title: AMB_200205_9mo_2A_3A_1_P1-4-M16-M7

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: M

value: 9 months


title: WT UVB 8

status: Public on Dec 30 2025

type: SRA

city: Birmingham

first: Pi-Ling

last: Chang

state: Alabama

address: 1675 University Blvd

department: Nutrition Sciences

country: USA

institute: University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used to convert the bcl images to FASTQ files.
Raw sequence reads were trimmed with Trim Galore version 0.6.5 using parameters --trim-n --trim1 --nextseq 20
Trimmed reads were aligned to the reference genome with STAR version 2.7.5a using paramters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the aligned BAM files with HTSeq-count version 0.11.3 using parameters -m union -r pos -t exon -i gene_id -a 10 - s no -f bam
Assembly: Gencode GRCm38 p6 Release M24
Supplementary files format and content: tab-delimited Excel file containing raw transcript abundances for each sample and Ensembl ID#

molecule: polyA RNA

organism: Mus musculus

source_name: Epidermis

growth_protocol: Not applicable

extract_protocol: Briefly, dorsal skins taken from euthanized mice were rinsed several times with DEPC water, followed by the addition of TRIzol™ Reagent (Thermo Fisher Scientific, Waltham, MA). The epidermis was scraped with a razor blade and transferred to tubes containing TRIzol™ Reagent. Total RNA isolated was sent to the UAB Genomic Core facility, analyzed for RNA integrity prior to RNA-seq.

treatment_protocol: WT, OPN-null and tg(K14-OP) male mice at 10 weeks of age were shaved 48 h prior to UVB exposure at 180 mJ/cm2. Dorsal skins of euthanized mice were harvested 24 h after UVB exposure.

tag: tissue

value: Epidermis

tag: genotype

value: WT

tag: treatment

value: UVB


title: Patient 1091 (Sample no 1320); H3K27ac ChIP-Seq - mets

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

description: Library name: K271320M

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
ATAC-seq: Downstream processing included alignment to hg19, peak calling, and differential accessibility analysis using the CHIPS pipeline and DESeq2.
RNA-seq: Reads were quality trimmed, aligned to the human genome with STAR, and transcript quantification and differential expression performed with Cufflinks and DESeq2.
Assembly: hg19
Supplementary files format and content: BigWig and peak text files (BED) were generated
Supplementary files format and content: fpkm_tracking

molecule: genomic DNA

organism: Homo sapiens

source_name: Metastasis; Ovary

extract_protocol:
Using a 2 mm2 core needle, one core was extracted from frozen RP tissue blocks in the areas marked on the corresponding slide. Frozen cores were pulverized using the Covaris CryoPrep system.
ATAC-seq: Frozen tissue cores (2 mm2 core, ~20 mg) were pulverized (Covaris CryoPrep), nuclei were isolated via iodixanol density gradient, and 50,000 nuclei were subjected to Tn5 transposition using the Omni-ATAC protocol; libraries were purified, PCR-amplified, and sequenced on an Illumina platform (150 bp paired-end).
RNA-seq: Total RNA was extracted from frozen tissue using Qiagen RNeasy columns with on-column DNase digestion, and 1  g RNA was used to prepare stranded polyA+ libraries (Illumina TruSeq); libraries were barcoded, pooled, and sequenced on an Illumina HiSeq 2500 (50 bp paired-end).
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

value: Metastasis; Ovary

tag: antibody

value: H3K27ac anitbody, Diagenode C15410196


title: oTr-0h-Ctrl 2

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Library name: oTr-0h-Ctrl 2

data_processing:
Raw fastq files were aligned to Sus scrofa Sscrofa11.1 genome and Ovis aries Oar3.1 genome assemblies using HISAT2 v.2.2.1.
Data were quantitated at a protein-coding mRNA level using Partek Flow bioinformatics software (https://www.partek.com/partek-flow/), with normalization by total read count (fragments per kilobase of transcript per million mapped reads, FPKM), and 75% distribution.
Differential gene expression was calculated using DESeq2. Genes were classified as differentially expressed (DEGs) if they met the following criteria: average FPKM>1 in at least one group, false discovery rate (q-value or FDR) <0.05, and ≥1.3-fold change in expression.
Assembly: Oar_v3.1 for Ovis aries; and Sscrofa11.1 for Sus scrofa
Supplementary files format and content: FPKM values

