title: Stereotaxic brain tumor biopsy, patient 18, Circumscribed glioma

city: Frankfurt

first: Katharina

last: Weber

address: Heinrich-Hoffmann-Straße 7

institute: University Hospital Frankfurt

data_processing: IDAT files were uploaded to molecularpathology.org (Heidelberg brain tumor classifier v11b4) to obtain calibrated scores for DNA methylation classes and subclasses, copy number variation profiles and MGMT promoter methylation status. Additional classification was performed using the Bethesda brain tumor classifier (v2) and EpiDiP. IDAT files were processed using R packages RnBeads for quality control and normalization (dasen method from wateRmelon package), and MethylCIBERSORT for reference-based tumor deconvolution. Genome build: hg19.

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_18

extract_protocol: Selected FFPE tissue samples were transferred into Eppendorf tubes using biopsy punches.

value: brain

value: Circumscribed glioma

value: female

value: FFPE stereotaxic biopsy


title: FFPE, LateStable,nr160

status: Public on Jul 22 2026

type: RNA

city: Bergen

first: Tony

last: Chen

address: Haukelandsveien 22

country: Norway

institute: Haukeland University Hospital

description: Human pancancer immune profiling panel primers and IDT-designed spike-in oligonucleotides targeting selected genes were added in the analysis

scan_protocol: Fluorescent detection system using nCounter MAX/FLEX Analysis System.

data_processing: Corresponding RCC files were generated for downstream analysis.

label: Fluorescently barcoded reporter probes

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

label_protocol: Four ng/ul was used for complementary cDNA synteshization using reverse transcription and amplification, and was thereafter subjected to hybridization with capture and reporter probes.

extract_protocol: RNAwas extracted from five to six microtome sliced, 3 um thick sections. miRNeasy extraction kit was used for RNA isolation.

tag: gender

value: Male


title: FFPE, LateProgressive,nr62

value: Female


title: FFPE, LateStable,nr65


title: PDAC_ex_vivo_slice, OT142, Culture_control, 48h, no_treatment

type: SRA

city: Huddinge

first: Tímea

last: Szekerczés

address: Alfred Nobels allé 8

department: LabMed

country: Sweden

institute: Karolinska Institutet

description:
Library name: OT142_48h_TC
Ex vivo culture 48 h; no selenite (treatment control)

library_source: transcriptomic

data_processing:
FASTQ processing was performed in the Chipster environment (CSC, Finland). Read quality was assessed with FastQC and summarized with MultiQC.
Adapter and quality trimming was performed with Trimmomatic v0.39 using TruSeq3-PE-2 adapters and a 4-bp sliding window (average Phred >= 15); reads shorter than 30 bp after trimming were discarded.
Trimmed reads were aligned to GRCh38 using STAR v2.7.10a.
Gene-level read counts were obtained with HTSeq-count v0.13.5 against Homo_sapiens.GRCh38.109 using paired-end mode and strandedness = reverse.
Differential expression was performed in edgeR (Chipster) using TMM normalization and a paired design (patient + group). Significance was defined as FDR < 0.05 (Benjamini-Hochberg).
Assembly: GRCh38; gene annotation: Homo_sapiens.GRCh38.109
Supplementary files format and content: Processed data files are tab-delimited TSV count tables generated by HTSeq-count (gene_id and raw read counts per sample)
Supplementary files format and content: Raw data are paired-end FASTQ files (R1/R2). Lane-level FASTQ files were merged per sample and read (R1 and R2) prior to submission.

source_name: pancreatic ductal adenocarcinoma tumor tissue

growth_protocol: Fresh PDAC tumor tissue was received in the pathology laboratory within ~20 min after surgery. Tumor tissue was sampled by a specialist pancreatic pathologist and cut into 350 um thick slices using a vibrating-blade microtome (Leica VT1200S) with a sapphire blade. Tissue slices were handled on ice in transport medium during preparation. The first slice was immediately formalin-fixed and FFPE-embedded as the 0 h baseline. Remaining slices were placed on 0.4 um pore, 30 mm Millicell membrane inserts in 35 mm culture dishes containing glutamine-free CMRL 1066 medium (Gibco 11530037) supplemented with 25 mM HEPES, 1 mM sodium pyruvate, ZnSO4, insulin-transferrin-selenite solution, 2.5% human AB serum, 1X Pen/Strep, and 100 nM diphenyl diselenide, and incubated at 37 C.

extract_protocol:
Total RNA was isolated from 10 um DNase-treated FFPE sections using the Maxwell RSC FFPE RNA Kit (Promega AS1440) according to the manufacturer. RNA quantity/quality was assessed using Qubit 4.0 with the RNA HS Assay Kit (Thermo Fisher Q32852).
Up to 50 ng total RNA per sample was used for library preparation with the SMARTer Total RNA-Seq Kit v2.5 Pico Input Mammalian (Takara 634411). RNA was thermally fragmented (94 C, 3 min) and reverse-transcribed with random N6 hexamers. Illumina adapters and sample barcodes were introduced during amplification; ribosomal cDNA was depleted by RNase H with mammalian R-probes; remaining fragments were re-amplified with universal adapter primers. Libraries were quantified (Qubit DNA HS, Q33230), normalized, pooled and sequenced on an Illumina NextSeq 500/550 Mid Output v2.5 (150 cycles) to generate 2 x 75 bp paired-end reads.

treatment_protocol: Slices were cultured for 48 h. Untreated slices were maintained to 48 h (48 h treatment control, no selenite). For treatment conditions, sodium selenite was added only during the second 24 h (24-48 h) at 5 uM or 15 uM.

tag: tissue

tag: treatment

value: no selenite (culture control)


title: PDAC_ex_vivo_slice, OT142, Baseline, 0h

description:
Library name: OT142_0h
0 h baseline; collected immediately after surgery; no ex vivo culture

value: pancreatic ductal adenocarcinoma tumor tissue

value: none (baseline)


title: PDAC_ex_vivo_slice, OT138, Selenite_15uM_(24-48h), 48h

description:
Library name: OT138_48h_Se_15uM
Ex vivo culture 48 h; sodium selenite 15 uM applied for 24 h during the second day (24-48 h)

value: sodium selenite 15 uM (24-48 h)


title: FFPE, LateStable,nr59


title: FFPE, LateStable,nr56


title: FFPE, LateStable,nr51


title: PDAC_ex_vivo_slice, OT138, Selenite_5uM_(24-48h), 48h

description:
Library name: OT138_48h_Se_5uM
Ex vivo culture 48 h; sodium selenite 5 uM applied for 24 h during the second day (24-48 h)

value: sodium selenite 5 uM (24-48 h)


title: PDAC_ex_vivo_slice, OT138, Baseline, 0h

description:
Library name: OT138_0h
0 h baseline; collected immediately after surgery; no ex vivo culture


title: FFPE, EarlyProgressive,nr150


title: PDAC_ex_vivo_slice, OT138, Culture_control, 48h, no_treatment

description:
Library name: OT138_48h_TC
Ex vivo culture 48 h; no selenite (treatment control)


title: FFPE, EarlyProgressive,nr140


title: PDAC_ex_vivo_slice, OT127, Selenite_15uM_(24-48h), 48h

description:
Library name: OT127_48h_Se_15uM
Ex vivo culture 48 h; sodium selenite 15 uM applied for 24 h during the second day (24-48 h)


title: FFPE, EarlyProgressive,nr123


title: FFPE, EarlyProgressive,nr95


title: PDAC_ex_vivo_slice, OT127, Selenite_5uM_(24-48h), 48h

description:
Library name: OT127_48h_Se_5uM
Ex vivo culture 48 h; sodium selenite 5 uM applied for 24 h during the second day (24-48 h)


title: FFPE, EarlyProgressive,nr83


title: PDAC_ex_vivo_slice, OT127, Culture_control, 48h, no_treatment

description:
Library name: OT127_48h_TC
Ex vivo culture 48 h; no selenite (treatment control)


title: FFPE, EarlyStable,nr152


title: PDAC_ex_vivo_slice, OT127, Baseline, 0h

description:
Library name: OT127_0h
0 h baseline; collected immediately after surgery; no ex vivo culture


title: PancPEC

city: Montpellier Cedex 5

first: Jacques

last: Colinge

address: 208 avenue des Apothicaires

country: France

institute: IRCM

description: Library name: sample 13

data_processing:
alignment with STAR 2.5.2b against Mus musculus and Homo sapiens genomes
gene count extraction with HTSeq-count
Assembly: GRCm38.89 and GRCh38.83
Supplementary files format and content: text files with read counts in tabular format

source_name: tumor

growth_protocol: PDX models were established from fresh tumor fragments obtained from the Pathology Department at the Comprehensive Cancer Center of Montpellier (ICM) after informed consent of the patients. A fragment of tumor (~8 mm3) was implanted into the inter-scapular fat pads of 3-4-week-old female Swiss-nude mice. Tumors were passaged onto a further cohort of mice before graft volume reached 1,000 mm3.

extract_protocol:
Quick-RNA Miniprep Kit (Zymo Research, #R1055)
2X75pB_30 M Reads

value: tumor


title: FFPE, EarlyStable,nr151


title: P8264

description: Library name: sample 12


title: FFPE, EarlyStable,nr58


title: FFPE, EarlyStable,nr64


title: P8121

description: Library name: sample 11


title: P6212

description: Library name: sample 9


title: FFPE, EarlyStable,nr63


title: FFPE, EarlyStable,nr61


title: P4604

description: Library name: sample 8


title: P7054_2

description: Library name: sample 10


title: FFPE, EarlyStable,nr60


title: FFPE, EarlyStable,nr54


title: P2846_wt

description: Library name: sample 7


title: FFPE, EarlyStable,nr53


title: P2846

description: Library name: sample 6


title: aipwh239(-/-)_4

city: Corvallis

first: Dante

last: Perone

state: Oregon

country: USA

institute: Oregon State University

description: Library name: D6

data_processing:
The cutadapt tool was used to trim adapter sequences, primers, and poly-A tails as well as quality trimming and filtering. Following trimming and filtering with cutadapt the median number of reads (x106) was 30.82, with the minimum being 27.85, and the maximum being 33.51.
The Star aligner was used to align reads in FASTQ format directly to the reference genome. The median percentage of uniquely mapped reads was 85.4%, with the minimum being 83.7% and the maximum being 86.7%.
Unique molecular identifier (UMI) tags were included in the samples and used to remove PCR duplicates. Reads with the same UMI that mapped to the same location are collapsed to one read. Following UMI collapsing the median percentage of remaining reads was 58.9% with the minimum being 54.6% and the maximum being 66.1%.
Transcript- and gene-level raw count matrices were generated which included 53,466 and 32,171 features, respectively.
Assembly: GRCz11
Supplementary files format and content: .xlsx, raw transcript and gene counts of all samples and types
Supplementary files format and content: .xlsx, separate DEG analysis results tables for each comparison referenced in the manuscript

molecule: polyA RNA

organism: Danio rerio

source_name: 5 whole 5 dpf larvae

extract_protocol:
A Thermo Fisher KingFisher Apex liquid handler system and a Zymo Quick-RNA MagBead kit were used to perform the extractions in a 96-well format. The Zymo kit requires an equal volume of ethanol to be mixed with the sample for extraction but has a max volume of 1000 µL. Since 550 µL of supernatant was collected, the final volume with ethanol was 1100 µL and had to be split between two extraction plates. Each sample was individually moved and equally divided between two extraction plates. The well position of the original sample plate was tracked throughout this process and into the sample submission. Ethanol and mag beads were added using a multichannel pipette and the extraction was carried out following the kit protocol including a DNase I digestion step. The RNA was eluted into 50 µL of UP water. Individual larval RNA samples were pooled following RNA extraction to reduce inter-replicate variation. Each pooled replicate was created by combining five individual samples. Samples with the highest concentration and RIN scores > 8 were selected to be pooled. The RIN and concentration of each sample was determined using an Agilent 4150 TapeStation System and an Invitrogen qubit fluorometer, respectively.
Library preparation was performed using the CORALL mRNA-Seq V2 whole transcriptome sequencing kit. 150bp paired end reads were sequenced on an AVITI sequencing platform

value: 5 whole 5 dpf larvae

tag: genotype


title: aipwh239(-/-)_3

description: Library name: C6


title: P1368

description: Library name: sample 4


title: P1219

description: Library name: sample 3


title: P2846_GR

description: Library name: sample 5


title: aipwh239(-/-)_2

description: Library name: B6


title: aipwh239(-/-)_1

description: Library name: A6


title: Ctrl_h_hPanc

description: Library name: sample 1

source_name: human normal pancreas

value: human normal pancreas


title: aipwh239(+/-)_4

description: Library name: D5


title: TGFb-Chip.GCCAAT.J1019.AHY7J3BGX9.L1-4.1

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

description: Library name: TGF-β1 -Chip

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2 with local read alignment
Peaks were called using MACS v2.1.0
Assembly: hg38
Supplementary files format and content: tab separated txt

molecule: genomic DNA

source_name: HSC

growth_protocol: Cells were cultured in IMDM, 15% FBS, 15% human serum, 1% penicillin/steptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
ChIP was performed using Diagenode Diagenode HighCell ChIP Kit (Cat# C01010060).
Illumina library prep kit was used to prepare ChIP-seq libraries

treatment_protocol: Cells were either treated with GDF11 (100 ng/mL) or TGFb1 (20 ng/mL)

tag: cell line

value: HSC

tag: cell type

value: stem cells and progenitors


title: aipwh239(+/-)_3

description: Library name: C5


title: TGFb-Chip.GCCAAT.J1019.AHY7J3BGX9.L1-4.1 (Input)

description: Library name: TGF-β1 -Input


title: aipwh239(+/-)_2

description: Library name: B5


title: Control-Chip.CGATGT.J1019.AHY7J3BGX9.L1-4.1 (Input)

description: Library name: control-Input


title: Control-Chip.CGATGT.J1019.AHY7J3BGX9.L1-4.1

description: Library name: control-Chip


title: aipwh239(+/+)_4

description: Library name: D4


title: aipwh239(+/-)_1

description: Library name: A5


title: colorectal cancer cells, patient_23

city: shanghai

first: He

last: Qian

address: No. 600 Yishan Road,  Shanghai, PRC, 200233.

country: China

institute: Shanghai Jiao Tong University

description:
Library name: tum_23
10X Genomics

library_source: transcriptomic single cell

data_processing:
Data Processing Pipeline: (1) Base Calling: Raw sequencing data were demultiplexed to FASTQ format using bcl2fastq (v5.0.1). (2) Alignment & Quantification: Processed through CellRanger (v7.0.0) using the 10x Genomics reference pipeline; reads aligned to GRCh38 human genome assembly; valid cell barcodes and unique molecular identifiers (UMIs) filtered; gene-cell count matrix generated via 3' transcript quantification (Pipeline details: 10x Genomics CellRanger Documentation, v7.0.0).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colorectal cancer tissue

extract_protocol:
All sample collection procedures complied with the regular routine in clinical practice. Tumor tissues and matched normal mucosa (≥5 cm from tumor margins) were collected from 18 patients (36 total samples). Fresh surgical specimens (≥100 mg/sample) were processed as follows: (1) Immediate transfer to pre-chilled RNase-free PBS (Ca²⁺/Mg²⁺-free) collection tubes maintained at 4°C; (2) Removal of blood clots and adipose tissue under sterile, ice-cold conditions; (3) Minced into 0.5 mm³ fragments using micro-scissors; (3) Triple-washed with pre-cooled PBS to eliminate debris. Fragments were enzymatically digested in dissociation buffer (0.35% collagenase IV, 2 mg/ml papain, 120 U/ml DNase I) at 37°C with 100 rpm agitation for 20 minutes. The reaction was quenched using PBS supplemented with 10% FBS. Cell suspensions were: (1) Mechanically dissociated via 10× pipetting with a 1 ml tip; (2) Sequentially filtered through 70 μm and 30 μm strainers; (3) Centrifuged at 300×g (4°C, 5 min); (4) Treated with 1× RBC Lysis Buffer (MACS 130-094-183) for 2–10 min at RT; (5) Labeled with Dead Cell Removal MicroBeads (MACS 130-090-101) for 15 min at RT; (6) Purified using MS Columns (130-042-201) with two additional centrifugation steps. Final viable cells were resuspended in 100 μl PBS containing 0.04% BSA. Cell viability (>85%) was verified by trypan blue exclusion. Concentrations (700–1,200 cells/μl) were quantified using a Countess II Automated Cell Counter (Thermo Fisher), meeting single-cell sequencing library preparation standards.
Single-cell suspensions were processed using the Chromium Single-Cell 3' Kit (v3, 10×Genomics) on a Chromium microfluidic chip, targeting capture of 8,000 individual cells. Following manufacturer protocols, captured cells underwent cDNA amplification and library preparation. Single-Cell Transcriptomic Analysis: (1) Preprocessing with Seurat (v4.1.0): Initial filtering: Retained cells with >500 detected genes and mitochondrial gene content ≤25%; data normalization: LogNormalize method applied; dimensionality reduction: PCA performed using top 2,000 variable genes; top 20 principal components retained; batch correction: Harmony algorithm implemented for dataset integration; clustering & visualization: Cell clusters identified and projected in 2D space using UMAP. (2) Differential Expression Analysis: Marker genes identified via FindAllMarkers function with thresholds:Expressed in ≥10% of cluster cells; Log₂ fold-change ≥0.26; Benjamini-Hochberg adjusted p-value ≤0.01.

value: colorectal cancer tissue

tag: Sex

tag: age

tag: tumor stage_(tnm)

value: Ⅰ

tag: genomic mutations

value: Wild


title: aipwh239(+/+)_3

description: Library name: C4


title: colorectal cancer cells, patient_21

description:
Library name: tum_21
10X Genomics

value: ⅢB


title: aipwh239(+/+)_1

description: Library name: A4


title: colorectal cancer cells, patient_19

description:
Library name: tum_19
10X Genomics

value: KRAS Exon-2


title: colorectal cancer cells, patient_20

description:
Library name: tum_20
10X Genomics


title: aipwh86(-/-)_4

description: Library name: D3


title: colorectal cancer cells, patient_18

description:
Library name: tum_18
10X Genomics

value: Male


title: aipwh86(-/-)_3

description: Library name: C3


title: aipwh86(-/-)_2

description: Library name: B3


title: aipwh86(-/-)_1

description: Library name: A3


title: colorectal cancer cells, patient_15

description:
Library name: tum_15
10X Genomics

value: ⅡA


title: colorectal cancer cells, patient_17

description:
Library name: tum_17
10X Genomics


title: aipwh86(+/-)_4

description: Library name: D2


title: colorectal cancer cells, patient_10

description:
Library name: tum_10
10X Genomics

value: KRAS Exon-4


title: aipwh86(+/-)_3

description: Library name: C2


title: aipwh86(+/-)_2

description: Library name: B2


title: colorectal cancer cells, patient_09

description:
Library name: tum_09
10X Genomics

value: Female


title: aipwh86(+/+)_4

description: Library name: D1


title: colorectal cancer cells, patient_08

description:
Library name: Tum8
10X Genomics


title: aipwh86(+/-)_1

description: Library name: A2


title: colorectal cancer cells, patient_06

description:
Library name: Tum6
10X Genomics

value: NRAS Exon-3


title: aipwh86(+/+)_2

description: Library name: B1


title: colorectal cancer cells, patient_04

description:
Library name: Tum_04
10X Genomics


title: aipwh86(+/+)_1

description: Library name: A1


title: colorectal cancer cells, patient_03

description:
Library name: tum_03
10X Genomics

value: ⅢC


title: colorectal cancer cells, patient_07

description:
Library name: Tum7
10X Genomics


title: colorectal cancer cells, patient_02

description:
Library name: tum_02
10X Genomics


title: HPMEC + TENT2sh-2

city: New Haven

first: Asawari

last: Korde

state: CT

address: 300 Cedar street, TAC S440, PO Box 208057

department: Internal Medicine, PCCSM section

institute: Yale University School of Medicine

description: Library name: TENT2sh-2_B22HVCGLT4_L002

data_processing:
Sequencing data were processed using standard Illumina pipelines for demultiplexing, alignment to the human genome, and quality control before downstream analyses. MiRNA abundance was estimated using miRge3(154) using human small RNA reference database (https://sourceforge.net/projects/mirge3/files/miRge3_Lib/). The mirGe3 analysis resulted in miRNA raw counts. The raw counts from mirGe3 analysis were used to estimate differentially expressed miRNAs were identified using DESeq2 (v 1.22.1)(155).
Assembly: GRCh38
Supplementary files format and content: .xlsx file with genes in the rows and samples in the column

source_name: HPMEC

growth_protocol: HPMECs (passage 4) cultured in EGM-2 Endothelial Cell Growth Medium-2 containing BulletKit (Lonza, CC-3162)

extract_protocol:
Total RNA were isolated from cells harvested in Trizol using the phenol-chloroform extraction protocol.
1ug of total RNA were used to prepare miRNA library. Total RNA quality and integrity were assessed by NanoDrop spectrophotometry and Agilent Bioanalyzer/Fragment Analyzer analysis. Samples with RNA integrity number (RIN) ≥7 were used for library preparation. Small RNA libraries were generated using the Qiagen miRNA Library Prep Kit (Cat# 331505) according to the manufacturer's instructions. Briefly, 3′ and 5′ adapters were ligated to miRNAs, followed by cDNA synthesis with unique molecular identifier (UMI) assignment, PCR amplification, and library purification. Library quality was assessed using an Agilent TapeStation and quantified by qPCR. Libraries were sequenced on an Illumina NovaSeq X platform using 100-bp paired-end reads, targeting 10–25 million reads per sample.

treatment_protocol: HPMECs were transduced by human TENT2 shRNA lentivirus for 36 hours, followed by serum starvation for 6 hours and treatment with PBS for 24 hours

value: HPMEC

value: Primary lung endothelial cells

value: TENT2 shRNA

value: 36 hr wih lenivirus + 24 hr PBS


title: HPMEC + TENT2sh-3

description: Library name: TENT2sh-3_B22HVCGLT4_L002


title: colorectal cancer cells, patient_01

description:
Library name: tum_01
10X Genomics


title: adjacent normal cells, patient_23

description:
Library name: nor_23
10X Genomics

source_name: adjacent normal mucosal tissue

value: adjacent normal mucosal tissue


title: HPMEC + Ctrlsh-3

description: Library name: Ctrlsh-3_B22HVCGLT4_L002

value: control


title: adjacent normal cells, patient_21

description:
Library name: nor_21
10X Genomics


title: HPMEC + Ctrlsh-2

description: Library name: Ctrlsh-2_B22HVCGLT4_L002


title: HPMEC + Ctrlsh-1

description: Library name: Ctrlsh-1_B22HVCGLT4_L002


title: adjacent normal cells, patient_20

description:
Library name: nor_20
10X Genomics


title: Raw sequencing data of H3K4me1 ChIP library from MCbs1 cell line.

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

description:
Library name: MCbs1_H3K4me1
MCbs1_H3K4me1

data_processing:
Raw ChIP-seq reads were first evaluated for quality using fastQC (v 0.12.1), which provides metrics including per-base sequence quality, GC content, duplication levels, read length distribution, k-mer profiles, and potential adapter contamination. Adapter sequences and low-quality bases were then trimmed using fastp to produce high-quality clean reads. For fastp, the adapters of pair-end data can be trimmed automatically by per-read overlap analysis, which seeks the overlap of each pair of reads. The processed reads were aligned to the human reference genome (GRCh38) using bwa (v 0.7.19). Then samtools (v 1.21) was used for sorting, indexing, and mapping quality assessment. Duplicates were marked using picard (v 3.4.0). Macs2 (v 2.2.6) was applied to identify peaks through peak calling. Differential binding site analysis was performed using MAnorm software, which allowed us to identify differential binding peaks. The threshold MA values (similar to log2 fold change) higher than 1.0 or lower than -1.0 were used to determine the differential binding peaks.
Assembly: GRCh38
Supplementary files format and content: narrowPeak format output from MACS2

source_name: breast

growth_protocol: To establish stable chronic IL-1-exposed sublines, MCF7 cells were cultured in DMEM/10% FB Essence (FBE) containing 0.5ng/mL IL-1α or 0.5ng/mL IL-1β for 6 months. Following chronic IL-1 exposure, cells were moved out of IL-1-containing medium and maintained in normal growth medium without IL-1 for phenotype characterization. Parental cell lines (MCF71) were cultured in vehicle control (1× phosphate buffer saline, PBS) alongside the sublines. Sublines: MCF7 chronic IL-1α subline termed MCas1, MCF7 chronic IL-1β sublines termed MCbs1.

extract_protocol:
MCF71, MCas1, and MCbs1 cells were crosslinked in 1% formaldehyde for 10 min at room temperature, followed by incubation with 125mM glycine for 5 minutes to quench formaldehyde. The cells were pelleted and washed twice with ice cold PBS. Chromatin was prepared by nuclear isolation followed by lysis. Lysates were sonicated using a Bioruptor® Pico (Diagenode) to obtain DNA fragments ranging from 200-600bp and cleared by centrifugation at 16,000g for 10 minutes at 4°C.
Supernatant (chromatin lysate) was incubated with either H3K4me1, H3K4me3 (both from Abcam), H3K27ac (Active Motif) or H3K27me3 (Diagenode) antibodies conjugated with DynabeadsTM Protein A beads (Invitrogen) overnight at 4°C. Next day, bead conjugated antibody-bound chromatin were collected using DynaMagTM-2 Magnet (Invitrogen) and washed extensively, followed by reverse crosslinking and DNA purification. Input and ChIP DNA libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) following the manufacturer's instructions and subjected to next-generation sequencing to obtain 25 million 50bp paired-end reads per sample.

treatment_protocol: We performed ChIP sequencing  and differential binding analysis for the parental (MCF71) and chronic IL-1 subline cells (MCas1, MCbs1) grown in normal growth medium (DMEM/10% FBE) in T75 flasks until 80% confluent. Cells were then collected for ChIP sequencing analysis to assess basal histone marks. Histone marks assayed: H3K4me1, H3K4me3, H3K27ac, H3K27me3

value: breast

value: Breast cancer


title: adjacent normal cells, patient_18

description:
Library name: nor_18
10X Genomics

value: Ⅰ


title: Raw sequencing data of H3K4me1 ChIP library from MCas1 cell line.

description:
Library name: MCas1_H3K4me1
MCas1_H3K4me1


title: Raw sequencing data of H3K4me1 ChIP library from MCF71 cell line.

description:
Library name: MCF71_H3K4me1
MCF71_H3K4me1


title: adjacent normal cells, patient_16

description:
Library name: nor_16
10X Genomics


title: adjacent normal cells, patient_17

description:
Library name: nor_17
10X Genomics


title: Raw sequencing data of H3K27me3 ChIP library from MCbs1 cell line.

description:
Library name: MCbs1_H3K27me3
MCbs1_H3K27me3


title: adjacent normal cells, patient_15

description:
Library name: nor_15
10X Genomics

value: Wild


title: Raw sequencing data of H3K27me3 ChIP library from MCas1 cell line.

description:
Library name: MCas1_H3K27me3
MCas1_H3K27me3


title: adjacent normal cells, patient_11

description:
Library name: nor_11
10X Genomics

value: KRAS Exon-2


title: Raw sequencing data of H3K27me3 ChIP library from MCF71 cell line.

description:
Library name: MCF71_H3K27me3
MCF71_H3K27me3


title: Raw sequencing data of H3K27ac ChIP library from MCbs1 cell line.

description:
Library name: MCbs1_H3K27ac
MCbs1_H3K27ac


title: adjacent normal cells, patient_10

description:
Library name: nor_10
10X Genomics

value: Male


title: adjacent normal cells, patient_09

description:
Library name: nor_09
10X Genomics

value: ⅡA


title: Raw sequencing data of H3K27ac ChIP library from MCas1 cell line.

description:
Library name: MCas1_H3K27ac
MCas1_H3K27ac


title: Raw sequencing data of H3K27ac ChIP library from MCF71 cell line.

description:
Library name: MCF71_H3K27ac
MCF71_H3K27ac


title: adjacent normal cells, patient_08

description:
Library name: Nor8
10X Genomics


title: adjacent normal cells, patient_07

description:
Library name: Nor7
10X Genomics


title: Raw sequencing data of H3K4me3 ChIP library from MCbs1 cell line.

description:
Library name: MCbs1_H3K4me3
MCbs1_H3K4me3


title: Raw sequencing data of H3K4me3 ChIP library from MCas1 cell line.

description:
Library name: MCas1_H3K4me3
MCas1_H3K4me3


title: adjacent normal cells, patient_04

description:
Library name: Nor_04
10X Genomics


title: adjacent normal cells, patient_03

description:
Library name: nor_03
10X Genomics


title: Raw sequencing data of input library of MCas1 cell line.

description: Library name: MCas1_input


title: CVID LN 3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Adapter- and quality-trimming was performed with Trimmomatic (v0.38), using the following parameters: HEADCROP:3 TRAILING:10 MINLEN:25
Single-end reads were then aligned to human genome (hg19) and read-per-gene was quantified using STAR (v2.5.2b). The following parameters were used: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Assembly: hg19
Supplementary files format and content: tab-delimited file including the raw read count per gene

source_name: Lymph node

extract_protocol:
RNA was harvested using Reasy mini plus kit (Qiagen).
Barcoded stranded mRNA-seq libraries were prepared from high-quality total RNA samples (200 ng/sample) using the Illumina TruSeq RNA Sample Preparation v2 Kit (Illumina).

value: Lymph node

value: Follicular T cells

tag: disease state

value: CVID


title: adjacent normal cells, patient_01

description:
Library name: nor_01
10X Genomics

value: Female

value: ⅢC


title: Raw sequencing data of input library of MCF71 cell line.

description: Library name: MCF71_input


title: aipwh239(+/+)_2

description: Library name: B4

value: 5 whole 5 dpf larvae


title: UPN5-TAZ

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: Library name: UPN5-TAZ

library_source: other

data_processing:
After adapter trimming with TrimGalore (--quality 20, --length 25), alignment was performed with bowtie2 (--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700), only properly paired reads, with no supplementay or secondary alignment, and mapping quality of at least 15 were retained for the subsequent steps. PCR duplicates were filtered out with picard MarkDuplicates tool. ChrY, mithocondrial mapping reads and blacklisted regions (hg38 v2) were also filtered out. Macs2 with broad parameters was adopted for peak calling. A catalog of regions was calculated after merging the peaks between the untreated and tazemetostat treated sample (bedtools merge). The table of counts was calculated with (bedtools map) taking into account the fold enrichment file generated with macs2 bdgcmp function. As an exploratory analysis, the log2FC was calculated considering Tazemetostat (n = 1) vs Untreated (n = 1) in order to capture the direction of signal enrichment, and using a threshold of 1 to describe the trend of gain and loss regions. Chipseeker annotatePeak function was adopted for annotating all the catalog regions (with parameters sameStrand = FALSE, ignoreOverlap = FALSE, ignoreDownstream = FALSE, overlap = "all", +/- 2000 bp around TSS and gencode v35). The track plots for rappresentative regions (ggcoverage) was generated over RPKM normalized bigwig file computed with bamCoverage function (deepTools).
Assembly: hg38
Supplementary files format and content: counts for each sample bed (output from bedtools map)
Library strategy: CUT&Tag

molecule: other

source_name: Bone marrow derived cells

growth_protocol: Culture medium reported in material and methos of the paper

extract_protocol:
Nuclei were extracted by incubating cells for 10 minutes on ice in 100 µL/sample of cold Nuclei Extraction buffer (composition reported in Material and Methods of the paper)
Illumina Tagment DNA TDE1 + custom indexing

treatment_protocol: Patient-derived AML cells untreated or ex-vivo treated with Tazemetostat (10uM)

value: Bone marrow derived cells

value: Bone Marrow

value: AML cells

value: tazemetostat


title: HD Tons 1

source_name: Tonsil

value: Tonsil

value: Healthy


title: UPN5-CTRL

description: Library name: UPN5-CTRL

value: untreated


title: colorectal cancer cells, patient_16

description:
Library name: tum_16
10X Genomics

value: colorectal cancer tissue

value: Ⅰ


title: CVID LN 1


title: d128 vSKO

city: Boston

first: Karl

middle: Russell

last: Koehler

state: MA

address: 3 Blackfan Circle

department: Otolaryngology-Head and Neck Surgery

institute: Boston Children's Hospital-Harvard Medical School

description:
Library name: vSKO-D128
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.1.2.
Ambient RNA was removed using SoupX v1.6.2.
Multiplets were identified using the scds v1.14.0 and excluded.
Cells exhibiting extremely low or high library sizes and number of gene features, falling outside the 95% confidence interval, as well as those displaying high mitochondrial content above the 10th percentile were excluded.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Organoid

growth_protocol: hPSC lines and culture All culture experiments were performed with the WTC-11 hiPSC lines mTagRFP-TUBA1B, mEGFP-TJP1 (passages 35-55) acquired from the Allen Institute for Cell Science and the Coriell Institute. Cells were cultured on 6-well TC-treated plates coated with Vitronectin Recombinant Human Protein (Fisher Scientific) at a concentration of 0.5 µg/cm2. Pluripotent stem cells were maintained in mTeSR medium with supplement (STEMCELL Technologies) and 100 µg/mL Normocin (Invivogen; hereafter, mTeSR). The medium was replenished every other day or eve-ryday depending on cell confluency and passaged at ~80% confluency (generally every 3-4 days). Cells were passaged in clusters of 3-6 cells on average with 0.5 mM EDTA.  hPSC differentiation into cvSkO and vSkO All steps take place in a biosafety cabinet unless stated otherwise. Pluripotent hPSC colonies were rinsed twice with 1x DPBS (Gibco), dissociated into single cells using StemPro Accutase Cell Dissociation Reagent (hereafter, Accutase; Gibco) and collected as a single cell suspension in mTeSR medium containing CEPT cocktail (final concentration in medium: 50 nM Chroman 1, MedChem Express; 5 µM Emricasan, SelleckChemicals; 1:1000 Polyamine Supplement, Sigma-Aldrich; 0.7 µM Trans-ISRIB, Tocris) and 100 µg/mL Normocin (Invivogen; here after: mTeSR + CEPT). On day minus 1, cells were distributed at a count of 3,500 cells in 100 µL mTeSR + CEPT per well for cvSkO and 800 cells in 100 µL mTeSR + CEPT per well for vSkO into 96-well U-bottom plates (Thermo Scientific). Aggregation was aided by centrifugation at RT, 110 rcf for 6 minutes. These cell aggregates were incubated in 37°C incubator under 5% CO2 for 24 hrs. On day 0, cells were transferred to new 96-well U-bottom plates in 100 µL of Essential 6 (Gibco) medium with 100 µg/mL Normocin (Invivogen; hereafter, E6), containing 2% Matrigel (Corning), 10 µM SB431542 (Reprocell), 4 ng/mL basic-FGF (PeproTech; herafter, bFGF), and 5 ng/mL BMP4 (PeproTech) to initiate non-neural ectoderm formation. On day 3, 200 µM  LDN-193189 (BMP inhibitor, Reprocell; hereafter, LDN), and 50 µg/mL of bFGF in E6 medium were added in a volume of 25 µL per well, making the final concentration of 200 nM LDN and 50 ng/mL bFGF per well and the final volume 125 µL per well. On day 6 of differentiation, day 6 LPMs (generated in parallel) were merged with the SKO aggregates in 75 µL of E6 medium, making the final volume 200 µL. Half of the medium was changed (removal of 100 µL of spent medium and addition of 100 µL of fresh E6 medium) on days 8 and 10. On day 12, to induce self-assembly of epidermis, all aggregates were transferred into individual wells of 24-well low-attachment plates (Thermo Sci-entific) in 500 µL of organoid maturation medium (OMM) containing 1% Matrigel. OMM is com-posed of Advanced DMEM/F12 (Gibco) and Neurobasal (Gibco) media at a 1:1 ratio, 1X Gluta-MAX™ supplement (Thermo Fisher Scientific), 0.5X B-27™ Minus Vitamin A supplement (Fisher Scientific), 0.5X N2 supplement (Fisher Scientific), 0.1 mM 2-Mercaptoethanol (Thermo Scien-tific), and 100 µg/mL Normocin (Invivogen). To maintain the aggregates in a floating culture for constant medium circulation, 24-well plates were placed on an orbital shaker shaking at a speed of 65 rpm in the 37°C incubator with 5% CO2. On differentiation day 15, half of the spent medium was replenished (removal of 250 µL of spent medium and addition of 250 µL of fresh medium) with OMM containing 1% Matrigel. Starting from day 18, half-medium change was performed every 2-3 days with fresh OMM without Matrigel, including once a week full-medium change. In-creasing the total volume of OMM per well to 1-1.5 mL was necessary when the aggregates ma-tured and grew larger to occupy approximately a quarter of the volume of the well.  hPSC differentiation into Lateral Plate Mesoderm (LPM) On day –minus 1, colonies of hPSCs were dissociated and seeded onto 96 well U-bottom low attachment plates (S-Bio) at a density of 3000 cells in 100 µL per well with mTeSR + CEPT medium. Aggregation was aided by centrifugation at RT, 110 rcf for 6 min. On day 0, aggregates were individually collected and washed thrice with DMEM/F12 GlutaMAX™  (Thermo Fisher Scientific), 1% Insulin-Transferrin Selenium (Thermo Scientific; hereafter, ITS) and 100 µg/mL Normocin (Invivogen). Aggregates were then transferred to new 96-well U-bottom plates (S-Bio) in 150 µL medium of DMEM/F12 GlutaM AX™ medium containing 1% ITS, 100 µg/mL Normocin, 10 ng/mL BMP4 (PeproTech), and 3 µM CHIR99021 (Reprocell; hereafter CHIR). On day 3, medium was entirely replaced with 150  µL of DMEM/F12 GlutaM AX™ medium containing 1% ITS, 100 µg/mL Normocin and 10 ng/mL human FGF8a (PeproTech).  hPSC differentiation into amnioids On day –minus 1, colonies of hPSCs were dissociated similarly to SkO differentiation protocol on day –minus 1 and seeded at the density of 800 cells in 100 µL per well of mTeSR + CEPT medium. Aggregation was aided by centrifugation at RT, 110 rcf for 6 min. On day 0, all cell aggregates were individually collected, washed thrice with E6 medium and transferred to new 96-well U-bottom plates in 100 µL of E6 medium containing 2% Matrigel (Corning), 10 µM SB431542 (Reprocell), 4 ng/mL bFGF (PeproTech), 5 ng/mL BMP4 (PeproTech) to initiate non-neural ectoderm and amnion epithelia formation. On day 3, 25 µL of E6 medium was added to supply nutrients. For generating Amnioid (amnion epithelia + mesenchyme), on day 6, amnion epithelium was merged with day 6 LPM (generated in parallel) in 75 µL of E6 medium, making the total volume 200 µL. The plate was centrifuged at RT, 300 rcf for 5 min to assist the assembly of LPM with the amnion epithelia. From day 6 to day 9, fusion occurs by the migration of LPM cells to cover the surface of the amnion epitheila, making an assembloid with epithelia layer facing inside and mesenchymal cells outside. On day 8, half-medium change with E6 medium was carried out to supply more nutrients, and centrifugation can be performed if the organoids did not start to merge. On day 10, half medium was changed again. From day 12 onwards, the protocol was same as cvSKO and vSKO differentiation. To promote the growth, amnioids at day 30 to day 40 can be transferred to 6-well plates or bigger containers.

extract_protocol:
Skin organoid dissociation for scRNA-seq To dissociate organoids into single cells, randomly selected day 6 organoids (n = 24) and day 28 organoids (n = 10) were pooled from each group. For day 104 aggregates, two representative skin organoids were collected. Briefly, organoids before day 30 were incubated with pre-warmed (37°C) TrypLE™ (Fisher Scientific) for total 8-30 min (depending on the organoid sizes and den-sities) in a 37°C incubator on a shaker at 65 rpm for a gentle swirl. For day 104 organoids, or-ganoids were first cut open and incubated with 10% Corning™ Dispase (Fisher Scientific) with CEPT for 30 min. During the incubation, the dissociation mixture was agitated every 3-10 min with gentle pipetting using wide-orifice p1000 and p200 tips (Mettler-Toledo) To aid the dissocia-tion, organoids were pipetted at 10-minute intervals -- first time gently with a wide-orifice p1000 (p200 for younger organoids; Rainin) tip and then with a regular p200 (Rainin) tip for subsequent intervals. For older organoids, if large cell chunks were remaining, the cell suspension was brief-ly spun down to collect larger chunks. The supernatant with Dispase-dissociated cells was saved in a separate tube while the larger chunks with treated with 300 µL of TrypLE™ with CEPT in the same manner as younger organoids. Once no visible chunks were remaining, the Dis-pase-dissociated cells suspension was mixed with the TrypLE™-dissociated cell suspension by pipetting. A neutralizing solution of cold 3% Bovine Serum Albumin (Millipore Sigma; hereafter, BSA) in culture medium with CEPT in a ratio of 1 (total cell suspension) : 2 (neutralizing solution) was added to the dissociated cell suspension to inactivate enzymatic activity. Then the cell sus-pension was centrifuged at RT, 230 rcf for 5.5 minutes, and resuspended in 1 mL of the cold neutralizing solution; this step was repeated twice. The suspension was then filtered through a 40 µm Flowmi™ cell strainer (Bel-Art™) into a 1.5 mL Eppendorf tube to eliminate any debris. Viability (live cell percentage) and live cell count was determined using Trypan Blue (Thermo Fisher Scientific), used at 1 (Trypan Blue) : 1 (Cell suspension) ratio, on a cell counting chamber slide and Invitrogen Countess II automated counter. Final cell concentration was ~1,000 cells/µL and >90% viability.
scRNA-seq cDNA library preparation and sequencing Single cell 3’ RNA-seq experiments were conducted using the Chromium platform (10x Ge-nomics) and the NovaSeq 6000 sequencer (Illumina, Inc). Approximately 17,000 cells (targeting for 10, 000 cells) per sample were added to a single cell master mix, following the Chromium Sin-gle Cell 3’ Reagent Kits v3 User Guide, CG000183 Rev C (10x Genomics). Day-6 samples were hash-tagged using CellPlex kit (10x Genomics) and pooled into one reaction of the Single Cell 3’ kit. Along with the single-cell gel beads and partitioning oil in separate wells of a Single Cell B Chip, the single cell reaction mixture was loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and Illumina library preparation. At each step, the quality of cDNA and library was examined by Bioanalyzer. The resulting library was sequenced in on Illumina NovaSeq 6000 using 28b plus 91b paired-end sequencing to a read depth of ~50,000 reads per cell.

