title: Total DNA from acute lymphoblastic leukemia patient 1113

city: XOCHIMILCO

first: ALAN

middle: ALBERTO

last: FONG LÓPEZ

state: CDMX

address: CALLE PRIVADA SAN LORENZO #45

country: Mexico

institute: INMEGEN

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1113

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to the Infinium MethylationEPIC BeadChip using the standard Illumina protocol.

scan_protocol: Arrays were scanned using the Illumina iScan or Illumina HiScan system with standard settings.

data_processing:
Raw IDAT files were processed using the ChAMP package (v.x.x.x) in R (v.x.x.x). Data normalization was performed using the [método usado, e.g., 'BMIQ' o 'Noob'] method. Probe filtering removed probes with a detection p-value > 0.01 in any sample, probes located on sex chromosomes, and cross-reactive probes.
File raw_signal.csv is linked as a supplementary file on the Series record.
Beta value: The ratio of the methylated probe intensity to the total intensity (sum of methylated and unmethylated probe intensities). Formula: Beta = M / (M + U + offset). File processed_matrix.csv is linked as a supplementary file on the Series record.

source_name: Bone marrow

label_protocol: Cy3 and Cy5

extract_protocol: QIAGEN Puregene Blood Core Kit

tag: disease state

value: acute lymphoblastic leukemia patient

value: Bone marrow

value: Male

tag: relapse

value: No

tag: death


title: Total DNA from acute lymphoblastic leukemia patient 1114

status: Public on Dec 04 2025

type: genomic

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1114

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: Sex

value: Female

value: Yes


title: Total DNA from acute lymphoblastic leukemia patient 1111

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1111


title: Total DNA from acute lymphoblastic leukemia patient 1108

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1108


title: Total DNA from acute lymphoblastic leukemia patient 1106

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1106


title: Total DNA from patient 1104 with discard acute lymphoblastic leukemia

description:
Total DNA from non leukemic patient
LAL1104

value: non leukemic patient


title: Total DNA from acute lymphoblastic leukemia patient 1110

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1110


title: Total DNA from acute lymphoblastic leukemia patient 1102

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1102


title: Total DNA from patient 1097 with discard acute lymphoblastic leukemia

description:
Total DNA from non leukemic patient
This sample was identified and filtered out during our rigorous quality control pipeline using the ChAMP package due to failing the detection p-value threshold (a standard QC metric for microarray data). It was not included in any of the downstream analyses reported in our study.
LAL1097


title: Total DNA from acute lymphoblastic leukemia patient 1093

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1093

source_name: Peripheral blood

value: Peripheral blood


title: Total DNA from acute lymphoblastic leukemia patient 1085

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1085


title: Total DNA from acute lymphoblastic leukemia patient 1087

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1087


title: Total DNA from acute lymphoblastic leukemia patient 1082

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1082


title: Total DNA from patient 1091 with discard acute lymphoblastic leukemia

description:
Total DNA from non leukemic patient
LAL1091


title: ALL survivor 4

city: Toronto

first: Sarah

middle: J.

last: Goodman

state: ON

address: PGCRL, 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC V1.0 Beadchip using standard Illumina protocol

scan_protocol: standard  protocol for Illumina HiScan

data_processing:
The raw IDAT files were processed into β-values, which quantify DNA methylation levels on a scale from 0 to 1, using the minfi package from Bioconductor in R v4.1.1. The data was then normalized using the preprocessIllumina function in minfi to correct for technical variation. The preprocessing pipeline included several filtering steps: removal of non-specific probes; exclusion of probes with detection p-values greater than 0.05 in more than 25% of samples; elimination of probes located near SNPs (within 10 bp of the CpG site or single base extension) or associated with SNPs having a minor allele frequency above 1%; removal of xyz probes with β-values of 0 or 1 in more than 0.25% of samples; exclusion of non-CpG probes; and filtering out probes located on sex chromosomes. Quality control was performed using standard minfi metrics such as median intensity plots, density distributions, and control probe assessments, with all samples passing QC and included in the final analysis.  The raw IDAT files were processed into β-values, which quantify DNA methylation levels on a scale from 0 to 1, using the minfi package from Bioconductor in R v4.1.1. The data was then normalized using the preprocessIllumina function in minfi to correct for technical variation. The preprocessing pipeline included several filtering steps: removal of non-specific probes; exclusion of probes with detection p-values greater than 0.05 in more than 25% of samples; elimination of probes located near SNPs (within 10 bp of the CpG site or single base extension) or associated with SNPs having a minor allele frequency above 1%; removal of probes with β-values of 0 or 1 in more than 0.25% of samples; exclusion of non-CpG probes; and filtering out probes located on sex chromosomes. Quality control was performed using standard minfi metrics such as median intensity plots, density distributions, and control probe assessments, with all samples passing QC and included in the final analysis.
processed value definition: normalized betas

source_name: primary

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications.

tag: cell line

value: primary

tag: cell type

value: Whole blood

value: M

tag: age at sample collection


title: Total DNA from acute lymphoblastic leukemia patient 1080

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1080


title: Total DNA from acute lymphoblastic leukemia patient 1078

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1078


title: Total DNA from acute lymphoblastic leukemia patient 1073

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1073


title: ALL survivor 2


title: Total DNA from acute lymphoblastic leukemia patient 1069

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1069


title: Total DNA from patient 1071 with discard acute lymphoblastic leukemia

description:
Total DNA from non leukemic patient
LAL1071


title: Total DNA from acute lymphoblastic leukemia patient 1068

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1068


title: Total DNA from acute lymphoblastic leukemia patient 1060

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1060


title: Total DNA from acute lymphoblastic leukemia patient 1063

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1063


title: Total DNA from acute lymphoblastic leukemia patient 1066

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1066


title: Total DNA from acute lymphoblastic leukemia patient 1058

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1058


title: Total DNA from acute lymphoblastic leukemia patient 1050

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1050


title: Total DNA from patient 1048 with discard acute lymphoblastic leukemia

description:
Total DNA from non leukemic patient
LAL1048


title: Total DNA from acute lymphoblastic leukemia patient 1051

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1051


title: Total DNA from acute lymphoblastic leukemia patient 1109

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1109


title: Total DNA from acute lymphoblastic leukemia patient 1049

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1049


title: Total DNA from acute lymphoblastic leukemia patient 1047

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1047


title: Total DNA from acute lymphoblastic leukemia patient 1046

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1046


title: Total DNA from acute lymphoblastic leukemia patient 1045

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1045


title: Total DNA from acute lymphoblastic leukemia patient 1084

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1084


title: Total DNA from acute lymphoblastic leukemia patient 1044

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1044


title: Total DNA from acute lymphoblastic leukemia patient 1043

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1043


title: Total DNA from acute lymphoblastic leukemia patient 1041

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1041


title: Total DNA from acute lymphoblastic leukemia patient 1042

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1042


title: Total DNA from acute lymphoblastic leukemia patient 1040

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1040


title: Total DNA from acute lymphoblastic leukemia patient 1039

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1039


title: Total DNA from acute lymphoblastic leukemia patient 1020

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1020


title: Total DNA from acute lymphoblastic leukemia patient 1077

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1077


title: Total DNA from acute lymphoblastic leukemia patient 1010

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1010


title: Total DNA from acute lymphoblastic leukemia patient 1027

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1027


title: Total DNA from acute lymphoblastic leukemia patient 1011

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1011


title: Total DNA from acute lymphoblastic leukemia patient 1009

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1009


title: Total DNA from acute lymphoblastic leukemia patient 1008

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1008


title: Total DNA from acute lymphoblastic leukemia patient 1007

description:
Total DNA from acute lymphoblastic leukemia patient
LAL1007


title: Total DNA from acute lymphoblastic leukemia patient 996

description:
Total DNA from acute lymphoblastic leukemia patient
LAL996


title: Total DNA from acute lymphoblastic leukemia patient 991

description:
Total DNA from acute lymphoblastic leukemia patient
LAL991


title: Total DNA from acute lymphoblastic leukemia patient 986

description:
Total DNA from acute lymphoblastic leukemia patient
LAL986


title: Total DNA from acute lymphoblastic leukemia patient 998

description:
Total DNA from acute lymphoblastic leukemia patient
LAL998


title: Total DNA from acute lymphoblastic leukemia patient 990

description:
Total DNA from acute lymphoblastic leukemia patient
LAL990


title: Total DNA from acute lymphoblastic leukemia patient 985

description:
Total DNA from acute lymphoblastic leukemia patient
LAL985


title: Total DNA from acute lymphoblastic leukemia patient 93

description:
Total DNA from acute lymphoblastic leukemia patient
LAL93


title: Total DNA from acute lymphoblastic leukemia patient 90

description:
Total DNA from acute lymphoblastic leukemia patient
LAL90


title: Total DNA from acute lymphoblastic leukemia patient 988

description:
Total DNA from acute lymphoblastic leukemia patient
LAL988


title: Total DNA from acute lymphoblastic leukemia patient 34

description:
Total DNA from acute lymphoblastic leukemia patient
LAL34


title: Total DNA from acute lymphoblastic leukemia patient 303

description:
Total DNA from acute lymphoblastic leukemia patient
LAL303


title: Very heavy drinker 1, post-induction

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

country: USA

institute: Wake Forest School of Medicine

hyb_protocol: Standard Illumina protocol

scan_protocol: iScan Illumina protocol

data_processing:
ChAMP package; BMIQ normalization, adjusted for Slide using Combat; sample "LD-P1" excluded because of poor data quality
processed value definition: beta values (Cox_EPIC_ChipAdj_042621.txt)

organism: Macaca mulatta

source_name: liver

extract_protocol: DNA was extracted from liver samples using the DNeasy Blood & Tissue Kits (Qiagen, Inc.).

treatment_protocol: Liver biopsies were performed to obtain samples before the induction phase. During the induction phase of 90 days, monkeys drank 0.5 g ethanol/kg/day, 1 g ethanol/kg/day, and 1.5 g ethanol/kg/day for 30 days at each dose. Liver biopsies were performed to obtain samples at the end of the induction phase.

value: liver

value: male

tag: treatment

value: post-induction


title: Very heavy drinker 2, post-induction


title: Very heavy drinker 3, post-induction


title: Light drinker 3, post-induction


title: Very heavy drinker 2, baseline

value: baseline


title: Light drinker 2, post-induction


title: Very heavy drinker 3, baseline


title: Light drinker 3, baseline


title: Very heavy drinker 1, baseline


title: Light drinker 2, baseline


title: Light drinker 1, baseline


title: Light drinker 1, post-induction


title: GA0055_Initial clinical diagnosis was stable GH

city: Xi'an

first: YuFeng

last: Liu

state: ShanXi

address: The First Affiliated Hospital of Xi'an Jiao Tong University

country: China

hyb_protocol: illumina protocol

data_processing: CHAPM package in R environment(v4.3)

source_name: peripheral blood

label_protocol: standard illumina protocol

extract_protocol: The peripheral blood DNA extraction process using a DNA extraction kit and the capture process for the methylation 450K array

value: peripheral blood

tag: initial clinical diagnosis

value: stable GH


title: GA0059_Initial clinical diagnosis was stable GH

institute: The First Affiliated Hospital of Xi'an Jiao Tong University


title: GA0036_Initial clinical diagnosis was stable GH


title: GA0058_Initial clinical diagnosis was stable GH


title: GA0045_Initial clinical diagnosis was stable GH


title: GA0016_Initial clinical diagnosis was stable GH


title: GA0054_Initial clinical diagnosis was stable GH


title: GA0047_Initial clinical diagnosis was stable GH


title: GA0022_Initial clinical diagnosis was stable GH


title: GA0029_Initial clinical diagnosis was stable GH


title: GA0031_Initial clinical diagnosis was GH to GO

value: GH to GO


title: GA0033_Initial clinical diagnosis was stable GH


title: GA0037_Initial clinical diagnosis was GH to GO


title: GA0010_Initial clinical diagnosis was stable GH


title: GA0004_Initial clinical diagnosis was stable GH


title: GA0012_Initial clinical diagnosis was stable GH


title: GA0038_Initial clinical diagnosis was stable GH


title: GA0021_Initial clinical diagnosis was stable GH


title: GA0024_Initial clinical diagnosis was GH to GO


title: GA0035_Initial clinical diagnosis was GH to GO


title: GA0026_Initial clinical diagnosis was stable GH


title: GA0049_Initial clinical diagnosis was stable GH


title: GA0018_Initial clinical diagnosis was stable GH


title: GA0046_Initial clinical diagnosis was GH to GO


title: GA0008_Initial clinical diagnosis was stable GH


title: GA0003_Initial clinical diagnosis was stable GH


title: GA0030_Initial clinical diagnosis was stable GH


title: GA0053_Initial clinical diagnosis was stable GH


title: GA0041_Initial clinical diagnosis was GH to GO


title: GA0011_Initial clinical diagnosis was GH to GO


title: GA0056_Initial clinical diagnosis was stable GH


title: H209A cells, polysome RNA, replicate 2

type: SRA

city: Chengdu

first: Haoning

last: Peng

state: Sichuan

address: No.37 Guoxue Alley, Wuhou District

department: Department of Thoracic Surgery

institute: West China Hospital, Sichuan University

description:
Library name: samples 16
H209A_poly_2
polysome_H209_H209A.profilling.expression_TPM_hg38.txt

library_source: other

data_processing:
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR
Count data were generated using HTSeq
Assembly: hg38
Supplementary files format and content: tab delimited text file includes read counts for each sample

molecule: other

growth_protocol: H82, H82R, H209 and H209A cells were maintained in RPMI 1640 supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Polysome-bound RNA were extracted from sucrose based fraction after polysome profiling using TRIzol LS (ThermoFisher) according to manufacturer’s protocol and were quantified by Nanodrop microvolume spectrophotometers (Thermo Fisher Scientific). Cytoplasmic RNA were extracted from cell lysate in hypotonic buffer (5 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 μg.ml-1 cycloheximide, 2 mM DTT, 100 U/ml RNase inhibitor (Promega), 0.5% sodium deoxycholate, 0.5% Triton X-100) using TRIzol LS and were quantified by Nanodrop as well.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations

value: SCLC cells

tag: genotype

value: WT

value: normal

tag: fraction

value: polysome RNA


title: H209A cells, polysome RNA, replicate 1

description:
Library name: samples 15
H209A_poly_1
polysome_H209_H209A.profilling.expression_TPM_hg38.txt


title: H209 cells, polysomal RNA, replicate 1

description:
Library name: samples 11
H209_poly_1
polysome_H209_H209A.profilling.expression_TPM_hg38.txt

value: polysomal RNA


title: H209 cells, cytoplasmic RNA, replicate 2

description:
Library name: samples 10
H209_input_2
polysome_H209_H209A.profilling.expression_TPM_hg38.txt

library_source: transcriptomic

molecule: cytoplasmic RNA

value: cytoplasmic RNA


title: H209A cells, cytoplasmic RNA, replicate 1

description:
Library name: samples 13
H209A_input_1
polysome_H209_H209A.profilling.expression_TPM_hg38.txt


title: H82R cells, polysomal RNA, replicate 2

description:
Library name: samples 8
H82R_poly_2
polysome_H82_H82R.profilling.expression_TPM_hg38.txt


title: H209 cells, polysomal RNA, replicate 2

description:
Library name: samples 12
H209_poly_2
polysome_H209_H209A.profilling.expression_TPM_hg38.txt


title: H209 cells, cytoplasmic RNA, replicate 1

description:
Library name: samples 9
H209_input_1
polysome_H209_H209A.profilling.expression_TPM_hg38.txt


title: H209A cells, cytoplasmic RNA, replicate 2

description:
Library name: samples 14
H209A_input_2
polysome_H209_H209A.profilling.expression_TPM_hg38.txt


title: TA5017_Initial clinical diagnosis was GO

value: GO


title: TA5012_Initial clinical diagnosis was GO


title: H82R cells, cytoplasmic RNA, replicate 1

description:
Library name: samples 5
H82R_input_1
polysome_H82_H82R.profilling.expression_TPM_hg38.txt


title: H82R cells, polysomal RNA, replicate 1

description:
Library name: samples 7
H82R_poly_1
polysome_H82_H82R.profilling.expression_TPM_hg38.txt


title: GA0023_Initial clinical diagnosis was GH to GO


title: H82 cells, polysomal RNA, replicate 1

description:
Library name: samples 3
H82_poly_1
polysome_H82_H82R.profilling.expression_TPM_hg38.txt


title: H82R cells, cytoplasmic RNA, replicate 2

description:
Library name: samples 6
H82R_input_2
polysome_H82_H82R.profilling.expression_TPM_hg38.txt


title: TA5016_Initial clinical diagnosis was GO


title: VSMC, Female, HGPS, P14

city: Ottawa

first: William

middle: L

last: Stanford

address: 501 Smyth Rd

institute: Ottawa Hospital Research Institute

description:
Library name: AG1B_hic_P14
hgps_p14_100kb_VC_TADs.bed
HGPS_P14_KR_mustache_loops.bedpe

library_source: genomic

data_processing:
Hi-C data was processed using the tools and workflow from HiCExplorer
Fastq files were aligned to Homo sapiens GRCh38 primary assembly (from GENCODE) using BWA-MEM version 0.7.17-r1188 with the following parameters: -A1 -B4 -E50 -L0 -t 20
Hi-C matrices for replicates were built using hicBuildMatrix at 5kb resolution and replicates were merged with hicSumMatrix for all downstream analysis.
Conversions between Hi-C formats, depending on the downstream analysis, were performed using hicConvertFormat tool
TADs and Loop files were created using replicated merged Hi-C files.
Assembly: Homo sapiens GRCh38 primary assembly (from GENCODE)
Supplementary files format and content: HDF5 (Hierarchical Data Format 5)

source_name: vascular smooth muscle cell

growth_protocol: VSMCs were maintained in Human vascular smooth muscle cell basal medium supplement with Smooth Muscle Growth Supplement and Gentamicin

extract_protocol:
Briefly, two cell lines of control and HGPS VSMCs (8 × 10^6 cells) were crosslinked in 1% formaldehyde for 10 min at room temperature and quenched with 0.2 M glycine. Crosslinked cells were pelleted by centrifugation and stored at -80 °C. Nuclei were isolated and chromatin was digested overnight with 100 U of DpnII (NEB). Following digestion, 5′ overhangs were filled in with biotin-14-dATP (Life Technologies) and blunt-end ligation was performed in situ for 4h. Crosslinks were reversed by proteinase K treatment, and DNA was purified by phenol:chloroform extraction, ethanol precipitation, and resuspension in low EDTA, tris-buffered water (TLE).
For library preparation, 40 µg of DNA from each sample was fragmented to 200–300 bp using a sonicator (Covaris). Fragmented DNA was size-selected with AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. The purified DNA fragments underwent end repair, after which biotinylated DNA was isolated using Streptavidin beads. Subsequently, polyA tailing and adapter ligation (Illumina TruSeq) were performed to generate the final libraries, and libraries were PCR-amplified and purified.

value: vascular smooth muscle cell

value: Female

value: HGPS

tag: age

tag: sample group

value: Female HGPS P14


title: VSMC, Male, HGPS, P7

description:
Library name: 0031C_hic_P7
hgps_p7_100kb_VC_TADs.bed
HGPS_P7_KR_mustache_loops.bedpe

value: Male

value: Male HGPS P7


title: TA5021_Initial clinical diagnosis was GO


title: VSMC, Female, Control, P14

description:
Library name: 0901C_hic_P14
ctrl_p14_100kb_VC_TADs.bed
CTRL_P14_KR_mustache_loops.bedpe

value: Control

value: Female Control P14


title: H82 cells, cytoplasmic RNA, replicate 2

description:
Library name: samples 2
H82_input_2
polysome_H82_H82R.profilling.expression_TPM_hg38.txt


title: H82 cells, cytoplasmic RNA, replicate 1

description:
Library name: samples 1
H82_input_1
polysome_H82_H82R.profilling.expression_TPM_hg38.txt


title: TA5020_Initial clinical diagnosis was GO

value: peripheral blood


title: TA5010_Initial clinical diagnosis was GO


title: VSMC, Male, Control, P7

description:
Library name: BJ1C_hic_P7
ctrl_p7_100kb_VC_TADs.bed
CTRL_P7_KR_mustache_loops.bedpe

value: Male Control P7


title: TA5018_Initial clinical diagnosis was GO


title: TA5011_Initial clinical diagnosis was GO


title: TA5014_Initial clinical diagnosis was GO


title: TA5009_Initial clinical diagnosis was GO


title: VSMC, Female, Control, P7

description:
Library name: 0901C_hic_P7
ctrl_p7_100kb_VC_TADs.bed
CTRL_P7_KR_mustache_loops.bedpe

value: Female Control P7


title: TA5008_Initial clinical diagnosis was GO


title: H82 cells, polysomal RNA, replicate 2

description:
Library name: samples 4
H82_poly_2
polysome_H82_H82R.profilling.expression_TPM_hg38.txt

value: SCLC cells

value: WT


title: TA5001_Initial clinical diagnosis was GO


title: VSMC, Male, Control, P14 (Input Ms), Rep2

description: Library name: 1681P_P14_Ms_igg

data_processing:
Sequencing data were processed using the nf-core cutandrun pipeline version 3.2.2
Peak calling for all CUT&Tag data was performed using SEACR (Sparse Enrichment Analysis for CUT&RUN) version 1.3 with parameters: target.bedgraph IgG.bedgraph norm stringent output.
All CUT&Tag signal tracks in bigWig format were generated using deeptools version 3.5.0 bamCoverage with RPGC normalization.
CTCF, SMC1A, HK27ac, H3K27me3, use IgG Rabbit (Rb). H3K36me3 used IgG Mouse (Ms).
Assembly: Homo sapiens GRCh38 primary assembly (from GENCODE)
Supplementary files format and content: bigWig, stringent.bed
Library strategy: CUT&Tag

extract_protocol:
Antibody associated DNA was released by incubation in 0.1% SDS, 16 mM EDTA at 50 °C for 1 h with proteinase K digestion.
DNA was purified using phenol:chloroform and libraries were amplified by PCR (12–15 cycles) with Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs) using dual-indexed barcoded primers.

value: IgG for H3K36me3 at P14


title: VSMC, Male, HGPS, P14 (Input Ms), Rep3

description: Library name: 0031C_P14_Ms_igg


title: TA5019_Initial clinical diagnosis was GO


title: VSMC, Female, HGPS, P14 (Input Ms), Rep1

description: Library name: AG1B_P14_Ms_igg


title: TA5003_Initial clinical diagnosis was GO


title: TA5013_Initial clinical diagnosis was GO


title: VSMC, Female, HGPS, P7 (Input Ms), Rep1

description: Library name: AG1B_P7_Ms_igg

value: IgG for H3K36me3 at P7


title: VSMC, Female, Control, P14 (Input Ms), Rep3

description: Library name: 0901C_P14_Ms_igg


title: VSMC, Male, Control, P7 (Input Ms), Rep1

description: Library name: BJ1C_P7_Ms_igg


title: VSMC, Male, HGPS, P7 (Input Ms), Rep3

description: Library name: 0031C_P7_Ms_igg


title: VSMC, Female, Control, P7 (Input Ms), Rep3

description: Library name: 0901C_P7_Ms_igg


title: TA5005_Initial clinical diagnosis was GO


title: VSMC, Male, HGPS, P14

description:
Library name: 0031C_hic_P14
hgps_p14_100kb_VC_TADs.bed
HGPS_P14_KR_mustache_loops.bedpe

value: Male HGPS P14


title: VSMC, Male, HGPS, P7 (Input Ms), Rep2

description: Library name: 1671Q_P7_Ms_igg


title: VSMC, Female, HGPS, P14, H3K36me3, Rep1

description: Library name: AG1B_H3K36me3_P14

value: Female HGPS P14 H3K36me3


title: GA0007_Initial clinical diagnosis was GH to GO

value: GH to GO


title: VSMC, Male, HGPS, P14, H3K36me3, Rep2

description: Library name: 1671Q_H3K36me3_P14

value: vascular smooth muscle cell

value: Male HGPS P14 H3K36me3


title: VSMC, Female, Control, P14 H3K36me3, Rep3

description: Library name: 0901C_H3K36me3_P14

value: Female Control P14 H3K36me3


title: VSMC, Male, HGPS, P14, H3K36me3, Rep3

description: Library name: 0031C_H3K36me3_P14


title: TA5015_Initial clinical diagnosis was GO

value: GO


title: VSMC, Male, Control, P14 H3K36me3, Rep1

description: Library name: BJ1C_H3K36me3_P14

value: Male Control P14 H3K36me3


title: TA5007_Initial clinical diagnosis was GO


title: TA5002_Initial clinical diagnosis was GO


title: VSMC, Male, Control, P7 (Input Ms), Rep2

description: Library name: 1681P_P7_Ms_igg


title: VSMC, Female, Control, P7, H3K36me3, Rep3

description: Library name: 0901C_H3K36me3_P7

value: Female Control P7 H3K36me3


title: VSMC, Male, Control, P14 H3K36me3, Rep2

description: Library name: 1681P_H3K36me3_P14


title: TA5004_Initial clinical diagnosis was GO


title: VSMC, Male, Control, P14

description:
Library name: BJ1C_hic_P14
ctrl_p14_100kb_VC_TADs.bed
CTRL_P14_KR_mustache_loops.bedpe

value: Male

value: Control

value: Male Control P14


title: VSMC, Male, HGPS, P7, H3K36me3, Rep2

description: Library name: 1671Q_H3K36me3_P7

value: Male HGPS P7 H3K36me3


title: VSMC, Male, HGPS, P7, H3K36me3, Rep3

description: Library name: 0031C_H3K36me3_P7


title: TA5006_Initial clinical diagnosis was GO

value: peripheral blood


title: VSMC, Female, HGPS, P7, H3K36me3, Rep1

description: Library name: AG1B_H3K36me3_P7

value: Female HGPS P7 H3K36me3


title: VSMC, Male, Control, P7, H3K36me3, Rep2

description: Library name: 1681P_H3K36me3_P7

value: Male Control P7 H3K36me3


title: VSMC, Female, HGPS, P14 (Input Rb), Rep1

description: Library name: AG1B_P14_Rb_igg

value: IgG for CTCF, SMC1a, H3K27me3, and H3K27ac at P14


title: VSMC, Male, Control, P7, H3K36me3, Rep1

description: Library name: BJ1C_H3K36me3_P7


title: VSMC, Male, HGPS, P14 (Input Rb), Rep3

description: Library name: 0031C_P14_Rb_igg


title: VSMC, Male, Control, P14 (Input Rb), Rep1

description: Library name: BJ1C_P14_Rb_igg


title: VSMC, Female, HGPS, P7 (Input Rb), Rep1

description: Library name: AG1B_P7_Rb_igg

value: IgG for CTCF, SMC1a, H3K27me3, and H3K27ac at P7


title: VSMC, Male, Control, P7 (Input Rb), Rep2

description: Library name: 1681P_P7_Rb_igg


title: VSMC, Male, HGPS, P7 (Input Rb), Rep3

description: Library name: 0031C_P7_Rb_igg


title: VSMC, Male, Control,  P7 (Input Rb), Rep1

description: Library name: BJ1C_P7_Rb_igg


title: VSMC, Female, Control, P7 (Input Rb), Rep3

description: Library name: 0901C_P7_Rb_igg


title: VSMC, Female, HGPS, P14, SMC1A, Rep1

description: Library name: AG1B_SMC1A_P14

value: Female HGPS P14 SMC1A


title: VSMC, Male, HGPS, P14, SMC1A, Rep3

description: Library name: 0031C_SMC1A_P14

value: Male HGPS P14 SMC1A


title: VSMC, Male, HGPS, P14, SMC1A, Rep2

description: Library name: 1671Q_SMC1A_P14

value: vascular smooth muscle cell


title: VSMC, Male, HGPS, P7, SMC1A, Rep3

description: Library name: 0031C_SMC1A_P7

value: Male HGPS P7 SMC1A


title: VSMC, Female, Control, P7, SMC1A, Rep3

description: Library name: 0901C_SMC1A_P7

value: Female Control P7 SMC1A


title: VSMC, Male, HGPS, P7, SMC1A, Rep2

description: Library name: 1671Q_SMC1A_P7


title: VSMC, Female, HGPS, P7, SMC1A, Rep1

description: Library name: AG1B_SMC1A_P7

value: Female HGPS P7 SMC1A


title: VSMC, Male, Control, P7, SMC1A, Rep1

description: Library name: BJ1C_SMC1A_P7

value: Male Control P7 SMC1A


title: VSMC, Male, Control, P7, SMC1A, Rep2

description: Library name: 1681P_SMC1A_P7


title: VSMC, Female, Control, P14 H3K27me3, Rep3

description: Library name: 0901C_H3K27me3_P14

value: Female Control P14 H3K27me3


title: VSMC, Male, Control, P14 (Input Rb), Rep2

description: Library name: 1681P_P14_Rb_igg


title: VSMC, Male, HGPS, P7 (Input Rb), Rep2

description: Library name: 1671Q_P7_Rb_igg


title: VSMC, Male, HGPS, P14 (Input Rb), Rep2

description: Library name: 1671Q_P14_Rb_igg

value: IgG for CTCF, SMC1a, H3K27me3, and H3K27ac


title: VSMC, Male, HGPS, P14, H3K27me3, Rep3

description: Library name: 0031C_H3K27me3_P14

value: Male HGPS P14 H3K27me3


title: VSMC, Male, HGPS, P14, H3K27me3, Rep2

description: Library name: 1671Q_H3K27me3_P14


title: VSMC, Female, HGPS, P14, H3K27me3, Rep1

description: Library name: AG1B_H3K27me3_P14

value: Female HGPS P14 H3K27me3


title: VSMC, Male, Control, P14 H3K27me3, Rep2

description: Library name: 1681P_H3K27me3_P14

value: Male Control P14 H3K27me3


title: VSMC, Female, Control, P14 SMC1A, Rep3

description: Library name: 0901C_SMC1A_P14

value: Female Control P14 SMC1A


title: VSMC, Male, Control, P14 SMC1A, Rep2

description: Library name: 1681P_SMC1A_P14

value: Male Control P14 SMC1A


title: VSMC, Female, Control, P7, H3K27me3, Rep3

description: Library name: 0901C_H3K27me3_P7

value: Female Control P7 H3K27me3


title: VSMC, Male, Control, P14 SMC1A, Rep1

description: Library name: BJ1C_SMC1A_P14


title: VSMC, Female, Control, P14 (Input Rb), Rep3

description: Library name: 0901C_P14_Rb_igg

value: IgG for CTCF, SMC1a, H3K27me3, and H3K27ac at P14


title: VSMC, Male, HGPS, P7, H3K27me3, Rep3

description: Library name: 0031C_H3K27me3_P7

value: Male HGPS P7 H3K27me3


title: VSMC, Male, HGPS, P14 (Input Ms), Rep2

description: Library name: 1671Q_P14_Ms_igg

value: IgG for H3K36me3 at P14


title: VSMC, Male, Control, P7, H3K27me3, Rep2

description: Library name: 1681P_H3K27me3_P7

value: Male Control P7 H3K27me3


title: VSMC, Male, Control, P7, H3K27me3, Rep1

description: Library name: BJ1C_H3K27me3_P7

value: vascular smooth muscle cell


title: VSMC, Female, HGPS, P7, H3K27me3, Rep1

description: Library name: AG1B_H3K27me3_P7

value: Female HGPS P7 H3K27me3


title: VSMC, Male, HGPS, P7, H3K27me3, Rep2

description: Library name: 1671Q_H3K27me3_P7


title: VSMC, Male, HGPS, P14, H3K27ac, Rep2

description: Library name: 1671Q_H3K27ac_P14

value: Male HGPS P14 H3K27ac


title: VSMC, Male, HGPS, P14, H3K27ac, Rep3

description: Library name: 0031C_H3K27ac_P14


title: VSMC, Female, Control, P14 H3K27ac, Rep3

description: Library name: 0901C_H3K27ac_P14

value: Female Control P14 H3K27ac


title: VSMC, Female, HGPS, P14, H3K27ac, Rep1

description: Library name: AG1B_H3K27ac_P14

value: Female HGPS P14 H3K27ac


title: VSMC, Male, Control, P14 H3K27ac, Rep2

description: Library name: 1681P_H3K27ac_P14

value: Male Control P14 H3K27ac


title: VSMC, Female, Control, P7, H3K27ac, Rep3

description: Library name: 0901C_H3K27ac_P7

value: Female Control P7 H3K27ac


title: VSMC, Male, Control, P14 H3K27ac, Rep1

description: Library name: BJ1C_H3K27ac_P14


title: VSMC, Male, HGPS, P7, H3K27ac, Rep3

description: Library name: 0031C_H3K27ac_P7

value: Male HGPS P7 H3K27ac


title: VSMC, Male, HGPS, P7, H3K27ac, Rep2

description: Library name: 1671Q_H3K27ac_P7


title: VSMC, Female, HGPS, P7, H3K27ac, Rep1

description: Library name: AG1B_H3K27ac_P7

value: Female HGPS P7 H3K27ac


title: VSMC, Male, Control, P7, H3K27ac, Rep2

description: Library name: 1681P_H3K27ac_P7

value: Male Control P7 H3K27ac


title: VSMC, Male, Control, P14 H3K27me3, Rep1

description: Library name: BJ1C_H3K27me3_P14

value: Male Control P14 H3K27me3


title: VSMC, Male, Control, P7, H3K27ac, Rep1

description: Library name: BJ1C_H3K27ac_P7


title: VSMC, Female, HGPS, P14, CTCF, Rep1

description: Library name: AG1B_CTCF_P14

value: Female HGPS P14 CTCF


title: VSMC, Female, Control, P14, CTCF, Rep3

description: Library name: 0901C_CTCF_P14

value: Female Control P14 CTCF


title: VSMC, Female, Control, P7, CTCF, Rep3

description: Library name: 0901C_CTCF_P7

value: Female Control P7 CTCF


title: VSMC, Male, Control, P14, CTCF, Rep2

description: Library name: 1681P_CTCF_P14

value: Male Control P14 CTCF


title: VSMC, Male, Control, P14, CTCF, Rep1

description: Library name: BJ1C_CTCF_P14


title: VSMC, Male, HGPS, P7, CTCF, Rep2

description: Library name: 1671Q_CTCF_P7

value: Male HGPS P7 CTCF


title: VSMC, Male, HGPS, P7, CTCF, Rep3

description: Library name: 0031C_CTCF_P7


title: UMUC3 shVIRMA2

city: Heidelberg

first: Jonas

last: Koch

address: Im Neuenheimer Feld 580

department: Epigenetics

country: Germany

institute: German Cancer Research Center

description: Library name: UMUC3_shVIRMA2

data_processing:
Adaptor sequences were trimmed using Trim Galore (version 0.6.6).
Reads were aligned using HISAT2 (version 2.2.1).
Mapped reads were quantified using featureCounts (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample.
Supplementary files format and content: tab-delimited text file including alternative polyadenylation events in patient and cell line samples.

molecule: total RNA

source_name: Bladder

growth_protocol: RT4 cells were cultured in McCoy’s 5A (modified) medium supplemented with 10% FBS and 1% penicillin/streptomycin. UM-UC-3 cells were cultured in DMEM high glucose medium supplemented with 10% FBS and 1% penicillin/streptomycin. Both cell lines were cultivated as adherent monolayers at 37°C in a humidified incubator with a 5% CO2 atmosphere.

extract_protocol:
Total RNA from tissue samples and cell lines were isolated using TRIzol. To remove residual gDNA contaminants, total RNA samples were DNase I-digested and further purified using the RNA Clean & Concentrator-5 kit (Zymo Research).
Libraries for RNA sequencing were prepared by the Genomics and Proteomics Core Facility of the German Cancer Research Center using the Illumina TruSeq Stranded RNA kit.

value: Bladder

value: urinary bladder carcinom

value: VIRMA knockdown


title: UMUC3 shVIRMA3

description: Library name: UMUC3_shVIRMA3


title: VSMC, Female, HGPS, P7

description:
Library name: AG1B_hic_P7
hgps_p7_100kb_VC_TADs.bed
HGPS_P7_KR_mustache_loops.bedpe

value: vascular smooth muscle cell

value: Female

value: HGPS

value: Female HGPS P7


title: VSMC, Male, Control, P7, CTCF, Rep1

description: Library name: BJ1C_CTCF_P7

value: Male Control P7 CTCF


title: RT4 shVIRMA2

description: Library name: RT4_shVIRMA2


title: UMUC3 shCtrl1

description: Library name: UMUC3_shCtrl1

value: Ctrl


title: RT4 shVIRMA3

description: Library name: RT4_shVIRMA3


title: VSMC, Female, HGPS, P7, CTCF, Rep1

description: Library name: AG1B_CTCF_P7

value: Female HGPS P7 CTCF


title: UMUC3 shCtrl2

description: Library name: UMUC3_shCtrl2


title: RT4 shVIRMA1

description: Library name: RT4_shVIRMA1


title: RT4 shCtrl3

description: Library name: RT4_shCtrl3


title: VSMC, Male, Control, P7, CTCF, Rep2

description: Library name: 1681P_CTCF_P7


title: UMUC3 shVIRMA1

description: Library name: UMUC3_shVIRMA1


title: RT4 shCtrl1

description: Library name: RT4_shCtrl1


title: UMUC3_shVIRMA3

description: Library name: UMUC3_shVIRMA3

data_processing:
Adaptor sequences were trimmed using Trim Galore (version 0.6.6).
Reads were aligned to the genome using STAR (version 2.7.10a) and to the transcriptome using bowtie (version 1.3.0)
Pileup was performed using samtools API pysam (version 1.19).
m6A calling was performed using the so-called GLORI-tools pipeline, which is available on github: https://github.com/liucongcas/GLORI-tools.
Assembly: GRCh38
Supplementary files format and content: tab-separated .csv files providing the detected m6A sites in every GLORI-sequenced sample.

molecule: polyA RNA

extract_protocol:
Total RNA from the cells was isolated with TRIzol. Small RNA fractions were depleted using the MEGAclear Transcription Clean-Up Kit (Thermo Fisher Scientific). Enrichment of mRNA was performed twice using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific). mRNA was then fragmented by incubation for 3 min at 94 °C using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Fragmented mRNA was then DNase I-treated and purified by the RNA Clean & Concentrator-5 kit (Zymo Research). Fragmented RNA samples were then subjected to the chemical deamination protocol. For RNA protection, 100 – 200 ng of fragmented mRNA supplemented with a synthetic Spike-In RNA oligonucleotide were added into protection buffer (1.32 M Glyoxal solution, 50 % DMSO, prepared in water) and incubated for 30 min at 50 °C in a thermal cycler. The RNA was further stabilized by adding 10 µL of freshly prepared saturated boric acid at RT, followed by incubation for 30 min at 50 °C in a thermal cycler. Protected RNA was then added into 50 µL of freshly prepared deamination buffer (1.5 M NaNO2, 80 mM MES (pH 6.0), 1.76 M Glyoxal solution, prepared in water), and incubated for 8 hours at 16 °C in a thermal cycler. After deamination, RNA was purified by ethanol precipitation ON at – 80 °C. Pelleted RNA was washed twice using 75 % ethanol and air-dried for 5 min at RT. Then, the RNA pellet was resuspended in 50 µL of deprotection buffer (500 mM triethylammonium acetate (pH 8.6), 47.5 % deionized formamide, prepared in water) and incubated for 10 min at 95 °C in a thermal cycler. Deprotected RNA was purified by ethanol precipitation for at least 30 min at – 80 °C. Pelleted RNA was washed twice using 75 % ethanol and air-dried for 5 min at RT. The RNA pellet was then resuspended in 50 µL of water and further purified using the RNA Clean & Concentrator-5 kit (Zymo Research). For sequencing library preparation, a two-step RNA end-repair protocol was pursued. RNA 3’-end dephosphorylation was performed by Antarctic phosphatase (New England Biolabs) treatment in a total reaction volume of 20 µL. The reaction was incubated for 30 min at 37 °C and inactivated for 2 min at 80 °C. Subsequently, RNA 5’-end phosphorylation was performed by T4 Polynucleotide Kinase (New England Biolabs) treatment in a total reaction volume of 50 µL. The reaction was incubated for 30 min at 37 °C, inactivated for 20 min at 65 °C, and purified using the RNA Clean & Concentrator-5 kit (Zymo Research).
The libraries were then prepared using the NEBNext Small RNA Library Prep Set for Illumina in combination with the NEBNext Multiplex Oligos for Illumina (Index Primer Sets 1 and 3) (New England Biolabs). Size selection of the libraries was performed via TBE-PAGE using 8 % TBE polyacrylamide gels (Thermo Fisher Scientific) selecting sequencing competent molecules in a size range of 160 – 250 bp.


title: VSMC, Male, HGPS, P14, CTCF, Rep2

description: Library name: 1671Q_CTCF_P14

value: Male HGPS P14 CTCF


title: VSMC, Male, HGPS, P14, CTCF, Rep3

description: Library name: 0031C_CTCF_P14


title: UMUC3_shVIRMA2

description: Library name: UMUC3_shVIRMA2


title: UMUC3_shVIRMA1

description: Library name: UMUC3_shVIRMA1


title: UMUC3_shCtrl3

description: Library name: UMUC3_shCtrl3


title: UMUC3_shCtrl1

description: Library name: UMUC3_shCtrl1


title: UMUC3 shCtrl3

description: Library name: UMUC3_shCtrl3


title: RT4_shVIRMA1

description: Library name: RT4_shVIRMA1


title: RT4_shVIRMA2

description: Library name: RT4_shVIRMA2


title: RT4_shCtrl3

description: Library name: RT4_shCtrl3


title: RT4_shCtrl2

description: Library name: RT4_shCtrl2


title: RT4_shVIRMA3

description: Library name: RT4_shVIRMA3


title: RT4_shCtrl1

description: Library name: RT4_shCtrl1


title: RT4 shCtrl2

description: Library name: RT4_shCtrl2


title: PDAC biopsies; Patients 2, 3, 4, 6, 8 ; C4D1, Cycle 12, baseline [combined]

city: Boston

first: Colin

last: Weekes

address: 55 Fruit Street

institute: Massachusetts General Hospital

description:
Library name: multiple_timepoints_patients_combined
Parse Biosciences Evercode WT V3

library_source: transcriptomic single cell

data_processing:
FASTQ files were prepared using bcl2fastq2 conversion software v2.20 via Illumina basespace sequencing hub. Pre-processing and alignment of FASTQ files were performed using the Parse Trailmaker Pipeline module v1.4.1. Briefly, FASTQ files were provided to the pipeline, and transcript sequences were aligned to the GRCh38 reference genome. Counts matrices filtered according to sample-specific barcode thresholds established within the pipeline were then downloaded for downstream analyses in R.
Assembly: Human GRCh38
Supplementary files format and content: Comma separated values files and matrix files

source_name: Pancreas tumor

extract_protocol:
STc buffer (146 mM NaCl, 20 mM Tricine, 1 mM CaCl2, and 21 mM MgCl2) and NSTcPA buffer (146 mM NaCl, 20 mM Tricine, 1 mM CaCl2, and 21 mM MgCl2, 0.2% NP-40, 0.01% BSA, 0.15 mM Spermine, 0.5 mM Spermidine) were prepared fresh. Tumor biopsies were lysed and nuclei isolated on a per-sample basis. Frozen tissues were then transferred into 500 mL of NSTcPA buffer containing DNA and RNA and minced for 8 minutes. Minced tissues were pipetted over a 40 mM filter into a 50 mL conical tube. The well was washed twice with 1 mL of NSTcPA buffer and twice with 1 mL of ST buffer and pipetted over the same filter for each subsequent wash. Subsequently, 1 mL of ST buffer was pipetted over the filter twice to further dilute the sample. The sample was then transferred to a 15 mL conical tube and centrifuged at 500 x g for 5 minutes at 4°C, with deceleration set to 5. The supernatant was removed, and the pellet was resuspended in 100-200 uL of PBS  /1% BSA, then pipetted through a 35 mM FACS tube. Nuclei were quantified using a disposable C-Chip hemocytometer, and up to 100,000 nuclei per sample were immediately fixed using the Evercode Low Input Cell Fixation kit according to manufacturer’s instructions. Nuclei samples were then stored at -80°C until all samples were ready to proceed with library preparation.
Sequencing library preparation with 12,500 cells per library was performed with the Evercode Whole Transcriptome v3 kit according to manufacturer’s instructions. Sublibrary quality control and quantification were performed using Qubit fluorometer, Agilent 4200 TapeStation, and KAPA qPCR analysis using a Quant studio 5, and sublibraries were then pooled to 4 nM for sequencing based on qPCR results. Seven sublibraries were pooled and submitted for sequencing in total.

value: Pancreas tumor

value: modified FOLFIRINOX + elraglusib + losartan (C4D1, cycle 12, or baseline)


title: RUNX2-OE-3, overexpression group

city: xi'an

first: Di

last: Zhang

state: shaanxi

address: No.76, Yanta West Road, Yanta District, Xi'an City, Shaanxi Province

institute: xi'an jiaotong university

description:
Library name: RUNX2-OE-3
RUNX2-overexpression sample replicate 3

data_processing:
Raw reads were quality-checked using FastQC.Low-quality reads and bases were filtered using fastp (v0.18.0). Reads were mapped to the ribosomal RNA database using Bowtie2 (v2.2.8). Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.3). Mapped reads were assembled using StringTie (v1.3.1) in a reference-based approach. Gene expression levels were quantified using RSEM to obtain FPKM values. Differentially expressed genes were analyzed with DESeq2 (|log₂FC| ≥ 1, adjusted p < 0.05). Functional enrichment (GO, KEGG, and DO analyses) was conducted with p < 0.05 as the significance threshold.
Assembly: Homo sapiens reference genome GRCh38 (hg38)
Supplementary files format and content: Processed data include normalized gene expression matrices (FPKM) and differential gene expression tables (gene ID, log₂ fold change, adjusted p-value) in tab-delimited text format.

growth_protocol: Human chondrocytes were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and maintained at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions. RNA integrity and concentration were assessed using Agilent 2100 Bioanalyzer and NanoDrop spectrophotomete
RNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit (NEB #7530, New England Biolabs, MA, USA) following the manufacturer’s protocol. Libraries were sequenced on an Illumina platform (Genedenovo Biotechnology Co., Ltd, Guangzhou, China) to generate approximately 6 Gb of clean data per sample.

treatment_protocol: Cells were transduced with lentiviral particles carrying RUNX2 overexpression vector or empty control vector. After 48 hours, stable expression was confirmed by qRT-PCR and western blot. Cells were harvested for total RNA extraction 72 hours post-transfection.

value: chondrocyte

value: Transduced with HBLV-h-RUNX2-3xflag-ZsGreen-PURO (RUNX4 overexpression lentivirus)

tag: batch


title: RUNX2-OE-2, overexpression group

description:
Library name: RUNX2-OE-2
RUNX2-overexpression sample replicate 2

value: Transduced with HBLV-h-RUNX2-3xflag-ZsGreen-PURO (RUNX3 overexpression lentivirus)


title: E-2-1

city: Zhuhai

first: Hongzhen

last: Tang

state: Guangdong

address: Cuijing Road, Qianshan, Xiangzhou District

institute: BioMega Spatiotemporal Pathology Research Center

description: Library name: E-2-1

data_processing:
Raw LACE-seq sequencing reads were subjected to quality control using fastp to remove low-quality bases and adapter sequences. The cleaned reads were then aligned to the reference genome with bowtie2. Finally, peak calling was performed with Piranha to identify enriched regions corresponding to RNA–protein interaction sites.
Assembly: hg38
Supplementary files format and content: file of .bed format contains ZFP36 binding sites
Library strategy: iCLIP

source_name: gastric cancer

extract_protocol:
HGC-27 cells were cultured in RPMI-1640 supplemented with 10% FBS at 37 °C, 5% CO₂ and harvested at ~70–80% confluence; monolayers were rinsed with ice-cold PBS and subjected immediately to laser-assisted UV crosslinking on ice to covalently fix endogenous ZFP36–RNA complexes. Crosslinked cells were lysed in CLIP lysis buffer containing RNase inhibitors, clarified by centrifugation, and (optionally) subjected to a brief, limiting RNase digestion to generate protected RNA fragments. ZFP36–RNA complexes were immunoprecipitated from cleared lysates using a ZFP36-specific antibody prebound to protein A/G magnetic beads, with incubation at 4 °C and subsequent high-salt/detergent stringency washes to minimize nonspecific binding. Bead-bound complexes were end-repaired as required, eluted and digested with proteinase K to release crosslinked RNA, and RNA was purified using silica-membrane spin columns. Purified RNA fragments underwent sequential 3′ and 5′ adaptor ligation, reverse transcription, and limited-cycle PCR with unique sample indices; libraries were size-selected to enrich ~50–150 nt inserts, quality-checked by Bioanalyzer and qPCR, pooled equimolarly, and subjected to Illumina paired-end sequencing. All steps were performed in four independent IP-only biological replicates processed in parallel.
Bead-bound ZFP36–RNA complexes were treated under RNase-controlled conditions to yield protected RNA fragments, then released by proteinase K digestion and purified on silica-membrane columns. Purified fragments were 3′-dephosphorylated and end-repaired as needed (T4 polynucleotide kinase, −ATP), ligated to a pre-adenylated 3′ RNA adapter using truncated T4 RNA ligase 2 (KQ), 5′-phosphorylated (T4 PNK, +ATP), and ligated to a 5′ RNA adapter with T4 RNA ligase 1. Reverse transcription was performed with a primer complementary to the 3′ adapter (optionally carrying an 8–12 nt UMI), followed by RNA hydrolysis and cDNA cleanup. Libraries were amplified by limited-cycle PCR to avoid over-cycling (cycle number determined by qPCR pre-tests), incorporating unique sample indices for each of the four IP replicates, and size-selected to enrich ~250–450 bp (insert ~50–150 nt plus adapters). Final libraries were quality-checked by capillary electrophoresis (Bioanalyzer/Fragment Analyzer) and fluorometric quantification, pooled equimolarly, and subjected to Illumina paired-end sequencing.

value: gastric cancer

value: Human gastric cancer cell


title: NC-1, negative control

description:
Library name: NC-1
Control sample replicate 1 (NC-1)

value: normal

value: Transduced with HBLV-ZsGreen-PURO (negative control lentivirus)


title: NC-3, negative control

description:
Library name: NC-3
Control sample replicate 3 (NC-3)


title: E-1-2

description: Library name: E-1-2


title: E-1-1

description: Library name: E-1-1


title: RUNX2-OE-1, overexpression group

description:
Library name: RUNX2-OE-1
RUNX2-overexpression sample replicate 1

value: Transduced with HBLV-h-RUNX2-3xflag-ZsGreen-PURO (RUNX2 overexpression lentivirus)


title: E-2-2

description: Library name: E-2-2


title: A549 cells,sh-NEAT1-16h-2

city: 福州市

first: 二英

last: 徐

state: 福建省

address: 福建农林大学金山校区

department: 福建省畜禽病原感染与免疫学重点实验室

institute: 动物科学学院

description: Library name: Sample5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencelow-quality sequence using CLC genomic benchwork (parameter: Quality limit: 0.05
Trimmed sequence reade were mapped to GRCh38 using CLC genomic benchwork (parametersmismat cost: 2inserton cost: 3 deledon cost 3 length fraction:0.8
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values each Sample

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% FBS and antiblotics in humidified atomosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit jOiagen). 1.3 ug of total RNA was used tor the constructon of sequencing libraries.
RNA Iibraries tor RNA-seq were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

treatment_protocol: 16 hours after influenza virus  infection


title: A549 cells,sh-NEAT1-16h-3

department: 福建省畜禽病原感染与免疫学重点实验室

description: Library name: Sample6


title: A549 cells,sh-luc-16h-2

department: 福建省畜禽病原感染与免疫学重点实验室

description: Library name: Sample2

value: sh-luc


title: A549 cells,sh-NEAT1-16h-1

department: 福建省畜禽病原感染与免疫学重点实验室

description: Library name: Sample4


title: A549 cells,sh-luc-16h-1

department: 福建省畜禽病原感染与免疫学重点实验室

description: Library name: Sample1


title: A549 cells,sh-luc-16h-3

department: 福建省畜禽病原感染与免疫学重点实验室

description: Library name: Sample3


title: SKBR3 tazemetosat + lapatinib REP 3

first: Naiara

last: Perurena

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital

description: Library name: SKBR3 COMBO-REP3

data_processing:
ATAC-seqs were read and aligned to the UCSC hg38 genome reference using ENCODE pipeline.
Peaks were called using MACS2. The consensus peaks were merged using GenomicRanges package in R.
bigWig files were generated using GenomicRanges package in R.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Nuclei were isolated from cells with >90% viability.
ATAC-Seq libraries were prepared using the Omni-ATAC-Seq protocol. Isolated nuclei were subjected to Tn5-mediated transposition. Transposed reactions were cleaned with the Zymo DNA Clean and Concentrator 5 kit. Next. Illumina adapter sequences and barcodes were added to the transposed DNA fragments. Amplified libraries were purified using the Zymo DNA Clean and Concentrator 5 kit, followed by a double-sided SPRIselect Bead cleanup (Beckman Coulter). Final libraries were analyzed on a 4200 TapeStation (Agilent Technologies) and quantified via quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific).

value: HER2+ breast cancer

value: WT

value: Tazemetostat + Lapatinib


title: SKBR3 tazemetosat + lapatinib REP 2

description: Library name: SKBR3 COMBO-REP2


title: iPSC-derived spinal motor neurons, UPF1 knockdown, batch 2, rep 1

city: Chicago

first: Evangelos

last: Kiskinis

state: IL

address: 303 E. Superior Street

department: Neurology

institute: Northwestern University Feinberg School of Medicine

description: Library name: M86UPFA

data_processing:
Raw reads were trimmed using cutadapt (v3.4) to remove Illumina universal adapter sequences (-a AGATCGGAAGAGC), trailing N bases (--trim-n), and bases with Phred score < 10 (-q 10,10), as well as any reads that were too short after trimming (-m 25). Trimmed reads were aligned to Gencode V38 (GRCh38.p13) using STAR (v.2.7.5a). The following flags were used during alignment: --twopassMode Basic, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --alignEndsType EndToEnd, as well as the “ENCODE options” flags provided by the STAR manual. Gene-level counts were quantified using featureCounts (v2.0.1).
Assembly: hg38 (GRCh38.p13, Gencode V38 gene annotations)
Supplementary files format and content: tab-delimited text file includes gene-level counts for each sample

source_name: iPSC-derived spinal motor neurons

growth_protocol: iPSCs were differentiated into spinal motor neurons (MNs) following a standard 2D differentiation protocol (Ortega et al., 2020). iPSCs were dissociated into single cells with Accutase and plated in mTESR1 supplemented with 10μM ROCK inhibitor (Y-27632, DNSK International)at a density of 1.2million/well of a 6-well plate. After two days, cells were washed with PBS, then fed daily with N2B27 media (50% DMEM:F12 / 50% Neurobasal media, supplemented with Non-Essential Amino Acids, Glutamax, N2, B27, all from Thermo Fischer Scientific) supplemented with 10μM SB431542 (DNSK International), 100nM LDN-193189 (DNSK International), 1μM Retinoic Acid (RA, Sigma-Aldrich), 1μM of Smoothened-Agonist (SAG, DNSK International) to induce spinal neural progenitors. After 6 days, the cells were fed daily with N2B27 medium supplemented with 1μM RA, 1μM SAG, 5μM DAPT (DNSK International) and 4μM SU5402 (DNSK International)to generate postmitotic spinal MNs. After an additional 7 days (day 14), the cells were dissociated using TryplE (Thermo Fischer Scientific) with added DNaseI (Worthington) and plated onto plates previously coated with Matrigel (BD Bioscences) at a density of 1 million/well of a 6-well plate. Cells were then fed every other day with Neurobasal media supplemented with Non-Essential Amino Acids, Glutamax, N2, B27 and the neurotrophic factors BDNF, CNTF, GDNF (10ng/mL,R&D systems) and Ascorbic acid (0.2μg/ml). In the first four days after plating, the medium was supplemented with EdU (10μM) to inhibit the growth of remaining proliferating progenitor cells. All cell cultures were maintained at 37°C, 5% CO2 without antibiotics and tested regularly for mycoplasma.

extract_protocol:
Cells were harversted in 1mL TRIzol Reagent (Thermo Fisher Scientific) per 1-3 million cells. Samples were added with chloroform (0.2mL), mixed and centrifuged at 4°C for 15 minutes at 12,000xg after 3 minutes of resting at room temperature. The aqueous phase containing the RNA was transferred to a new tube and added with 5µg of RNase-free Glycogen (Thermo Fisher Scientific). The aqueous phase was added with 0.5mL of isopropanol, incubated for 25 minutes at room temperature and centrifuged for 10 minutes at 15,000xg at 4°C.
Samples were sent to Novogene for strand-specific polyA-purified library preparation and 150bp paired-end (PE150) sequencing

treatment_protocol: For transient knockdown experiments, pre-designed siRNAs (Ambion Silencer Selector ThermoFisher Scientific) were transfected using Lipofectamine RNAiMAX(Invitrogen) according to manufacturer guidelines. Briefly, for each well of a 6-well plate, we mixed siRNA with lipofectamine RNAiMAX reagent in 200mL Opti-MEM medium and incubated the solution for 20min at RT. We added 800mL of cell culture medium, delivering a total of 1000mL per well. For UPF1, 40pmol of a single siRNA were used per each well of a 6-well plate, 5, 10 and 15 days before cell culture collection. For TDP-43KD, 20pmol of each of three siRNAs were used 3, 6, 9 and 12 days before cell culture collection.

value: iPSC-derived spinal motor neurons

value: UPFkd


title: iPSC-derived spinal motor neurons, UPF1 knockdown, batch 2, rep 2

description: Library name: M86UPFB


title: iPSC-derived spinal motor neurons, TDP-43 and UPF1 double knockdown, batch 2, rep 2

description: Library name: M86TUB

value: TDPkd+UPFkd


title: iPSC-derived spinal motor neurons, TDP-43 knockdown, batch 2, rep 2

description: Library name: M86TDPB

value: TDPkd


title: NC-2, negative control

description:
Library name: NC-2
Control sample replicate 2 (NC-2)


title: iPSC-derived spinal motor neurons, scramble, batch 2, rep 2

description: Library name: M86SCRB

value: Scr


title: iPSC-derived spinal motor neurons, scramble, batch 2, rep 1

description: Library name: M86SCRA


title: iPSC-derived spinal motor neurons, UPF1 knockdown, batch 1, rep 2

description: Library name: M85UPFB


title: iPSC-derived spinal motor neurons, TDP-43 knockdown, batch 1, rep 1

description: Library name: M85TDPA


title: iPSC-derived spinal motor neurons, TDP-43 and UPF1 double knockdown, batch 1, rep 1

description: Library name: M85TUA


title: iPSC-derived spinal motor neurons, scramble, batch 1, rep 1

description: Library name: M85SCRA


title: iPSC-derived spinal motor neurons, scramble, batch 1, rep 2

description: Library name: M85SCRB


title: iPSC-derived spinal motor neurons, UPF1 knockdown, batch 1, rep 1

description: Library name: M85UPFA


title: SKBR3 tazemetosat + lapatinib REP 1

description: Library name: SKBR3 COMBO-REP1


title: LM3-si1

first: Jun

last: Wu

address: Guoxue street

institute: West   32 China Hospital, Sichuan University

description: Library name: sample4

data_processing:
Cutadapt (version: cutadapt-1.9) was used to obtain high-quality clean reads, and the reads of all the samples were subsequently aligned to the human reference genome using HISAT2.
Assembly: HG38
Supplementary files format and content: 1_genes_fpkm_expression.xlsx

extract_protocol:
Huh7 and LM3 cells with and without SRSF11 knockdown were subjected to RNA-seq. Total RNA was extracted from these cells with a TRIzol reagent kit. Next, quality control of the extracted RNA was performed using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA) and Bioanalyzer 2100 (Agilent, CA, USA).
The captured mRNA was subsequently fragmented using the NEBNextR Magnesium RNA Fragmentation Module (cat. E6150S, USA). The fragmented RNA was used for library construction.

value: liver

value: hepatocellular carcinoma cell lines


title: iPSC-derived spinal motor neurons, TDP-43 knockdown, batch 1, rep 2

description: Library name: M85TDPB


title: LM3-siCTL

description: Library name: sample6


title: NC_IP

description: Library name: sample2

data_processing:
Cutadapt (version: cutadapt-1.9) was used to obtain high-quality clean reads, and the reads of all the samples were subsequently aligned to the human reference genome using HISAT2.
Assembly: HG38
Supplementary files format and content: binding_protein_gene_expr.txt

extract_protocol:
RNAs that bind to SRSF11 were identified with RIP kit (BersinBio, Guangzhou, China). In brief, polysome lysis buffer mixed with protease inhibitors and RNase inhibitors was used to lyse the cells on ice. After the DNA was removed, the anti-SRSF11 antibody or anti-Flag antibody and an equal amount of anti-IgG antibody were added to the lysis mixture, which was subsequently incubated at 4°C for 16 h. Then, protein A/G beads were used to collect immunoprecipitates. Finally, TRIzol was used to extract RNA from immunoprecipitated samples and input samples.
High-quality RNA was broken into short fragments via fragmentation buffer, and a library was constructed via the KCTM Digital Stranded mRNA Library Prep Kit (Seqhealth Technology. Co., Ltd., Wuhan, China).


title: Huh7-si2

description: Library name: sample2


title: iPSC-derived spinal motor neurons, TDP-43 and UPF1 double knockdown, batch 1, rep 2

description: Library name: M85TUB


title: Huh7-siCTL

description: Library name: sample3


title: NC_input

description: Library name: sample1


title: Huh7-si1

description: Library name: sample1


title: LM3-si2

description: Library name: sample5


title: Gradient_9_10_D

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

description: Library name: Gradient_9_10_D

data_processing:
TIGER (“Tools for Integrative Genome analysis of Extracellular sRNAs”), an in-house small RNA sequencing analysis pipeline, was used to quantify small RNAs[1]. Briefly, Cutadapt (v4.5)[2] was used to trim 3’ adapters for raw reads. All reads with less than 16 nucleotides were designated as “too short” and discarded. Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc).
The adaptor-trimmed reads were mapped to the GENCODE GRCh38.p13 genome, addition to rRNA and tRNA reference sequences, by Bowtie1 (v1.3.1)[3] allowing only one mismatch.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited file with small RNA raw counts

source_name: Epithelial

growth_protocol: 2D: DiFi and CC-CR cells were cultured in DMEM medium supplemented with 10% bovine growth serum, 1% glutamine, 1% non-essential amino acids, and 1% penicillin–streptomycin at 37 °C in a 5% CO2 humidified incubator. All cell culture media was purchased from Corning Cellgro and all cell culture supplements were from Hyclone, unless stated otherwise. Cells were cultured until 80% confluent, then washed 3X with PBS and cultured in serum-free medium for 48 h prior to collection of EVs and NVEPs. A total of three separate 2D pools of DiFi medium (1,360 mL) were harvested from 68 plates with 20 mL of medium isolated when culturing about 5.1 x 109 cells total. Medium was concentrated and used to isolate UC-purified EV pellets (EVp), exomeres, and supermeres, as described5,16. 3D: Hollow fiber bioreactors were loaded with 1-5 x 108 DiFi or CC-CR cells, allowed to reach an equilibrium growth phase based on glucose utilization (using 1-2 mg of glucose per day), and medium was harvested and processed as described11,12, except for the following modifications. With each harvest, 20 mL of conditioned medium was centrifuged sequentially at 250g and 2,500g for 10 min each (Thermoscientfic Xpro series centrifuge) to remove cellular debris. Medium was then gravity filtered through a Millex 0.22-µm pore syringe filter (Millipore Sigma, Burlington, MA). Four separate pools of around 400 mL of conditioned medium were generated and distributed concurrently. Each pool was divided into 60 mL aliquots for purification by UC, FPLC, or cushion-DGUC (C-DGUC), with the remainder kept in reserve for quality control (QC) or other experiments.

extract_protocol:
Mutant AlkB enzyme mix was generated through purification of AlkB wild-type protein (pET30a-AlkB ΔN11) (Addgene), D135S mutant protein (pET30a-AlkB-D135S), and D135T mutant protein (pET28a(+)-AlkB-D135T) (Addgene), which were expressed in BL21(DE3) competent E. coli cells (New England Biolabs Inc). Protein expression was induced by 1 mM isopropyl β-d-1-thiogalactopyranoside with 5 uM iron sulfate for 4 h at 30 °C. Cells were centrifuged and resuspended in Buffer A (10 mM Tris-HCL pH 7.4, 300 mM NaCl, 2 mM CaCl2, 10 mM MgCl2, 2 mM 2-mercaptoethanol, 5% glycerol) containing protease inhibitors. Samples were lysed by sonication. Supernatants were loaded onto a Ni-NTA column (Qiagen) pre-equilibrated with Buffer A and eluted using 250 μM of imidazole. Fractions containing purified AlkB proteins were pooled and dialyzed against storage buffer (30 mM Tris pH 8, 2 mM 2-mercaptoethanol), then supplemented with 30% glycerol and snap frozen. RNA demethylation was performed in a 50 μL reaction volume containing 1 μM purified AlkB (wt, D135S, and D135T) enzymes, 25 mM MES buffer pH 6.0, 2 mM MgCl2, 270 mM KCl, 2 mM L-ascorbic acid, 300 μM α-ketoglutarate, 283 μM (NH4)2Fe(SO4)2, and 1 U/mL SUPERaseIn RNase Inhibitor. Reactions were carried out at 25 °C for 2 h then stopped by the addition of EDTA. RNA was re-purified using RNeasy Mini Kit (Qiagen, 74104) and used as input for sRNA sequencing library preparation.
Libraries were prepared using NEXTFlex Small RNA-seq kit v3 (Perkin Elmer) and size-selected using Pippin Prep (Sage). Libraries were quantified with Qubit (Thermo Fisher) and assessed using Bioanalyzer high-sensitivity DNA chips (Agilent). Paired-end sequencing (PE-150) using equimolar concentrations of multiplexed libraries were completed using NovaSeq6000 (S4, Illumina) by the Vanderbilt Technologies for Advanced Genomics Core.

treatment_protocol: UC-based isolation of EVs and NVEPs UC-based EV and NVEP isolation was performed as previously described with detailed protocol published5,16. Specifically, 2D serum-free conditioned medium was centrifuged for 15 min at 1,000g to remove cellular debris and the resulting supernatant was then filtered through a 0.22 μm polyethersulfone filter (Nalgene). The filtrate from 2D conditioned media was concentrated using a centrifugal concentrator with a 100,000 Dalton molecular-weight cutoff (Millipore). The concentrate or 3D conditioned media was then subjected to UC at 167,000g for 4 h in a SW32 Ti swinging-bucket rotor (Beckman Coulter) and the resulting sEV pellet was resuspended in PBS containing 25 mM HEPES (pH 7.2) and washed by centrifuging again at 167,000g for 4 h. The washed pellet was designated as EVp. To isolate exomeres, the supernatant collected from the 4 h UC was ultracentrifuged at 167,000g for 16 h. The resulting pellet was resuspended in PBS containing 25 mM HEPES (pH 7.2) and washed by centrifuging again at 167,000g for 16 h. The washed pellet was designated as exomeres. To isolate supermeres, the supernatant from the pelleting of exomeres was subjected to UC at 367,000g using a Beckman Coulter SW55 Ti rotor (k factor of 48, Beckman Coulter) for 16 h. The resulting pellet was resuspended in PBS containing 25 mM HEPES (pH 7.2) and was designated supermeres.  Density gradient ultracentrifugation The isolation of sEVs, heavy EVs, and non-vesicular fractions using C-DGUC has been previously described24. In brief, the conditioned 60 mL 3D sourced aliquots were spun at 10,000g for 30 min in a Ti 45 (Beckman Coulter) at 4 °C. The supernatant from 10,000g spin was concentrated with Centricon Plus-70 centrifugal filter (cat no. UFC710008, Millipore) at 4°C to 30 mL. The concentrate was overlaid onto a 2 mL cushion of 60% iodixanol (OptiPrep) and centrifuged at 100,000g for 4 h in a SW32 rotor (Beckman Coulter) at 4°C. For the preparation of the density gradient, the 40% iodixanol layer was made by transferring the bottom 3 mL of the cushion (which includes 1 mL of collected EVs and 2 mL of 60% iodixanol) into a new tube. The 20%, 10%, and 5% iodixanol dilutions were prepared by diluting OptiPrep with 0.25 M sucrose/10 mM Tris, pH 7.5. Three mL of each iodixanol dilution were subsequently layered on top of the 40% layer. The density gradients were spun at 100,000g for 18 h in a SW40 rotor (Beckman Coulter) at 4°C. After this centrifugation step, 1 mL density gradient fractions were collected. Fractions 6, 7, 9. 10, and 12 were diluted in 2.5 mL PBS and centrifuged at 100,000g for 3h in a TLA-110 rotor at 4 oC. To quantitate the size and concentration of these fractions, nanoparticle tracking analysis was performed using a Particle Metrix ZetaView PMX 110. Final pellets were resuspended in 100 µL of PBS for C-DGUC. To quantitate the size and concentration of these fractions, nanoparticle tracking analysis (NTA) was performed using a Particle Metrix ZetaView PMX 110.   Size-exclusion chromatography Size-exclusion chromatography (SEC) was performed on an AKTA Purifier fast-protein liquid chromatography (FPLC) system (GE) with two inline Superose 6 Increase resin columns (Cytiva). Samples were filtered off-line using 0.22 µm spin-filters and 0.5 mL of filtered sample was injected into the FPLC. Samples were run at a flow rate of 0.3 mL per min and fractionated into 1.5 mL wells of 96-deep well plates. Colorimetric assays for phosphatidylcholine (PC) (FujiFilm, NC9993780), total cholesterol (Pointe Scientific, 7510, 7509), total protein by BCA (Thermo Scientific, cat. 23225), and triglycerides (Pointe Scientific, 23-666-412) were performed, per the manufacturer’s instructions. Total RNAs were quantified in each fraction by SYTO RNASelect (Thermo Scientific, S32703) and a sRNA standard curve, as described previously25. The supermere samples were a result of combining fractions 19-24, and exomeres samples were pooled from fractions 14-17.

value: Epithelial

value: DiFi

tag: sample type

tag: cell culturing_condition

tag: isolation method

value: Gradient


title: VSMC, Male, Control, P14 (Input Ms), Rep1

description: Library name: BJ1C_P14_Ms_igg

value: vascular smooth muscle cell

value: IgG for H3K36me3 at P14


title: Gradient_9_10_C

description: Library name: Gradient_9_10_C


title: iPSC-derived spinal motor neurons, TDP-43 knockdown, batch 2, rep 1

description: Library name: M86TDPA


title: iPSC-derived spinal motor neurons, TDP-43 and UPF1 double knockdown, batch 2, rep 1

description: Library name: M86TUA


title: Gradient_9_10_A

description: Library name: Gradient_9_10_A


title: Gradient_6_7_D

description: Library name: Gradient_6_7_D


title: Gradient_9_10_B

description: Library name: Gradient_9_10_B


title: Gradient_6_7_C

description: Library name: Gradient_6_7_C


title: Gradient_6_7_B

description: Library name: Gradient_6_7_B


title: Gradient_6_7_A

description: Library name: Gradient_6_7_A


title: FPLC_Supermere_D

description: Library name: FPLC_Supermere_D

value: Supermere

value: FPLC


title: FPLC_Supermere_C

description: Library name: FPLC_Supermere_C


title: Gradient_12_D

description: Library name: Gradient_12_D


title: Gradient_12_A

description: Library name: Gradient_12_A


title: FPLC_Exomere_D

description: Library name: FPLC_Exomere_D

value: Exomere


title: Gradient_12_C

description: Library name: Gradient_12_C


title: FPLC_Exomere_A

description: Library name: FPLC_Exomere_A


title: 3D_UC_sEV_C

description: Library name: 3D_UC_sEV_C

value: sEV

value: UC


title: UMUC3_shCtrl2

description: Library name: UMUC3_shCtrl2

value: Bladder

value: urinary bladder carcinom

value: Ctrl


title: FPLC_Exomere_C

description: Library name: FPLC_Exomere_C


title: 3D_UC_Supermere_B

description: Library name: 3D_UC_Supermere_B


title: FPLC_Supermere_B

description: Library name: FPLC_Supermere_B


title: 3D_UC_sEV_B

description: Library name: 3D_UC_sEV_B


title: 3D_UC_Exomere_B

description: Library name: 3D_UC_Exomere_B


title: 3D_UC_Exomere_C

description: Library name: 3D_UC_Exomere_C


title: 3D_UC_Supermere_C

description: Library name: 3D_UC_Supermere_C


title: FPLC_Supermere_A

description: Library name: FPLC_Supermere_A


title: 3D_UC_Supermere_A

description: Library name: 3D_UC_Supermere_A


title: 3D_UC_Exomere_A

description: Library name: 3D_UC_Exomere_A


title: 2D_UC_sEV_B

description: Library name: 2D_UC_sEV_B


title: 2D_UC_sEV_A

description: Library name: 2D_UC_sEV_A


title: 2D_UC_sEV_C

description: Library name: 2D_UC_sEV_C


title: 2D_UC_Supermere_B

description: Library name: 2D_UC_Supermere_B


title: 2D_UC_Supermere_C

description: Library name: 2D_UC_Supermere_C


title: 2D_UC_Exomere_C

description: Library name: 2D_UC_Exomere_C


title: 2D_UC_Exomere_B

description: Library name: 2D_UC_Exomere_B


title: 2D_UC_Supermere_A

description: Library name: 2D_UC_Supermere_A


title: Gradient_12_B

description: Library name: Gradient_12_B


title: 3D_UC_sEV_A

description: Library name: 3D_UC_sEV_A


title: FPLC_Exomere_B

description: Library name: FPLC_Exomere_B


title: IL-17Ai, Synovial tissue biopsie, SpA15 (PsA), treatment, week 12

city: Amsterdam

first: Nataliya

last: Yeremenko

state: North Holland

address: Meibergdreef 9

department: Department of Rheumatology and Clinical Immunology

country: Netherlands

institute: Amsterdam University Medical Centers

description:
Library name: SpA15_wk12
Column name in IL-17Ai_raw_counts.txt : BP0570

data_processing:
Adapter sequnces and low-quality reads were removed with Trimmomatic 0.38
Sequence reads were mapped to the reference genome (USCS hg19 assembly) with HISAT2 v2.1.0
HTseq was used to build raw transcription profile as a read counts for each gene and each sample
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimeted txt file with raw counts for each gene (raw) and each sample (column)
Supplementary files format and content: First column 'GeneID' is ENTREZ GeneID

source_name: synovial tissue biopsie

extract_protocol:
Total RNA was extracted from the snap-frozen whole-tissue synovial biopsies using RNA Stat-60 (Tel-Test Inc), treated with DNase I (Invitrogen) and cleaned using RNeasy columns (79254, Qiagen) according to manufacturer's instructions. RNA concentration and integrity were measured using the Qubit RNA BR Assay kit (Life Technologies) and the Agilent 2100 Bioanalyzer (Agilent Technologies), correspondingly.
cDNA libraries were constructed with Illumina TruSeq™ RNA Sample Preparation Kit (Illumina) using 1 µg of total RNA with RNA integrity number (RIN) ≥ 7.

value: synovial tissue biopsie

tag: subject

tag: time

tag: spa subtype


title: IL-17Ai, Synovial tissue biopsie, SpA16 (PsA), treatment, week 12

description:
Library name: SpA16_wk12
Column name in IL-17Ai_raw_counts.txt : BP0568

tag: tissue


title: IL-17Ai, Synovial tissue biopsie, SpA18 (PsA), baseline, week 0

description:
Library name: SpA18_wk0
Column name in IL-17Ai_raw_counts.txt : BP0580

value: baseline

value: PsA


title: IL-17Ai, Synovial tissue biopsie, SpA12 (PsA), treatment, week 12

description:
Library name: SpA12_wk12
Column name in IL-17Ai_raw_counts.txt : BP0432


title: IL-17Ai, Synovial tissue biopsie, SpA17 (PsA), treatment, week 12

description:
Library name: SpA17_wk12
Column name in IL-17Ai_raw_counts.txt : BP0614


title: IL-17Ai, Synovial tissue biopsie, SpA16 (non_PsA), baseline, week 0

description:
Library name: SpA16_wk0
Column name in IL-17Ai_raw_counts.txt : BP0503


title: IL-17Ai, Synovial tissue biopsie, SpA9 (PsA), baseline, week 0

description:
Library name: SpA9_wk0
Column name in IL-17Ai_raw_counts.txt : BP0235


title: IL-17Ai, Synovial tissue biopsie, SpA6 (PsA), baseline, week 0

description:
Library name: SpA6_wk0
Column name in IL-17Ai_raw_counts.txt : BP0228


title: IL-17Ai, Synovial tissue biopsie, SpA9 (PsA), treatment, week 12

description:
Library name: SpA9_wk12
Column name in IL-17Ai_raw_counts.txt : BP0316


title: IL-17Ai, Synovial tissue biopsie, SpA6 (PsA), treatment, week 12

description:
Library name: SpA6_wk12
Column name in IL-17Ai_raw_counts.txt : BP0320


title: IL-17Ai, Synovial tissue biopsie, SpA7 (PsA), baseline, week 0

description:
Library name: SpA7_wk0
Column name in IL-17Ai_raw_counts.txt : BP0229


title: IL-17Ai, Synovial tissue biopsie, SpA15 (non_PsA), baseline, week 0

description:
Library name: SpA15_wk0
Column name in IL-17Ai_raw_counts.txt : BP0506


title: IL-17Ai, Synovial tissue biopsie, SpA12 (PsA), baseline, week 0

description:
Library name: SpA12_wk0
Column name in IL-17Ai_raw_counts.txt : BP0382


title: IL-17Ai, Synovial tissue biopsie, SpA7 (PsA), treatment, week 12

description:
Library name: SpA7_wk12
Column name in IL-17Ai_raw_counts.txt : BP0318


title: IL-17Ai, Synovial tissue biopsie, SpA5 (non_PsA), baseline, week 0

description:
Library name: SpA5_wk0
Column name in IL-17Ai_raw_counts.txt : BP0207


title: IL-17Ai, Synovial tissue biopsie, SpA2 (non_PsA), treatment, week 12

description:
Library name: SpA2_wk12
Column name in IL-17Ai_raw_counts.txt : BP0195


title: IL-17Ai, Synovial tissue biopsie, SpA3 (non_PsA), baseline, week 0

description:
Library name: SpA3_wk0
Column name in IL-17Ai_raw_counts.txt : BP0171


title: IL-17Ai, Synovial tissue biopsie, SpA1 (PsA), treatment, week 12

description:
Library name: SpA1_wk12
Column name in IL-17Ai_raw_counts.txt : BP0181


title: 2D_UC_Exomere_A

description: Library name: 2D_UC_Exomere_A

tag: cell line


title: IL-17Ai, Synovial tissue biopsie, SpA2 (non_PsA), baseline, week 0

description:
Library name: SpA2_wk0
Column name in IL-17Ai_raw_counts.txt : BP0131


title: IL-17Ai, Synovial tissue biopsie, SpA5 (non_PsA), treatment, week 12

description:
Library name: SpA5_wk12
Column name in IL-17Ai_raw_counts.txt : BP0293


title: IL-17Ai, Synovial tissue biopsie, SpA1 (PsA), baseline, week 0

description:
Library name: SpA1_wk0
Column name in IL-17Ai_raw_counts.txt : BP0120


title: IL-17Ai, Synovial tissue biopsie, SpA3 (non_PsA), treatment, week 12

description:
Library name: SpA3_wk12
Column name in IL-17Ai_raw_counts.txt : BP0227


title: IL-17Ai, Synovial tissue biopsie, SpA18 (PsA), treatment, week 12

description:
Library name: SpA18_wk12
Column name in IL-17Ai_raw_counts.txt : BP0616


title: siWTAP1

city: Qing Dao

first: Chan

last: Li

address: Jiangsu Road No. 16, Shinan District, Qingdao

department: Department of Obstetrics and Gynecology

institute: The Affiliated Hospital of Qingdao University

description: Library name: SAMPLE 4

data_processing:
Data filtering
Comparative analysis
Expression analysis
Functional analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each example

source_name: Placenta

extract_protocol:
Sample purity detected by Nanof Hortomel ® spectrophotometer (Thermofischer Semerfiche); Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA) was used to test RNA samples Integrity and concentration of the product.
The 3' end of eukaryotic mRNA had a polyA tail structure, and magnetic beads with Oligo(dT) were used for enrichment and purification. Fragmentation Buffer is added to the purified mRNA to make the fragments short. Then, the fragmented RNA was used as a template, and the first strand of cDNA was synthesized by random primers for reverse transcription, and the second strand of cDNA was synthesized by adding 2nd Strand Marking Buffer and 2nd Strand/End Repair Enzyme Mix. After end repair, base A was added, sequencing adapter was added, the target fragment was recovered by magnetic bead screening, and PCR amplification was carried out to complete the entire library preparation.

value: Placenta

tag: cell type

value: Trophoblast


title: siWTAP2

description: Library name: SAMPLE 5


title: IL-17Ai, Synovial tissue biopsie, SpA17 (PsA), baseline, week 0

description:
Library name: SpA17_wk0
Column name in IL-17Ai_raw_counts.txt : BP0575


title: siWTAP3

description: Library name: SAMPLE 6


title: NC2

description: Library name: SAMPLE 2


title: NC3

description: Library name: SAMPLE 3


title: NC1

description: Library name: SAMPLE 1


title: 376-H3K27ac

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

description: Library name: B4

data_processing:
Raw reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments by FastQC and Trimmomatic. The trimmed reads were aligned to the reference human genome version hg38 or mouse geneome version mm10 with the program Bowtie2 v2.3.4. Aligned reads were sorted and indexed using SAMtools. Peak calling was performed using MACS2 v2.1.4.
Assembly: hg38
Supplementary files format and content: wig
Library strategy: CUT&Tag

source_name: pbmc

extract_protocol:
Anti-H3K27ac (Active Motif, Cat#391330)  CUT&Tag was performed according to the manufacturer's instruction (Active Motif, Cat#53160).
Anti-H3K27ac (Active Motif, Cat#391330)  CUT&Tag libraries were performed according to the manufacturer's instruction (Active Motif, Cat#53160).

value: pbmc

value: T cell


title: Hu8H9-H3K27ac

description: Library name: B2


title: HRMEC, HG2, PES1 (ChIP)

city: Hefei

first: Sha

address: anhui hefei jingkai furong road 678

institute: Second Affiliated Hospital of Anhui Medical University

description: Library name: HRMEC_HG2,ChIP

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. The clean reads were mapped to the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks. IGV 7 software was used to visualize called peaks from ChIP-seq samples. Called peaks were then annotated using R package ChIPseeker. And HOMER (http://homer.ucsd.edu/homer/download.html，v4.11.1) were used to find de novo and known motif. Differential peaks analysis was performed using R package  Diffbind for experimental design with replication.
Assembly: hg38
Supplementary files format and content: bigWig,narrowPeak

source_name: HRMEC

extract_protocol:
Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. Extract chromatin from cross-linked cells by adding Lysis Buffer.Sonicate chromatin DNA to fragments ranging from 100 to 500 bp.
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X)和 End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min. And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15min. USER Enzyme was added to remove base U of adaptor at 37°C for 5min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads.

