40X read

value: 1nM R1881 + 7.7 um Venetoclax in 10% CSS  24 Hr


title: LNCaP-DMSO-1

description: 40X read

value: Prostate


title: breast tumor Z157T


title: breast tumor Z148T


title: N2A-LaminB1-Dam IlluminaDamID1

city: St Lucia

first: Seth

last: Cheetham

state: Queensland

address: Australian Institute of Bioengineering and Nanotechnology

country: Australia

institute: University of Queensland

library_source: genomic

data_processing:
Nanopore reads were aligned to the mouse genome (mm10) or human genome (hg38) using Minimap2  with the options -a --MD --cs=long -x map-ont. Mapped reads were filtered for map quality using SAMtools view -q 10 and converted to bigwig format using deepTools bamCoverage. Short-read DamID was mapped using minimap2 44 and filtered for alignment quality using samtools view -q 10.
Lamin-associated domains were identified by binning reads from LaminB1-DamID samples into 20 kb bins using bedtools coverage. Ratios of LaminB1-Dam/(Dam+1) were calculated using awk and Lamin-associated domains called using HMMt27. Consensus LADs (between the Nanopore-DamID undiluted and 1:1/10 dilution and between the two Illumina replicates) were determined using intersectBed.
CTCF Nanopore-DamID peaks were called by first binning reads from both replicates separately into GATC fragment bins using BEDtools53 coverage. To remove bias from amplified regions of the HEK293T genome, we normalised the Nanopore DamID coverage by readcount and HEK293T Nanopore WGS coverage. The two replicates were then quantile normalised and averaged. Peaks were called on the average coverage using the DamID peak caller47 (https://github.com/owenjm/find_peaks). Peaks were only considered if they were present in both WGS-normalised and unnormalised peak sets.
Assembly: mm10 or hg38
Supplementary files format and content: Bed files containing Lamin associated domains or CTCF binding sites
Supplementary files format and content: Bigwig files containing genomic coverage
Supplementary files format and content: Bedgraph files containing CTCF average genomic coverage normalised to WGS coverage

molecule: genomic DNA

extract_protocol:
Dam fusion protein expression was induced with 2μg/mL doxycycline and genomic DNA (gDNA) was extracted from one million cells cultured in Nunc™ T75 flasks using an NEB Monarch® gDNA extraction kit according to manufacturer's instructions, with the exception of using inversion rather than vortexing for mixing.
For Nanopore-DamID 2.5μg of gDNA was dephosphorylated by the addition of 5μl of 10X NEB Cutsmart® buffer and 1μl of QuickCIP (NEB) in a total volume of 48μL. The reaction was mixed by gentle flicking and incubated at 37°C for 30 minutes. The QuickCIP was then heat inactivated at 80°C for 5 min. 2μl of DpnI (NEB) was added to the reaction, mixed by gently flicking and incubated at 37°C overnight. DNA was A-tailed by addition of 1μL 10mM dATPs and 1μL of Klenow exo- (NEB) and incubation at 37°C for 1hr. The digested DNA was purified using the Qiagen QiaQuick™ PCR Purification kit (which purifies fragments <10kb) and eluted in 60μL of H2O. The DNA was prepared for ONT sequencing with the DNA Ligation Sequencing Kit (LSK110), starting from the adaptor ligation step and using the Short Fragment Buffer. For Illumina-DamID libraries were prepared according to the protocol in Marshall et al., 2016, Nature Protocols) using the NEBnext UltraII kit for Illumina library construction.
Nanopore DamID or Illumina-DamID


title: LNCaP BCL2-OE-R1881-2

description: 40X read

treatment_protocol: R1881 TREATED  for 24 hrs in 60-70% confluent cells

value: Human BCL2 cDNA Overexpressed

value: 1nM R1881 in 10% CSS  24 Hr


title: GCU54

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v38) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCh38.p7 GENCODE r38
Supplementary files format and content: Comma-separated file with raw counts

source_name: prostate cancer

growth_protocol: LNCaP cells were transfected with siRNA against UPF1, RCOR1 or non-targeting control siRNA. At 48h post transfection, cells were treated with 5nM R1881 or vehicle (ethanol). Biological triplicates were performed for each treatment group. Cells were harvested in Trizol reagent 48h later.

extract_protocol:
RNA was extracted using Trizol reagent and purified using RNAeasy columns
RNA-Seq libraries were prepared from 500 ng total RNA by using an RNA HyperPrep Kit along with RiboErase (HMR) kit.

value: prostate cancer

value: prostate adenocarcinoma

tag: transfection

value: UPF1 siRNA


title: Vehicle, Muscle, 03

description:
Library name: Sample 3
vehicle_V.03

value: the red regions of the gastrocnemius muscle

value: male

value: Vehicle


title: N2A-Dam IlluminaDamID


title: breast tumor Z145T


title: GCR53

treatment_protocol: LNCaP cells were transfected with siRNA against UPF1, RCOR1 or non-targeting control siRNA. At 48h post transfection, cells were treated with 5nM R1881 or vehicle (ethanol). Biological triplicates were performed for each treatment group. Cells were harvested in Trizol reagent 48h later.

value: LNCaP

value: RCOR1 siRNA


title: breast tumor Z139T


title: LNCaP BCL2-OE-DMSO-2

description: 40X read

value: Prostate cancer Cell

value: DMSO in 10% CSS  24 Hr


title: GCO52

value: control siRNA


title: breast tumor Z138T

value: primary tumor tissue

value: female


title: Rag2-/-SiteI.3Pr-/-3

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

data_processing:
Raw reads were trimmed to remove Truseq adapters and bases from the 3’ end with quality scores less than 20 using cutadapt; trimmed reads shorter than 40bp were discarded. Trimmed reads were aligned to the reference genome using STAR. ENSEMBL genes were quantified using FeatureCounts.
Strand-specific enrichment tracks (bigWig) were generated by first converting the bam files to bed using bedtools bamtobed, reversing the orientation of R2 reads to match that of R1. Separate bedgraph files for + and - strands were created using bedtools genomecov using the “-strand” flag, and counts were normalized to reads per billion bases in the library. Bedgraph files were converted to bigWig using UCSC tool bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigwig files were generated after converting the mm10 files to mm9

source_name: BM pro-B cells

growth_protocol: Pro-B cells were isolated from Rag2-/-SiteI.3Pr-/- BM using anti-CD19 magnetic microbeads (MACS, Miltenyi) according to the manufacturer’s instructions. B cells cultured 1x10^6 cells/ml in RPMI, glutamine (4 mM), penicillin (200 U/ml)-streptomycin (200 mg/ml), b-mercaptoenthanol (50 mM), supplemented with FCS (10% vol/vol.).   Rag2-/-SiteI.3Pr-/- pro-B cells that were cultured with IL7 and expanded in ex vivo culture for 5 days.

extract_protocol: Total RNA was prepared from Rag2-/-Site I.3Pr-/- pro-B cells. RNA was extracted using TRIzol (Life Technologies) and genomic DNA (gDNA) was eliminated using the genomic DNA wipeout buffer in the QuantiTect Reverse Transcription Kit (Qiagen). RNA was purified using with the RNeasy Kit (Qiagen), ribosomal RNA was eliminated using the Ribo-Zero Magnetic Gold Kit (Illumina), processed with the NEBNext Ultra Directional RNA Library Prep Kit (Illumina) and sequenced on the Illumina HiSeq system.

value: BM derived  Rag2-/-SiteI.3Pr-/- pro-B cells

value: ex vivo IL7 expansion  5 days


title: Rag2-/-SiteI.3Pr-/-2


title: GCR50


title: GCU51


title: breast tumor Z069T


title: breast tumor Z042T


title: Rag2-/-SiteI.3Pr-/-1


title: LNCaP CONT PLVX-R1881-2

description: 40X read

value: Prostate

value: WT-Empty Vector


title: GCO49

value: prostate cancer


title: LNCaP CONT PLVX-DMSO-2

description: 40X read


title: N2A-LaminB1-Dam IlluminaDamID2


title: breast tumor M389T


title: hECs media control

description: 10x Genomics

source_name: EPCs AD

value: EPCs AD

value: endothelial cells

value: media control


title: GCR47

value: prostate adenocarcinoma


title: breast tumor M315T


title: LNCaP BCL2-OE-R1881-1

description: 40X read

value: Human BCL2 cDNA Overexpressed

value: 1nM R1881 in 10% CSS  24 Hr


title: breast tumor M318T


title: GCU48

value: LNCaP

value: UPF1 siRNA


title: LNCaP CONT PLVX-DMSO-1

description: 40X read

value: Prostate cancer Cell

value: DMSO in 10% CSS  24 Hr


title: breast tumor M250T

value: primary tumor tissue


title: LNCaP BCL2-OE-FBS2

description: 40X read

growth_protocol: Cells Cultures in 10% Fetal Bovine Serum or 10% Charcoal Stripped Serum in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Cultured Medium Supplemented with 10% FBS or CSS (Charcoal Stripped Serum)

value: 10% FBS 28 days


title: LNCaP BCL2-OE-CSS2

description: 40X read

value: 10% CSS 28 days


title: LNCaP CONT PLVX-R1881-1

description: 40X read


title: GCO46

value: control siRNA


title: LNCaP BCL2-OE-DMSO-1

description: 40X read

value: Prostate


title: LNCaP BCL2-OE-FBS1

description: 40X read


title: GCR44

value: vehicle

value: RCOR1 siRNA


title: GCU45

value: prostate cancer


title: breast tumor M098T

value: female


title: Wild type Brain, biological rep3

city: Taipei

first: Keng-Mao

last: Liao

state: Taipei

address: Rm. 521-1, 5F., No.1, Changde St., Zhongzheng Dist

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from wild type mice brain

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Mouse Genome 430_2 GeneChip (Affymetrix). GeneChips were then washed, stained and read by Affymetrix GeneChip Scanner 3000 7G

scan_protocol: GeneChips were read by Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GeneSpring GX 14.8 (Sillicon Genetics) and GC-RMA was used as normalization method.

label: biotin

source_name: Brain from wild type mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Standard housing conditions; mice sacrificed on the 14th day post-birth