molecule: total RNA

organism: Ovis aries

source_name: oTr1 Cells

extract_protocol:
The RNA from pTr2 and oTr1 cells was extracted by TRIzol following the mannual.
For RNA sequencing (RNA-seq) of pTr2 and oTr1 cells treated with or without arginine, total RNA (350 ng per samples) was used to generate sequencing libraries using the TruSeq Stranded Total RNA with Ribo-zero Plus kit (Illumina), following the manufacturer’s instruction.

tag: cell line

value: oTr1 Cells

tag: cell type

value: ovine trophectoderm cells

value: wildtype

value: 0 mM Arginine

tag: time


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-M19

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

tag: strain

tag: brain region

value: FC

tag: gender

tag: age


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-M20


title: Patient 1301/1319; H3K27ac ChIP-Seq - mets 2

description: Library name: K271319M

source_name: Metastasis; Adrenal

value: Metastasis; Adrenal


title: Patient 256; H3K27ac ChIP-Seq - mets

description: Library name: K27256M

source_name: Metastasis; Soft Tissue

value: Metastasis; Soft Tissue


title: WT UVB 6


title: WT UVB 7


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-L8


title: Patient 1077/1284/1308; H3K27ac ChIP-Seq - mets 3

description: Library name: K271308M

source_name: Metastasis; abdominal wall

value: Metastasis; abdominal wall


title: OPN KO noTx 10

value: OPN KO

value: noTx


title: cMPC, dKO 3

type: RNA

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

description: Gene expression in mast cells cultured in vitro  affected by knockout of Roquin1 and Roquin2

hyb_protocol: 7.5 µg biotinylated cRNA was hybridized to an identical lot of Affymetrix GeneChip MOE430 2.0 (16 hours, 45°C) following the manufacturer’s instructions.

scan_protocol: Images were scanned using a GeneChip® Scanner 3000 7G with autoloader and command console software (both Affymetrix).

data_processing: Array normalization and expression value calculation was performed using DNA-Chip Analyzer (www.dchip.org).

source_name: In vitro cultured peritoneal mast cells deficient for Roquin 1 and 2

label_protocol: 50 ng of total RNA were used for biotin labeling (Affymetrix GeneChip whole transcript sense target-labeling kit).

growth_protocol: To generate cPMCs, bulk peritoneal cells were cultured in suspension in mast cell medium: DMEM (Gibco) supplemented with 10% fetal calf serum (PAA), 2% supernatant from X63/0 cells expressing IL-3 (gift from Ton Rolink), 0.5% supernatant from CHO cells expressing SCF (gift from Patrice Dubreuil), Glutamax (Gibco), Non Essential Amino Acids (Gibco), 50 μM 2-mercaptoethanol (Merck), and 25 mM Hepes (PAN). To generate BMMCs , bulk bone marrow cells were cultured in suspension in mast cell medium: DMEM (Gibco) supplemented with 10% fetal calf serum (PAA), 2% supernatant from X63/0 cells expressing IL-3,  Glutamax (Gibco), Non Essential Amino Acids (Gibco), 50 μM 2-mercaptoethanol (Merck), and 25 mM Hepes (PAN).

extract_protocol: RNA was extracted using a Qiagen RNAeasy Micro kit according to manufacturer's manual

treatment_protocol: Four weeks after the initiation of cPMC and BMMC cultures, the knockout of both Roquin1 and Roquine2  was achieved by culturing the cells in medium containing 1 μM 4-hydroxytamoxifen (Sigma-Aldrich) for 7 days. After that all mast cells were cultured in DMEM (Gibco) supplemented with 10% fetal calf serum (PAA), 2% supernatant from X63/0 cells expressing IL-3, 0.5% supernatant from CHO cells expressing SCF, Glutamax (Gibco), Non Essential Amino Acids (Gibco), 50 μM 2-mercaptoethanol (Merck), and 25 mM Hepes (PAN).

value: CkitCreERT2 Roquin1FF Roquin2FF


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-L7

value: M

value: 9 months


title: Patient 1301/1319; H3K27ac ChIP-Seq - mets 1

description: Library name: K271301M


title: BMMC, WT2

source_name: In vitro cultured bone marrow derived  mast cells


title: BMMC, WT1


title: cPMC, WT2

source_name: In vitro cultured peritoneal mast cells


title: OPN KO noTx 9

value: Epidermis


title: BMMC, dKO 2

source_name: In vitro cultured bone marrow derived  mast cells deficient for Roquin 1 and 2


title: cPMC, WT1


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-L20


title: In vitro mixture, 9 cell-types, mix24

type: genomic

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

description: genomic DNA part of double extraction (RNA/DNA)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: The raw DNA methylation intensity data files (IDAT) were processed with the lumi and methylumi R packages. We performed pre-normalization filtering (removing probes containing SNP, high intensity probes, not detected probes). We performed normalization using color balance adjusment and between sample normalisation by the "quantile" method.

label: Cy3, Cy5

source_name: 9 cell-types mixture

label_protocol: Standard Illumina Protocol

extract_protocol: For all samples, DNA/RNA was extracted using the ALLPrep tissue kit (Qiagen, Venlo, The Netherlands) following the manufacturer’s instructions.

value: 9 cell-types mixture


title: Patient 1077/1284/1308; H3K27ac ChIP-Seq - mets 2

description: Library name: K271284M

source_name: Metastasis; soft tissue

value: Metastasis; soft tissue


title: OPN KO noTx 8


title: cMPC, dKO 1


title: cPMC, WT3


title: cMPC, dKO 2


title: BMMC, WT3


title: BMMC, dKO 3


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-L19


title: In vitro mixture, 9 cell-types, mix23


title: OPN KO UVB 16

value: UVB


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-K8


title: Patient 1247; H3K27ac ChIP-Seq - mets

description: Library name: K271247A

source_name: Metastasis; Lung

value: Metastasis; Lung

value: H3K27ac anitbody, Diagenode C15410196


title: In vitro mixture, 9 cell-types, mix21


title: Patient 1230; H3K27ac ChIP-Seq - mets

description: Library name: K271230M

source_name: Metastasis; Liver

value: Metastasis; Liver


title: In vitro mixture, 9 cell-types, mix20


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-K20


title: Patient 1226; H3K27ac ChIP-Seq - local tumor

description: Library name: K271226T

source_name: Primary; Kidney tumor

value: Primary; Kidney tumor


title: OPN KO UVB 14


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-K19

value: FC


title: In vitro mixture, 9 cell-types, mix19


title: Patient 1247; H3K27ac ChIP-Seq - mets 2

description: Library name: K271247B

source_name: Metastasis; lymph node

value: Metastasis; lymph node


title: In vitro mixture, 9 cell-types, mix17


title: Patient 1226; H3K27ac ChIP-Seq - mets

description: Library name: K271226M

source_name: Metastasis; adrenal

value: Metastasis; adrenal


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-J20


title: In vitro mixture, 9 cell-types, mix22


title: K14 OPN UVB 3

source_name: Epidermis

value: K14 OPN


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-J19


title: K14 OPN noTx 2


title: In vitro mixture, 9 cell-types, mix16


title: K14 OPN noTx 1


title: Patient 1174; H3K27ac ChIP-Seq - mets

description: Library name: K271174M

source_name: Metastasis; Pancreas

value: Metastasis; Pancreas


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-J7


title: Patient 1058 (sample no 1189); H3K27ac ChIP-Seq - mets

description: Library name: K271189M

source_name: Metastasis; Spine

value: Metastasis; Spine


title: OPN KO UVB 15

value: OPN KO


title: BMMC, dKO 1

value: CkitCreERT2 Roquin1FF Roquin2FF


title: OPN KO UVB 13


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-K7

value: M

value: 9 months


title: In vitro mixture, 9 cell-types, mix15

value: 9 cell-types mixture


title: Patient 1169; H3K27ac ChIP-Seq - mets

description: Library name: K271169M

source_name: Metastasis; Brain

value: Metastasis; Brain


title: Patient 1226; H3K27ac ChIP-Seq - normal

description: Library name: K271226N

source_name: Normal Kidney

value: Normal Kidney


title: K14 OPN UVB 2

value: Epidermis

value: UVB


title: K14 OPN noTx 11

value: noTx


title: In vitro mixture, 9 cell-types, mix18


title: In vitro mixture, 9 cell-types, mix14


title: Patient 1168; H3K27ac ChIP-Seq - mets

description: Library name: K271168M

source_name: Metastasis; Omentum

value: Metastasis; Omentum

value: H3K27ac anitbody, Diagenode C15410196


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-I8

value: FC


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-I7


title: In vitro mixture, 9 cell-types, mix13


title: Patient 1166; H3K27ac ChIP-Seq - mets

description: Library name: K271166M

source_name: Metastasis; Adrenal

value: Metastasis; Adrenal


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-J8


title: K14 OPN UVB 1

value: K14 OPN


title: 40w - WT - islet cells 4

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HTZvsWT.xlsx
40wt-30010-020

data_processing:
All analysis were carried out using CLC Genomics Workbench (version 12.0.2) and CLC Genomics Server (version 11.0.2).
Adapter and quality trimming was done by “Trim Reads” tool from CLC Genomics Workbench. While adapters are often removed directly by the sequencer, part of the adapter region may be included in the sequenced reads. Such adapters artefacts were removed by identifying read-through adapter sequences, whereby the 3’ end of one read includes the reverse complement of the adapter from the other read.
Further, reads were trimmed based on quality scores and ambiguous nucleotides, e.g. due to stretches of Ns. A maximum of 2 ambiguous nucleotides were allowed in a read.
The QC reports were generated by “QC for Sequencing Reads” tool from CLC Genomics Workbench, and can be found in [2] Quality Control, assess and visualize statistics on: Sequence-read lengths and base- coverages, nucleotide-contributions and base-ambiguities, quality scores as emitted by the base-caller, over-represented sequences and hints suggesting contamination events.
Read mapping and gene quantification were done by “RNA-seq Analysis” tool from CLC Genomics Workbench.
Principal Component Analyses (PCA) were performed on the gene expression profile using the “PCA for RNA-seq” tool from CLC Genomic Workbench.
Genome_build: ENSEMBL Mus musculus GRCm38
Supplementary_files_format_and_content: xlsx file include normalized TPM values for each sample as well as fold change

source_name: Pancreatic islet cells

extract_protocol:
Pancreas were digested with collagenase, islets extracted with histopaque gradient, and mRNA extracted using the Qiagen RNeasy Micro Kit (50)
Illumina TruSeq Stranded mRNA Library Prep Kit

value: mixed background

tag: glyceamia

value: normal

value: wt

value: 40 weeks old


title: In vitro mixture, 9 cell-types, mix12


title: 40w - WT - islet cells 3

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HTZvsWT.xlsx
40wt-30010-022


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-I19

value: M


title: Patient 1136; H3K27ac ChIP-Seq - mets

description: Library name: K271136M


title: Patient 1164; H3K27ac ChIP-Seq - mets

description: Library name: K271164M

value: Metastasis; Pancreas


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-I20

value: 9 months


title: 40w - WT - islet cells 1

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HTZvsWT.xlsx
40wt-30010-021


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-H7


title: Patient 957 (sample no 1131); H3K27ac ChIP-Seq - mets

description: Library name: K271131M

value: Metastasis; Lung


title: Patient 1120 (sample no 1124); H3K27ac ChIP-Seq - mets

description: Library name: K271124M

source_name: Metastasis; lung

value: Metastasis; lung


title: In vitro mixture, 9 cell-types, mix10

value: 9 cell-types mixture


title: In vitro mixture, 9 cell-types, mix9


title: 40w - Beta-cell Hnf1a fl/wt - islet cells 2

description:
QNS30010_Expression Browser-40w-HMZvsHTZ.xlsx
QNS30010_Expression Browser-40w-HTZvsWT.xlsx
40htz-30010-030

value: hyperglyceamia

value: htz


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-H20


title: In vitro mixture, 9 cell-types, mix13rep2


title: Patient 1120; H3K27ac ChIP-Seq - local tumor

description: Library name: K271120T

value: Primary; Kidney tumor


title: 40w - Beta-cell Hnf1a fl/wt - islet cells 1

description:
QNS30010_Expression Browser-40w-HMZvsHTZ.xlsx
QNS30010_Expression Browser-40w-HTZvsWT.xlsx
40htz-30010-029


title: 40w - WT - islet cells 2

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HTZvsWT.xlsx
40wt-30010-019


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-H19


title: Patient 1120; H3K27ac ChIP-Seq - normal

description: Library name: K271120N

value: Normal Kidney

value: H3K27ac anitbody, Diagenode C15410196


title: 40w - Beta-cell Hnf1a fl/fl - islet cells 4

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HMZvsHTZ.xlsx
40hmz-30010-023

value: hmz


title: Pure, CD4 T cells

source_name: CD4 T cells

value: CD4 T cells


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-G7

value: FC


title: Patient 1091; H3K27ac ChIP-Seq - local tumor

description: Library name: K271091T


title: Patient 1091; H3K27ac ChIP-Seq - normal

description: Library name: K271091N


title: 40w - Beta-cell Hnf1a fl/fl - islet cells 3

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HMZvsHTZ.xlsx
40hmz-30010-025

value: mixed background


title: Pure, Cancer Basal

source_name: Cancer Basal

value: Cancer Basal


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-H8


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-G8


title: In vitro mixture, 9 cell-types, mix11

source_name: 9 cell-types mixture


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-G20


title: Pure CD8, T Cells

source_name: CD8, T Cells

value: CD8, T Cells


title: Patient 1077/1284/1208; H3K27ac ChIP-Seq - mets 1

description: Library name: K271077M

source_name: Metastasis; bone

value: Metastasis; bone


title: 40w - Beta-cell Hnf1a fl/fl - islet cells 1

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HMZvsHTZ.xlsx
40hmz-30010-024

value: 40 weeks old


title: 40w - Beta-cell Hnf1a fl/fl - islet cells 2

description:
QNS30010_Expression Browser-40w-HMZvsWT.xlsx
QNS30010_Expression Browser-40w-HMZvsHTZ.xlsx
40hmz-30010-026


title: Pure, B cells

source_name: B cells

value: B cells


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-G19

value: M

value: 9 months


title: Patient 1058; H3K27ac ChIP-Seq - tumor

description: Library name: K271058T

source_name: Primary; Kidney tumor


title: 6w - WT - islet cells 3

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HTZvsWT.xlsx
6wt-30010-003

value: normal

value: wt

value: 6 weeks old


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-F8


title: Pure, Cancer Classical

source_name: Cancer Classical

value: Cancer Classical


title: Pure, Fibroblast

source_name: Fibroblast

value: Fibroblast


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-F7


title: Pure, Macrophages

source_name: Macrophages

value: Macrophages


title: 6w - WT - islet cells 2

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HTZvsWT.xlsx
6wt-30010-004


title: 6w - WT - islet cells 1

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HTZvsWT.xlsx
6wt-30010-001


title: Patient 1022; H3K27ac ChIP-Seq - mets

description: Library name: K271022M

source_name: Metastasis; Diaphragm

value: Metastasis; Diaphragm

value: H3K27ac anitbody, Diagenode C15410196


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-F20

value: FC


title: Patient 1014; H3K27ac ChIP-Seq - local tumor

description: Library name: K271014T

value: Primary; Kidney tumor


title: 6w - Beta-cell Hnf1a fl/wt- islet cells 2

description:
QNS30010_Expression Browser-6w-HTZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6htz-30010-016

value: mixed background

value: hyperglyceamia

value: htz


title: Pure, