title: CG4

value: clean seawater

value: control


title: Mouse 9: T cells with combo

status: Public on Feb 23 2022

type: RNA

city: Gaithersburg

first: Eric

last: Tu

state: MD

address: 1 Medimmune way

country: USA

institute: AstraZeneca

description:
RE807-RMS37481-44
Gene expression data from xenograft tumors of combo-treated mouse.

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized on Human Genome U133 Plus 2.0 GeneChip arrays (Affymetrix) according to manufacturer’s instruction.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Data capture and array quality assessments were performed with the GeneChip Operating Software tool. Normalization of gene expression profiles was performed by using robust multi-array average method. Probesets with highest sample variance among multiple probesets per gene were selected and used for downstream analyses. Differential gene expression analysis was carried out by R package LIMMA with linear modeling and empirical Bayes moderation.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Xenograft tumors from combo-treated mouse

label_protocol: RNA was converted to biotin-labeled cRNA using MessageAmp™ Premier RNA Amplification Kit (Thermo Fisher Scientific) according to manufacturer’s instruction.

growth_protocol: NSG mice at 6-8 weeks were used in the study. Mice were treated with antibodies for 17 days before the tumors were harvested.

extract_protocol: Total RNA was derived from cells using RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction.

treatment_protocol: Tumors were cut into smaller fragments that were placed into tumor digestion enzyme buffer (RPMI + DNase + Collagenase) to process to single cell suspension using gentleMACS Dissociator (Miltenyi Biotec).

tag: mouse strain

value: NSG

tag: tissue

value: NSCLC tumor

tag: treatment

value: combo


title: CG3

type: SRA

city: Dalian

first: dongxu

last: gao

address: Heishijiao

country: China

institute: Dalian Ocean University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome (Takifugu_rubripes_Ensemble_92) using Hisat2 v2.0.5.
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.
Genome_build: Takifugu_rubripes_Ensemble_92
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for  all sample

organism: Takifugu rubripes

source_name: gill

growth_protocol: T. rubripes (average size 118 ± 7.5 g) were obtained from a local supplier (Tianzheng Industrial, Dalian, China) and acclimated for approximately 7 days in a temperature controlled room (19 ± 1 ◦C).

extract_protocol:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fish were put into the aquaria with the bacteria at concentration of 2.5×10e7 CFU/mL for 12 h of immersion exposure. At 12 h fish were transferred to clean seawater and maintained for 7 days. Control groups were maintained in the clean seawater all the time. Spleen and gill tissues were collected in both symptomatic treatment fish and control fish at 7 day.

tag: average size

tag: infection

value: gill


title: Control 5 months, replicate 4

city: Montreal

first: Roberta

middle: M

last: Palmour

state: Quebec

address: 1033 Pine West

department: Psychiatry

country: Canada

institute: McGill

description: mRNA expression data from the hippocampus of vervet green monkeys sacrificed at 5 months after birth

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: GeneChips were scanned using the Affymetrix GeneTitan at the McGill Genome Center

data_processing: The data were analyzed with FlexArray software and the Bioconductor package in R. These data were normalized using the Robust Multi-Array (RMA) normalization method. Probe sets have been trimmed for present/absent calls, annotation, and where multiple probe sets were available for a single gene only the probe set showing the highest mean expression value was selected

organism: Chlorocebus aethiops

source_name: Chlorocebus aethiops hippocampus sacrificed at 5 months post sucrose exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: miRNeasy Qiazol extraction performed according to manufacturers specifications

treatment_protocol: Whole hippocampus was extracted and placed in a 1 ml sterile vial containing GITC

tag: age

value: Sacrificed at 5 months

tag: ethanol exposure

value: Pre Natal sucrose exposure


title: Expo_Rep1_D

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

data_processing:
Reads were mapped onto the E. coli genome (version U0009.3, GenBank) using the Burrows-Wheeler alignment method (version 0.7.12-r1069). Counting was performed with HTSeq-count version 0.6.1p1 using the « intersection non empty » mode.
Supplementary_files_format_and_content: Matrix of read counts for every gene (in total for 4488 genes)

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: E. coli MG1655 was grown in batch cultures in a bioreactor at 37°C, pH 7.0 and 350 rpm, in M9 medium supplemented with 3 g/L glucose. All cultures were inoculated at an OD600nm of 0.1 after overnight preculture. The partial pressure of oxygen was continuously monitored during the culture and maintained above 30%. Cells were collected in the exponential phase at an OD600nm of ~1.3, and in the stationary phase 1 h after glucose depletion at an OD600nm of ~3.4.

extract_protocol:
Total RNA was extracted using the RNeasy Midi kit (Qiagen, Germantown, MD, USA) and quantified using a Nanodrop® spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The 23S/16S and 16S/23S ratios in each subfraction were calculated using the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and used to pool the subfractions into seven fractions labelled A to G. Fraction A consisted of subfractions containing DNAs, free RNAs, and free small and large ribosomal subunits. In fractions B to G, the 23S/16S ratio was constant, at about 1.8, corresponding to entire ribosomes. The 1st peak (fraction B) was attributed to the monosome. The 2nd, 3rd, and 4th peaks were attributed to 2, 3, and 4 ribosomes, respectively.
Ribosomal RNA was removed using the Ribo-ZeroRM Magnetic Kit (Illumina, San Diego, CA, USA). Then 10 ng ribodepleted RNA was used to construct a sequencing library using the Ion Total RNA-Seq Kit v2 Kit and the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific, Waltham, MA, USA). The library was constructed and (100 base pair [bp]) single-end sequencing on an Ion Torrent system equipped with an Ion P1 Chip Kit was performed by the GeT-BioPuces platform (http://get-biopuces.insa-toulouse.fr/). These experiments were repeated with three independent cultures.

treatment_protocol: Translation was arrested by adding 0.1 mg/mL chloramphenicol. Cells were harvested, washed twice, and resuspended in lysis buffer (20 mM Tris HCl pH 8, 140 mM KCl, 40 mM MgCl2, 0.5 mM DTT, 100 μg/ml chloramphenicol, 1 mg/ml heparin, 20 mM EGTA, 1% Triton X-100). Heparin was used as a RNase inhibitor. After mechanical cell disruption with glass beads, mRNA-ribosome complexes were size-separated on a sucrose gradient (10 to 50% (w/v) in polysome gradient buffer (same composition as lysis buffer except for heparin at a final concentration of 0.5 mg/ml)) into 24 subfractions.

tag: strain


title: C3_Healthy subject

city: Fuzhou

first: Jie-feng

last: Huang

address: No 20, Chazhong road, Taijiang district

institute: First affiliated hospital of Fujian Medical University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, 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: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Healthy subject

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 9 subjects were enrolled in the study. They were classified into three groups: three healthy subjects (healthy group), three OSA without AMI and three OSA with AMI. The main symptoms of three AMI patients were chest pain or chest tightness, with dynamic alterations of electrocardiogram and dynamic changes of myocardial injury markers, and confirmed by coronary angiography. The three AMI patients were all diagnosed as ST-segment elevation myocardial infarction (STEMI) with ST-segment elevation in electrocardiograms. The study was also approved by the Ethics Committee of the First Affiliated Hospital of Fujian Medical University and written informed consent was obtained from all participants prior to the study.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissues from pancreatic tissues and promptly cooled at -80℃ refrigerator.

value: plasma

tag: subject status

value: Healthy subject

tag: molecule subtype

value: circRNA


title: CG2


title: Mouse 7: T cells with combo

description:
RE807-RMS37481-42
Gene expression data from xenograft tumors of combo-treated mouse.


title: Mouse 9: T cells with MEDI9447

description:
RE807-RMS37481-34
Gene expression data from xenograft tumors of oleclumab-treated mouse.

source_name: Xenograft tumors from oleclumab-treated mouse

value: oleclumab


title: Mouse 10: T cells with MEDI9447

description:
RE807-RMS37481-35
Gene expression data from xenograft tumors of oleclumab-treated mouse.


title: Mouse 6: T cells with combo

description:
RE807-RMS37481-41
Gene expression data from xenograft tumors of combo-treated mouse.


title: CG1


title: Mouse 6: T cells with MEDI9447

description:
RE807-RMS37481-31
Gene expression data from xenograft tumors of oleclumab-treated mouse.


title: C2_Healthy subject


title: C1_Healthy subject


title: VhS4

source_name: spleen

value: Vibrio harveyi at concentration of 2.5x 10e7 CFU/mL

value: Vibrio harveyi infection

value: spleen


title: B3_OSA without AMI

source_name: OSA without AMI

value: OSA without AMI


title: Control 5 months, replicate 1


title: Mouse 10: T cells with MEDI4736

description:
RE807-RMS37481-25
Gene expression data from xenograft tumors of durvalumab-treated mouse.

source_name: Xenograft tumors from durvalumab-treated mouse

value: durvalumab


title: Mouse 9: T cells with MEDI4736

description:
RE807-RMS37481-24
Gene expression data from xenograft tumors of durvalumab-treated mouse.


title: Mouse 8: T cells with MEDI4736

description:
RE807-RMS37481-23
Gene expression data from xenograft tumors of durvalumab-treated mouse.


title: VhS3


title: VhS2


title: Mouse 7: T cells with MEDI9447

description:
RE807-RMS37481-32
Gene expression data from xenograft tumors of oleclumab-treated mouse.


title: Mouse 7: T cells with MEDI4736

description:
RE807-RMS37481-22
Gene expression data from xenograft tumors of durvalumab-treated mouse.


title: Fetal alcohol exposed, 5 months replicate 3

source_name: Chlorocebus aethiops hippocampus sacrificed at 5 months after prenatal alcohol exposure

value: Pre Natal Alcohol Exposure


title: Mouse 9: T cells with isotype

description:
RE807-RMS37481-14
Gene expression data from xenograft tumors of isotype-treated mouse.

source_name: Xenograft tumors from isotype-treated mouse

value: isotype


title: Expo_Rep1_A


title: CS4

value: clean seawater

value: control


title: B2_OSA without AMI


title: Mouse 10: T cells with isotype

description:
RE807-RMS37481-15
Gene expression data from xenograft tumors of isotype-treated mouse.

value: NSG

value: NSCLC tumor


title: Mouse 8: T cells with isotype

description:
RE807-RMS37481-13
Gene expression data from xenograft tumors of isotype-treated mouse.