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

treatment_protocol: No special treatment; mice sacrificed on the 14th day post-birth, and the brain was extracted for analysis

value: Brain

value: Wild type


title: LNCaP BCL2-OE-CSS1

description: 40X read

value: Human BCL2 cDNA Overexpressed


title: breast tumor P494T


title: Wild type Brain, biological rep1


title: Wild type Brain, biological rep2


title: breast tumor P049T


title: LNCaP CONT plvx-FBS2

description: 40X read

value: WT-Empty Vector


title: GCU42

value: LNCaP

value: prostate adenocarcinoma


title: breast tumor P021T


title: Knock out Brain, biological rep2

description: Gene expression data from knockout mice brain

source_name: Brain from knockout mice

value: miR-137 KO


title: Knock out Brain, biological rep1


title: Wild type liver, biological rep2

source_name: Liver from wild type mice

treatment_protocol: No special treatment; mice sacrificed on the 14th day post-birth, and the liver was extracted for analysis

value: Liver

value: WT


title: Wild type liver, biological rep1


title: Wild type liver, biological rep3


title: GCR38


title: GCO43


title: Knock out Brain, biological rep3


title: GCR41


title: LNCaP CONT plvx-css2

description: 40X read

value: Prostate cancer Cell


title: LNCaP CONT plvx-FBS1

description: 40X read

value: 10% FBS 28 days


title: breast tumor Z168T

value: primary tumor tissue


title: GCO40

value: control siRNA


title: breast tumor Z188T


title: GCU39

value: vehicle

value: UPF1 siRNA


title: A transgenic line of Arabidopsis thaliana, pCORTEX:GFP

city: Blacksburg

first: Song

last: Li

state: Virginia

address: 1880 Pratt Drive Blacksburg

department: School of Plant and Environmental Sciences

institute: Virginia Tech

description:
Library name: CORTEX
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v7.1.0
Assembly: Arabidopsis thaliana Col-0
Supplementary files format and content: Seurat object and Hierarchical Data Formats h5 file

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Sample preparation for scRNA-seq was performed as described (Ryu at al., 2019). Arabidopsis thaliana seeds were surface sterilized using a 30% (v/v) bleach, 0.1% (v/v) Triton X-100 solution for 10 min and incubated on Murashige and Skoog (MS) growth media covered with 100/47 mm mesh. The square dishes are oriented vertically and incubated under continuous light condition at 22°C for 4~5 days after gemination (~ 2-2.5cm long roots). At 4~5 d after germination, the primary root tips were cut 1/3 from root tips and put them into a 35mm petri dish containing a 70um strainer and 4 mL enzyme solution (1.25% [w/v] Cellulase [“ONOZUKA” R-10, Yakult], 0.1%[w/v] Pectolyase [P-3026, Sigma-Aldrich], 0.4 M Mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin). The sample was incubated on the orbital shaker at 85 rpm for 1 hour at 25°C. After incubation, the protoplast solution was filtered through a 70μm filter, and then through a 40μm filter twice in 50ml conical tubes. The filtered solution was centrifuged at 500g for 10 min at 22°C using a swinging bucket rotor and discard supernatant. The protoplasts were resuspended using 500μL Solution A (0.4 M Mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin) and transferred to a 2ml round bottom tube. After centrifugation at 200g for 6 min, the pelleted protoplasts resuspended with 30–50 μL Solution A to achieve the desired cell concentration (~1,000 protoplasts/μL) after cell counting.
The protoplasts were loaded into Chromium microfluidic chips (Next GEM Single Cell 3’ kit) and barcoded with a 10X Chromium Controller (10X Genomics). The mRNA from barcoded cells was then reverse-transcribed, and sequencing libraries were prepared using reagents from a Chromium Single Cell 3’ v3.1 reagent kit (10X Genomics) following the manufacturer’s guidelines. The cDNA and final library quality were confirmed using a Bioanalyzer (Agilent). Sequencing was performed with Illumina NovaSeq 6000 according to the manufacturer’s instructions.

value: Root

value: various cell types in root

value: Diploid

value: transgenic line

tag: batch


title: A transgenic line of Arabidopsis thaliana, pSCR:GFP

description:
Library name: SCR
10X Genomics


title: breast tumor Z183T

value: female


title: breast tumor Z187T


title: A transgenic line of Arabidopsis thaliana, pWER:GFP

description:
Library name: WER
10X Genomics


title: LNCaP CONT plvx-css1

description: 40X read

value: Prostate

value: WT-Empty Vector

value: 10% CSS 28 days


title: Knock out liver, biological rep3

source_name: Liver from knockout mice

value: miR-137 knockout


title: breast tumor Z265T


title: CUT&RUN of CD34+ HSPCs at day11 of erythroid differentiation: BRD4 CUT&RUN replicate2

city: Ann Arbor

first: Kaiwen

last: Deng

state: Michigan

address: 3305 NCRC Building 520

institute: University of Michigan

description: CUT&RUN was performed using 1 million nuclei with spefic antibodies(1:100 dilute); library was prepared with NEBNext UltraII DNA Library Prep Kit for Illumina

data_processing:
The BRD4 CNR datasets were processed using the CUT&RUNTools (https://bitbucket.org/qzhudfci/cutruntools/src) using the default trimming and alignment settings
Paired-end sequencing reads were first trimmed with Trimmomatic to remove adaptor and low-quality sequences using the parameters ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25, where the “Truseq3.PE.fa” are the adapters provided by the tool.
Reads were aligned to the reference human genome hg38 assembly with bowtie2
Alignment results were recorded in BAM files and sorted, indexed, marked duplications with Picard MarkDuplicate function, and filtered with SAMtools to discard unmapped reads (-f 3 -F 4 -F 8). Fragments of sizes less than 120 bp were kept for downstream analysis.
MACS2 version 2.1.4 was used to call peaks from the BAM files with narrowPeak setting, q-value cutoff of 0.01, and with --SPMR which normalizes the signal intensity
Assembly: GRCh38
Supplementary files format and content: bigWig files (.bw) storing the normalized pile-ups of the reads
Supplementary files format and content: narrow peak files (.narrowPeak) storing the peaks called by MACS2
Library strategy: CUT&RUN

source_name: not applicable

extract_protocol:
PB-CD34+ HSPCs were differentiated in a standard 3-phase erythroid differentiation culture for 11 days before collection for CUT&RUN. CUT&RUN experiments were carried out as described (Skene PJ, et al. Nat Protoc. 2018) with minor modiﬁcations. Brieﬂy, nuclei from 106 cells were isolated from cells at day11 of differentiation and conjugated to Concanavalin A-coated magnetic beads. The nuclei:bead slurry was incubated with primary antibody (BRD4 or IgG) at 4°C overnight. Protein A/G-MNase (Epicypher) was incubated according to manufacturer’s instructions for 2 hours at 4°C and subsequently activated by CaCl2 at 0°C. After MNase digestion for 2 hours, the reaction was terminated by adding an equal volume of STOP buffer (170 mM NaCl, 20 mM EGTA, 0.05% Digitonin, 50 µg/mL RNase A and 25 µg/mL glycogen). The protein-DNA complexes were released by incubation at 37°C for 30 minutes. After proteinase K digestion at 55°C for 1 hour, the samples were then subjected to DNA purification by phenol-chloroform extraction.
Library preparation was performed following a modified protocol for TF-targeted short fragments using NEBNext Ultra II DNA Library Prep Kit as described (Liu N, et al. Cell. 2018). Brieﬂy, the dA-tailing reaction was modified to 50 °C for 1 hr. After adaptor ligation, 1.75 x volume of size-selection beads was added to increase the recovery of short fragments. DNA was then PCR amplified for 12 cycles with reduced amount of universal and individual index primers. After PCR ampliﬁcation, size selection of 160-350 bp fragments was carried out by sequentially adding 0.6 x and 0.6 x volume of beads. The quantity and size distribution of DNA in the libraries was measured using a Qubit ﬂuorometer and Bioanalyzer, respectively. Libraries were sequenced on the Illumina Novaseq (S4) platform by paired-end sequencing. All experiments were carried out in independent duplicates from 2 different CD34+ cell donors.

value: not applicable

value: PB-CD34+ HSPC at day11 of erythroid differentiation


title: S. Typhi treated with 2 µg/ml rifmapin (RIF). Exp3.

city: Ithaca

first: Jeongmin

last: Song

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

description: Library name: RIF_2ugml_3

data_processing:
The pooled library was sequenced with the MinION Flow cell (R9.4.1) using MinKNOW v21.06.0 (ONT). The raw reads were base called, filtered (minimum q score > 7), de-barcoded, and aligned with ISP2825 CDS sequences using Guppy v5.0.11 (ONT, RRID: SCR_023196). The raw reads were normalized and analyzed with DESeq2 (α=0.01)
Supplementary files format and content: normalized_RNAseq

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: S. Typhi

extract_protocol:
S. Typhi was grown in LB overnight and 50 µl of culture was inoculated into 2 ml of 86 mM NaCl-LB containing 0.1% DMSO (control) or 2 µg/ml rifampin. When OD600nm reached 0.9-1.0, 1.5 ml of the culture was pelleted at 8,000 ×g for 2 min; the pellets were immediately resuspended in 1 ml of RNAprotect Bacteria Reagent (Qiagen, cat# 76506) and incubated for 10 min at room temperature. The bacterial pellets were stored at -80°C overnight. On the following day, total RNAs were isolated using RNeasy mini kit (Qiagen, cat# 74104) with in-column DNase digestion (Qiagen, cat# 79254).
RNA quantity and quality were evaluated using NanoDrop 2000 spectrophotometer (ThermoFisher), Qubit 4 fluorometer (ThermoFisher), and standard RNA gel electrophoresis. The following two-step bacterial rRNA depletion procedures were performed to obtain high-quality mRNA samples. First, 5 µg total RNA was treated with RNASEOUT (Invitrogen, cat# 10777019) and Terminator 5'-Phosphate-Dependent Exonuclease (Lucigen, cat# TER51020) for 1 hr at 37°C. Second, the remaining rRNA in the sample was further depleted with NEBNext® rRNA Depletion Kit for bacteria (NEB cat# E7850L). After rRNA depletion, the random-primed double-stranded cDNA (dscDNA) library was prepared with the Maxima H Minus Double-Stranded cDNA Synthesis Kit (ThermoFisher, cat# K2561). The purified dscDNA library was end-repaired (NEB, #cat E7546L) and barcoded (ONT, #cat EXP-NBD104). All the barcoded samples were pooled for adaptor ligation (AMII, part of ONT EXP-NBD104). RNAclean XP beads (Beckman Coulter, #cat A63987) and AMPure XP beads (Beckman Coulter, cat # A63880) were used at each step that requires RNA and DNA purification, respectively.