value: HRMEC

value: High Glucose


title: HRMEC, HG2, PES1 (Input)

description: Library name: HRMEC_HG2,INPUT


title: MGA271-H3K27ac

description: Library name: B3


title: HRMEC, NG2, PES1 (Input)

description: Library name: HRMEC_NG2,INPUT


title: HRMEC, NG2, PES1 (ChIP)

description: Library name: HRMEC_NG2,ChIP


title: HRMEC, NG1, PES1 (Input)

description: Library name: HRMEC_NG1,INPUT


title: HRMEC, HG1, PES1 (ChIP)

description: Library name: HRMEC_HG1,ChIP


title: Ctrl-H3K27ac

description: Library name: B1


title: HRMEC, NG1, PES1 (ChIP)

description: Library name: HRMEC_NG1,ChIP


title: A549 cells, ASONC1

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description:
Library name: ASONC1
Column name in FPKM_allsamples.txt: ASONC1

data_processing:
Hisat2 software was used for the alignment to the hg38 reference genome with default parameters. The expression count matrix was obtained by FeatureCounts.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRch38
Supplementary files format and content: txt file include FPKM values for each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Negative Control


title: A549 cells, OE1

description:
Library name: OE1
Column name in FPKM_allsamples.txt: OE1

value: Overexpression of AFAP1-AS1


title: A549 cells, ASONC2

description:
Library name: ASONC2
Column name in FPKM_allsamples.txt: ASONC2


title: A549 cells, vector1

description:
Library name: Vector1
Column name in FPKM_allsamples.txt: Vector1

value: Vecctor


title: A549 cells, OE2

description:
Library name: OE2
Column name in FPKM_allsamples.txt: OE2


title: A549 cells, vector2

description:
Library name: Vector2
Column name in FPKM_allsamples.txt: Vector2


title: KS_A3

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

description:
Library name: 6350-JMZ-S1-C
FFPE from Patient

data_processing:
The raw original FASTQ files were generated through 10X Visium pipeline with the respective TIFF image file using v1 and v2 probe with 5 KSHV spiked in the probes respectively.
A combined reference of HG38 with adding Human herpesvirus 8 strain GK18 (NC_009333) (spaceranger_hg38_kshv_refrence.gz) and a probe set V2 (Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K.csv)
Processed FASTQ files were aligned to a custom reference with KSHV genome (NC_009333.1) added using SpaceRanger “count” module (version 3.0.0) (supplementary files: spaceranger_hg38_kshv_refrence.gz, Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K2.csv or Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K.csv).
Assembly: spaceranger_hg38_kshv_refrence
Supplementary files format and content: positions.csv.gz, positions_list.csv.gz: list of barcodes and their coordinations
Supplementary files format and content: feature.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: *.tif.gz: Tiff file for the tissue
Supplementary files format and content: *.json.gz: Spots information
Supplementary files format and content: *.png.gz: Spots information
Library strategy: Spatial Transcriptomics

source_name: cutaneous KS tumor

extract_protocol:
FFPE treated samples were deparaffinized with investigator placed sections, H&E stained, imaged and decrosslinked.
The tissue was permeabilized and 10X Genomics human transcriptome V1 probes were hybridized to the mRNA overnight for KS_A1, KS_A2, and KS_A3. For KS_B1, KS_B2, and KS_B3 and KS_B4 the same process was performed with V2 and spiked KSHV genes (listed in Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K2.csv).  The probes were ligated, released from the tissue, captured on the spatially barcoded spots and subjected to extension followed by denaturation per manufacturer protocol.

value: cutaneous KS tumor


title: KS_B4

description:
Library name: 7630-JMZ-S2-D
FFPE from Patient


title: A549 cells, ASO1

description:
Library name: ASO1
Column name in FPKM_allsamples.txt: ASO1

value: Knockdown AFAP1-AS1


title: MLO_DJ1KO_organoid_5_replicate_1

type: other

city: Singapore

first: Matas

last: Vitkauskas

address: 60 Biopolis St.

department: Genome Institute of Singapore

country: Singapore

institute: A*star research entities

description:
60
DJ-1 KO

hyb_protocol: Following cryosectioning, sections were fixed for 1 min with ice-cold 4% PFA then 3:1 MeOH:acetic acid for 5 min, with 3x5 min washes with cold PBS in between. Air-dried coverslips were stored at −20°C. Coverslips were thawed and permeabilized with 70% EtOH at 4°C for 48 h, and incubated with wash buffer for 2 h in a 47°C incubator, before 48 h incubation at 47°C with 75–100 uM of encoding probe library. Before imaging, coverslips were washed twice with wash buffer for 15 min at 47°C, stained with DAPI, then washed twice with 2X saline-sodium citrate buffer.

scan_protocol: Imaging was performed on a commercial platform using a custom-built microscope.

data_processing:
Images of individual hybridization rounds were merged by z-stack and stitched to get joint X-Y coordinates per organoid section. RNA spots were decoded from the codebook using logic outlined in section “design and construction of the MERFISH encoding probes”. Cell segmentation of DAPI+ images staining for cell nuclei were segmented using CellPose v2.0 (Pachitariu & Stringer, 2022). The obtained .png cell mask and .hdf5 spot files were then put into a custom spot assignment script that assigns spots to cells within the cell area from the cell mask. Spots assigned to unsegmented areas were filtered out.
total counts of RNA spots per sample for each gene in the MERFISH panel.

source_name: human midbrain-like organoids

growth_protocol: hMLOs were generated as previously published (Jo, et al., 2016) (Jo, et al., 2021). In brief, TrypLE-Express-dissociated hPSCs were seeded into a V-bottom 96-well culture plate (Sumitomo Bakelite) in neuronal induction media with the ROCK inhibitor thiazovivin, which was removed after 24 h. Neuronal induction medium, used for the first three days, contained DMEM/F12:Neurobasal (1:1), N2 supplement (1:100), B27 without vitamin A (1:50), GlutaMAX (1%), minimum essential media-nonessential amino acid (1%), and β-mercaptoethanol (0.1%) (all Invitrogen) supplemented with 1 μg/ml heparin (Sigma-Aldrich), 10 μM SB431542 (Stemgent), 200 ng/ml Noggin (Prospec), and 0.8 μM CHIR99021 (Reagents Direct). On day 3, 100 ng/ml SHH-C25II and 100 ng/ml FGF8 (both R&D Systems), along with 0.5 μM purmorphamine (Stemgent), were added for midbrain patterning. On day 7, media was completely removed and organoids were embedded in reduced growth factor Matrigel and left to solidify in a 37°C incubator for 30 min, then grown in tissue growth induction medium containing Neurobasal, 1:100 N2 supplement, 1:50 B27 without vitamin A, 1% GlutaMAX, 1% minimum essential media-nonessential amino acid, and 0.1% β-mercaptoethanol supplemented with 2.5 μg/ml insulin (Sigma-Aldrich), 200 ng/ml laminin (Sigma-Aldrich), 100 ng/ml SHH-C25II, and 100 ng/ml FGF8. On day 8, hMLOs were transferred using a wide-bore pipette tip into low-attachment 6-well-plates (Costar) in final differentiation media, consisting of Neurobasal medium, N2 supplement (1:100), B27 without vitamin A (1:50), GlutaMAX (1%), minimum essential media-nonessential amino acid (1%), β-mercaptoethanol (0.1%), 10ng/ml BDNF (Peprotech), 10 ng/ml GDNF (Peprotech), 100 μM ascorbic acid (Sigma-Aldrich), and 125 μM db-cAMP (Sigma-Aldrich), and were cultured on orbital shakers for maintenance.

extract_protocol: Following manufacturer’s protocol, 50 units of papain enzyme (Worthington) was activated with 1 mM L-cysteine and 0.5 μM EDTA in Earle's Balanced Salt Solution (EBSS) (Thermo Fisher), and DNase I (Worthington) added. hMLOs were finely chopped with a scalpel and then resuspended in papain enzyme mix. The slurry was incubated at 37°C, 5% CO2 for 45 min on a rotator, and then triturated. Cells were spun down at 300xg for 5 min and washed twice in EBSS containing ovalbumin (Worthington) and BSA.

treatment_protocol: Cell lines were generated via CRISPR/Cas9 genome editing using similar methods as previously reported7, using gRNAs (5’-GATTTGACTGACCGCCAGCGTGG-3’ and 5’-GTTCGCTCTAAACAAAACAGTGG-3’) cloned into the lentiCRISPRv2 plasmid (Addgene plasmid #52961) to mediate knockout of the PARK7 gene.

tag: tag


title: MLO_DJ1KO_organoid_3_replicate_2

description:
60
DJ-1 KO

label_protocol: RNA spots were decoded from the codebook using logic outlined in section “design and construction of the MERFISH encoding probes”.


title: KS_B3

description:
Library name: 7630-JMZ-S2-A
FFPE from Patient


title: KS_B2

description:
Library name: 7630-JMZ-S1-D
FFPE from Patient


title: KS_A2

description:
Library name: 6350-JMZ-S1-B
FFPE from Patient


title: HRMEC, HG1, PES1 (Input)

last: Liu

description: Library name: HRMEC_HG1,INPUT

tag: treatment


title: MLO_DJ1KO_organoid_5_replicate_2

description:
60
DJ-1 KO


title: KS_A1

description:
Library name: 6350-JMZ-S1-A
FFPE from Patient


title: A549 cells, ASO2

description:
Library name: ASO2
Column name in FPKM_allsamples.txt: ASO2


title: MLO_DJ1KO_organoid_1_replicate_7

description:
60
DJ-1 KO


title: MLO_DJ1KO_organoid_1_replicate_5

description:
60
DJ-1 KO


title: MLO_DJ1KO_organoid_3_replicate_1

description:
60
DJ-1 KO


title: MYEOV_KD#1_S3

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

description: Library name: Sample 8

data_processing:
Adaptor and low-quality sequences were trimmed from the raw reads and the trimmed reads were aligned to the reference genome using the STAR program (version 2.6.1d). Differential expression analyses were performed by the DESeq2 R package (version 1.28.0).
Assembly: hg38
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample

source_name: Cultured corneal epithelial cells

extract_protocol:
Human donor corneas were obtained from eye banks. The central cornea was removed by an 8mm disposable biopsy punch and the corneal endothelium was removed mechanically. After 1 h incubation with PluriSTEM Dispase II Solution at 37 °C, limbal epithelial cells were scraped and incubated with TrypLE Express Enzyme at 37 °C for 30 min to dissociate. Dissociated limbal epithelial cells were cultured and treated with siRNAs (Control, MYEOV knockdown #1, and MYEOV knockdown #2).  Transfection was repeated on day 2 and day 4 and the cells were harvested on day 7 for RNA extraction.
After the removal of rRNA, approximately 500 ng of total RNA underwent library preparation with the Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research). RNA-seq libraries were sequenced on an Illumina NovaSeq to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.

value: Cultured corneal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 3, MYEOV knockdown #1


title: MYEOV_KD#1_S2

description: Library name: Sample 5

value: Sample 2, MYEOV knockdown #1


title: MLO_DJ1KO_organoid_1_replicate_4

description:
60
DJ-1 KO


title: Control_S3

description: Library name: Sample 7

value: Sample 3, Control


title: MLO_DJ1KO_organoid_1_replicate_3

description:
60
DJ-1 KO


title: MYEOV_KD#2_S2

description: Library name: Sample 6

value: Sample 2, MYEOV knockdown #2


title: MLO_DJ1KO_organoid_1_replicate_2

description:
60
DJ-1 KO


title: MLO_DJ1KO_organoid_1_replicate_1

description:
60
DJ-1 KO


title: Control_S2

description: Library name: Sample 4

value: Sample 2, Control


title: MYEOV_KD#2_S1

description: Library name: Sample 3

value: Sample 1, MYEOV knockdown #2


title: MYEOV_KD#1_S1

description: Library name: Sample 2

value: Sample 1, MYEOV knockdown #1


title: MLO_WT_organoid_6_replicate_3

description: GIS-Human-140-v1.0; Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015). RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science (New York, N.Y.), 348(6233), aaa6090. https://doi.org/10.1126/science.aaa6090

tag: organoid id

value: WT


title: Control_S1

description: Library name: Sample 1

value: Sample 1, Control


title: MLO_WT_organoid_6_replicate_2

tag: genotype


title: COJO-PBMC-TIL-2-W5

city: Solna

first: Lucas

last: Arruda

address: Nanna Svartz väg  4

country: Sweden

institute: CuraCell AB

description: Library name: S11732Nr53

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014). Quality trimming of the reads has not been performed. The FASTQ files were downsampled to 2 million read pairs before TCR analysis. Overlapping paired reads were merged into single reads before reconstruction of the CDR3β regions using NGmerge (Gaspar 2018). Only read pairs that could be successfully merged into a single read were kept for further analysis. Reconstruction of T cell receptor sequences was performed using RTCR (Gerritsen et al. 2016).
Assembly: hg38
Supplementary files format and content: csv files contain the assembled CDR3 sequences

source_name: Blood

extract_protocol:
RNA was extracted using MagMax (Thermo Fisher)
AmpliSeq™ for Illumina® TCR beta-SR Panel (Illumina)

value: Blood

value: PBMC


title: MLO_WT_organoid_4_replicate_2


title: COJO-TIL-3

description: Library name: S11732Nr54

source_name: TIL

value: TIL

value: T-cells


title: MLO_WT_organoid_4_replicate_1


title: MLO_WT_organoid_2_replicate_5