value: Organoid

tag: day

value: day 128


title: colorectal cancer cells, patient_11

description:
Library name: tum_11
10X Genomics

value: Male

value: KRAS Exon-2


title: d104 cvSKO

description:
Library name: SKIN-D104
10x Genomics

value: day 104


title: HD Tons 3

value: Follicular T cells


title: HD Tons 4


title: HD Tons 2


title: d28 cSKO

description:
Library name: SKIN-D28
10x Genomics

value: day 28


title: CVID LN 2

value: Lymph node

value: CVID


title: d28 Amnioid

description:
Library name: AMNION-D28-A-GEX
10x Genomics


title: CVID LN 4


title: UPN13_ARA

data_processing:
Reads quality control - FastQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters -s 2 --minOverlap 10)
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

source_name: AML blasts in culture, AraC, day 5

extract_protocol:
miRNeasy Mini Kit (QIAGEN)
Illumina Stranded mRNA Prep Ligation (Illumina)

value: AML blasts in culture, AraC, day 5

tag: disease

value: Primary AML patient

value: M

value: ARA-C at 410nM , day 0 and day 3


title: d28 SE

description:
Library name: AMNION-D28-LF-GEX
10x Genomics


title: CMO-multiplexed 4 d6 samples: d6 SEO, d6 SEO (+d3 LDN), d6 cSKO, d6 LPM

description:
Library name: pool4D6-Amnion-AmnionWL-SKIN-LPM
SKIN-D6, AMNION-D6-NO-LF, AMNION-D6-WL-NO-F and LPMESO-D6 share the same raw file.
10x Genomics

value: day 6

tag: cmo


title: UPN11_ARA

value: AML cells

value: F


title: Brain MG

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

description: Library name: Sample 9

data_processing:
The sequencing reads were first aligned to the Ensembl mouse reference genome GRCm39 with STRA (version 2.7.3a). The duplicated reads were removed using samtools software (version 1.16.1). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

organism: Mus musculus

source_name: brain

extract_protocol:
Brain tissue from adult mice was mechanically and enzymatically dissociated, and vascular fragments were isolated, followed by further digestion to obtain a single-cell suspension.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: brain

value: tissue

value: MG


title: UPN10_ARA


title: Brain FB

description: Library name: Sample 8

value: FB


title: UPN05_ARA


title: Brain vSMC

description: Library name: Sample 7

value: vSMC


title: UPN03_ARA


title: adjacent normal cells, patient_19

description:
Library name: nor_19
10X Genomics

value: adjacent normal mucosal tissue

value: Female

value: Ⅰ

value: KRAS Exon-2


title: Brain aSMC

description: Library name: Sample 6

value: aSMC


title: UPN02_ARA

value: AML blasts in culture, AraC, day 5


title: Brain PC

description: Library name: Sample 5

value: PC


title: UPN13_CTRL

source_name: AML blasts, Control, day 5

value: AML blasts, Control, day 5

value: Primary AML patient

value: M

value: Control


title: Brain CP-EC

description: Library name: Sample 4

value: CP-EC


title: Brain vEC

description: Library name: Sample 3

value: brain

value: vEC


title: UPN11_CTRL

value: AML cells

value: F


title: UPN10_CTRL


title: Brain capilEC

description: Library name: Sample 2

value: tissue

value: capilEC


title: UPN05_CTRL


title: Brain aEC

description: Library name: Sample 1

value: aEC


title: UPN03_CTRL


title: Brain single cell 391

description: Library name: Sample 391

data_processing:
The sequencing reads were first aligned to the Ensembl mouse reference genome GRCm39 with STRA (version 2.7.3a). The duplicated reads were removed using samtools software (version 1.16.1). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

value: endothelial


title: UPN02_CTRL


title: Brain single cell 390

description: Library name: Sample 390


title: ATAC-seq, Human LCL, Nutlin, 1 hour, rep 2

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

data_processing:
Read quality was assessed using FastQC (v0.11.5).
Read quality and adapter trimming was done using BBMap (v38.05) bbduk with options ktrim=r qtrim=10, k=23, mink=11, hdist=1, maq=10, minlen=25, tpe, tbo, literal=AAAAAAAAAAAAAAAAAAAAAAA, ref= The FASTA file containing common adapters found in https://github.com/Dowell-Lab/Nascent-Flow/blob/master/bin/adapters.fa.
Mapping was done using HISAT2 (v2.1.0) with options --new-summary --very-sensitive --no-spliced-alignment to each species' reference genomes.
Converted mapped SAM to BAM files using Samtools (v1.8) view -F 4 to remove unmapped reads.
Read duplicates were removed using Sambamba (v0.6.6) markdup with options --remove-duplicates, --overflow-list-size=300000.
Bedgraph files were obtained using deepTools (v3.0.1) bamCoverage with options --binSize 1, --normalizeUsing CPM.
Assembly: Human (Homo sapiens) datasets were mapped to hg38,  and Bonobo (Pan paniscus) datasets were mapped to panPan3.
Supplementary files format and content: The *.bigwig are bigwig visualization files normalized for coverage using deepTools using --normalizeUsing RPKM.

growth_protocol: The human, chimp, bonobo, gorilla, orangutan, gibbon, rhesus, baboon, squirrel monkey, owl monkey, and cow LCLs were cultured in RPMI-1640 media (Gibco Ref. 72400-047), 15% FBS (R&D Systems Ref. S11150), and 100 U/mL Penicillin-Streptomycin (Gibco Ref. 15140-122). The chicken LCLs were cultured in RPMI-1640 media (Gibco Ref. 72400-047), 10% FBS (R&D Systems Ref. S11150), 5% Chicken serum (Sigma Ref. C5405-100ML), 10% Tryptose phosphate broth (Sigma Ref. T8154), 0.05 mM β-mercaptoethanol (MP Ref. 194834), and 100 U/mL Penicillin-Streptomycin (Gibco Ref. 15140-122). All LCLs were cultured using vent-cap T-25 flasks (Corning 430639), and kept at a confluency between 400,000 cells/mL and 800,000 cells/mL during cell culture at 37°C with 5% CO2, except for the chicken LCLs which were kept between 1,000,000 cells/mL and 2,500,000 cells/mL.

extract_protocol: The ATAC-seq libraries were made following the [Corces2017] (https://doi.org/10.1038/nmeth.4396) protocol. Briefly, after the 1 hour treatments, the 100,000 cells were transferred from their 12-well plate wells to 1.8 mL eppendorf tubes, and centrifuged at 500 x g for 7 minutes at 4°C. The supernatant was carefully removed and replaced with 50 μL of ice-cold lysis buffer (water with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, 0.1% Tween-20, 0.01% Digitonin), the cells resuspended 4 times pipetting up and down, and incubated on ice for 5 minutes. Then, added 1 mL of wash buffer (water with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and the tubes inverted 4 times to mix. The tubes were centrifuged at 500 x g for 10 minutes at 4°C and the supernatant was carefully removed without disturbing the small cell pellet. The pellets were then carefully resuspended by pipetting 6 times with 50 μL of the transposition mix (25 μL Tagment DNA Buffer Illumina Ref. 15027866, 2.5 μL Tagment DNA Enzyme 1 Illumina Ref. 15027865, 0.5 μL Digitonin diluted 1:1 with water, 0.5 μL 10% Tween-20, 5 μL water, 16.5 μL PBS), and were incubated for 30 minutes in a heat block at 37°C, flicking the tube often. Afterwards, the samples were cleaned using the DNA Clean and Concentrator-5 Kit (Zymo Research Ref. D4014) following the manufacturer's instructions, and eluted in 21 μL elution buffer. Then, a PCR pre-amplification was done using NEBNext Ultra II Q5 Master Mix (NEB Ref. M0544S) using 5 cycles. Then, a qPCR was done using NEBNext Ultra II Q5 Master Mix, SYBR Gold (Life Tech Ref. S11494), and 5 μL of the pre-amplified sample, and the results used to determine the additional number of extra PCR cycles using Nextera DNA CD Indices (Illumina Ref. 20015882), which was just 1 additional cycle. The post-amplified ATAC-libraries were cleaned-up with the DNA Clean and Concentrator-5 Kit (Zymo Research Ref. D4014). The libraries were size-selected to remove DNA fragments greater than 1000 bp with a Sage Science BluePippin. The ATAC-seq libraries were quantified with Qubit HS DNA assay and their fragment size-distributions determined with Agilent HS D5000 ScreenTape. All samples were processed in parallel. After the samples were pooled and size-selected, they were cleaned-up using AMPure XP beads (Beckman Coulter Ref. A63881) at 1.5x volume and eluted into 20 μL of EB buffer (Qiagen Ref. 19086).

treatment_protocol: The human and bonobo LCLs were used for obtaining ATAC-seq libraries. They were treated for 1 hour with either 20 μM Nutlin-3a (Sigma Ref. SML0580), treated for 1 hour with either 100 U/mL of human IFN-α2 (Proteintech Ref. HZ-1066), or treated with 0.001% DMSO as a negative control. The treatments were done in 12-well plate wells so that each well had 100,000 cells in 2 mL volume. Each condition was prepared in duplicates, and all samples were processed in parallel.

value: Female

value: Lymphoblastoid cell line

value: WT

value: Nutlin

tag: time

value: 1 hour


title: adjacent normal cells, patient_06

description:
Library name: Nor6
10X Genomics

value: adjacent normal mucosal tissue

value: ⅢB

value: NRAS Exon-3


title: Brain single cell 389

description: Library name: Sample 389


title: ATAC-seq, Human LCL, Nutlin, 1 hour, rep 1


title: Raw sequencing data of input library of MCbs1 cell line.

description: Library name: MCbs1_input

value: breast

value: Breast cancer


title: Raw sequencing data of H3K4me3 ChIP library from MCF71 cell line.

description:
Library name: MCF71_H3K4me3
MCF71_H3K4me3


title: ATAC-seq, Human LCL, hsIFNa2, 1 hour, rep 2


title: Brain single cell 388

description: Library name: Sample 388

value: brain


title: ATAC-seq, Human LCL, hsIFNa2, 1 hour, rep 1


title: Brain single cell 386

description: Library name: Sample 386


title: Brain single cell 387

description: Library name: Sample 387


title: adjacent normal cells, patient_02

description:
Library name: nor_02
10X Genomics

value: Male

value: Wild


title: ATAC-seq, Human LCL, DMSO, 1 hour, rep 2

value: DMSO


title: ATAC-seq, Human LCL, DMSO, 1 hour, rep 1


title: Brain single cell 385

description: Library name: Sample 385


title: Brain single cell 384

description: Library name: Sample 384


title: Brain single cell 383

description: Library name: Sample 383


title: MycCaP cells, Olaparib2

city: Chicago

first: ping

last: xie

state: IL

address: 300 E Superior St, Tarry 4-726

institute: Northwestern University Feinberg School of Medicine, Chicago , Illinois, US

description: Library name: Bzh_PX_38S_OC2_MJ

data_processing:
Check the quality of the raw sequencing data using FastQC.
Data were trimmed using Trimmotatic to romove adapter contamination.
Sequences are aligned to the appropriate mouse reference genome using STAR aligner. The gene quantification was done using HTSeq-count.
Different gene expression was analyzed using DESeq2.
Assembly: mm39
Supplementary files format and content: LSMean values for each sample

source_name: prostate cancer

growth_protocol: MycCaP cells were maintained in DMEM with 10% FBS plus antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted with Direct-zol RNA miniprop plus of zymo
The libraries were made with NEBNext Ultra II kit

treatment_protocol: Treated with vehicle and olaparib for 24 hours

value: prostate cancer

value: MycCaP

value: Epithelial cells

value: wild type

value: Olaparib


title: Brain single cell 382

description: Library name: Sample 382

value: endothelial


title: MycCaP cells, Vehicle3

description: Library name: Bzh_PX_38S_CC3_MJ

value: Vehicle


title: MycCaP cells, Olaparib1

description: Library name: Bzh_PX_38S_OC1_MJ


title: Brain single cell 380

description: Library name: Sample 380


title: Brain single cell 381

description: Library name: Sample 381


title: MycCaP cells, Vehicle2

description: Library name: Bzh_PX_38S_CC2_MJ


title: Brain single cell 379

description: Library name: Sample 379


title: MycCaP cells, Vehicle1

description: Library name: Bzh_PX_38S_CC1_MJ


title: Brain single cell 378

description: Library name: Sample 378


title: HK2 cells, USAG1_OE_3

city: Zhengzhou

first: Xiaohu

last: Li

state: Henan

address: 1 Jianshe E Rd, Erqi District

department: Department of Kidney Transplantation

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: Sample 6
Column L in genes_fpkm_expression.csv: count.USAG1_OE_3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: kidney

value: Proximal Tubular Epithelial Cells

value: WT


title: d104 Amnioid

description:
Library name: AMNION-D104
10x Genomics

value: Organoid

value: day 104


title: Brain single cell 377

description: Library name: Sample 377


title: HK2 cells, USAG1_OE_2

description:
Library name: Sample 5
Column K in genes_fpkm_expression.csv: count.USAG1_OE_2


title: Brain single cell 376

description: Library name: Sample 376


title: HK2 cells, USAG1_OE_1

description:
Library name: Sample 4
Column J in genes_fpkm_expression.csv: count.USAG1_OE_1


title: Brain single cell 374

description: Library name: Sample 374


title: HK2 cells, Cont3

description:
Library name: Sample 3
Column I in genes_fpkm_expression.csv: count.Cont_3


title: HK2 cells, Cont2

description:
Library name: Sample 2
Column H in genes_fpkm_expression.csv: count.Cont_2


title: Brain single cell 375

description: Library name: Sample 375


title: Brain single cell 373

description: Library name: Sample 373


title: Brain single cell 372

description: Library name: Sample 372


title: HK2 cells, Cont1

description:
Library name: Sample 1
Column G in genes_fpkm_expression.csv: count.Cont_1


title: Mossy cells_Ventral_rep5

city: Daegu

first: Yong-Seok

last: Oh

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

country: South Korea

institute: Daegu-Gyeongbuk Institute of Science and Technology (DGIST)

data_processing:
Reads were then aligned to the mouse reference genome (GRCm38) with STAR version 2.5.2b.
Read counts per gene were calculated with HTseq-count version 0.7.2.
Differential expression analysis on raw read counts was performed in R  using edgeR package.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hippocampus

extract_protocol:
RNA was precipitated using TRAP assay, and purificated with Rneasy Micro Kit (QIAGEN).
Ovation RNAseq V2 kit (NuGene) was used with 500 pg of RNA for cDNA synthesis. Sequencing libraries were constructed by a TruSeq RNA library Prep Kit v2 (illumina).
Libraries were sequenced for 50 bp paired-end on Illumina HiSeq2500 using Rapid V2 sequencing chemistry (Illumina).

value: Hippocampal mossy cells (ventral)

tag: strain

value: MC-TRAP (Drd2-Cre;Eef1a1LSL.eGFPL10a/+)

value: Hippocampus


title: Brain single cell 371

description: Library name: Sample 371

value: brain


title: Brain single cell 370

description: Library name: Sample 370


title: Mossy cells_Ventral_rep4


title: Mossy cells_Ventral_rep3


title: Brain single cell 369

description: Library name: Sample 369


title: Mossy cells_Ventral_rep2


title: Mossy cells_Ventral_rep1


title: Mossy cells_Dorsal_rep4

value: Hippocampal mossy cells (dorsal)


title: Brain single cell 366

description: Library name: Sample 366


title: Brain single cell 367

description: Library name: Sample 367


title: Mossy cells_Dorsal_rep5


title: Brain single cell 365

description: Library name: Sample 365


title: Brain single cell 364

description: Library name: Sample 364


title: Mossy cells_Dorsal_rep3


title: Brain single cell 363

description: Library name: Sample 363


title: Mossy cells_Dorsal_rep1


title: Brain single cell 362

description: Library name: Sample 362


title: Mossy cells_Dorsal_rep2


title: Brain single cell 361

description: Library name: Sample 361


title: Traditional cerebral organoids (N) for originating iPSC sample 514

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 35/GF-127, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
Library name: Sample_514N
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.

data_processing:
Post deplexing, the paired-end sequence files (.fastq) per sample were quality inspected using the FastQC tool 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:11) and low quality calls (TRAILING:2 SLIDINGWINDOW:4:15 MINLEN:15) using the Trimmomatic tool 0.39 (http://www.usadellab.org/cms/?page=trimmomatic). Surviving intact pairs of reads per sample were then reference aligned to the human genome (GRCh38.p13) using hisat2 v2.2.1 (--phred33 --rna-strandness RF --dta --fr --no-discordant --no-mixed --known-splicesite-infile). To sort and index the resulting alignment files, samtools v1.13 was used. To evaluate the quality and coverage of alignment, the bam_stat.py and geneBody_coverage.py scripts available as part of RSeQC v4.0.0 were used. For transcript assembly and merging of output across samples, stringtie v2.1.4 was used in conjunction with gencode.v38.annotation.gtf. To compare the results post merge, gffcompare v0.11.6 was used. For gene enumeration, the function extractGeneExpression available in Ballgown v2.22.0 was used, returning raw linear counts per gene; including those for novel assemblies.
Assembly: GRCh38.p13
Supplementary files format and content: tab-deliminated text files include raw linear counts per gene.

source_name: Embryoid bodies differentiated from blood-derived iPSCs

growth_protocol: Embryoid bodies were derived from iPSCs using AggreWellTM plates (Stemcell Technologies, Canada) according to manufacturer’s instruction. Briefly, iPSCs were dissociated into single cells by treatment with Accutase dissociation buffer (Invitrogen) and counted. One million cells per well were seeded onto a low attachment 24-well AggreWell plate in E8 Flex medium with Rock inhibitor Y-27632 (10 ìM). After 24 hours, embryoid bodies were formed and transferred to new 24 well plates pretreated with anti-adherence rinsing solution (Stemcell Technologies) at ~10 spheres per well in 1 ml of E8 Flex medium.

extract_protocol:
At 4 weeks old, total RNA was extracted from each 3D organoid sample using the Qiagen kit following the manufacturer’s protocol,  RNA quantity and integrity was assessed and confirmed after via Bioanalyzer (Agilent, Santa Clara, CA).
500 ng of total RNA was used per sample in conjunction with the TruSeq® Stranded Total RNA Library Prep kit (Illumina, San Diego, CA). Library quality was checked by the Bioanalyzer and quantitated by the Qubit (ThermoFisher Scientific). Equimolar quantities from each sample library was pooled then sequencing on a Next-Seq550. RTA 1.13.48 and CASAVA 1.8.2. software were used after sequencing for basecalling and deplexing.

treatment_protocol: To form 3D organoids consisting of neural and endothelial cells, 48 hours after being transferred to a new plate, the embryoid bodies were coated by adding ice-cold Matrigel drop wisely (25 ul/500 ul medium) into the medium and then incubated in a 5% CO2 incubator at 37.C for 4 hours. The endothelial cell induction process was done following modifications to a protocol that used in 2D endothelial induction from iPSCs. Briefly, 500 ul of medium consisting of DMEM/F12, 1X B27 supplements and Activin A (125 ng/ml) was added on top of  the spheres followed by incubation for 24 hours. Then 500 ul medium was replaced with freshly made E8 Flex consisting of 10 ng/ml BMP4 followed by another 25 ul of ice-cold Matrigel overlay and incubation for 72 hours. The medium was then changed with DMEM/F12 consisting of 1X B27 supplement, 1 mM 8-bromo-cAMP, 100 ng/ml vascular endothelial growth factor (VEGF) and antibiotics for 72 hours. After that, half medium was changed with DMEM/F12 medium consisting of 1X N2 supplements, 1X B27 supplements, 50 ng/ml VEGF and antibiotic-antimycotic was done every other day to facilitate neural differentiation and maintain the growth of the organoids. The organoids were transferred to a 6 well plate pretreated with antiadherence rising solution after 2 weeks in culture to avoid over-crowding of cells. 3D cerebral organoids without endothelial cell induction were also derived from iPSCs using the Kit from Stem Cell technologies with modifications. Following the embryoid body formation using the Aggrewells, the neural induction and expansion were done as instructed and at day 5, the Matrigel was used to coat the spheroids drop wisely. The organoids were then changed to maturation media for further neuronal maturation.

value: blood-derived iPSC

value: neural embryoid

value: iPSC-induced 3D embyonic transformation

tag: batch


title: Brain single cell 360

description: Library name: Sample 360


title: Endothelial containing neural organoid (E) for originating iPSC sample 514

description:
Library name: Sample_514E
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.

value: Embryoid bodies differentiated from blood-derived iPSCs

value: neural and endothelial embryoid


title: Endothelial containing neural organoid (E) for originating iPSC sample 513

description:
Library name: Sample_513E
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Traditional cerebral organoids (N) for originating iPSC sample 513

description:
Library name: Sample_513N
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Brain single cell 359

description: Library name: Sample 359

value: endothelial


title: Brain single cell 358

description: Library name: Sample 358


title: Endothelial containing neural organoid (E) for originating iPSC sample 512

description:
Library name: Sample_512E
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Brain single cell 357

description: Library name: Sample 357


title: Brain single cell 356

description: Library name: Sample 356


title: Traditional cerebral organoids (N) for originating iPSC sample 512

description:
Library name: Sample_512N
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Traditional cerebral organoids (N) for originating iPSC sample 511

description:
Library name: Sample_511N
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Brain single cell 354

description: Library name: Sample 354


title: Brain single cell 355

description: Library name: Sample 355


title: Endothelial containing neural organoid (E) for originating iPSC sample 511

description:
Library name: Sample_511E
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Traditional cerebral organoids (N) for originating iPSC sample 508

description:
Library name: Sample_508N
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Brain single cell 353

description: Library name: Sample 353


title: Endothelial containing neural organoid (E) for originating iPSC sample 508

description:
Library name: Sample_508E
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Traditional cerebral organoids (N) for originating iPSC sample 504

description:
Library name: Sample_504N
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Brain single cell 351

description: Library name: Sample 351


title: Brain single cell 352

description: Library name: Sample 352


title: Brain single cell 350

description: Library name: Sample 350


title: Endothelial containing neural organoid (E) for originating iPSC sample 504

description:
Library name: Sample_504E
Enumerated expression are linear raw counts output from the Stringtie-Ballgown pipeline.


title: Brain single cell 349

description: Library name: Sample 349


title: IM63_Severe

city: Nijmegen

first: Niels

last: Velthuijs

address: Houtlaan 4

department: Cell Biology

country: Netherlands

institute: Radboud University

description: Library name: IM63_Severe

data_processing:
Preprocessing and quality control were performed using the ATAC-seq pipeline from seq2science (v1.2.5) for adapter trimming (fastp), alignment (bwa-mem2, hg38), filtering of valid reads, applying a Tn5 shift, and creating a trackhub using default settings. Based on read numbers, duplicate read ratios, TSSE enrichment, and FriP, low-quality and outlying samples were removed.
We removed all paired-end information from the BAM files and called peaks using macs3 (v3.0.4) on the pooled BAM files per group. Using the combine_peaks and coverage_table scripts from GimmeMotifs (v0.18.0), we merged the three sets of peaks into a consensus set of 200bp-wide peaks and counted reads per sample in these peaks. Peaks were filtered for having at least 0.3 CPM in more than 15 samples of a single patient group.
Assembly: Hg38
Supplementary files format and content: Counts.tsv contains all called peaks (rows, first column describes peak locations) and all samples (columns, as described in samples.txt)

source_name: Blood

extract_protocol:
Ficoll PBMC isolation followed by MACS pan-monocyte isolation kit on fresh blood
https://doi.org/10.1002/0471142727.mb2129s109

value: Blood

tag: donor group

value: Severe

value: Monocyte


title: IM62_Severe

description: Library name: IM62_Severe

tag: tissue


title: Brain single cell 348

description: Library name: Sample 348


title: Brain single cell 347

description: Library name: Sample 347


title: RGL25a

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: FFPE tissue-based spatial transcriptome profiling

data_processing:
Raw seqeuencing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to the reference genome and transcriptome abundance was calculated using Space Ranger following the manufacturer's manual.
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings.
Assembly: hg38
Supplementary files format and content: RGL25a_barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: RGL25a_features.tsv.gz: list ofr gene ID's
Supplementary files format and content: RGL25a_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: RGL25a_aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: RGL25a_detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: RGL25a_scalefactors_json.json: scalefactors in json format
Supplementary files format and content: RGL25a_tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: RGL25a_tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: RGL25a_tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tissue section (5 µm-thick) was prepared with tissue microtome for the Visum Spatial Transcriptome profiling.
Spatial transcriptome sequencing library was prepared using 10x Genomics Visium Spatial Gene expression slides & Reagent kit according to the manufacturer's protocol.

value: Liver

value: Metabolic dysfunction-associated steatotic liver disease


title: IM60_Severe

description: Library name: IM60_Severe


title: Brain single cell 346

description: Library name: Sample 346


title: IM59_Severe

description: Library name: IM59_Severe


title: Brain single cell 345

description: Library name: Sample 345


title: IM58_Severe

description: Library name: IM58_Severe


title: Brain single cell 344

description: Library name: Sample 344


title: IM57_Severe

description: Library name: IM57_Severe


title: Brain single cell 343

description: Library name: Sample 343


title: IM55_Severe

description: Library name: IM55_Severe


title: Brain single cell 342

description: Library name: Sample 342


title: IM54_Severe

description: Library name: IM54_Severe


title: Brain single cell 341

description: Library name: Sample 341


title: Brain single cell 340

description: Library name: Sample 340


title: IM53_Severe

description: Library name: IM53_Severe


title: aipwh86(+/+)_3

description: Library name: C1

data_processing:
The cutadapt tool was used to trim adapter sequences, primers, and poly-A tails as well as quality trimming and filtering. Following trimming and filtering with cutadapt the median number of reads (x106) was 30.82, with the minimum being 27.85, and the maximum being 33.51.
The Star aligner was used to align reads in FASTQ format directly to the reference genome. The median percentage of uniquely mapped reads was 85.4%, with the minimum being 83.7% and the maximum being 86.7%.
Unique molecular identifier (UMI) tags were included in the samples and used to remove PCR duplicates. Reads with the same UMI that mapped to the same location are collapsed to one read. Following UMI collapsing the median percentage of remaining reads was 58.9% with the minimum being 54.6% and the maximum being 66.1%.
Transcript- and gene-level raw count matrices were generated which included 53,466 and 32,171 features, respectively.
Assembly: GRCz11
Supplementary files format and content: .xlsx, raw transcript and gene counts of all samples and types
Supplementary files format and content: .xlsx, separate DEG analysis results tables for each comparison referenced in the manuscript

source_name: 5 whole 5 dpf larvae

extract_protocol:
A Thermo Fisher KingFisher Apex liquid handler system and a Zymo Quick-RNA MagBead kit were used to perform the extractions in a 96-well format. The Zymo kit requires an equal volume of ethanol to be mixed with the sample for extraction but has a max volume of 1000 µL. Since 550 µL of supernatant was collected, the final volume with ethanol was 1100 µL and had to be split between two extraction plates. Each sample was individually moved and equally divided between two extraction plates. The well position of the original sample plate was tracked throughout this process and into the sample submission. Ethanol and mag beads were added using a multichannel pipette and the extraction was carried out following the kit protocol including a DNase I digestion step. The RNA was eluted into 50 µL of UP water. Individual larval RNA samples were pooled following RNA extraction to reduce inter-replicate variation. Each pooled replicate was created by combining five individual samples. Samples with the highest concentration and RIN scores > 8 were selected to be pooled. The RIN and concentration of each sample was determined using an Agilent 4150 TapeStation System and an Invitrogen qubit fluorometer, respectively.
Library preparation was performed using the CORALL mRNA-Seq V2 whole transcriptome sequencing kit. 150bp paired end reads were sequenced on an AVITI sequencing platform

value: 5 whole 5 dpf larvae


title: IM51_Severe

description: Library name: IM51_Severe


title: Brain single cell 339

description: Library name: Sample 339


title: IM50_Severe

description: Library name: IM50_Severe


title: IM49_Severe

description: Library name: IM49_Severe


title: Brain single cell 338

description: Library name: Sample 338


title: IM48_Severe

description: Library name: IM48_Severe


title: Brain single cell 337

description: Library name: Sample 337


title: IM47_Severe

description: Library name: IM47_Severe


title: HPMEC + TENT2sh-1

description: Library name: TENT2sh-1_B22HVCGLT4_L002

source_name: HPMEC

value: HPMEC

value: Primary lung endothelial cells

value: TENT2 shRNA

tag: treatment

value: 36 hr wih lenivirus + 24 hr PBS


title: Brain single cell 336

description: Library name: Sample 336

value: brain


title: IM46_Severe

description: Library name: IM46_Severe


title: Brain single cell 335

description: Library name: Sample 335


title: Brain single cell 334

description: Library name: Sample 334


title: Brain single cell 368

description: Library name: Sample 368


title: IM45_Severe

description: Library name: IM45_Severe


title: IM44_Severe

description: Library name: IM44_Severe


title: Brain single cell 333

description: Library name: Sample 333


title: Brain single cell 332

description: Library name: Sample 332


title: IM43_Severe

description: Library name: IM43_Severe


title: IM41_Nonsymptomatic

description: Library name: IM41_Nonsymptomatic

value: Nonsymptomatic


title: Brain single cell 331

description: Library name: Sample 331


title: Brain single cell 329

description: Library name: Sample 329


title: Brain single cell 330

description: Library name: Sample 330


title: IM40_Nonsymptomatic

description: Library name: IM40_Nonsymptomatic


title: Brain single cell 328

description: Library name: Sample 328


title: IM38_Mild

description: Library name: IM38_Mild

value: Mild


title: IM37_Nonsymptomatic

description: Library name: IM37_Nonsymptomatic


title: Brain single cell 327

description: Library name: Sample 327


title: IM39_Mild

description: Library name: IM39_Mild


title: IM35_Nonsymptomatic

description: Library name: IM35_Nonsymptomatic


title: Brain single cell 326

description: Library name: Sample 326


title: Brain single cell 325

description: Library name: Sample 325


title: IM34_Nonsymptomatic

description: Library name: IM34_Nonsymptomatic


title: Brain single cell 324

description: Library name: Sample 324


title: IM33_Mild

description: Library name: IM33_Mild


title: Brain single cell 323

description: Library name: Sample 323


title: IM31_Mild

description: Library name: IM31_Mild


title: Brain single cell 322

description: Library name: Sample 322


title: Brain single cell 321

description: Library name: Sample 321


title: IM29_Nonsymptomatic

description: Library name: IM29_Nonsymptomatic


title: Brain single cell 319

description: Library name: Sample 319


title: Brain single cell 320

description: Library name: Sample 320


title: IM24_Mild

description: Library name: IM24_Mild


title: IM23_Nonsymptomatic

description: Library name: IM23_Nonsymptomatic


title: IM30_Nonsymptomatic

description: Library name: IM30_Nonsymptomatic


title: IM21_Mild

description: Library name: IM21_Mild


title: IM22_Mild

description: Library name: IM22_Mild


title: Brain single cell 317

description: Library name: Sample 317


title: Brain single cell 318

description: Library name: Sample 318


title: IM20_Mild

description: Library name: IM20_Mild


title: Brain single cell 316

description: Library name: Sample 316


title: Brain single cell 315

description: Library name: Sample 315


title: IM19_Nonsymptomatic

description: Library name: IM19_Nonsymptomatic


title: Brain single cell 314

description: Library name: Sample 314


title: IM18_Nonsymptomatic

description: Library name: IM18_Nonsymptomatic


title: Brain single cell 313

description: Library name: Sample 313


title: IM16_Nonsymptomatic

description: Library name: IM16_Nonsymptomatic


title: Brain single cell 310

description: Library name: Sample 310


title: Brain single cell 311

description: Library name: Sample 311


title: IM15_Nonsymptomatic

description: Library name: IM15_Nonsymptomatic


title: Brain single cell 312

description: Library name: Sample 312


title: IM14_Mild

description: Library name: IM14_Mild


title: Brain single cell 307

description: Library name: Sample 307


title: IM13_Nonsymptomatic

description: Library name: IM13_Nonsymptomatic


title: Brain single cell 309

description: Library name: Sample 309


title: Brain single cell 308

description: Library name: Sample 308


title: IM11_Mild

description: Library name: IM11_Mild


title: IM10_Nonsymptomatic

description: Library name: IM10_Nonsymptomatic


title: Brain single cell 305

description: Library name: Sample 305


title: IM09_Mild

description: Library name: IM09_Mild


title: Brain single cell 304

description: Library name: Sample 304


title: IM08_Mild

description: Library name: IM08_Mild


title: Brain single cell 302

description: Library name: Sample 302


title: Brain single cell 303

description: Library name: Sample 303


title: IM07_Nonsymptomatic

description: Library name: IM07_Nonsymptomatic


title: Brain single cell 301

description: Library name: Sample 301


title: Brain single cell 300

description: Library name: Sample 300


title: Brain single cell 299

description: Library name: Sample 299


title: T47Dbs1 PBS biorep 1

description: Library name: 341-13

data_processing:
Fastq files were checked for quality using fastqc and fastq_screen and were quality trimmed using fastq-mcf
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using TopHat
duplicates were marked using picard-tools, read counts were generated using featureCounts and differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: The Excel files contain RNA-seq differential expression analysis results, gene overlap analyses identifying shared and unique differentially expressed genes, genes of interest (GOI), and Gene Ontology (GO) over-representation analysis (ORA) results with associated enrichment statistics.

growth_protocol: To establish stable chronic IL-1-exposed sublines, MCF7 cells were cultured in DMEM/10% FB Essence (FBE) containing 0.5ng/mL IL-1α or 0.5ng/mL IL-1β for 6 months and T47D cells were cultured in RPMI 1640/10% FBE containing 0.5 ng/mL IL-1α or IL-1β for 6 months (7 months for the T47Dbs1 subline due to slowed prolifer-ation and expansion). Following chronic IL-1 exposure, cells were moved out of IL-1-containing medium and maintained in normal growth medium without IL-1 for phenotype characterization. Parental cell lines (MCF71, T47D1) were cultured in vehicle control (1× phosphate buffer saline, PBS) alongside the sublines. Sublines: MCF7 chronic IL-1α subline termed MCas1, MCF7 chronic IL-1β sublines termed MCbs1, T47D chronic IL-1α subline termed T47Das1, and termed T47D chronic IL-1β subline T47Dbs1.

extract_protocol:
RNA was extracted from cells treated with cytokines using GeneJET RNA Purification kit (Thermo Fisher Scientific, Waltham, MA; K0732) as per manufacturer’s instructions. Genomic DNA contamination was removed by treating 1 ug of RNA with 1 U of DNase-I (Thermo scientific, Waltham, MA; EN0521) following manufacturer’s instructions.
RNA-seq was performed by the Genome Center at tThe University of Texas at Dallas (Richardson, TX). Total RNA library was prepared using Illumina Truseq Stranded Total RNA prep Gold kit (Illumina). The prepared libraries were sequenced on an Illumina NextSeq 500 platform (San Diego, CA) with 100bp single-end reads.

treatment_protocol: We performed RNA sequencing (RNA-seq) and differential gene expression analysis for the parental (MCF71, T47D1) cells treated acutely with vehicle control, 25ng/mL IL-1α or 25ng/mL IL-1β for 4 days and for the chronic IL-1 sublines (MCas1, MCbs1, T47Das1, T47Dbs1) grown in vehicle control only.

value: breast cancer


title: Brain single cell 298

description: Library name: Sample 298


title: T47Das1 PBS biorep 3

description: Library name: 341-12


title: Brain single cell 297

description: Library name: Sample 297


title: T47Das1 PBS biorep 2

description: Library name: 341-11


title: Brain single cell 296

description: Library name: Sample 296


title: Brain single cell 295

description: Library name: Sample 295


title: T47D-1 acute IL-1b biorep 3

description: Library name: 341-9


title: T47D-1 acute IL-1b biorep 2

description: Library name: 341-8


title: Brain single cell 293

description: Library name: Sample 293


title: Brain single cell 292

description: Library name: Sample 292


title: T47D-1 acute IL-1b biorep 1

description: Library name: 341-7


title: T47D-1 acute IL-1a biorep 3

description: Library name: 341-6


title: Brain single cell 291

description: Library name: Sample 291


title: T47D-1 acute IL-1a biorep 2

description: Library name: 341-5


title: Brain single cell 290

description: Library name: Sample 290


title: T47D-1 acute IL-1a biorep 1

description: Library name: 341-4


title: T47D-1 PBS biorep 3

description: Library name: 341-3


title: Brain single cell 288

description: Library name: Sample 288


title: T47D-1 PBS biorep 2

description: Library name: 341-2


title: T47D-1 PBS biorep 1

description: Library name: 341-1


title: Brain single cell 285

description: Library name: Sample 285


title: MycCaP cells, Olaparib3

description: Library name: Bzh_PX_38S_OC3_MJ

value: prostate cancer

value: MycCaP

value: Epithelial cells

tag: genotype

value: wild type

value: Olaparib


title: IM17_Nonsymptomatic

description: Library name: IM17_Nonsymptomatic

value: Blood

value: Monocyte


title: MCbs1 PBS biorep 2

description: Library name: 300-14

tag: cell line


title: Brain single cell 284

description: Library name: Sample 284

tag: cell type

value: endothelial


title: MCbs1 PBS biorep 1

description: Library name: 300-13


title: Brain single cell 283

description: Library name: Sample 283


title: MCas1 PBS biorep 3

description: Library name: 300-12


title: Brain single cell 282

description: Library name: Sample 282


title: Brain single cell 281

description: Library name: Sample 281


title: MCas1 PBS biorep 2

description: Library name: 300-11


title: MCas1 PBS biorep 1

description: Library name: 300-10


title: Brain single cell 280

description: Library name: Sample 280

value: microglia


title: MCF7-1 acute IL-1b biorep 3

description: Library name: 300-9


title: Brain single cell 279

description: Library name: Sample 279


title: MCF7-1 acute IL-1b biorep 2

description: Library name: 300-8


title: Brain single cell 278

description: Library name: Sample 278


title: MCF7-1 acute IL-1b biorep 1

description: Library name: 300-7


title: Brain single cell 277

description: Library name: Sample 277


title: MCF7-1 acute IL-1a biorep 3

description: Library name: 300-6


title: T47Dbs1 PBS biorep 2

description: Library name: 341-14


title: Brain single cell 276

description: Library name: Sample 276


title: MCF7-1 acute IL-1a biorep 2

description: Library name: 300-5


title: Brain single cell 275

description: Library name: Sample 275


title: MCF7-1 acute IL-1a biorep 1

description: Library name: 300-4


title: MCF7-1 PBS biorep 3

description: Library name: 300-3


title: Brain single cell 273

description: Library name: Sample 273


title: MCF7-1 PBS biorep 2

description: Library name: 300-2


title: Brain single cell 274

description: Library name: Sample 274


title: Brain single cell 272

description: Library name: Sample 272


title: MCF7-1 PBS biorep 1

description: Library name: 300-1


title: Brain single cell 271

description: Library name: Sample 271


title: ko-CRC9-POR_3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11b (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Endothelial

growth_protocol: Cells cultured in endothelial growth media (EGM) prior to RNA isolation

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and all 18ul of total RNA was used as input for Watchmaker_RNA_Library_Prep_Kit_with_Polaris™_Depletion"]="Watchmaker RNA Library Prep Kit with Polaris™ Depletion following manufacture’s protocol (Watchmaker Genomics). Sequencing was performed on the NextSeq2000 platform (Illumina) using P4 flowcell with 72bp single-end setup.

treatment_protocol: No treatment, basal conditions

value: Endothelial

value: HAEC

value: human aortic endothelial cells

value: POR-/-

value: Basal


title: Brain single cell 270

description: Library name: Sample 270

value: brain


title: ko-CRC9-POR_2

description: Library name: Sample 5


title: Brain single cell 269

description: Library name: Sample 269


title: ko-CRC9-POR_1

description: Library name: Sample 4


title: Brain single cell 268

description: Library name: Sample 268


title: Brain single cell 267

description: Library name: Sample 267


title: WT_3

description: Library name: Sample 3

value: NTC


title: WT_2

description: Library name: Sample 2


title: Brain single cell 266

description: Library name: Sample 266


title: WT_1

description: Library name: Sample 1


title: Brain single cell 265

description: Library name: Sample 265


title: ko-CRC9-POR_4

description: Library name: Sample 8

growth_protocol: Cells cultured in endothelial growth media (EGM) prior to RNA isolation. Initially, mixed cultures were prepared containing non-target control (NTC) and POR-/- cells expressing CFP or YFP, including reciprocal labelling conditions (NTC-CFP/POR-/--YFP and NTC-YFP/POR-/--CFP) mixed at a 1:1 ratio.

value: HUVEC

value: Human umbilical vein endothelial cells

value: POR-/-/YFP


title: Brain single cell 264

description: Library name: Sample 264


title: Brain single cell 263

description: Library name: Sample 263


title: ko-CRC9-POR_2

description: Library name: Sample 6

value: POR-/-/CFP


title: Brain single cell 262

description: Library name: Sample 262


title: ko-CRC9-POR_3

description: Library name: Sample 7


title: ko-CRC9-POR_1

description: Library name: Sample 5


title: Brain single cell 261

description: Library name: Sample 261


title: Brain single cell 260

description: Library name: Sample 260


title: WT_4

description: Library name: Sample 4

value: NTC/YFP


title: WT_3

description: Library name: Sample 3


title: Brain single cell 258

description: Library name: Sample 258


title: Brain single cell 259

description: Library name: Sample 259


title: WT_2

description: Library name: Sample 2

value: NTC/CFP


title: WT_1

description: Library name: Sample 1


title: Brain single cell 257

description: Library name: Sample 257


title: OL70504

city: 北京市

first: Zhaochen

last: Wang

address: 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

description: Library name: F9O

data_processing:
Clean paired-end RNA-seq reads were aligned to the Bos taurus reference genome (ARS-UCD1.2) using HISAT2 (v2.2.1) with default settings except that only uniquely mapping reads were retained.
Gene-level read quantification was performed with featureCounts (Subread) using parameters -t exon -g gene_id against the corresponding GTF annotation.
Assembly: ARS-UCD1.2
Supplementary files format and content: counts_hisat2_all.txt

organism: Bos taurus

source_name: ovary

extract_protocol:
For single oocytes and cumulus cells (CCs), cells were lysed directly using the Single Cell Full-Length mRNA Amplification Kit (Vazyme). For mural granulosa cells (MGCs), total RNA was extracted using standard protocols.
For oocytes and CCs, cDNA was amplified using the SMART-seq2 protocol and libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). For MGCs, standard bulk RNA-seq libraries were constructed. All libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: ovary

value: Oocyte

value: oocyte from large follicle (11.6mm)


title: Brain single cell 256

description: Library name: Sample 256

value: microglia


title: OL72101

description: Library name: F7O

value: oocyte from large follicle (11.3mmmm)


title: OL71801

description: Library name: F8O

value: oocyte from large follicle (11.5mm)


title: Brain single cell 254

description: Library name: Sample 254


title: Brain single cell 255

description: Library name: Sample 255


title: OL62803

description: Library name: F6O

value: oocyte from large follicle (11.2mm)


title: Brain single cell 253

description: Library name: Sample 253


title: OL50505

description: Library name: W5O


title: Brain single cell 252

description: Library name: Sample 252


title: OL70703

description: Library name: F5O

value: oocyte from large follicle (10.2mm)


title: Brain single cell 251

description: Library name: Sample 251


title: OL62802

description: Library name: F4O


title: Brain single cell 250

description: Library name: Sample 250


title: Brain single cell 249

description: Library name: Sample 249


title: OL72102

description: Library name: F3O

value: oocyte from large follicle (10.0mm)


title: OL70503

description: Library name: F2O


title: Brain single cell 248

description: Library name: Sample 248

value: brain


title: Brain single cell 247

description: Library name: Sample 247


title: OL71802

description: Library name: F1O

value: oocyte from large follicle (9.6mm)


title: OM71001

description: Library name: D10O

value: oocyte from medium follicle (7.1mm)


title: Brain single cell 246

description: Library name: Sample 246


title: OM72404

description: Library name: D9O

value: oocyte from medium follicle (7.0mm)


title: OM71805

description: Library name: D8O


title: Brain single cell 244

description: Library name: Sample 244


title: Brain single cell 245

description: Library name: Sample 245


title: OM71804

description: Library name: D7O


title: OM72403

description: Library name: D5O

value: oocyte from medium follicle (6.7mm)


title: Brain single cell 243

description: Library name: Sample 243


title: OM71002

description: Library name: D6O


title: Brain single cell 239

description: Library name: Sample 239


title: Brain single cell 242

description: Library name: Sample 242


title: OM71704

description: Library name: D4O

value: oocyte from medium follicle (6.4mm)


title: Brain single cell 241

description: Library name: Sample 241


title: OM72104

description: Library name: D2O

value: oocyte from medium follicle (6.2mm)


title: Brain single cell 240

description: Library name: Sample 240


title: OM70502

description: Library name: D3O


title: Brain single cell 238

description: Library name: Sample 238