value: S. Typhi

value: WT

value: 2 µg/ml RIF


title: CUT&RUN of CD34+ HSPCs at day11 of erythroid differentiation: IgG CUT&RUN replicate2


title: breast tumor Z182T

value: primary tumor tissue


title: A transgenic line of Arabidopsis thaliana, enhancer trap PET111

description:
Library name: PET111
10X Genomics

value: enhancer trap PET111


title: CUT&RUN of CD34+ HSPCs at day11 of erythroid differentiation: BRD4 CUT&RUN replicate1


title: GCO37

value: prostate cancer

value: LNCaP

value: prostate adenocarcinoma

value: vehicle

value: control siRNA


title: Knock out liver, biological rep1

value: Liver


title: LS Precipitated withdrawal (Nal)

city: Seattle

first: Rhiana

middle: Catherine

last: Simon

state: WA

address: 1959 NE Pacific St

department: Anesthesiology & Pain Medicine

institute: University of Washington

description: 10x Genomics

data_processing:
Demultiplexing, genome alignment, and processing of gene expression matrices were carried out using CellRanger v3.1.0 (samples 1-3) / Cellranger-6.1.2 (samples 4-5)
Assembly: mm10
Library strategy: snRNA-seq

molecule: nuclear RNA

source_name: Septal complex

extract_protocol:
Each day for 3 days prior to tissue collection, all animals were habituated to the procedure room for ~2 hours to control for environmentally-induced immediate early gene activity. On the day of sacrifice, mice were sequentially euthanized with sodium pentobarbital (> 90 mg kg-1 Somnasol) and transcardially perfused with ice-cold NMDG (96 mM NMDG, 2.5 mM KCl, 1.35 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na+ ascorbate, 3 mM Na+pyruvate, 0.6 mM glutathione-ethyl-ester, 2 mM N-acetyl-cysteine, 0.5 mM CaCl2, 10 mM MgSO4; pH 7.35–7.40, 300-305 mOsm, continuously oxygenated with 95% O2 and 5% CO2). This NMDG solution was also used for tissue sectioning and for a collection bath. Both the perfusion solution and recovery bath included an inhibitor cocktail containing 500 nM TTX, 10 μM APV, 10 μM DNQX, 5 μM actinomycin, and 37.7 μM anysomycin, as described previously29. 250 μm thick coronal sections containing septum were rapidly harvested using a Leica Vibratome (VT1200). The septal complex was then rapidly microdissected, flash-frozen on powdered dry ice, and stored at -80 °C. We intended to reduce nucleus accumbens contamination as much as possible. To this end, our tissue sections primarily ranged from +1.10 mm through 0.0 mm with respect to Bregma. We also excluded the medial septum and diagonal band level to and ventral to the accumbens. Once tissue from all animals were collected and stored, we proceeded with nuclear isolation. The following steps were all performed on ice. Also note that the PBS used here was Ca2+ and Mg2+ free. For each experimental group, we pooled all mice into the same tube containing a hypertonic lysis buffer (10mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal, 0.2 U/μl Lucigen NxGen RNase inhibitor). Nuclei were extracted using a glass dounce homogenizer (DWK, #885300-0002) via 5-10 reps of pestle A and 5 reps of pestle B. Nuclei were then incubated in lysis buffer for 5 min. Next, the nuclear extract was moved into a clean tube, diluted to ~5-6 ml using a wash buffer (1X PBS, 1% BSA, 0.2 U/μl RNase inhibitor), and strained into a new 50 ml conical tube using a 40 μm cell strainer (pluriSelect, # 43-50040-51). Strained nuclei were centrifuged for 10 min, 500 x g at 4 °C. The resulting pellet was then retained. To purify our nuclei, we used density gradient centrifugation, where we prepared a two-layer column containing a 25% and 30% iodixanol (OptiPrep, Sigma-Aldrich, #D1556) gradient. Briefly, we suspended the nuclear pellet in a homogenate solution (0.25M Sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tris-HCl, pH 7.8-8.0, and 0.2 U/μl RNase inhibitor), and combined the resuspended pellet 1:1 with a 50% iodixanol solution (50% OptiPrep, 25 mM KCl, 5 mM MgCl2, 20 mM Tris-HCl, 1% BSA, 0.2 U/μl RNase inhibitor, pH 7.8-8.0) in a clean 15-ml conical tube. This creates a 25% iodixanol layer. Next, we prepare a 30% iodixanol layer (30% OptiPrep, 25 mM KCl, 5 mM MgCl2, 20 mM Tris-HCl, 1% BSA, 0.2 U/μl RNase inhibitor) and underlaid the 25% iodixanol layer with this 30% layer using a 18G needle. This density gradient column was then centrifuged for 15 min, 3000 x g at 4 °C. The resulting purified and invisible pellet was then resuspended in wash buffer. Nuclei were stained with propidium iodide and assessed for yield and quality using a disposable Neubauer hemocytometer (INCYTO, #DHC-N01) on a fluorescent microscope (Zeiss ApoTome.2). Final nuclear concentration was adjusted to 1,000 nuclei per μl in preparation for single nucleus capture.
Approximately 10,000 nuclei per experimental group were captured and single-nucleus cDNA libraries were constructed using the Chromium Single Cell 3' v3 (samples 1-3) and Chromium NextGEM platform (samples 4-5) according to manufacturer’s instructions. Libraries for samples 1-3 were sequenced using an Illumina 4400 HiSeq platform to a target output of ~ 350,000,000 reads, and libraries 4-5 were sequenced using an Illumina NovaSeq 6000 for a target output of ~350,000,000 reads

treatment_protocol: A total of 30 wildtype mice (~8 weeks) were used for single-nucleus RNA-sequencing. Animals were assigned to one of the following groups: saline (Sal; saline only), chronic morphine (Mor; escalating morphine), naloxone (Nal; escalating morphine plus naloxone), acute morphine (Mor-single; saline 13x, one dose of 10 mg kg-1 morphine) and naloxone only (Nal-no-mor; saline 13x, one dose of 1 mg kg-1 naloxone). Each experimental group included 3 male and 3 female mice that were pooled into the same reaction.

tag: brain region

value: Septal complex

value: 8 weeks

value: Brain

value: Morphine 14x, 7 days, 2x day; 1 mg/kg naloxone 1 hr following final morphine dose; collected 1 hr following final dose


title: ips_3

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

institute: Kyoto University Graduate School of Pharmaceutical Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner.

data_processing: The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

source_name: ips

label_protocol: The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

growth_protocol: Human iPSC was cultured and exposed to the chemicals for 3 days

extract_protocol: cDNA labeling was performed according to the manufacturer’s instructions.

treatment_protocol: Total RNA was extracted by spin column method and transcribed to cDNA.

value: Human iPS cells

value: ips


title: breast tumor Z267T

source_name: breast tumor

value: female


title: LS Chronic morphine (Mor)

description: 10x Genomics

value: WT

value: Morphine 14x, 7 days, 2x day, collected 1 hr following final dose


title: ips_2


title: RA100BPA20_2


title: ips_1


title: Knock out liver, biological rep2

value: miR-137 knockout


title: breast tumor Z084T

value: primary tumor tissue


title: HD_donor4_Tet1_sgRNAs

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
Library name: ESCD9_2
HD_donor4_Editor_1_sgRNAs

data_processing:
Read quality was evaluated using FastQC (v. 0.11.9). Raw reads were trimmed for adapters and low-quality tails (quality < Q20) with BBDuk (v. 38.92); moreover, the first 10 nucleotides were force-trimmed for low quality. Reads shorter than 35 bp after trimming were removed.
Trimmed reads were aligned to the human reference genome (hg38) using STAR (v. 2.7.9a). Raw gene counts were obtained in R-4.1.1 using the featureCounts function of the Rsubread R package (v. 2.8.1) and the GENCODE v44 basic gene annotation for hg38 human reference genome.
Gene counts were normalized to counts per million mapped reads (CPM) and to fragments per kilobase of exon per million mapped reads (FPKM) using the edgeR R package (v. 3.34.1); only genes with a CPM greater than 1 in at least 3 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: FPKM obtained using edgeR

source_name: Blood

growth_protocol: Cells were cultured in pre-activation medium for 48 h before electroporation and 72 h after the electroporation

extract_protocol:
Total RNA was isolated from control or edited mobilized HD or bone marrow derived-SCD HSPCs using the RNeasy Kit (QIAGEN)
RNA-seq libraries were prepared starting from 100 ng of total RNA using Watchmaker RNA kit with Polaris Depletion - rRNA/Globin (HMR) as recommended by the manufacturer.

treatment_protocol: Cells were electroporated with a combination of epigenome editors mRNA and sgRNA targeting the HBG promoters, and then cultured for 3 additional days. Cells electroporated with TE buffer only or with epigenome editors mRNA only were used as controls.

value: Blood

value: HD CD34+ HSPCs

value: HD

value: electroporated with Tet1 mRNA and -28,-115,-197 and -211 sgRNA


title: breast tumor Z256T


title: S. Typhi treated with 2 µg/ml rifmapin (RIF). Exp2.

description: Library name: RIF_2ugml_2

value: S. Typhi

value: 2 µg/ml RIF


title: 4T1 tumor, rep 4

description: Visium 10X spatial transcriptomics

data_processing: Sequencing data were processed with Space Ranger version 2.0.0 (10X Genomics).

source_name: Primary tumor

extract_protocol:
Tumors were excised 4 weeks after implantation. FFPE tissue blocks were cut down to approximately 6.5 mm x 6.5 mm in size and sectioned onto the capture areas of the Visium slide according to 10X Genomics Tissue Preparation Guide CG000408. Slides were then deparaffinized and H&E-stained according to the 10X Genomics Demonstrated Protocol CG000409 and imaged at the Animal & Tissue Imaging Core Facility at CSHL.
Visium Mouse Transcriptome Probe Kit (PN-1000365, 10X Genomics)

treatment_protocol: 4T1 tumors were orthotopically implanted into BALB/C mice. Tumors were collected 4 weeks after tumor implantation.

value: Primary tumor

value: WT, BALB/C

value: Orthotopic 4T1 tumor-bearing


title: Genomic DNA from 403H cell model

type: genomic

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

institute: National Cancer Institute

hyb_protocol: Bisulphite converted DNA (Zymo Z-96 DNA Methylation Kit Deep-Well Cat#D5004) was amplified, fragmented, and hybridized to the Human Methylation EPIC V1 Beadchip (CAT# WG-317-1003) using standard Illumina protocol

scan_protocol: Arrays are read by iScan with standard recommended Illumina scanner settings

data_processing: Data was run through the ChAMP package’s EPIC pipeline resulting in a matrix of normalized methylation beta values for further analysis

label: Cy3 and Cy5

source_name: Cell Line

label_protocol: Cy3 and Cy5

extract_protocol: gDNA was extracted using DNeasy Blood & Tissue Kit (Qiagen), according to manufacturer’s instructions.

value: Cell Line

value: IDH-mutant high grade astrocytoma patient derived cell line

value: IDH-mutant


title: 4T1 tumor, rep 3

description: Visium 10X spatial transcriptomics


title: breast tumor Z229T

data_processing:
data extraction: Feature Extraction version software (v11.5.1.1, Agilent) with default parameters for miRNA (Grid: 046064_D_F_20141006)
Total gene signal for all miRNA genes on the microarrays was extracted from the Feature extraction reports, quantile normalized, and log2 transformed with the help of AgiMicroRna and Linear Models for Microarray Data (limma) R/Bioconductor software packages (v3.17). The genes detected in less than 75% of samples or having intensities less than 20 percentile were excluded from further analysis.

extract_protocol: Total RNA was extracted from fresh frozen tumor tissue using the TRIzol reagent (Thermo Fisher Scientific) following the manufacturer’s protocol.

value: female


title: breast tumor Z223T


title: S. Typhi treated with 2 µg/ml rifmapin (RIF). Exp1.

description: Library name: RIF_2ugml_1

value: WT


title: breast tumor Z206T


title: CUT&RUN of CD34+ HSPCs at day11 of erythroid differentiation: IgG CUT&RUN replicate1

value: not applicable

value: PB-CD34+ HSPC at day11 of erythroid differentiation


title: RA500_2

value: Human iPS cells


title: RA500_3


title: S. Typhi treated with 0.1% DMSO. Exp3.

description: Library name: RIF_nontreated_3

value: 0.1% DMSO


title: S. Typhi treated with 0.1% DMSO. Exp2.

description: Library name: RIF_nontreated_2


title: breast tumor Z194T

value: primary tumor tissue


title: RA100_3


title: RA100BPA20_3


title: 4T1 tumor, rep 2

description: Visium 10X spatial transcriptomics


title: breast tumor M408T


title: RA500_1


title: S. Typhi treated with 0.1% DMSO. Exp1.

description: Library name: RIF_nontreated_1


title: breast tumor Z320T


title: SCD_donor3_Tet1_sgRNAs

description:
Library name: ESCD7_11
SCD_donor3_Editor_1_sgRNAs

source_name: Bone marrow

value: Bone marrow

value: SCD CD34+ HSPCs

value: SCD


title: LS Saline (Sal)

description: 10x Genomics

value: Septal complex

value: 8 weeks

value: Brain

value: Saline 14x, 7 days, 2x day, collected 1 hr following final dose


title: breast tumor P044T


title: Primary tumor LLC cancer cells from PAD4-DN mice, rep 2

data_processing:
Abundances were estimated using Kallisto
Assembly: GRCm39
Supplementary files format and content: TSV file. Contains estimated counts and TPM

extract_protocol: Tumors were excised and digested to single cells with Collagenase/Hyaluronidase, stained for CD45 for FACS and TdTomato+ CD45- cells were sorted for each sample. Then total RNA was extracted using a Qiagen RNeasy Plus kit, according to the manufacturer?s instructions. We then measured the concentration of the total RNA using Qubit (Thermo Fisher) and Agilent RNA 6000 Nano kit (Cat. ID: 5067-1511) to analyze its quality. Libraries were made using the Kapa mRNA Hyper prep protocol: the mRNA is captured with oligo-dT beads and then fragmented using heat and magnesium. The first cDNA strand is synthesized using random priming. Then, this step is followed by a combined second strand synthesis and A-tailing, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporates dUTP into the second cDNA strand, and adds dAMP to the 3? ends of the resulting dscDNA. The next steps are Illumina adaptor ligation and then library amplification using high-fidelity, low-bias PCR. The strand marked with dUTP is not amplified, allowing strand-specific sequencing. As starting material, we used 100 ng of total RNA in 50 ?l of DNase-free water. For fragmentation, we incubated the samples 6 minutes at 85°C (fragments of 300?400 bp). For PCR enrichment, we used 13 cycles. Quality control for the final libraries was done using Qubit (DNA HS assay) and Bioanalyzer (DNA HS assay), then we pooled the samples and checked the final library using the Kapa qPCR. Sequencing was done using the Illumina NextSeq 500/550 Mid Output Kit v2.5 (~24M single-end 75-cycles reads for each sample).

treatment_protocol: LLC tumors were subcutaneously implanted in the flank of B6 mice. Tumors were collected 4 weeks after tumor implantation.

value: Primary tumor

value: LLC cancer cells

value: Subcutaneous LLC tumor-bearing


title: breast tumor M420T

value: female


title: HD_donor4_Ctr_TE

description:
Library name: ESCD9_1
HD_donor4_Ctr_TE

value: Blood

value: HD CD34+ HSPCs

value: HD

value: electroporated with TE buffer only


title: SCD_donor3_CBP+Tet1_sgRNAs

description:
Library name: ESCD7_12
SCD_donor3_Editor_1_2_sgRNAs

value: electroporated with CBP+Tet1 mRNA and -28,-115,-197 and -211 sgRNA


title: breast tumor Z315T

value: primary tumor tissue


title: Genomic DNA from 403L cell model

value: Cell Line

value: IDH-mutant low grade astrocytoma patient derived cell line

value: IDH-mutant


title: Primary tumor LLC cancer cells from WT mice, rep 2

value: WT


title: SCD_donor3_Ctr_CBP+Tet1

description:
Library name: ESCD7_10
SCD_donor3_Editor_1_2

value: Bone marrow

value: SCD CD34+ HSPCs

value: SCD

value: electroporated with CBP+Tet1 mRNA only


title: SCD_donor2_Tet1_sgRNAs

description:
Library name: ESCD7_7
SCD_donor2_Editor_1_sgRNAs

value: electroporated with Tet1 mRNA and -28,-115,-197 and -211 sgRNA


title: 4T1 tumor, rep 1

description: Visium 10X spatial transcriptomics

value: Primary tumor

value: WT, BALB/C

value: Orthotopic 4T1 tumor-bearing


title: RA100BPA20_1

value: Human iPS cells


title: DMSO_3

source_name: DMSO

value: DMSO


title: Primary tumor LLC cancer cells from PAD4-DN mice, rep 1

value: LLC cancer cells

value: Subcutaneous LLC tumor-bearing


title: RA100_1


title: breast tumor Z297T

value: primary tumor tissue

value: female


title: BPA20_3


title: Primary tumor LLC cancer cells from WT mice, rep 1


title: RA100_2


title: DMSO_1


title: breast tumor Z303T


title: SCD_donor2_CBP+Tet1_sgRNAs

description:
Library name: ESCD7_8
SCD_donor2_Editor_1_2_sgRNAs

value: electroporated with CBP+Tet1 mRNA and -28,-115,-197 and -211 sgRNA


title: Blood neutrophils, Ly6c-low, rep 3

extract_protocol:
Blood was drawn into EDTA tubes. Blood was RBC-lysed and stained with Ly6G and Ly6C. Ly6G+ neutrophils were sorted based on their expession of Ly6C (Ly6C-high and Ly6C-low)
Kapa mRNA Hyper prep protocol

treatment_protocol: 4T1 tumors were orthotopically implanted into BALB/C mice. Blood was collected 4 weeks after tumor implantation.

value: Blood

tag: ly6c status

value: low

value: Neutrophils


title: SCD_donor2_Ctr_CBP+Tet1

description:
Library name: ESCD7_6
SCD_donor2_Editor_1_2

value: Bone marrow

value: SCD CD34+ HSPCs


title: DMSO_2


title: SCD_donor3_Ctr_TE

description:
Library name: ESCD7_9
SCD_donor3_Ctr_TE

value: SCD

value: electroporated with TE buffer only


title: PKD2_IFT88KO_org

city: Jinan

first: liqiang

last: guo

address: No. 107, Wenhua West Road

institute: Qilu Hospital

description: Library name: PKD2_IFT88KO_org

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then 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: HISAT2 v2.0.5
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney cells

extract_protocol:
RNA libaries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: kidney cells

value: Organoid

value: cilia-KO


title: Blood neutrophils, Ly6c-low, rep 2

value: WT, BALB/C

value: Orthotopic 4T1 tumor-bearing


title: BPA20_1

value: Human iPS cells


title: BPA20_2


title: PKD2_org

description: Library name: PKD2_org

value: WT


title: SCD_donor2_Ctr_TE

description:
Library name: ESCD7_5
SCD_donor2_Ctr_TE


title: SCD_donor1_CBP+Tet1_sgRNAs

description:
Library name: ESCD7_4
SCD_donor1_Editor_1_2_sgRNAs


title: Blood neutrophils, Ly6c-low, rep 1


title: PKD1_IFT88KO_org

description: Library name: PKD1_IFT88KO_org


title: SCD_donor1_Tet1_sgRNAs

description:
Library name: ESCD7_3
SCD_donor1_Editor_1_sgRNAs

value: electroporated with Tet1 mRNA and -28,-115,-197 and -211 sgRNA


title: Blood neutrophils, Ly6c-high, rep 3

value: high


title: Ref - Log phase - Rep3

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression at log-phase in Yeast Minimal Medium

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Reference Strain RNA isolate

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Both mutant and reference strain were grown overnight in 100 mL of YPD at 30℃ x 150 rpm.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Reference strain


title: Ref - Log phase - Rep2


title: breast tumor Z309T

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

institute: National Institute of Public Health

value: primary tumor tissue

value: female


title: PKD1_org

description: Library name: PKD1_org


title: Blood neutrophils, Ly6c-high, rep 2

value: Blood

value: Neutrophils


title: SCD_donor1_Ctr_TE

description:
Library name: ESCD7_1
SCD_donor1_Ctr_TE

value: Bone marrow

value: SCD CD34+ HSPCs


title: Ref - Log phase - Rep1


title: Blood neutrophils, Ly6c-high, rep 1


title: SCD_donor1_Ctr_CBP+Tet1

description:
Library name: ESCD7_2
SCD_donor1_Editor_1_2

value: SCD

value: electroporated with CBP+Tet1 mRNA only


title: IVC_Spc_TSA_wash_SCP3_1

status: Public on May 14 2025

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Raw reads were processed with Trim Galore to remove adaptor sequences and poor quality bases.
Trimmed reads were then aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters.
Picard was used to remove PCR duplicates.
Peaks were called using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: The UCSC Genome Browser utility, bedGraphToBigWig, was used to transform the bedgraph ﬁles to bigwig ﬁles
Supplementary files format and content: bigwig file for each sample

source_name: testis

extract_protocol:
Generally, spermatocytes isolated from mouse testis or NIH3T3 cells were collected, followed by ChIP-seq library preparation.
ChIP-seq libraries were prepared using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, China) according to the manufacturer’s protocol. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.

value: testis

value: spermatocyte

tag: chip antibody

value: TSA and washout


title: F3 - Log phase - Rep3

source_name: Resistant  Strain RNA isolate

value: Resistant strain


title: CON_IFT88KO_org

state: Shandong

description: Library name: CON_IFT88KO_org

value: kidney cells

value: Organoid

tag: genotype

value: cilia-KO


title: CON _org

description: Library name: CON _org

tag: tissue

value: WT


title: IVC_Spc_TSA_wash_SCP3_2


title: IVC_Spc_TSA_SCP3_1

value: TSA


title: IgG_mus_3T3

value: IgG


title: SCP3_rab_3T3


title: F3 - Log phase - Rep1


title: IVC_Spc_WT_Pol_1

value: PolII


title: IVC_Spc_WT_SCP3_2


title: F3 - Log phase - Rep2


title: IVC_Spc_WT_Pol_2


title: IVC_Spc_WT_IgG


title: IVC_Spc_a_SCP3_2


title: IVC_Spc_a_Pol_2


title: IVC_Spc_a_IgG


title: IVC_Spc_a_Pol_1


title: SCP3_HFD_Spc_2


title: IgG_16_hx_Spc_mus


title: SCP3_16_hx_Spc_2


title: SCP3_16_hx_Spc_1


title: IVC_Spc_TSA_SCP3_2


title: Pol_HFD_Spc_2


title: SCP3_HFD_Spc_1


title: gH2AX_HFD_Spc_2


title: SCP1_adult_Spc_2


title: gH2AX_HFD_Spc_1


title: SCP3_mus_3T3


title: SCP3_Scml2_KO_Spc_1


title: IVC_Spc_WT_SCP3_1


title: SCP1_adult_Spc_1


title: gH2AX_Spc_2


title: SCP3_Scml2_KO_Spc_2


title: Pol_P10_Spc_1


title: IVC_Spc_a_SCP3_1


title: Pol_adult_Spc_2


title: gH2AX_P10_Spc_1


title: gH2AX_P10_Spc_2


title: IgG_mus_adult_Spc


title: gH2AX_Spc_1


title: Pol_P10_Spc_2


title: SCP3_Spc_adult_1


title: SCP3_4wk_Rb_2


title: SCP3_4wk_Rb_1


title: Pol_HFD_Spc_1


title: SCP3_Spc_adult_2


title: SCP3_4wk_mus_2


title: IgG_mus_4wk_Spc


title: SCP3_P10_Spc_2


title: IgG_rab_4wk_Spc


title: SCP3_P10_Spc_1


title: IgG_mus_P10_Spc


title: Pol_adult_Spc_1


title: Blood neutrophil, 0h, RA replicate39

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

data_processing:
Reads were aligned to the human genome (hg38) using HISAT2 (v2.2.0)
Counts were generated using featureCounts in R (v3.6.3) profiving the hg38 GTF file (iGenomes)
Assembly: hg38
Supplementary files format and content: Raw gene counts

molecule: polyA RNA

source_name: Neutrophil

growth_protocol: Neutrophils were isolated from whole blood by centrifugation through density-gradient reagent (Ficoll-Paque). Erythrocytes were removed by hypotonic lysis with ammonium chloride buffer.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen RNAeasy cleanup including on-column DNase digest
100bp Paired-end reads

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

value: Neutrophil

value: RA


title: Blood neutrophil, 0h, RA replicate43


title: Blood neutrophil, 0h, RA replicate41


title: Blood neutrophil, 0h, RA replicate38


title: Blood neutrophil, 0h, RA replicate40


title: Blood neutrophil, 0h, RA replicate37


title: Blood neutrophil, 0h, RA replicate36


title: Blood neutrophil, 0h, RA replicate35


title: Blood neutrophil, 0h, RA replicate32


title: Blood neutrophil, 0h, RA replicate31


title: Blood neutrophil, 0h, RA replicate33


title: Blood neutrophil, 0h, RA replicate28


title: Blood neutrophil, 0h, RA replicate29


title: Blood neutrophil, 0h, RA replicate26


title: Blood neutrophil, 0h, RA replicate27


title: Blood neutrophil, 0h, RA replicate24


title: SCP3_4wk_Mus_1


title: Blood neutrophil, 0h, RA replicate22


title: Blood neutrophil, 0h, RA replicate25


title: Blood neutrophil, 0h, RA replicate23


title: Blood neutrophil, 0h, RA replicate18


title: Blood neutrophil, 0h, RA replicate42


title: Blood neutrophil, 0h, RA replicate21


title: Blood neutrophil, 0h, RA replicate19


title: Blood neutrophil, 0h, RA replicate20


title: Blood neutrophil, 0h, RA replicate17


title: Blood neutrophil, 0h, RA replicate15


title: Blood neutrophil, 0h, RA replicate34


title: Blood neutrophil, 0h, RA replicate12


title: Blood neutrophil, 0h, RA replicate16


title: Blood neutrophil, 0h, RA replicate14


title: Blood neutrophil, 0h, RA replicate13


title: Blood neutrophil, 0h, RA replicate3


title: Blood neutrophil, 0h, RA replicate11


title: Blood neutrophil, 0h, RA replicate10


title: Blood neutrophil, 0h, Healthy control replicate5

value: Healthy


title: Blood neutrophil, 0h, Healthy control replicate4


title: Blood neutrophil, 0h, RA replicate30


title: HIT2_IFN_REP5 [ATAC-Seq]

city: Nijmegen

first: Nick

last: Keur

address: Geert Grooteplein Zuid 10

department: Internal medicine

country: Netherlands

institute: Radboudumc

description:
HIT2_IFN_REP5
HUVEC_IFN_countTable.tsv

data_processing:
Quality of ATACseq reads was assessed using FASTQC, and adapters were trimmed using TrimGalore. Subsequently, reads were aligned to the human genome (GRCh38) using BWA. We excluded reads mapped to mitochondrial DNA and retaining only properly paired reads with high mapping quality (MAPQ score >10, qualified reads) using SAMTools for further analysis. Next, duplicate reads were eliminated with the Picard tools using the MarkDuplicates program and narrow peaks were called using MACS with parameters –narrow_peak, --paired_end, fdr 0.05). A peak was deemed genuine if present in a minimum of 3 biological replicates.
Assembly: GRCh38.p13
Supplementary files format and content: Count matrix
Supplementary files format and content: Bigwig

source_name: umbilical cord tissue

growth_protocol: HUVECs (lonza) were cultured in EGM-2 medium (Promocell). Experiments were executed on cells at P3.

extract_protocol:
ECs were dissociated by trypsin, and 50,000 cells were collected in PBS. A 50 µl of reaction mix containing Transposase enzyme, buffer (Illumina Tagment DNA TDE1 enzyme and buffer kit), and Digitonin (2%) (Promega) was added to the cell pellet as recommended (Corces et al., 2016). The reaction was incubated at 37 oC for 30 min with agitation at 300 rpm, before purifying with a Qiagen MinElute PCR purification kit. The transposed DNA was stored at -20 oC to wait until all samples were ready for PCR amplification.
The transposed DNA fragments were amplified for 4-6 cycles (NEBNext High-Fidelity 2X PCR Master mix), before being cleaned again with a Qiagen MinElute PCR purification kit. DNA fragments (100-1000 bp) were selected from the library by bead purifications (Agencourt AMPure XP beads, Fisher Scientific). The quantity and quality of the ATACseq libraries were calculated by Bioanalyzer (Agilent TapeStation), HS D1000. The libraries were pooled together and sequenced by BGI on the DNBSEQ platform with dual index.

treatment_protocol: HUVECs were stimulated with TNF-α (PeproTECH, 300-01A) at 10 ng/ml or IFN-γ (10 ng/ml) for 4 hours (‘1hit’). To mimic repetitive stimulations, ECs were first exposed to stimuli for 24 hours. The cells were then washed and incubated in control medium EGM-2 for 48 hours before the second hit of the same stimuli was added (‘2hits). The responses of twice exposed cells (‘2hits’) were compared with cells that were exposed only once to stimuli (‘1hit’), which took place always on the same day the second hits were added. Two control conditions were also added by cells that were exposed to no stimulation but only medium control (’CTRL1-EGM’), and cells that received only one hit of stimulation on the day of the 1st hit of stimulation (‘CTRL2-Stimuli’).