title: A2_OSA with AMI

source_name: OSA with AMI

value: OSA with AMI


title: T0503GCT-normal-cerebrum_L004

city: Cincinnati

first: Frank

state: OHIO

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Normal human cerebrum (autopsy)

data_processing:
Bowtie for reads alignment
HTSeq for mapping reads to each gene.
Genome_build: hg38
Supplementary_files_format_and_content: .txt

source_name: brain

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit according to manufacturer's instructions (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
Bulk RNA-Seq

treatment_protocol: SYC-435, 15 mg/kg per day, i.p. for 28 days; Radiation treatment, 2 Gy/day, for 5 days; and combination treatment with SYC-435(i.p. 15 mg/kg per day for 28 days), Temozolomide(50 mg/kg/per day), and radiation(2Gy/day for 5 days).

value: human autopsy

tag: genotype

value: normal

value: No Treatment


title: Mouse 7: T cells with isotype

description:
RE807-RMS37481-12
Gene expression data from xenograft tumors of isotype-treated mouse.


title: A3_OSA with AMI

value: plasma

value: circRNA


title: Mouse 5: No T cells

description:
RE807-RMS37481-5
Gene expression data from xenograft tumors of untreated mouse.

source_name: Xenograft tumors from untreated mouse

value: untreated


title: Mouse 6: T cells with MEDI4736

description:
RE807-RMS37481-21
Gene expression data from xenograft tumors of durvalumab-treated mouse.


title: T0503GCT-normal-cerebrum_L003

description: Normal human cerebrum (autopsy)


title: Mouse 6: T cells with isotype

description:
RE807-RMS37481-11
Gene expression data from xenograft tumors of isotype-treated mouse.


title: VhS1

value: Vibrio harveyi at concentration of 2.5x 10e7 CFU/mL

value: Vibrio harveyi infection


title: 6-10B + P-Evs

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

description: Sample 2 (BEXO)

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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

source_name: NPC cells

growth_protocol: NPC cells were treated with or without P-EVs and cultured in 10%FBS RPMI medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: NPC cells were treated with or without P-EVs for 48h.

tag: cell type

value: Nasopharyngeal epithelial cancer cells


title: Mouse 8: T cells with MEDI9447

description:
RE807-RMS37481-33
Gene expression data from xenograft tumors of oleclumab-treated mouse.

value: oleclumab


title: 5-8F NC (P-Ev control)

description: Sample 3 (FNC)


title: 5-8F + P-Evs

description: Sample 4 (FEXO)


title: 6-10B NC (P-Ev control)

description: Sample 1 (BNC)


title: CS1

value: spleen


title: Mouse 3: No T cells

description:
RE807-RMS37481-3
Gene expression data from xenograft tumors of untreated mouse.


title: A1_OSA with AMI


title: Mouse 8: T cells with combo

description:
RE807-RMS37481-43
Gene expression data from xenograft tumors of combo-treated mouse.

value: combo


title: T0503GCT-normal-cerebrum_L001

description: Normal human cerebrum (autopsy)


title: NDF4

city: Hangzhou

first: qianqian

last: pang

state: Zhejiang

address: Qingchun road

department: Plastic Surgery

institute: The First Affiliated Hospital, School of Medicine, Zhejiang University,

description: Gene expression of demal fibroblasts

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software (version 11.0.1.1) .

source_name: normal dermal fibroblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was amplified and transcribed using a random priming method (Arraystar Super RNA Labeling Kit; Arraystar) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: normal skin dermal fibroblasts and keloid dermal fibroblasts

extract_protocol: Total RNA was extracted from cells using TRIzol reagent and quantified using the NanoDrop ND-1000.

treatment_protocol: Cells were cultured in DMEM, comprising of 10% FBS, penicillin (100 U/ml) and streptomycin (100 ug/ml) in 5% CO2 at 37°C in the incubator

value: skin


title: T0503GCT-normal-cerebrum_L002

description: Normal human cerebrum (autopsy)


title: D0322GBM-normal-cerebrum_L003

description: Normal human cerebrum (autopsy)


title: NDF3

description: Gene expression of demal fibroblasts


title: CS2

value: clean seawater

value: control


title: B1_OSA without AMI

value: OSA without AMI


title: NDF2

description: Gene expression of demal fibroblasts


title: Mouse 4: No T cells

description:
RE807-RMS37481-4
Gene expression data from xenograft tumors of untreated mouse.

value: NSG

value: NSCLC tumor


title: 32C_#1

city: Gainesville

first: Kaylie

last: Padgett-Pagliai

state: Florida

address: 2033 Mowry Road, Lab 325 CGRC

institute: University of Florida

data_processing:
Raw sequences were modified to trim the Illumina sequencing adapter using Cutadapt.
Sequence processing using the Sickle tool to verify the quality of the samples prior to further analyses.
Sequences were mapped against the genome of L. crescens BT-1 using Bowtie2.
The mapped mRNA sequences were aligned using Samtools.
mRNA sequences were counted using the HTseq tool.
Genome_build: Liberibacter crescens BT-1 (NC_019907.1)
Supplementary_files_format_and_content: Processed data files are in the form of an Htseq .txt file with gene counts.
Supplementary_files_format_and_content: *DESeq2_results.txt: Processed data files are in the form of an DESeq2 results file in a .txt file with differential expression data.

organism: Liberibacter crescens BT-1

source_name: L. crescens BT-1, 32C

growth_protocol: L. crescens BT-1 cultures were cultured at 25°C in the presence and absence of 100 mM sucrose, or 0.05% DMSO. For the heat stress, L. crescens cells were grown at 32°C. L. crescens BT-1 cells were collected at OD600= 0.3 (mid-exponential phase) by centrifugation at 8000 rpm, at 4 °C.

extract_protocol:
Total RNA was extracted with the RiboPure-Bacteria (Life Technologies) kit following the manufacturer’s protocol. The quality of isolated RNA samples was examined in an Agilent 2100 Bioanalyzer. The rRNA was depleted using the MICROBExpress Bacterial mRNA enrichment kit (Life Technologies) according to the manufacturer’s instructions.
Single end RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and followed by sequencing using a HiSeq2500 system. RNA sequencing was performed by the Genome Sciences Facility at Penn State University in Hershey, PA. The assays were performed in duplicates, and approximately 2million reads were obtained for each library.


title: D0322GBM-normal-cerebrum_L001

description: Normal human cerebrum (autopsy)

value: human autopsy

value: normal


title: NC2-normal-cerebrum_L003

description: Normal human cerebrum (autopsy)

value: No Treatment


title: V0914-SYC435-15mg-bioD5_L004_R1_001

description: Mus musculus Xenograft

value: NOD SCID

value: IDH1 mutation


title: Sucrose 100 mM_#1

source_name: L. crescens BT-1, sucrose

value: Sucrose


title: V0914-SYC435-15mg-bioD5_L003_R1_001

description: Mus musculus Xenograft


title: Sucrose 100 mM_#2


title: V0914-SYC435-15mg-bioD5_L002_R1_001

description: Mus musculus Xenograft


title: D0322GBM-normal-cerebrum_L004

description: Normal human cerebrum (autopsy)


title: V0914-SYC435-15mg-bioD5_L001_R1_001

description: Mus musculus Xenograft


title: 25C-control_#2

source_name: L. crescens BT-1, 25C


title: NC2-normal-cerebrum_L004

description: Normal human cerebrum (autopsy)


title: NC2-normal-cerebrum_L001

description: Normal human cerebrum (autopsy)


title: NDF1

description: Gene expression of demal fibroblasts


title: MLVATP-735

city: Beltsville

first: Damarius

middle: S

last: FLEMING

state: Maryland

address: 10300 Baltimore Ave Bldg 1040, Barc East

department: ARS

institute: USDA

data_processing:
Alignment to the Sscrofa 11.1 reference genome was carried out using Hisat2 version 2.1.0+galaxy5
Raw counts were generated using FeatureCounts  and the Ensembl Sscrofa11.1.104 GTF file.
Differential gene expression using DeSeq2 version 2.11.40.6. The parameters were set to use poscounts for the estimateSizeFactors to account for genes with zero counts and the fit type was set to local with all other parameters tuned to default.
Genome_build: Sus_scrofa.Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited raw gene counts

organism: Sus scrofa

source_name: Liver

extract_protocol:
Representative samples of liver tissue were extracted from several locations within the liver and combined, placed in tubes containing RNA later and frozen, RNA sent ISU DNA center for processing.
3’ Quantseq fwd kit and the Illumina Hiseq 4000 to produce twenty 100bp single-end reads

value: Liver

tag: timepoint

value: 14 days post infection

value: Commercial vaccine and PRRSV challenge


title: KDF3

description: Gene expression of demal fibroblasts

source_name: keloid dermal fibroblasts

value: keloid


title: KDF4

description: Gene expression of demal fibroblasts


title: 32C_#2


title: 25C-control_#1


title: V0914-TMZ-XRT-bioD5_L004

description: Mus musculus Xenograft

value: SYC-435 treatment


title: D0322GBM-normal-cerebrum_L002

description: Normal human cerebrum (autopsy)


title: MLVATP-733


title: V0914-TMZ-XRT-bioD5_L003

description: Mus musculus Xenograft


title: KDF1

description: Gene expression of demal fibroblasts


title: NC2-normal-cerebrum_L002

description: Normal human cerebrum (autopsy)


title: KDF2

description: Gene expression of demal fibroblasts


title: V0914-TMZ-XRT-bioD5_L002

description: Mus musculus Xenograft


title: V0914-SYC435-15mg-sur_L004

description: Mus musculus Xenograft

value: Temozolomide/Radiation


title: V0914-SYC435-15mg-sur_L002

description: Mus musculus Xenograft


title: MLVATP-738


title: MLVATP-732


title: V0914-SYC435-15mg-sur_L003

description: Mus musculus Xenograft


title: V0914-SYC435-15mg-sur_L001

description: Mus musculus Xenograft


title: MLVATP-737


title: V0914-SYC-435-15mg-TMZXRT-bio-day5_L004

description: Mus musculus Xenograft


title: V0914-SYC-435-15mg-TMZXRT-bio-day5_L003

description: Mus musculus Xenograft


title: ShamP-796

value: Sham vaccine and PRRSV challenge


title: V0914-SYC-435-15mg-TMZXRT-bio-day5_L002

description: Mus musculus Xenograft


title: DMSO_#2

source_name: L. crescens BT-1, DMSO

value: DMSO


title: V0914-SYC-435-15mg-TMZXRT-bio-day5_L001

description: Mus musculus Xenograft


title: V0914-SYC-435-15mg-TMZXRT-sur_L004

description: Mus musculus Xenograft


title: ShamP-793


title: V0914-SYC-435-15mg-TMZXRT-sur_L003

description: Mus musculus Xenograft


title: ShamP-795


title: V0914-SYC-435-15mg-TMZXRT-sur_L002

description: Mus musculus Xenograft


title: DMSO_#1


title: V0914-TMZ-XRT-bioD5_L001

description: Mus musculus Xenograft


title: V0914-TMZXRT-sur_L004

description: Mus musculus Xenograft


title: ShamP-798


title: CS3

value: clean seawater

value: control

value: spleen


title: V0914-SYC-435-15mg-TMZXRT-sur_L001

description: Mus musculus Xenograft


title: V0914-TMZXRT-sur_L003

description: Mus musculus Xenograft


title: ShamP-797


title: V0914-TMZXRT-sur_L002

description: Mus musculus Xenograft


title: V0914-TMZXRT-sur_L001

description: Mus musculus Xenograft


title: V0914-Untreated-sur_L004

description: Mus musculus Xenograft

value: No treatment


title: V0914-Untreated-sur_L002

description: Mus musculus Xenograft


title: V0914-Untreated-sur_L003

description: Mus musculus Xenograft


title: MLV129-766

value: Novel vaccine and PRRSV challenge


title: MLV129-763


title: MLV129-769


title: MLV129-765


title: MLV129-761


title: V0914-Untreated-sur_L001

description: Mus musculus Xenograft


title: GM12878-Pol2-S5-4H8-50K-1

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: nMOWChIP-seq data. Name format: Sample-target-cell/nuclei number-replicate number

library_source: genomic

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2. Uniquely mapped reads were filtered for known blacklisted genome regions using Samtools55 and bedtools56 to remove ChIP-seq artifacts.
Reads were extended by 100 bp on either ends
Sample was normalized and input subtracted. The reference genome was then divided into 100-bp bins and ChIP-seq signal for each bin was counted for both ChIP and input samples.
Sample was converted to BigWig format
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

molecule: genomic DNA

source_name: GM12878 cell line

growth_protocol: GM12878 cells were obtained from Coriell Institute for Medical Research. Cells were cultured in RPMI-1640 medium (30-2001, ATCC) with 15% fetal bovine serum (16000-044, Gibco) and 1% pen-strep (Invitrogen) at 37°C, 5% CO2. Cells were subcultured every 3 d to maintain exponential growth. C57BL/6J mice were purchased from Jackson Laboratory and maintained in the animal facility with 12-h light/12-h dark cycles and food and water ad libitum. 8-week old male mice were sacrificed by compressed CO2 followed by cervical dislocation. Mouse brains were rapidly dissected, frozen on dry ice and stored at -80°C. This study was approved by the Institutional Animal Care and Use Committee (IACUC) at Virginia Tech.

extract_protocol:
GM12878 protocol: Cells were centrifuged at 1,600 g for 5 min and resuspended in DPBS. Our experiments usually started with 4×10^5 cells/nuclei suspended in 100 µl of DPBS. 1 µl of PIC, 1 µl of 100 mM PMSF and 100 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added, mixed by vortexing and incubated at room temperature for 10 min. 10 µl of 100 mM CaCl2 and 2.5 µl 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 22 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing fragmented chromatin was collected into a new 1.5 ml tube and placed on ice. Chromatin volume equal to the stated number of cells per assay was taken and used for nMOWChIP, diluted to 60 µl loading volume with IP buffer if needed. Mouse protocol: A mouse brain was put on ice and PFC and cerebellum were dissected for nuclei isolation. The following steps are performed on ice and centrifugation performed at 4°C. Tissue was placed in 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)¬2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use]. Tissue was homogenized in the grinder set (D9063, Sigma-Aldrich) by slowly douncing 15 times with pestle A and 25 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. The supernatant was removed and the pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by pipetting. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. If mixed nuclei (without separation of neurons and glia) were used for MOWChIP directly, the nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS). If nuclei labeling and FACS sorting were conducted, 500 µl of 2% normal goat serum (50062Z, Life Technologies) in DPBS was added to the nuclei pellet and incubated for 10 min before resuspending. Anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was diluted with DPBS to 2 ng/µl. 8 µl of anti-NeuN was added to each 500 µl of nuclei suspension and incubated at 4°C for 1 h on a rotator. The labeled nuclei were then sorted using FACS (BD FACSAria, BD Biosciences). 8 µl of non-labeled nuclei were saved as unstained control prior to addition of anti-NeuN antobody. The concentration of nuclei suspension after FACS was typically low (~1.2×10^5/ml). The nuclei were re-concentrated by adding 200 µl of 1.8 M sucrose, 5 µl of 1M CaCl2 and 3 µl of 1M Mg(Ac)2 to 1 ml of the nuclei suspension. The mixture was incubated on ice for 15 min and centrifuged at 1800g for 15 min. Supernatant was removed and the nuclei pellet was resuspended in DPBS. Nuclei were digested using the same steps as GM12878 cells.
Libraries were constructed using Accel-NGS 2S Plus DNA Library kit (Swift Biosciences) following the manufacturer’s instructions. 1× EvaGreen dye (Biotium) was added to the amplification mixture to monitor the PCR amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library fragment size was examined using TapeStation (Agilent) and the concentration was quantified with KAPA Library Quantification kit (Kapa Biosystems). Libraries were pooled accordingly for sequencing by Illumina HiSeq 4000 SR50 mode.

tag: cell line

tag: antibody


title: GM12878-Pol2-S5-4H8-50K-2


title: Control_S13_RBMX_TSS

city: Pieve Emanuele

first: Giampaolo

last: Trivellin

state: Lombardy

address: Via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

data_processing:
Library strategy: 4C-seq
Sequencing data were demultiplexed and mapped to human reference genome (GRCh37/hg19). Reads located in restriction fragments flanked by restriction recognition sites of the same enzyme, in fragments smaller than 40 bp or within a window of 10 kb around the viewpoint were filtered out. Mapped reads were then converted to read counts per restriction fragment of first restriction enzyme.
For visualization, all samples were normalized for million mapped reads (reads per million, RPM) for a given genomic region (chrX:135,000,000-137,000,000, hg19) and smoothened using a 10-fragment running window algorithm.
To compare interaction profiles of patients to control, subtraction of normalized reads was applied. To reduce variability among control samples, an average profile from three independent control samples was used for subtraction.
Genome_build: human genome GRCh37/hg19

source_name: Blood

extract_protocol:
4C-seq libraries were prepared following the published protocol (van de Werken et al., 2012). For GPR101 and S6 breakpoint viewpoints, Csp6 and DpnII were used for the first and second digestion, repsectively. For RBMX and VGLL1 viewpoints, DpnII and Csp6 were used for the first and second digestion, repsectively. Parallel PCR reactions were performed to amplify from a total of 1 µg template per 4C library and viewpoint. PCR reactions were pooled and purified using 1.8x volume of AMPure XP beads (Agencourt, A63881).
Samples were indexed and sequenced with Ilumina Hi-Seq technology according to standard procedures.

treatment_protocol: Approximately, 1 × 106 to 2.5 × 106 cells from cultured lymphoblastoid cells or nucleated cell isolates from peripheral blood samples were used as input material for 3C library preparation. Trypsinized or disaggregated cells were filtered through 40 µm cell strainer and pelleted by centrifugation at 500x g. Cells were fixed in 5 ml of 2 % formaldehyde in 10 % FCS/ PBS and incubated for 10 minutes at room temperatures to cross-link chromatin. The reaction was quenched with glycine at a final concentration of 0.125 M and incubation at room temperature for 5 minutes. Cells were pelleted by centrifugation for 5 minutes at 500x g at 4ºC and washed on ice twice with 1x PBS. Cell pellets were either snap frozen in liquid nitrogen or processed for nuclei extraction. For nuclei extraction, fixed cells were resuspended in 2 ml freshly prepared lysis buffer (50 mM Tris pH7.5; 150 mM NaCl; 5 mM EDTA; 0.5 % NP-40; 1.15 % Triton X-100; 1x Roche Complete protease inhibitors) and incubated for 10 minutes on ice. Nuclei were pelleted by centrifugation for 5 minutes, 800x g at 4ºC and washed with 1x PBS.

value: Blood

tag: clinical phenotype

value: healthy control

tag: viewpoint

value: RBMX TSS


title: Control_S13_VGLL1_TSS

value: VGLL1 TSS


title: Control_S13_GPR101_TSS

value: GPR101 TSS


title: WM3248_6 µM rep 3

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 839 Health Science Ct.

department: Dermatology

institute: University of California, Irvine

description:
6 uM WM3248 9/17
nR093-L3-G3-P045-TGAGATCG-TCAGTTGC

data_processing:
trimmomatic to remove adaptors
Alignment to human reference genome with Tophat v2.1 (in conjunction with Bowtie2 v2.2.7 and Samtools v1.9)
Tuxedo Suite (Cufflinks v2.2.1) used to process reads
CummeRbund R v4.0.3 to visualize data
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: gene_exp.diff

growth_protocol: Cells were maintained in Tu2% (80% MCDB153, 20% Leibovitz's L-15, 2% FBS, 5 ug/mL Insulin Bovine, 1.68 mM CaCl2, sterilized by using 0.22 um filter) pH 7.2-7.4

extract_protocol:
RLT lysis buffer were added to adhered cells 24 h after treatment and RNA was extracted using a RNeasy Kit (Qiagen)
Poly-A Enrichment Library Construction

treatment_protocol: Cells were seeded at 8.4 x 10^4 cells per 6-well plate. Next day, cells were treated with ARN22089 at 0, 4, or 6 uM and harvested 24 h after treatment

value: Human melanoma cell line

value: treated 6 uM ARN22089 for 24 h


title: WM3248_6 µM rep 2

description:
6 uM WM3248 9/5
nR093-L3-G3-P042-TGAATGCG-CCATATCG


title: Control_S9_VGLL1_TSS


title: WM3248_6 µM rep 1

description:
6 uM WM3248 9/2
nR093-L3-G3-P039-AACAGTTG-AATTCACT


title: NPC-5

city: ShangHai

first: Yunguang

address: 320, Yueyang Road

institute: Center for Excellence in Molecular Cell Science, CAS

data_processing:
Sequenced reads were mapped to hg19 genome with TopHat
Fragments per kilobase of exon per million mapped reads (FPKM) values were determined  using Cufflinks as the gene expression measurements.
Genes with FPKM values <1 in all  samples were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Normal pancreatic ductal organoid

extract_protocol:
PDPCOs and NPOs in Matrigel were collected and washed with precooled PBS before lysis with 1 ml of TRIzol (Invitrogen, 15596018), and otal RNA was extracted according to the manufacturer‟s instructions.
A total amount of 3 μg RNA per sample was used as input material for RNA sample preparation. Ribosomal RNA was removed with a Globin-Zero Gold rRNA Removal Kit (Illumina, E7750X), and rRNA-free residue was cleaned up by ethanol precipitation. RNA-seq libraries were generated using a NEBNext Ultra RNA Library Prep Kit (New England Biolabs, E7530L) according to the manufacturer's instructions.