value: umbilical cord tissue

value: Human umbilical vein endothelial cells (HUVECs)

tag: time point


title: HIT2_IFN_REP2 [ATAC-Seq]

description:
HIT2_IFN_REP2
HUVEC_IFN_countTable.tsv


title: HIT2_IFN_REP4 [ATAC-Seq]

description:
HIT2_IFN_REP4
HUVEC_IFN_countTable.tsv


title: HIT2_IFN_REP3 [ATAC-Seq]

description:
HIT2_IFN_REP3
HUVEC_IFN_countTable.tsv


title: Blood neutrophil, 0h, RA replicate7


title: CTRL2_IFN_REP5 [ATAC-Seq]

description:
CTRL2_IFN_REP5
HUVEC_IFN_countTable.tsv


title: Blood neutrophil, 0h, RA replicate6


title: CTRL2_IFN_REP3 [ATAC-Seq]

description:
CTRL2_IFN_REP3
HUVEC_IFN_countTable.tsv


title: Blood neutrophil, 0h, RA replicate9


title: Blood neutrophil, 0h, RA replicate4


title: Blood neutrophil, 0h, RA replicate5


title: Blood neutrophil, 0h, RA replicate2


title: Blood neutrophil, 0h, Healthy control replicate3


title: Blood neutrophil, 0h, Healthy control replicate2


title: Blood neutrophil, 0h, Healthy control replicate1


title: HIT1_IFN_REP4 [ATAC-Seq]

description:
HIT1_IFN_REP4
HUVEC_IFN_countTable.tsv


title: HIT2_IFN_REP1 [ATAC-Seq]

description:
HIT2_IFN_REP1
HUVEC_IFN_countTable.tsv


title: Blood neutrophil, 0h, RA replicate8


title: HIT2_TNF_REP4 [ATAC-Seq]

description:
HIT2_TNF_REP4
HUVEC_TNF_countTable.tsv


title: CTRL2_IFN_REP4 [ATAC-Seq]

description:
CTRL2_IFN_REP4
HUVEC_IFN_countTable.tsv


title: CTRL2_IFN_REP2 [ATAC-Seq]

description:
CTRL2_IFN_REP2
HUVEC_IFN_countTable.tsv


title: CTRL2_IFN_REP1 [ATAC-Seq]

description:
CTRL2_IFN_REP1
HUVEC_IFN_countTable.tsv


title: HIT1_IFN_REP2 [ATAC-Seq]

description:
HIT1_IFN_REP2
HUVEC_IFN_countTable.tsv


title: Blood neutrophil, 0h, RA replicate1


title: HIT1_IFN_REP1 [ATAC-Seq]

description:
HIT1_IFN_REP1
HUVEC_IFN_countTable.tsv


title: CTRL2_TNF_REP3 [ATAC-Seq]

description:
CTRL2_TNF_REP3
HUVEC_TNF_countTable.tsv


title: HIT2_TNF_REP5 [ATAC-Seq]

description:
HIT2_TNF_REP5
HUVEC_TNF_countTable.tsv


title: HIT1_TNF_REP5 [ATAC-Seq]

description:
HIT1_TNF_REP5
HUVEC_TNF_countTable.tsv


title: HIT2_TNF_REP3 [ATAC-Seq]

description:
HIT2_TNF_REP3
HUVEC_TNF_countTable.tsv


title: HIT1_TNF_REP3 [ATAC-Seq]

description:
HIT1_TNF_REP3
HUVEC_TNF_countTable.tsv


title: HIT2_TNF_REP2 [ATAC-Seq]

description:
HIT2_TNF_REP2
HUVEC_TNF_countTable.tsv


title: HIT1_TNF_REP2 [ATAC-Seq]

description:
HIT1_TNF_REP2
HUVEC_TNF_countTable.tsv


title: HIT2_TNF_REP1 [ATAC-Seq]

description:
HIT2_TNF_REP1
HUVEC_TNF_countTable.tsv


title: CTRL1_EGM_REP3 [ATAC-Seq]

description:
CTRL1_EGM_REP3
HUVEC_IFN_countTable.tsv
HUVEC_TNF_countTable.tsv


title: CTRL1_EGM_REP2 [ATAC-Seq]

description:
CTRL1_EGM_REP2
HUVEC_IFN_countTable.tsv
HUVEC_TNF_countTable.tsv


title: CTRL2_TNF_REP4 [ATAC-Seq]

description:
CTRL2_TNF_REP4
HUVEC_TNF_countTable.tsv


title: HIT1_IFN_REP3 [ATAC-Seq]

description:
HIT1_IFN_REP3
HUVEC_IFN_countTable.tsv


title: HIT1_TNF_REP4 [ATAC-Seq]

description:
HIT1_TNF_REP4
HUVEC_TNF_countTable.tsv


title: HIT2_IFN_REP5

description:
HIT2_IFN_REP5
HUVEC_IFN_countTable.tsv

data_processing:
raw sequence reads were  filtered using SOAPnuke. We applied filters which included the removal of sequence adapters, contamination check, and the removal of poor-quality reads (Q ≥ 33). Subsequently, the processed data were evaluated for subsequent quality control using FastQC (version 0.11.9) and MultiQC (version 1.14). The remaining filtered data were then aligned and annotated using the human GENCODE Version 39 (GRCh38.p13) genome using the STAR Aligner (version 2.7.10a) with default parameters. Finally, quantification of reads per gene was performed using STAR's --quantMode GeneCounts.
Assembly: GRCh38
Supplementary files format and content: Count matrix

growth_protocol: HUVECs (Lonza) were cultured in EGM-2 (Promocell) medium. Experiments were executed on cells at P3.

extract_protocol:
Cells were washed in PBS and quickly lysed in the lysis buffer of the MirVanva MagMax RNA isolation kit (Thermofisher) and stored at -20 oC until isolation. RNA was isolated manually according to the manufacturer’s instructions. RNA concentration and integrity were determined using the Bioanalyzer (Agilent D2000). All samples had a RNA integrity number (RIN) score  of at least 8. Of these samples 300 ng of RNA were sent to BGI Hongkong for library prep and sequencing on the DNBSEQ platform to achieve paired-end and 150 bp read length.
Strand-specific mRNA libraries were prepared at BGI, following their inhouse protocol for DNBseq platform


title: CTRL2_TNF_REP1 [ATAC-Seq]

description:
CTRL2_TNF_REP1
HUVEC_TNF_countTable.tsv


title: HIT1_TNF_REP1 [ATAC-Seq]

description:
HIT1_TNF_REP1
HUVEC_TNF_countTable.tsv


title: CTRL1_EGM_REP5 [ATAC-Seq]

description:
CTRL1_EGM_REP5
HUVEC_IFN_countTable.tsv
HUVEC_TNF_countTable.tsv


title: HIT2_IFN_REP1

description:
HIT2_IFN_REP1
HUVEC_IFN_countTable.tsv


title: CTRL2_IFN_REP5

description:
CTRL2_IFN_REP5
HUVEC_IFN_countTable.tsv


title: HIT1_IFN_REP5 [ATAC-Seq]

description:
HIT1_IFN_REP5
HUVEC_IFN_countTable.tsv


title: CTRL2_TNF_REP5 [ATAC-Seq]

description:
CTRL2_TNF_REP5
HUVEC_TNF_countTable.tsv


title: CTRL1_EGM_REP4 [ATAC-Seq]

description:
CTRL1_EGM_REP4
HUVEC_IFN_countTable.tsv
HUVEC_TNF_countTable.tsv


title: HIT2_IFN_REP4

description:
HIT2_IFN_REP4
HUVEC_IFN_countTable.tsv


title: CTRL2_IFN_REP2

description:
CTRL2_IFN_REP2
HUVEC_IFN_countTable.tsv


title: HIT2_IFN_REP2

description:
HIT2_IFN_REP2
HUVEC_IFN_countTable.tsv


title: HIT1_IFN_REP5

description:
HIT1_IFN_REP5
HUVEC_IFN_countTable.tsv


title: CTRL1_EGM_REP1 [ATAC-Seq]

description:
CTRL1_EGM_REP1
HUVEC_IFN_countTable.tsv
HUVEC_TNF_countTable.tsv


title: HIT1_IFN_REP4

description:
HIT1_IFN_REP4
HUVEC_IFN_countTable.tsv


title: CTRL2_IFN_REP1

description:
CTRL2_IFN_REP1
HUVEC_IFN_countTable.tsv


title: HIT2_IFN_REP3

description:
HIT2_IFN_REP3
HUVEC_IFN_countTable.tsv


title: HIT1_IFN_REP2

description:
HIT1_IFN_REP2
HUVEC_IFN_countTable.tsv


title: HIT2_TNF_REP3

description:
HIT2_TNF_REP3
HUVEC_TNF_countTable.tsv


title: HIT1_IFN_REP3

description:
HIT1_IFN_REP3
HUVEC_IFN_countTable.tsv


title: HIT2_TNF_REP4

description:
HIT2_TNF_REP4
HUVEC_TNF_countTable.tsv


title: HIT1_IFN_REP1

description:
HIT1_IFN_REP1
HUVEC_IFN_countTable.tsv


title: CTRL2_TNF_REP4

description:
CTRL2_TNF_REP4
HUVEC_TNF_countTable.tsv


title: HIT2_TNF_REP2

description:
HIT2_TNF_REP2
HUVEC_TNF_countTable.tsv


title: HIT2_TNF_REP1

description:
HIT2_TNF_REP1
HUVEC_TNF_countTable.tsv


title: HIT2_TNF_REP5

description:
HIT2_TNF_REP5
HUVEC_TNF_countTable.tsv


title: CTRL2_TNF_REP1

description:
CTRL2_TNF_REP1
HUVEC_TNF_countTable.tsv


title: CTRL2_IFN_REP4

description:
CTRL2_IFN_REP4
HUVEC_IFN_countTable.tsv


title: HIT1_TNF_REP5

description:
HIT1_TNF_REP5
HUVEC_TNF_countTable.tsv


title: HIT1_TNF_REP4

description:
HIT1_TNF_REP4
HUVEC_TNF_countTable.tsv


title: CTRL2_TNF_REP2

description:
CTRL2_TNF_REP2
HUVEC_TNF_countTable.tsv


title: HIT1_TNF_REP3

description:
HIT1_TNF_REP3
HUVEC_TNF_countTable.tsv


title: CTRL2_IFN_REP3

description:
CTRL2_IFN_REP3
HUVEC_IFN_countTable.tsv


title: HIT1_TNF_REP1

description:
HIT1_TNF_REP1
HUVEC_TNF_countTable.tsv


title: HIT1_TNF_REP2

description:
HIT1_TNF_REP2
HUVEC_TNF_countTable.tsv


title: CTRL1_EGM_REP5


title: CTRL1_EGM_REP4


title: CTRL1_EGM_REP3


title: CTRL1_EGM_REP2


title: sham_DEN_3

city: Boston

first: Shadmehr

last: Demehri

address: 149 13th Street

institute: Cutaneous Biology Research Center, Harvard Medical School

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of 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 browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, 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 (Mortazavi et al., 2008).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Mus liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Liver

value: Liver cells

value: Sham+DEN


title: CTRL1_EGM_REP1


title: HBV_DEN_2

value: HBV+DEN


title: sham_DEN_1


title: HBV_DEN_3


title: CTRL2_TNF_REP5

description:
CTRL2_TNF_REP5
HUVEC_TNF_countTable.tsv


title: HBV_DEN_1


title: CTRL2_TNF_REP3

description:
CTRL2_TNF_REP3
HUVEC_TNF_countTable.tsv


title: DNA from resected tumor tissue of radiation-induced glioma N22-F72

city: Hidaka

first: Mitsuaki

middle: Shirahata

last: Shirahata

state: Saitama

department: Neurosurgery/Neuro-oncology

institute: Saitama Medical University International Medical Center

description: DNA from radiation-induced glioma patient

hyb_protocol: Bisulphite converted DNA was hybridized to Illumina Infinium MethylationEPIC v2.0 Kits using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).
The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

source_name: radiation-induced glioma

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from resected tumor tissue using Maxwell® RSC Genomic DNA Kit

value: radiation-induced glioma


title: buccal swab 1051

city: Singapore

first: Dennis

last: Wang

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina protocol for Illumina Infinium Human Methylation EPICarray

scan_protocol: Standard Illumina protocol

data_processing:
R/RStudio
The filtered and normalized (preprocessNoob) average Betas use in this study are represented in the Sample Data table

label: Cy5 and Cy3

source_name: buccal swab 1051

extract_protocol: Genomic DNA was extracted from buccal swab samples using IsoHelix DNA Extreme Kit/Qiasymphony SP following the standard protocol

value: buccal swab

tag: age(month)


title: buccal swab 1050

source_name: buccal swab 1050


title: buccal swab 1049

source_name: buccal swab 1049


title: buccal swab 1047

source_name: buccal swab 1047


title: buccal swab 1046

source_name: buccal swab 1046


title: buccal swab 1048

source_name: buccal swab 1048


title: buccal swab 1045

source_name: buccal swab 1045


title: buccal swab 1042

source_name: buccal swab 1042


title: buccal swab 1043

source_name: buccal swab 1043


title: buccal swab 1041

source_name: buccal swab 1041


title: buccal swab 1044

source_name: buccal swab 1044


title: buccal swab 1038

source_name: buccal swab 1038


title: buccal swab 1037

source_name: buccal swab 1037


title: buccal swab 1035

source_name: buccal swab 1035


title: buccal swab 1036

source_name: buccal swab 1036


title: sham_DEN_2

source_name: Mus liver

tag: treatment


title: buccal swab 1030

source_name: buccal swab 1030


title: buccal swab 1031

source_name: buccal swab 1031


title: buccal swab 1033

source_name: buccal swab 1033


title: buccal swab 1032

source_name: buccal swab 1032


title: buccal swab 1027

source_name: buccal swab 1027


title: buccal swab 1029

source_name: buccal swab 1029


title: buccal swab 1028

source_name: buccal swab 1028


title: buccal swab 1026

source_name: buccal swab 1026


title: buccal swab 1025

source_name: buccal swab 1025


title: buccal swab 1020

source_name: buccal swab 1020


title: buccal swab 1023

source_name: buccal swab 1023


title: buccal swab 1022

source_name: buccal swab 1022


title: buccal swab 1024

source_name: buccal swab 1024


title: buccal swab 1016

source_name: buccal swab 1016


title: buccal swab 1014

source_name: buccal swab 1014


title: buccal swab 1021

source_name: buccal swab 1021


title: buccal swab 1040

source_name: buccal swab 1040


title: buccal swab 1013

source_name: buccal swab 1013


title: buccal swab 1019

source_name: buccal swab 1019


title: buccal swab 1015

source_name: buccal swab 1015


title: buccal swab 1039

source_name: buccal swab 1039


title: buccal swab 1008

source_name: buccal swab 1008


title: buccal swab 1009

source_name: buccal swab 1009


title: buccal swab 1012

source_name: buccal swab 1012


title: buccal swab 1011

source_name: buccal swab 1011


title: buccal swab 1017

source_name: buccal swab 1017


title: buccal swab 1034

source_name: buccal swab 1034


title: buccal swab 1007

source_name: buccal swab 1007


title: buccal swab 1010

source_name: buccal swab 1010


title: buccal swab 1005

source_name: buccal swab 1005


title: buccal swab 1003

source_name: buccal swab 1003


title: buccal swab 1004

source_name: buccal swab 1004


title: buccal swab 1006

source_name: buccal swab 1006


title: buccal swab 1000

source_name: buccal swab 1000


title: buccal swab 1002

source_name: buccal swab 1002


title: buccal swab 1001

source_name: buccal swab 1001


title: buccal swab 998

source_name: buccal swab 998


title: buccal swab 1018

source_name: buccal swab 1018


title: buccal swab 999

source_name: buccal swab 999


title: buccal swab 996

source_name: buccal swab 996


title: buccal swab 995

source_name: buccal swab 995


title: buccal swab 997

source_name: buccal swab 997


title: buccal swab 994

source_name: buccal swab 994


title: buccal swab 990

source_name: buccal swab 990


title: buccal swab 991

source_name: buccal swab 991


title: buccal swab 993

source_name: buccal swab 993


title: buccal swab 986

source_name: buccal swab 986


title: buccal swab 987

source_name: buccal swab 987


title: buccal swab 988

source_name: buccal swab 988


title: buccal swab 985

source_name: buccal swab 985


title: buccal swab 992

source_name: buccal swab 992


title: buccal swab 984

source_name: buccal swab 984


title: buccal swab 982

source_name: buccal swab 982


title: buccal swab 981

source_name: buccal swab 981


title: buccal swab 978

source_name: buccal swab 978


title: buccal swab 980

source_name: buccal swab 980


title: buccal swab 975

source_name: buccal swab 975


title: buccal swab 977

source_name: buccal swab 977


title: buccal swab 979

source_name: buccal swab 979


title: buccal swab 976

source_name: buccal swab 976


title: buccal swab 972

source_name: buccal swab 972


title: buccal swab 974

source_name: buccal swab 974


title: buccal swab 973

source_name: buccal swab 973


title: buccal swab 971

source_name: buccal swab 971


title: buccal swab 969

source_name: buccal swab 969


title: buccal swab 968

source_name: buccal swab 968


title: buccal swab 967

source_name: buccal swab 967


title: buccal swab 966

source_name: buccal swab 966


title: buccal swab 964

source_name: buccal swab 964


title: buccal swab 989

source_name: buccal swab 989


title: buccal swab 965

source_name: buccal swab 965


title: buccal swab 963

source_name: buccal swab 963


title: buccal swab 962

source_name: buccal swab 962


title: buccal swab 960

source_name: buccal swab 960


title: buccal swab 983

source_name: buccal swab 983


title: buccal swab 958

source_name: buccal swab 958


title: buccal swab 961

source_name: buccal swab 961


title: buccal swab 957

source_name: buccal swab 957


title: buccal swab 959

source_name: buccal swab 959


title: buccal swab 955

source_name: buccal swab 955


title: buccal swab 954

source_name: buccal swab 954


title: buccal swab 953

source_name: buccal swab 953


title: buccal swab 951

source_name: buccal swab 951


title: buccal swab 949

source_name: buccal swab 949


title: buccal swab 950

source_name: buccal swab 950


title: buccal swab 948

source_name: buccal swab 948


title: buccal swab 947

source_name: buccal swab 947


title: buccal swab 956

source_name: buccal swab 956


title: buccal swab 952

source_name: buccal swab 952


title: buccal swab 944

source_name: buccal swab 944


title: buccal swab 970

source_name: buccal swab 970


title: buccal swab 943

source_name: buccal swab 943


title: buccal swab 942

source_name: buccal swab 942


title: buccal swab 940

source_name: buccal swab 940


title: buccal swab 946

source_name: buccal swab 946


title: buccal swab 941

source_name: buccal swab 941


title: buccal swab 937

source_name: buccal swab 937


title: buccal swab 938

source_name: buccal swab 938


title: buccal swab 936

source_name: buccal swab 936


title: buccal swab 934

source_name: buccal swab 934


title: buccal swab 935

source_name: buccal swab 935


title: buccal swab 932

source_name: buccal swab 932


title: buccal swab 931

source_name: buccal swab 931


title: buccal swab 933

source_name: buccal swab 933


title: buccal swab 930

source_name: buccal swab 930


title: buccal swab 929

source_name: buccal swab 929


title: buccal swab 924

source_name: buccal swab 924


title: buccal swab 927

source_name: buccal swab 927


title: buccal swab 923

source_name: buccal swab 923


title: buccal swab 922

source_name: buccal swab 922


title: buccal swab 925

source_name: buccal swab 925


title: buccal swab 945

source_name: buccal swab 945


title: buccal swab 926

source_name: buccal swab 926


title: buccal swab 921

source_name: buccal swab 921


title: buccal swab 920

source_name: buccal swab 920


title: buccal swab 918

source_name: buccal swab 918


title: buccal swab 917

source_name: buccal swab 917


title: buccal swab 915

source_name: buccal swab 915


title: buccal swab 912

source_name: buccal swab 912


title: buccal swab 939

source_name: buccal swab 939


title: buccal swab 916

source_name: buccal swab 916


title: buccal swab 914

source_name: buccal swab 914


title: buccal swab 911

source_name: buccal swab 911


title: buccal swab 902

source_name: buccal swab 902


title: buccal swab 903

source_name: buccal swab 903


title: buccal swab 908

source_name: buccal swab 908


title: buccal swab 910

source_name: buccal swab 910


title: buccal swab 905

source_name: buccal swab 905


title: buccal swab 906

source_name: buccal swab 906


title: buccal swab 900

source_name: buccal swab 900


title: buccal swab 899

source_name: buccal swab 899


title: buccal swab 896

source_name: buccal swab 896


title: buccal swab 894

source_name: buccal swab 894


title: buccal swab 895

source_name: buccal swab 895


title: buccal swab 919

source_name: buccal swab 919


title: buccal swab 892

source_name: buccal swab 892


title: buccal swab 891

source_name: buccal swab 891


title: buccal swab 889

source_name: buccal swab 889


title: buccal swab 887

source_name: buccal swab 887


title: buccal swab 886

source_name: buccal swab 886


title: buccal swab 885

source_name: buccal swab 885


title: buccal swab 893

source_name: buccal swab 893


title: buccal swab 884

source_name: buccal swab 884


title: buccal swab 883

source_name: buccal swab 883


title: buccal swab 877

source_name: buccal swab 877


title: buccal swab 878

source_name: buccal swab 878


title: buccal swab 897

source_name: buccal swab 897


title: buccal swab 880

source_name: buccal swab 880


title: buccal swab 879

source_name: buccal swab 879


title: buccal swab 876

source_name: buccal swab 876


title: buccal swab 882

source_name: buccal swab 882


title: buccal swab 872

source_name: buccal swab 872


title: buccal swab 874

source_name: buccal swab 874


title: buccal swab 873

source_name: buccal swab 873


title: buccal swab 890

source_name: buccal swab 890


title: buccal swab 888

source_name: buccal swab 888


title: buccal swab 871

source_name: buccal swab 871


title: buccal swab 870

source_name: buccal swab 870


title: buccal swab 869

source_name: buccal swab 869


title: buccal swab 928

source_name: buccal swab 928


title: buccal swab 907

source_name: buccal swab 907


title: buccal swab 868

source_name: buccal swab 868


title: buccal swab 866

source_name: buccal swab 866


title: buccal swab 867

source_name: buccal swab 867


title: buccal swab 860

source_name: buccal swab 860


title: buccal swab 857

source_name: buccal swab 857


title: buccal swab 859

source_name: buccal swab 859


title: buccal swab 856

source_name: buccal swab 856


title: buccal swab 864

source_name: buccal swab 864


title: buccal swab 865

source_name: buccal swab 865


title: buccal swab 858

source_name: buccal swab 858


title: buccal swab 855

source_name: buccal swab 855


title: buccal swab 881

source_name: buccal swab 881


title: buccal swab 854

source_name: buccal swab 854


title: buccal swab 875

source_name: buccal swab 875


title: buccal swab 852

source_name: buccal swab 852


title: buccal swab 862

source_name: buccal swab 862


title: buccal swab 861

source_name: buccal swab 861


title: buccal swab 863

source_name: buccal swab 863


title: buccal swab 851

source_name: buccal swab 851


title: buccal swab 850

source_name: buccal swab 850


title: buccal swab 853

source_name: buccal swab 853


title: buccal swab 846

source_name: buccal swab 846


title: buccal swab 848

source_name: buccal swab 848


title: buccal swab 849

source_name: buccal swab 849


title: buccal swab 845

source_name: buccal swab 845


title: buccal swab 843

source_name: buccal swab 843


title: buccal swab 844

source_name: buccal swab 844


title: buccal swab 841

source_name: buccal swab 841


title: buccal swab 840

source_name: buccal swab 840


title: buccal swab 838

source_name: buccal swab 838


title: buccal swab 837

source_name: buccal swab 837


title: buccal swab 901

source_name: buccal swab 901


title: buccal swab 842

source_name: buccal swab 842


title: buccal swab 839

source_name: buccal swab 839


title: buccal swab 834

source_name: buccal swab 834


title: buccal swab 836

source_name: buccal swab 836


title: buccal swab 832

source_name: buccal swab 832


title: buccal swab 827

source_name: buccal swab 827


title: buccal swab 829

source_name: buccal swab 829


title: buccal swab 831

source_name: buccal swab 831


title: buccal swab 825

source_name: buccal swab 825


title: buccal swab 833

source_name: buccal swab 833


title: buccal swab 847

source_name: buccal swab 847


title: buccal swab 830

source_name: buccal swab 830


title: buccal swab 824

source_name: buccal swab 824


title: buccal swab 822

source_name: buccal swab 822


title: buccal swab 821

source_name: buccal swab 821


title: buccal swab 820

source_name: buccal swab 820


title: buccal swab 817

source_name: buccal swab 817


title: buccal swab 819

source_name: buccal swab 819


title: buccal swab 835

source_name: buccal swab 835


title: buccal swab 816

source_name: buccal swab 816


title: buccal swab 815

source_name: buccal swab 815


title: buccal swab 813

source_name: buccal swab 813


title: buccal swab 810

source_name: buccal swab 810


title: buccal swab 811

source_name: buccal swab 811


title: buccal swab 814

source_name: buccal swab 814


title: buccal swab 826

source_name: buccal swab 826


title: buccal swab 904

source_name: buccal swab 904


title: buccal swab 812

source_name: buccal swab 812


title: buccal swab 809

source_name: buccal swab 809


title: buccal swab 806

source_name: buccal swab 806


title: buccal swab 804

source_name: buccal swab 804


title: buccal swab 823

source_name: buccal swab 823


title: buccal swab 805

source_name: buccal swab 805


title: buccal swab 807

source_name: buccal swab 807


title: buccal swab 828

source_name: buccal swab 828


title: buccal swab 808

source_name: buccal swab 808


title: buccal swab 802

source_name: buccal swab 802


title: buccal swab 818

source_name: buccal swab 818


title: buccal swab 798

source_name: buccal swab 798


title: buccal swab 797

source_name: buccal swab 797


title: buccal swab 799

source_name: buccal swab 799


title: buccal swab 796

source_name: buccal swab 796


title: buccal swab 795

source_name: buccal swab 795


title: buccal swab 794

source_name: buccal swab 794


title: buccal swab 792

source_name: buccal swab 792


title: buccal swab 793

source_name: buccal swab 793


title: buccal swab 790

source_name: buccal swab 790


title: buccal swab 791

source_name: buccal swab 791


title: buccal swab 788

source_name: buccal swab 788


title: buccal swab 787

source_name: buccal swab 787


title: buccal swab 786

source_name: buccal swab 786


title: buccal swab 803

source_name: buccal swab 803


title: buccal swab 784

source_name: buccal swab 784


title: buccal swab 781

source_name: buccal swab 781


title: buccal swab 782

source_name: buccal swab 782


title: buccal swab 779

source_name: buccal swab 779


title: buccal swab 800

source_name: buccal swab 800


title: buccal swab 780

source_name: buccal swab 780


title: buccal swab 801

source_name: buccal swab 801


title: buccal swab 777

source_name: buccal swab 777


title: buccal swab 775

source_name: buccal swab 775


title: buccal swab 778

source_name: buccal swab 778


title: buccal swab 773

source_name: buccal swab 773


title: buccal swab 776

source_name: buccal swab 776


title: buccal swab 774

source_name: buccal swab 774


title: buccal swab 771

source_name: buccal swab 771


title: buccal swab 772

source_name: buccal swab 772


title: buccal swab 769

source_name: buccal swab 769


title: buccal swab 789

source_name: buccal swab 789


title: buccal swab 909

source_name: buccal swab 909


title: buccal swab 766

source_name: buccal swab 766


title: buccal swab 767

source_name: buccal swab 767


title: buccal swab 785

source_name: buccal swab 785


title: buccal swab 765

source_name: buccal swab 765


title: buccal swab 783

source_name: buccal swab 783


title: buccal swab 762

source_name: buccal swab 762


title: buccal swab 761

source_name: buccal swab 761


title: buccal swab 759

source_name: buccal swab 759


title: buccal swab 760

source_name: buccal swab 760


title: buccal swab 763

source_name: buccal swab 763


title: buccal swab 757

source_name: buccal swab 757


title: buccal swab 758

source_name: buccal swab 758


title: buccal swab 755

source_name: buccal swab 755


title: buccal swab 756

source_name: buccal swab 756


title: buccal swab 754

source_name: buccal swab 754


title: buccal swab 770

source_name: buccal swab 770


title: buccal swab 753

source_name: buccal swab 753


title: buccal swab 752

source_name: buccal swab 752


title: buccal swab 750

source_name: buccal swab 750


title: buccal swab 749

source_name: buccal swab 749


title: buccal swab 751

source_name: buccal swab 751


title: buccal swab 745

source_name: buccal swab 745


title: buccal swab 746

source_name: buccal swab 746


title: buccal swab 744

source_name: buccal swab 744


title: buccal swab 913

source_name: buccal swab 913


title: buccal swab 743

source_name: buccal swab 743


title: buccal swab 742

source_name: buccal swab 742


title: buccal swab 741

source_name: buccal swab 741


title: buccal swab 764

source_name: buccal swab 764


title: buccal swab 768

source_name: buccal swab 768


title: buccal swab 739

source_name: buccal swab 739


title: buccal swab 740

source_name: buccal swab 740


title: buccal swab 736

source_name: buccal swab 736


title: buccal swab 738

source_name: buccal swab 738


title: buccal swab 737

source_name: buccal swab 737


title: buccal swab 898

source_name: buccal swab 898


title: buccal swab 735

source_name: buccal swab 735


title: buccal swab 731

source_name: buccal swab 731


title: buccal swab 748

source_name: buccal swab 748


title: buccal swab 721

source_name: buccal swab 721


title: buccal swab 722

source_name: buccal swab 722


title: buccal swab 732

source_name: buccal swab 732


title: buccal swab 718

source_name: buccal swab 718


title: buccal swab 717

source_name: buccal swab 717


title: buccal swab 733

source_name: buccal swab 733


title: buccal swab 734

source_name: buccal swab 734


title: buccal swab 713

source_name: buccal swab 713


title: buccal swab 711

source_name: buccal swab 711


title: buccal swab 747

source_name: buccal swab 747


title: buccal swab 724

source_name: buccal swab 724


title: buccal swab 710

source_name: buccal swab 710


title: buccal swab 727

source_name: buccal swab 727


title: buccal swab 728

source_name: buccal swab 728


title: buccal swab 725

source_name: buccal swab 725


title: buccal swab 726

source_name: buccal swab 726


title: buccal swab 723

source_name: buccal swab 723


title: buccal swab 716

source_name: buccal swab 716


title: buccal swab 715

source_name: buccal swab 715


title: buccal swab 712

source_name: buccal swab 712


title: buccal swab 720

source_name: buccal swab 720


title: buccal swab 709

source_name: buccal swab 709


title: buccal swab 704

source_name: buccal swab 704


title: buccal swab 730

source_name: buccal swab 730


title: buccal swab 729

source_name: buccal swab 729


title: buccal swab 706

source_name: buccal swab 706


title: buccal swab 708

source_name: buccal swab 708


title: buccal swab 707

source_name: buccal swab 707


title: buccal swab 700

source_name: buccal swab 700


title: buccal swab 696

source_name: buccal swab 696


title: buccal swab 693

source_name: buccal swab 693


title: buccal swab 705

source_name: buccal swab 705