value: Pancreas

value: Organoid

tag: disease state

value: Normal pancreatic ductal


title: NPC-7

tag: tissue


title: CAS-NEN-4

source_name: NEN organoid

value: Pancreatic cancer


title: CAS-DAC-9

source_name: PDAC organoid


title: CAS-DAC-89


title: Control_S9_RBMX_TSS


title: NPC-4


title: CAS-DAC-88


title: WM3248_4 µM rep 2

description:
4 uM WM3248 9/5
nR093-L3-G3-P041-ACTTCCTG-AGTCGCGA

tag: treatment

value: treated 4 uM ARN22089 for 24 h


title: WM3248_4 µM rep 3

description:
4 uM WM3248 9/17
nR093-L3-G3-P044-TCTTACTC-GTCACAAG


title: CAS-IPMN-4

source_name: IPMN organoid


title: WM3248_4 µM rep 1

description:
4 uM WM3248 9/2
nR093-L3-G3-P038-TGCCGTAA-GTGCATCC


title: CAS-DAC-86


title: 25 mg/kg [T15]

data_processing:
trimmomatic to remove adaptors
Alignment to human reference genome with hisat2/2.1.0 and then used XenofilteR to remove the mouse contaimination from the human reads
featureCounts was used to check counts
DESeq2 in R to generated counts
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: counts

source_name: PDX (BRAFV600E, PTPN11N58S)

growth_protocol:
PDX (BRAFV600E, PTPN11N58S) was inserted into a small incision on either side of the anesthetized NSG mice.
Mice were monitored until the tumors reached 100-200 mm3 to start drug treatment.

extract_protocol:
a small chunk of PDX tumor was collect and lysed in RLT lysis buffer. RNA was extracted using a Rneasy Kit (Qiagen) and send to the Genomic Core Faicility at UCI
Poly-A Enrichment Library Construction

treatment_protocol:
ARN22089 was dissolved for 10 or 25 mg/kg doses in 100 uL of vehicle (80% saline, 10% Tween80, and 10% PEG400).
Mice were treated with 100 uL of vehicle or inhibitor via intravenous (IV) tail vein injection of ARN22089 inhibitor twic a week as the tumor grow for four weeks.
When vehicle treated tumors reached endpoint (1500 mm3), tumors were collected

value: PDX (BRAFV600E, PTPN11N58S)

value: 25 mg/kg


title: WM3248_0 µM rep 2

description:
0 uM WM3248 9/5
nR093-L3-G3-P040-TGTTAACA-TTCAGTGA

value: untreated (DMSO)


title: CAS-DAC-85


title: CAS-DAC-84


title: WM3248_0 µM rep 3

description:
0 uM WM3248 9/17
nR093-L3-G3-P043-ACTTGTAC-AAGCATGG


title: HFD 16W_2

first: Chen

last: Zhiyun

address: No. 9, Street 9, Xiasha economic development zone, Jianggan district

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

data_processing:
The average insert size for the paired-end libraries was 300 bp (±50 bp). After removing the low-quality reads, de novo assembly of the transcriptome was performed with Trinity version 2.4.0. The transcripts were grouped into clusters based on sharing sequences. The longest transcript in the cluster was kept as the “Unigene”.
All assembled Unigenes were aligned against the following database: NCBI non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), Swiss-Prot (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
The expression levels of Unigenes were quantified using Salmon program by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (P value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analyses were again performed on the differentially expressed Unigenes by ggplot2 Rrscript.
Supplementary_files_format_and_content: The xlsx file contains the nomalized expression levels of the mRNAs from the 18 samples

organism: Meriones unguiculatus

source_name: liver

growth_protocol: The mice were exposed to continuous light and 12:12 h light/dark cycle, and provided with food and water ad libitum.

extract_protocol:
Total RNA was extracted using Trizol regent (Invitrogen, CA, USA) according to the manufacturer's procedure.
The total RNA were quantified by a 2100 Bioanalyzer (Agilent Technologies) and purified by RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN (RNA integrity number) >7.0. Approximately 10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Then the mRNA was randomly broken into short fragments by fragmentation buffer. Next, the cleaved RNA fragments were reverse-transcribed to generate the final cDNA library following the protocol of the mRNA-Seq sample preparation kit (Illumina, San Diego, USA). The mRNA sequencing was performed on Hiseq4000 platform with 150PE strategy and Hiseq4000 platform with 150 strategyThe average insert size for the paired-end libraries was 350 bp (±50 bp). After removing the low-quality reads, de novo assembly of the transcriptome was performed with Trinity version 2.4.0. The transcripts were grouped into clusters based on sharing sequences. The longest transcript in the cluster was kept as the “Unigene”.

treatment_protocol: After one week of adaptive feeding, 36 male gerbils (body weight 40~60g) were randomly divided into two groups, namely normal feeding diet (ND) group and high-fat diet (HFD) group. Each group was divided into three time points of 4-week (4W), 8-week (8W) and 16-week (16W), with 6 gerbils in each group. The gerbils in ND group were fed with normal feed and had water freely. The gerbils in HFD group were fed with high-fat diet and had water freely. The high-fat diet consists of 80.5% ordinary feed, 10% egg yolk powder, 7% lard bile, 2% cholesterol and 0.5% No. 3 bile salt. The ordinary feed and high-fat feed are processed and produced by the Zhejiang Academy of Medical Sciences Center of Laboratory Animals.

tag: tag

tag: diet

value: High-fat diet

tag: time point

value: 16 weeks


title: ND 16W_2

value: Normal diet


title: ND 16W_3


title: WM3248_0 µM rep 1

description:
0 uM WM3248 9/2
nR093-L3-G3-P037-TGCAGTCG-CTGTAGTG


title: Control_S9_GPR101_TSS

value: Blood

value: healthy control


title: HFD 16W_3


title: CAS-DAC-83


title: S13_GPR101_TSS

value: X-linked acrogigantism


title: HFD 16W_1


title: ND 16W_1


title: CAS-DAC-82


title: 25 mg/kg [T14]


title: 25 mg/kg [T13]


title: S6_breakpoint

value: breakpoint


title: S9_GPR101_TSS

value: GPR101 TSS


title: 25 mg/kg [T12]


title: CAS-DAC-81


title: S7_GPR101_TSS


title: HFD 8W_2

value: 8 weeks


title: HFD 8W_1


title: 25 mg/kg [T11]


title: HFD 8W_3


title: CAS-DAC-80

value: Pancreas


title: CAS-DAC-8

value: Organoid


title: 10 mg/kg [T10]

value: 10 mg/kg


title: S6_RBMX_TSS

value: RBMX TSS


title: ND 8W_3


title: S6_VGLL1_TSS

value: VGLL1 TSS


title: ND 8W_2


title: CAS-DAC-79

value: Pancreatic cancer


title: ND 8W_1


title: CAS-DAC-78


title: 10 mg/kg [T08]

value: PDX (BRAFV600E, PTPN11N58S)


title: BC376_PBMC_Tumor

city: Duarte

first: Peter

middle: P

last: Lee

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

institute: Beckman Research Institute at City of Hope

description: BD Precise Platform

data_processing:
The raw counts were imputed by scImpute R package (v0.0.7) with kcluster = 5.
The imputed counts were analyzed by Seurat R package (v3.1.4). Briefly, nonviable cells (defined as the cells in which more than 20% expressing genes are mitochondrial genes) were removed. In addition, the potential empty well or duplets (defined as cells in which less than 200 genes are expressed or more than 2500 genes are expressed, respectively) were also discarded for further analysis
The normalization was implemented by Seurat with default settings.
The top 1,000 most variable protein-encoding genes were selected for principle component analysis. Based on the two heuristic methods in Seurat (modified Jack Straw procedure and ranking variance method), the top 12 principal components were used for the further non-linearly dimensional reduction (i.e., tSNE) and clustering analysis.
Genome_build: hg18
Supplementary_files_format_and_content: Both raw counts and imputed counts were provided here with the meta-data table for each cell

molecule: polyA RNA

source_name: CD8+ T cells from PBMC and tumor

extract_protocol:
CD8+ T cells were stained with monoclonal antibodies for CD8, PD-1, CD39, CD103, CD69, CD137, and CCR7 as described above and then single-cell index sorted using a BD ARIA III FACS system into BD Genomics Precise WTA 96 well plates for whole transcriptome analysis.
Single-cell libraries were prepared as recommended.

value: PBMC + Tumor

tag: patient


title: S2_GPR101_TSS


title: CAS-DAC-76


title: HFD 4W_3

value: High-fat diet

value: 4 weeks


title: S6_GPR101_TSS


title: CAS-DAC-77


title: HFD 4W_2


title: 10 mg/kg [T06]


title: BC304_PBMC

description: BD Precise Platform

source_name: CD8+ T cells from PBMC

value: PBMC


title: CAS-DAC-75


title: vehicle [T04]

value: vehicle


title: HFD 4W_1


title: CAS-DAC-73


title: ND 4W_2

value: Normal diet


title: CAS-NEN-3


title: BC308_T+LN_Normal_p4

description: BD Precise Platform

source_name: CD8+ T cells from tumor positive lymph nodes and normal breast tissue

value: Tumor-positive LN + Normal


title: BC304_Tumor_Normal

description: BD Precise Platform

source_name: CD8+ T cells from tumor and normal breast tissue

value: Tumor + Normal


title: vehicle [T05]


title: ND 4W_1


title: ND 4W_3


title: BC308_T+LN_Normal_P3

description: BD Precise Platform


title: CAS-DAC-72


title: vehicle [T02]


title: CAS-DAC-71


title: Mix_circRNA

city: Shenyang

first: Zhiyong

last: Liu

state: Liaoning Province

address: Dongling Road 120

institute: Shenyang Agriculral University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to identify circRNAs.
Genome_build: BRAD：Brassica_rapa_v3.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

organism: Brassica rapa subsp. pekinensis

source_name: root, stem and leaf

growth_protocol: The DH ‘FT’ seeds were seeded in the greenhouse of Shenyang Agricultural University after vernalization at 4 ℃ for 20 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: The seedlings with four true leaves included roots, stems, and leaves (Mix), and anthers at different developmental stages (Ant) were sampled

value: whole seedlings with four true leaves included roots, stems, and leaves


title: TL_7

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: minfi and RnBeads R packages

label: Cy5 and Cy3

source_name: tolerogenic monocyte-derivated Dendritic Cells (TL)

label_protocol: Standard Illumina Protocol

growth_protocol: PBMCs were isolated using Ficoll-Paque gradient centrifugation. MOs were isolated from PBMCs using positive selection with MACS CD14 microbeads (Miltenyi Biotec). Cells were resuspended in RPMI Medium 1640 + GlutaMAXTM-1 (Gibco, Life Technologies) containing 10% fetal bovine serum, 100 unit’s/mL penicillin, and 100 μg/mL streptomycin. For TolDC differentiation, the medium was supplemented with 10 ng/mL human IL-4, 10 ng/mL GM-CSF (PeproTech), and 10 nM of Vitamin D3 or calcitriol (Sigma Aldrich)

extract_protocol: DNA was extracted with Maxwell RSC Clutured Cells DNA kit (Promega)

value: tolerogenic monocyte-derived Dendritic Cells

value: presence of the active form of vitamin D (calcitriol)

tag: days of culture


title: 10 mg/kg [T09]


title: vehicle [T01]


title: CAS-DAC-70

value: Pancreas

value: Organoid


title: Vector_3_P13

city: Shenzhen

first: Liyun

last: Gong

address: Nanhai Road 3688 number

institute: Shenzhen University

data_processing:
Illumina Casava2.19 software used for basecalling
fastp v0.20.0 for quality control
HISAT2 version 2.1.0 for mapping reads to the grch38 genome with parameter "-p 4 --dta-cufflinks"
featureCounts v1.6.1 was used to count reads mapped to each gene with arguments '-T 4 -p -t exon -Q 20 -g gene_id'
R package Deseq2 for analysis of differential gene expression under two conditions
Genome_build: grch38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HCT-116 cell

growth_protocol: HCT-116 was cultured in Dulbecco's modified Eagle's medium (DMEM) (HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA).

extract_protocol:
HCT-116 RNA was harvested using Trizol reagent and using the total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Removing the medium and washed twice with PBS, then added 1 ml Trizol to culture dish and transferred the lysate to 1.5ml tube.

value: colon

value: wild type

value: Trizol


title: BC379_Tumor

description: BD Precise Platform

source_name: CD8+ T cells from tumor

value: Tumor


title: CAS-DAC-7

value: Pancreatic cancer


title: CAS-DAC-69


title: Healthy-3rd-4

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

data_processing:
RNA-seq data were processed quality control (QC), trimming and mapping to the human reference genome hg38 using CLC Genomics Workbench. Gene expression level was measured based on the transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: SARS-CoV-2 naïve

extract_protocol:
Total RNA was extracted from PBMCs by using the RNeasy Mini Kit. A total amount of 100 ng total RNA per sample was used to prepare for the rRNA-depleted cDNA library by Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: three dose of inactivated vaccine

tag: time

value: 14 days after vaccination


title: Vector_1_P12

tag: genotype


title: MBC35_LN

description: BD Precise Platform

source_name: CD8+ T cells from LN

value: LN


title: CAS-DAC-68

tag: cell type


title: TL_6


title: TL_10


title: DC_10

source_name: monocyte-derivated Dendritic Cells (DC)

value: monocyte-derived Dendritic Cells

value: absence of the active form of vitamin D (calcitriol)


title: MO_9

source_name: monocytes (MO)

value: monocytes


title: MBC35_PBMC

description: BD Precise Platform

value: PBMC


title: CAS-DAC-67


title: DC_9


title: Healthy-3rd-3


title: Healthy-3rd-1


title: 10 mg/kg [T07]

value: PDX (BRAFV600E, PTPN11N58S)

value: 10 mg/kg


title: CAS-DAC-66


title: BC379_PBMC_Normal

description: BD Precise Platform

source_name: CD8+ T cells from PBMC and normal breast tissue

value: PBMC + Normal


title: Golph3_2_P12


title: Golph3_3_P13


title: TL_9

value: tolerogenic monocyte-derived Dendritic Cells

value: presence of the active form of vitamin D (calcitriol)


title: vehicle [T03]

value: vehicle


title: DC_7


title: Golph3_1_P8

value: colon

value: wild type


title: BC361_PBMC

description: BD Precise Platform


title: BC365_Tumor

description: BD Precise Platform

value: Tumor


title: Healthy-2nd-6

value: two dose of inactivated vaccine


title: CAS-DAC-65

source_name: PDAC organoid

value: Pancreas

value: Organoid

value: Pancreatic cancer


title: Healthy-2nd-5

value: 14 days after vaccination


title: Vector_2_P11

value: Trizol


title: NEN organoid [CAS-NEN-2]

data_processing:
Illumina adapter sequences as well as transposase sequences were trimmed  with Trimmomatic.
The reads were mapped to the human reference genome hg19 with Bowtie v1.0.0.
Duplicate reads were removed with SAMtools v0.1.19.
Only uniquely aligned reads were used for peak calling with Hotspot using default parameters (http://www.uwencode.org/proj/hotspot/).
Quantile normalization was then performed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized openness values for each sample

source_name: Pancreas

extract_protocol:
PDPCOs in Matrigel were collected and washed with precooled PBS. Cells were washed once with 200 μl of cold PBS buffer and were then centrifuged for 5 min at 500 × g and 4°C. The supernatant was removed and discarded. The cell pellet was resuspended in 50 μl of cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) by gently pipetting up and down. The cells were immediately centrifuged at 500Xg for 5 min at 4°C to collect nuclei, and the transposition reaction was immediately continued.
ATAC-seq libraries were generated using a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the Illumina Nova platform, and 150 bp paired-end reads were generated. Libraries that contained less than 15 million aligned, deduplicated reads were sequenced again, and the additional reads were pooled prior to deduplication.

value: NEN organoid

tag: Sex

value: Male

value: Body

value: Pancreatic Cancer

value: Pancreatic Neuroendocrine Tumor

value: PANET

value: IV


title: NEN organoid [CAS-NEN-4]

value: Tail

value: NEC


title: CAS-DAC-63


title: NEN organoid [CAS-NEN-3]

value: Female

value: Head

value: IA


title: MO_7

value: monocytes


title: FNA12_Tumor_P10

description: BD Precise Platform

value: Tumor


title: Healthy-2nd-2

value: PBMC

value: two dose of inactivated vaccine


title: NEN organoid [CAS-NEN-1]

value: Pancreatic cancer


title: BC331_Normal

description: BD Precise Platform

source_name: CD8+ T cells from normal breast tissue

value: Normal


title: Ant_circRNA

source_name: anther

value: anther


title: BC361_Tumor

description: BD Precise Platform


title: DC_6

value: monocyte-derived Dendritic Cells

value: absence of the active form of vitamin D (calcitriol)


title: CAS-DAC-64

value: Pancreas

value: Organoid


title: PDAC organoid [CAS-DAC-9]

description:
Exocrine_PDPCO_ATAC_openness.txt
PDPCO_drug_screening.txt

value: PDAC organoid

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: Pancreatic Ductal Adenocarcinoma

value: PAAD

value: 2 - Moderately differentiated

value: IIB


title: MO_6

value: monocytes


title: Healthy-2nd-4

value: PBMC

value: 14 days after vaccination


title: BC341_PBMC_Tumor

description: BD Precise Platform

source_name: CD8+ T cells from PBMC and tumor

value: PBMC + Tumor


title: FNA12_Tumor_P11

description: BD Precise Platform

value: Tumor


title: Healthy-2nd-1

value: two dose of inactivated vaccine


title: CAS-DAC-60

value: Pancreatic cancer


title: BC331_PBMC

description: BD Precise Platform

source_name: CD8+ T cells from PBMC


title: Healthy-2nd-3


title: CAS-DAC-6


title: Healthy-1st-5

value: one dose of inactivated vaccine


title: CAS-DAC-62

value: Pancreas


title: MO_10


title: CellSelex_HumanIslet_cycle0

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

data_processing:
Data processing was done using HiSeq’s Real Time Analysis (RTA) from Casava software. Base calling files were transformed into zipped FASTQ files containing raw reads with base qualities. These raw read files were then filtered by Illumina’s internal filter resulting in 2 FASTQ files (1 per read) containing all pass-filter reads. FASTQ files were used as input for frequency evaluation and Clustal-Ω and for APTANI analysis. Please see Van Simaeys et al "RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutic to human β cells " nature communication 2022 for specific primers and conditions.
Genome_build: Aptamers were selected using clustal omega and  APTANI, a computational method for the identification of target-specific aptamers from HT-SELEX data and secondary structure information. Briefly, APTANI first calculates the relative enrichment of each individual aptamer sequence produced by the HT-SELEX process and then, for each aptamer with an enrichment higher than a pre-selected threshold, predicts all secondary structures in a specific energy range and extracts the motifs represented in these structures. As a result, APTANI returns a list of aptamers, ranked by their abundance and by the presence of structural motifs. Here we used APTANI on HT-SELEX data from 8  cycles selection on human islet, then on the 8th cycle of aptamers selected on mouse islet (cycle 9) and then on two chimeric cycles (mouse aptamers on human islets). Parameters were set at default values and the enrichment and motif frequency thresholds were set at 0.01% and 0.05%, respectively.
Supplementary_files_format_and_content: Processed data files contains the frequencies of the unique aptamer sequences found in each analyzed SELEX cycle. Frequency files are structured listing the unique sequence on a single line, followed by a semicolon and then the frequency value in scientific notation. Sequences are listed in a ranked fashion, from the most frequent one (i.e. the one showing higher presence in the investigated SELEX cycle) to those showing lower frequencies, usually in the range of 10e-8.

organism: synthetic construct

source_name: random aptamer library

extract_protocol: cDNA from cycles 1-8 in the HT “cluster-cell” and cycles M8, M8H1 and M8H2 from the toggle cell SELEX were sampled for HT-sequencing by tagging aptamers’ constant region with two sequential PCRs. The first PCR reactions were performed in 100 µl of water containing 1X PCR buffer, MgCl2 solution (1.5 mM), dNTPs (200 µM each), DNA template (5 ng/µl) recombinant Taq polymerase (5 U, Invitrogen) and the PFA and PRA primers corresponding to each cycle described above. The reactions were performed in the GS482 thermocycler (G-STORM) using the following program: 95ºC 5’, 5x (95ºC 1’, 56ºC 30”, 72ºC 30”), 72ºC 10’. PCR was purified via gel extraction using the QIAquick Gel Extraction Kit (QIAGEN) following manufacturer instructions. The second PCR was performed using the same condition described above but using the UFB and PRB primers  and the following cycles: 95ºC 5’, 6x (95ºC 30’’, 65ºC 30’’, 72ºC 30”), 72ºC 10’. Products were purified by gel extraction, quality evaluated via bio-analyzer (Agilent). Library quantitation and pooling took place at the Hussman Institute for Human Genomics-Center for Genome Technology using the KAPA Library Quantification Kit for Illumina platforms (part# KK4854). 10-13 pM of pooled samples were loaded on the Illumina cBot for cluster generation according to manufacturer's recommendations. Sequencing was performed on an Illumina HiSeq 2000/2500 (HCS 2.0.12.0) using the reagents provided in the Illumina TruSeq PE Cluster Kit v3 and the TruSeq SBS Kit-HS (200 cycle) kit.

tag: description

value: SELEX random library cycle 0


title: PDAC organoid [CAS-DAC-7]

value: PDAC organoid

value: Female

value: Tail

value: 3 - Poorly differentiated


title: CAS-DAC-61

value: Organoid


title: Healthy-1st-4


title: CAS-IPMN-3

source_name: IPMN organoid


title: Healthy-1st-3


title: PDAC organoid [CAS-DAC-6]

value: Male

value: Head

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: Pancreatic Ductal Adenocarcinoma

value: PAAD

value: 2 - Moderately differentiated


title: CellSelex_MouseHumanIslet_cycleM8H2

value: Toggle SELEX library after 8 selection cycles against mouse islets followed by 2 selection cycle against human islets


title: PDAC organoid [CAS-DAC-5]

value: Pancreatic cancer

value: IIB


title: CellSelex_MouseHumanIslet_cycleM8H1

value: Toggle SELEX library after 8 selection cycles against mouse islets followed by 1 selection cycle against human islets


title: CAS-DAC-58

value: Pancreas


title: Healthy-1st-1

value: PBMC

value: one dose of inactivated vaccine

value: 14 days after vaccination


title: CAS-DAC-57


title: PDAC organoid [CAS-DAC-4]

value: PDAC organoid

value: Body

value: 3 - Poorly differentiated


title: Healthy-3rd-2

value: three dose of inactivated vaccine


title: CAS-DAC-56

value: Organoid


title: CellSelex_MouseIslet_cycle9

value: Toggle SELEX library after 8 selection cycles against mouse islets


title: Patient-1st-5

source_name: SARS-CoV-2 recovered


title: PDAC organoid [CAS-DAC-8]

value: Female

value: Head

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: Pancreatic Ductal Adenocarcinoma

value: IB


title: ACC organoid [CAS-ACC-1]

value: ACC organoid

value: Pancreatic cancer

value: Pancreatic Acinar Cell Carcinoma

value: PAAC

value: III


title: Patient-1st-4

value: PBMC

value: one dose of inactivated vaccine

value: 14 days after vaccination


title: CellSelex_HumanIslet_cycle8

value: Cluster SELEX library from selection against human islets cycle 8


title: PDAC organoid [CAS-DAC-42]

value: PDAC organoid

value: Male

value: PAAD

value: 3 - Poorly differentiated


title: Patient-1st-3


title: CellSelex_HumanIslet_cycle7

value: Cluster SELEX library from selection against human islets cycle 7


title: CAS-DAC-55

value: Pancreas

value: Organoid


title: PDAC organoid [CAS-DAC-41]

value: Head

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: Pancreatic Ductal Adenocarcinoma

value: 2 - Moderately differentiated

value: IB


title: CellSelex_HumanIslet_cycle6

value: Cluster SELEX library from selection against human islets cycle 6


title: CAS-DAC-53

value: Pancreatic cancer


title: Healthy-1st-2

value: PBMC

value: one dose of inactivated vaccine

value: 14 days after vaccination


title: PDAC organoid [CAS-DAC-3]

value: PDAC organoid

value: Male

value: IIB


title: Patient-1st-1


title: Patient-1st-2


title: CAS-DAC-52


title: CellSelex_HumanIslet_cycle4

value: Cluster SELEX library from selection against human islets cycle 4


title: CAS-IPMN-2

value: Pancreas


title: CellSelex_HumanIslet_cycle5

value: Cluster SELEX library from selection against human islets cycle 5


title: Control-5

value: No inactivated vaccine

value: 0 day


title: PDAC organoid [CAS-DAC-39]

value: Body

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: PAAD


title: PDAC organoid [CAS-DAC-38]

value: Head

value: Pancreatic Ductal Adenocarcinoma

value: IV


title: CAS-DAC-50

value: Organoid

value: Pancreatic cancer


title: PDAC organoid [CAS-DAC-37]

value: PDAC organoid

value: Female

value: 2 - Moderately differentiated

value: IIA


title: Control-4

value: PBMC


title: PDAC organoid [CAS-DAC-36]


title: CAS-DAC-5

value: Pancreas


title: CAS-DAC-54


title: Control-3

value: No inactivated vaccine


title: CellSelex_HumanIslet_cycle1

value: Cluster SELEX library from selection against human islets cycle 1


title: PDAC organoid [CAS-DAC-35]

value: Male

value: IIB


title: CellSelex_HumanIslet_cycle3

value: Cluster SELEX library from selection against human islets cycle 3


title: Control-1

value: 0 day


title: CellSelex_HumanIslet_cycle2

value: Cluster SELEX library from selection against human islets cycle 2


title: CAS-NEN-2

source_name: NEN organoid


title: PDAC organoid [CAS-DAC-34]

value: Body

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: Pancreatic Ductal Adenocarcinoma

value: PAAD

value: 3 - Poorly differentiated

value: IB


title: CAS-ACC-1

source_name: ACC organoid

value: Organoid

value: Pancreatic cancer


title: Control-2

value: PBMC


title: CAS-NEN-1

value: Pancreas


title: PDAC organoid [CAS-DAC-33]

value: PDAC organoid

value: Female

value: Head

value: 2 - Moderately differentiated

value: III


title: PDAC organoid [CAS-DAC-32]


title: CAS-DAC-42


title: CAS-DAC-41


title: PDAC organoid [CAS-DAC-31]

value: Male

value: IIB


title: PDAC organoid [CAS-DAC-30]

value: Pancreatic Cancer


title: CAS-DAC-4


title: CAS-DAC-39


title: PDAC organoid [CAS-DAC-2]

value: Body

value: Pancreatic Adenocarcinoma


title: Human_SSNS_3

city: HangZhou

first: Danni

address: 3333 Binsheng Rd, Hangzhou,Zhejiang

institute: Children's Hospital Affiliated to Zhejiang University

description: Gene expression of urinary sediment cells in children with INS before steroid therapy

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for 12-16 hours per the manufacturer’s recommendations.  Hybridized samples were run on the NanoString nCounter preparation station using the high-sensitivity protocol, in which excess capture and reporter probes were removed and transcript-specific ternary complexes were immobilized on a streptavidin-coated cartridge.

scan_protocol: The samples were scanned at maximum scan resolution on the nCounter Digital Analyzer.

data_processing: Gene expression data for each individual sample were normalized by quantile normalization. Gene counts collected from the NanoString scanner were used as input variables with a reference distribution generated using a pool of counts from all samples and 770 genes (excluding data from positive and negative control probes).

source_name: Human,SSNS

label_protocol: Per sample, 50 ng of total RNA in a final volume of 5 μl was mixed with a 3′ biotinylated capture probe and a 5′ reporter probe tagged with a fluorescent barcode from the custom gene expression code set.

extract_protocol: 10 mL of urine samples were centrifuged at 3000g for 10 min at 4C immediately after collection. The supernatant was discarded, and the urinary cell pellet mixture were mixed with RNAlater (Invitrogen, CA, USA) and stored at 80C until further use. RNA was extracted from the cell mixture using an EX3600 instrument with the magnetic bead method (catalog: Z-ME-0044, Shanghai Zhijiang Biotechnology Ltd. Co).

value: female

tag: sediment

value: Urinary sediment

tag: disease

value: steroid-resistant nephrotic syndrome


title: Human_SSNS_2

value: male


title: Human_SRNS_2

source_name: Human,SRNS


title: PDAC organoid [CAS-DAC-29]

value: Pancreatic cancer

value: Pancreatic Ductal Adenocarcinoma

value: PAAD

value: 3 - Poorly differentiated

value: IIA


title: Human_SRNS_3


title: PDAC organoid [CAS-DAC-28]

value: PDAC organoid

value: Head


title: CAS-DAC-38

value: Pancreas

value: Organoid


title: 197

description: SAMPLE 8

hyb_protocol: Total RNA was hybridized overnight at 65°C for 14 to 18 hours as per manufacturers’ recommendations.

scan_protocol: RNA transcripts were detected using Nanostring PanCancer Immune Panel with nCounter technology (Nanostring Technologies).

data_processing:
Quality control and normalization of data were performed with nSolver Analysis Software version 4.0 and the measured gene expression values were normalized to the geometric mean of 40 housekeeping genes. Advanced analysis was conducted using nCounter Advanced Analysis Software version 2.0.115. Heatmaps were generated using the ComplexHeatmap R package (v2.1.1).
Normalized log2 count data

source_name: breast tumor

extract_protocol: RNA was extracted from 10µm thick slices of unbaked formalin fixed paraffin embedded (FFPE) tissue using Qiagen miRNeasy FFPE kits.

tag: age

tag: grade

value: texlo


title: 192

description: SAMPLE 6

value: texhi


title: 193

description: SAMPLE 7


title: 186

description: SAMPLE 5


title: CAS-DAC-37

tag: tissue

tag: disease state


title: Human_SRNS_1


title: Micro-organoid-STAR-low_2

city: Utrecht

first: Maria

middle: Christine

last: Heinz

address: Heidelberglaan 100

department: Molecular Cancer Research

country: Netherlands

institute: University Medical Center Utrecht

description: Cells derived from size-filtered, small organoids were sorted for STAR-low expression prior to bulk RNAseq.

data_processing:
Reads were aligned with Hisat2 (version 2.0.4) with enabled alignment tailoring for transcript assemblers.
Reads per gene were counted with htseq-count script (Hisat2 software suite, strandness disabled, identification attribute set to gene_id).
Genes with no reads in any of the samples were excluded from analysis.
Differential gene expression was performed with DESeq2 package.
Significantly changing genes were called after Walt test followed by correction for multiple testing (Benjamini-Hochberg method).
Data visualisation was performed upon normalisation, log2 transformation, and noise-stabilisation using the rlogTransformation function of the DESeq2 package.
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing transcript counts (PCR duplicates have been removed)

source_name: Colorectal cancer

growth_protocol: Engineered human colorectal cancer organoids (APCKO/KO; KRASG12D/-; TP53KO/KO; SMAD4 KO/KO) were grown from single cells following trypsinisation for 12 days in Matrigel (Corning). Growth media was refreshed every 2-3 days. Growth media contained Advanced DMEM/F12 (Invitrogen), supplemented with 10 mM Hepes (Invitrogen), 1% GlutaMAX (Invitrogen), 1% Penicillin-Streptomycin (Lonza) as well as 1x B27 supplement (Invitrogen), 1.25 mM N-Acetyl-L-cysteine (Sigma-Aldrich), 10 mM Nicotinamide (Sigma-Aldrich), 500 nM A83-01 (Tocris), and 10 µM SB202190 (Gentaur).

extract_protocol:
RNA was extracted using the RNeasy Mini RNA extraction kit (Qiagen, Cat. No. 74106) according to the manufacturer’s instructions with DNaseI treatment.
Up to 73ng RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems). In short, oligo hybridisation and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94⁰C for 6:30 min. First strand synthesis, second strand synthesis, and A-tailing were performed according to protocol. For the adapter ligation, a 1.5μM stock was used (NextFlex DNA barcodes, Bioo Scientific). First and second post-ligation cleanup were performed according protocol. The library was amplified in 13 cycles and the subsequent cleanup was performed using a 0.8x bead-based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer (Agilent Technologies) and the library concentration was measured using the KAPA Library Quantification Kit (KAPA Biosystems). Sequencing was performed using an Illumina NextSeq 500, while 50‐bp paired‐end reads were generated.

treatment_protocol: Organoids were harvested with 1 mg/mL Dispase II (Life Technologies) and pelleted by gentle spinning at 300xg, 4 min, 4°C. The organoid suspension was first applied onto a 100 µm strainer (VWR), while organoids passing the filter were collected in a 50 mL falcon tube. Organoids trapped in the filter (>100µm) were isolated using 10 mL of Advanced DMEM/F12, pelleted and kept on ice (big organoids). Next, to collect organoids of 40-70 µm in diameter, the flow-through of the 100 µm strainer was subjected first to a 70 µm strainer (VWR) and subsequently to a 40 µm strainer (VWR). Organoids trapped in the 40 µm strainer were washed out with 10 mL of Advanced DMEM/F12, pelleted, and kept on ice (small organoids). Next, organoid subfractions were trypsinized to single cells using TrypsinEDTA (Sigma-Aldrich), trypsin activity was blocked with trypsin inhibitor (Sigma-Aldrich) at a 1:1 ratio, and single cells were pelleted by spinning at 550xg, 4min, 4°C. To visualise dead cells on FACS, 1.5 µM DRAQ7 (Cell Signaling Technologies) was added to growth medium containing 10 µM Y-27632 (Gentaur). On FACS, alive cells with STAR expression being high, medium (mid) or negative (neg) were collected duplicates or triplicates (10,000-20,000 cells each). Samples were pelleted and snap-frozen until processed further.

tag: organoid size

value: micro

tag: star level

value: low

tag: technical replicate


title: PVtt cell line PVtt treated with TGFbeta1

city: Beijing

first: Pengyuang

last: Yang

address: 15 Datun Road, Chaoyang District

department: Key Laboratory of Infection and Immunity of CAS

institute: Institute of Biophysics, Chinese Academy of Sciences

description: TGFbeata1 treated replicate 3 of 4

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using an Affymetrix 428 scanner and Imagene version 4 software.

data_processing: Data analysis was carried out using Imagene, version 5.1 and Genesight version 4 (Biodiscovery Inc). The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy5/Cy3 fluorescence ratios from each pair samples.

source_name: PVtt TGFbeta1 treated

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: cells were maintained in high glucose DMEM (Gibco) supplemented with 10% FBS (Hyclone), 100 μg/mL penicillin and 100 U/mL streptomycin. The cells were incubated at 37 ℃ in a humidified atmosphere of 5 % CO2.

extract_protocol: Total RNA (HCC cell lines) were extracted by Trizol (Invitrogen, USA) following the manufacturer’s protocols.

treatment_protocol: Recombinant human TGFβ1 was purchased from Peprotech (Peprotech Inc., USA) and used at the concentration of 2.5 ng/mL.

tag: cell line

value: PVtt

value: Hepatocellular

source_name: PVtt


title: Huh7 cell line Huh7 treated with TGFbeta1

description: TGFbeata1 treated replicate 2 of 4

source_name: Huh7 TGFbeta1 treated


title: PDAC organoid [CAS-DAC-27]

source_name: Pancreas

value: Male

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: 2 - Moderately differentiated

value: III


title: HepG2 cell line HepG2 treated with TGFbeta1

description: TGFbeata1 treated replicate 4 of 4

source_name: HepG2 TGFbeta1 treated


title: 213

description: SAMPLE 9


title: Micro-organoid-STAR-low_1


title: CAS-DAC-35

source_name: PDAC organoid

value: Pancreatic cancer


title: Human_SSNS_1

value: male

value: Urinary sediment

value: steroid-resistant nephrotic syndrome


title: MHCC cell line MHCC treated with TGFbeta1

description: TGFbeata1 treated replicate 1 of 4

source_name: MHCC TGFbeta1 treated

value: MHCC

source_name: MHCC


title: 390

description: SAMPLE 36


title: PDAC organoid [CAS-DAC-26]

value: PDAC organoid

value: Head

value: Pancreatic Ductal Adenocarcinoma

value: PAAD


title: CAS-DAC-34

value: Pancreas

value: Organoid


title: 384

description: SAMPLE 34

value: texlo


title: PDAC organoid [CAS-DAC-24]

value: Male

value: IIB


title: 382

description: SAMPLE 33


title: Micro-organoid-STAR-mid_1

description: Cells derived from size-filtered, small organoids were sorted for STAR-medium expression prior to bulk RNAseq.

value: micro

value: medium


title: CAS-DAC-32


title: PDAC organoid [CAS-DAC-25]

value: Female

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: 2 - Moderately differentiated

value: IB


title: 389

description: SAMPLE 35


title: Micro-organoid-STAR-high_1

description: Cells derived from size-filtered, small organoids were sorted for STAR-high expression prior to bulk RNAseq.

value: high


title: PDAC organoid [CAS-DAC-23]

value: PDAC organoid

value: Pancreatic cancer

value: 3 - Poorly differentiated

value: III


title: Macro-organoid-STAR-low_3

description: Cells derived from size-filtered, big organoids were sorted for STAR-low expression prior to bulk RNAseq.

value: macro

value: low


title: 374

description: SAMPLE 32

value: texlo


title: CAS-DAC-31

value: Pancreas

value: Organoid


title: CAS-DAC-36


title: PDAC organoid [CAS-DAC-22]

value: Male

value: Body

value: Pancreatic Ductal Adenocarcinoma

value: PAAD


title: 166

description: SAMPLE 4

value: texhi


title: 373

description: SAMPLE 31


title: CAS-DAC-30


title: CAS-DAC-3


title: 287

description: SAMPLE 30


title: Macro-organoid-STAR-low_2


title: PDAC organoid [CAS-DAC-21]

value: Pancreatic Cancer

value: Pancreatic Adenocarcinoma

value: 2 - Moderately differentiated

value: IIB


title: PDAC organoid [CAS-DAC-20]

value: PDAC organoid

value: Pancreatic cancer

value: Female

value: Head


title: Micro-organoid-STAR-mid_2

value: micro

value: medium


title: Macro-organoid-STAR-low_1

value: macro

value: low


title: CAS-DAC-29

value: Pancreas

value: Organoid


title: CAS-DAC-33


title: PDAC organoid [CAS-DAC-1]

value: Pancreatic Ductal Adenocarcinoma

value: IB


title: Macro-organoid-STAR-mid_3

description: Cells derived from size-filtered, big organoids were sorted for STAR-medium expression prior to bulk RNAseq.


title: Micro-organoid-STAR-high_2

value: high


title: Macro-organoid-STAR-mid_2


title: PDAC organoid [CAS-DAC-19]

value: Body

value: Pancreatic Cancer

value: PAAD

value: 3 - Poorly differentiated


title: CAS-DAC-28


title: 225

description: SAMPLE 28

value: texhi


title: 242

description: SAMPLE 29


title: 214

description: SAMPLE 27


title: Macro-organoid-STAR-mid_1


title: CAS-DAC-25

value: Pancreatic cancer


title: CAS-DAC-26


title: Macro-organoid-STAR-high_3

description: Cells derived from size-filtered, big organoids were sorted for STAR-high expression prior to bulk RNAseq.


title: 96

description: SAMPLE 26


title: PDAC organoid [CAS-DAC-14]

value: PDAC organoid

value: Male

value: Pancreatic Adenocarcinoma

value: IIB


title: PDAC organoid [CAS-DAC-15]

value: Head

value: 2 - Moderately differentiated


title: CAS-DAC-23

value: Pancreas


title: CAS-DAC-24

value: Organoid


title: PDAC organoid [CAS-DAC-16]

value: Tail

value: Pancreatic Ductal Adenocarcinoma

value: III


title: 17086-15

description: SAMPLE 25

value: texlo


title: Macro-organoid-STAR-high_2

value: macro

value: high


title: PDAC organoid [CAS-DAC-13]

value: Female

value: Pancreatic Cancer

value: PAAD

value: IA


title: 380

description: SAMPLE 24


title: Macro-organoid-STAR-high_1


title: CAS-DAC-22

value: Pancreatic cancer


title: PDAC organoid [CAS-DAC-12]

value: PDAC organoid

value: Male

value: Pancreatic Adenocarcinoma

value: IIA


title: 378

description: SAMPLE 23


title: CAS-DAC-21

value: Pancreas


title: PDAC organoid [CAS-DAC-11]

value: Head

value: 2 - Moderately differentiated

value: IB


title: 371

description: SAMPLE 22

value: texhi


title: 165

description: SAMPLE 3

value: texlo


title: CAS-DAC-20

value: Organoid


title: CAS-DAC-27


title: PDAC organoid [CAS-DAC-18]

value: Tail

value: Pancreatic Ductal Adenocarcinoma

value: III


title: IPMN organoid [CAS-IPMN-1]

value: IPMN organoid

value: Pancreatic Cancer

value: Intraductal Papillary Mucinous Neoplasm

value: Intraductal Papillary Mucinous Neoplasm with invasion

value: IPMN


title: 367

description: SAMPLE 21


title: 351

description: SAMPLE 20


title: 98

description: SAMPLE 2


title: CAS-DAC-2

value: Pancreatic cancer


title: CAS-DAC-18


title: NCI-H1963, PolII

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 or STAR 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with different concentrations of iBAP for 24 hours, with DMSO as negative control

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

tag: treatment

value: normal cells

tag: phenotype

tag: chip antibody

value: anti-Pol II (CST #14958)


title: 341

description: SAMPLE 19

tag: group


title: 339

description: SAMPLE 18


title: CAS-DAC-16

last: Li

value: Pancreas

tag: cell type


title: NCI-H1963, BAP1

value: anti-BAP1 (home made)


title: CAS-DAC-14


title: 338

description: SAMPLE 17

value: texhi


title: NCI-H1963, H2AUb

value: anti-H2AK119Ub (CST #8240S)


title: 318

description: SAMPLE 15

value: texlo


title: CAS-DAC-13

value: Organoid


title: 335

description: SAMPLE 16


title: NCI-H1963, H2AUb_DMSO

value: treated with DMSO


title: CAS-DAC-15


title: NCI-H1963, RING1B

value: anti-RING1B (CST #5694)


title: NCI-H1963, H2AUb_iBAPII

value: treated with iBAPII


title: 317

description: SAMPLE 14


title: CAS-DAC-12


title: NCI-H1963, ASCL1_DMSO

value: anti-ASCL1 (CST #43666S)


title: NCI-H1963, BAP1_iBAPII


title: CAS-DAC-11


title: 17086-12

description: SAMPLE 13


title: NCI-H1963, ASCL1_iBAPII


title: 291

description: SAMPLE 12


title: CAS-DAC-19


title: NCI-H1963, BAP1_DMSO


title: CAS-IPMN-1


title: CAS-DAC-1


title: 262

description: SAMPLE 11


title: 258

description: SAMPLE 10


title: NCI-H1963, shRNF2_2, rep1

value: transduced with RNF2 specific shRNA #2


title: 94

description: SAMPLE 1


title: org2019_3391B_T33_MixN2018_Chronic50days

city: Milano

first: Nicolò

last: Caporale

state: MI

address: Via Adamello, 16

institute: European Institute of Oncolology

data_processing:
RNA-seq quantification was performed directly from the reads using Salmon 6.1, using the hg38 Refseq annotation.
Only genes with at least 20 reads in at least 2 samples were included; small (<200 nt) genes, ribosomal RNA genes, and fusion genes were excluded.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: TotalSumExp.RData: SummarisedExperiment (https://bioconductor.org/packages/SummarizedExperiment) including count matrix and metadata for all the samples.
Supplementary_files_format_and_content: counts.csv: Count matrix for all the samples. Names of the columns are matched to the Sample titles.

source_name: Cortical brain organoids

growth_protocol: For the differentiation of cortical brain organoids, we used the protocol described by (Paşca et al., PMID: 26005811), with minor modifications to improve its efficiency, as we previously showed (PMID: 31607568). Human fetal primary neural stem cells (HFPNSC) were provided by Dr. Steve Pollard’s laboratory and cultured according to the published protocols (PMID: 23934830).

extract_protocol:
Total RNA was isolated with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA was quantified with Nanodrop and then the integrity was evaluated with Agilent 2100 Bioanalyzer (only if the quality ratios were not optimal after Nanodrop analysis). TruSeq Stranded Total RNA LT Sample Prep Kit, Illumina was used to run the library for each sample. Sequencing is performed with the Illumina HiSeq 2000 platform, sequencing on average 10 million 50bp paired-end reads per sample.

treatment_protocol:
For EDC chemical exposure of HFPNSC, cells were seeded in 6-well plates. When 70-80% confluency was reached, 0.1% DMSO or the other compounds diluted in DMSO, namely the 5 different concentrations of MIX N (from 0.1X to 1000X), 0.04 nM BPA, 10 μM T3 were added to the culture medium and used to culture cells for 48 hours or for 15 days (in the chronic setting), adding the chemical every time media change was performed (every other day). After the exposure cells were collected for RNA extraction.
For EDC chemical exposure of organoids, 0.1% DMSO, or the other compounds diluted in DMSO, MIX N in the 2 different concentrations used (1X and 1000X), 0.04 nM BPA or 10 uM T3 was added to the culture media and used to culture cells from day 0 to day 50.

value: hiPSC-derived cortical brain organoids

tag: Stage

value: Day 50

tag: passage

tag: Sex

value: Female

value: Chronic 50 days


title: org2019_3391B_T32_MixN2018_Chronic50days


title: NCI-H1963, shRNF2_1, rep2

value: small cell lung cancer

value: Low passages (6-10)

value: transduced with RNF2 specific shRNA #1

value: normal cells


title: NCI-H1963, shRNF2_1, rep1


title: NCI-H1963, shNONT, rep2

value: transduced with non-targeting shRNA


title: org2019_3391B_T31_MixN2018_Chronic50days


title: NCI-H1963, shNONT, rep1


title: SLE, 407

city: Stanford

first: Gloria

last: Yiu

address: CCSR Building Room 2215

institute: Stanford University

description: SLE

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their software package: https://www.fluidigm.com/products-services/instruments/biomark-hd
For the normalization, the average geomean of three housekeeping genes: B2M, GAPDH, and ACTB was subtracted from the average of each sample duplicate
Fold change was not utilized in the calculation of determining the interferon signature

label: FAM

source_name: SLE, PBMCs

label_protocol: For 10-50 ng total RNA of each sample, reverse transcription of the RNA to cDNA was performed at 50°C for 15 minutes using the High-Capacity Reverse Transcription kit (ABI). RT was performed directly on a 96-well PCR plate (ABI). PreAmp was performed on a thermocycler using the TaqMan PreAmp Master Mix Kit (Invitrogen) added to cDNA and pooled Taqman assays. RT enzyme was inactivated and the Taq polymerase reaction was started by bringing the sample to 95°C for 2 minutes. The cDNA was preamplified by denaturing for 10 cycles at 95°C for 15 seconds, annealing at 60°C for 4 minutes. The resulting cDNA product was diluted 1:2 with 1X TE buffer (Invitrogen). 2X Applied Biosystems Taqman Master Mix, Fluidigm Sample Loading Reagent, and preamplified cDNA were mixed and loaded into the 48.48 Dynamic Array (Fluidigm) sample inlets, followed by loading 10X assays into the assay inlets. Manufacturer’s instructions for chip priming, pipetting, mixing, and loading onto the BioMark system were followed. Real-time PCR was carried out with the following conditions: 10 min at 95°C, followed by 50 cycles of 15 sec at 95°C and 1 min at 60°C.

extract_protocol: 3ml of whole blood was collected into a Tempus Blood RNA Tube (Life Technologies #4342792) and frozen at -20°C for a minimum of 30 days. Batched samples were thawed and processed for RNA extraction using a Tempus RNA Isolation Kit (Life Technologies #4380204). All RNA samples were stored at -80°C prior to use. Samples were analyzed 3 using a Bioanalyzer (Agilent Technologies) to confirm RNA quality prior to assay. All samples had RNA Integrity Numbers (RIN) > 7.9.

value: SLE

value: PBMCs

value: whole blood

tag: gender

value: F

tag: age

tag: ifn score

tag: ifn classification

value: intermediate


title: SLE, 396

description: SLE

tag: disease state

tag: tissue

value: IFN-H


title: org2019_3391B_DMSO4_MixN2018_Chronic50days

value: DMSO


title: SLE, 419

description: SLE

value: IFN-L


title: NCI-H1963, iBAPII_20uM, rep2

value: treated with 20 mM of iBAPII


title: SLE, 328

description: SLE


title: NCI-H1963, iBAPII_20uM, rep1


title: org2019_3391B_DMSO2_MixN2018_Chronic50days

value: hiPSC-derived cortical brain organoids

value: Day 50


title: SLE, 310

description: SLE


title: NCI-H1963, iBAPII_10uM, rep2

value: treated with 10 mM of iBAPII


title: org2019_3391B_DMSO1_MixN2018_Chronic50days

value: Female

value: Chronic 50 days


title: NCI-H1963, shRNF2_2, rep2

value: small cell lung cancer

value: Low passages (6-10)

value: transduced with RNF2 specific shRNA #2


title: SLE, 416

description: SLE

value: SLE


title: org2019_3391B_BPA0.04X4_MixN2018_Chronic50days


title: NCI-H1963, iBAP_20uM, rep2

value: treated with 20 mM of iBAP

value: normal cells


title: SLE, 269

description: SLE

value: PBMCs

value: whole blood

value: F


title: SLE, 341

description: SLE

value: intermediate


title: SLE, 265

description: SLE

value: IFN-L


title: NCI-H1963, iBAPII_10uM, rep1


title: org2019_3391B_DMSO3_MixN2018_Chronic50days

value: DMSO


title: org2019_3391B_BPA0.04X3_MixN2018_Chronic50days

value: hiPSC-derived cortical brain organoids


title: RHE DMSO 72h #4

city: Issy-les-Moulineaux

first: Georgios

last: Stamatas

address: 1, rue Camille Desmoulins

department: Consumer Health R&D

institute: Johnson & Johnson Santé Beauté France

hyb_protocol: washed and scanned according to the manufacturer’s instructions

scan_protocol: Scanner G2505C (Agilent Technologies)

data_processing: Proprietary R algorism

source_name: RHE DMSO 72h

growth_protocol: RHE from Episkin growth with EGF and albumine, experimets (treatments were performed without EGF and Alb)

extract_protocol: RHE extracted in RLT buffer + B mercaptoethanol 1%

treatment_protocol: Afatinib 100 nM

tag: tissue source

value: reconstructed Human Epidermis (RHE)

value: Keratinocytes


title: SLE, 326

description: SLE


title: RHE DMSO 72h #2


title: org2019_3391B_BPA0.04X2_MixN2018_Chronic50days

value: Day 50

value: Female


title: RHE DMSO 72h #3


title: SLE, 249

description: SLE


title: NCI-H1963, iBAP_20uM, rep1

tag: cell line

value: small cell lung cancer


title: SLE, 246

description: SLE


title: NCI-H1963, iBAP_10uM, rep2

tag: passages

value: Low passages (6-10)

value: treated with 10 mM of iBAP


title: org2019_3391B_BPA0.04X1_MixN2018_Chronic50days

tag: treatment

value: Chronic 50 days


title: NCI-H1963, iBAP_10uM, rep1

tag: phenotype


title: RHE DMSO 72h #1


title: SLE, 232

description: SLE

value: SLE


title: org2019_3391B_CNT4_MixN2018_Chronic50days

value: CNT


title: RHE AFA 72h #4

source_name: RHE AFA 72h

value: AFA


title: RHE AFA 72h #3


title: RHE AFA 72h #2


title: org2019_3391B_CNT3_MixN2018_Chronic50days


title: RHE DMSO 6h #4

source_name: RHE DMSO 6h


title: RHE DMSO 6h #3


title: NCI-H1963, DMSO, rep2

value: treated with DMSO

value: normal cells


title: SLE, 228

description: SLE

value: PBMCs

value: whole blood

value: F

value: intermediate


title: org2019_3391B_CNT2_MixN2018_Chronic50days

value: hiPSC-derived cortical brain organoids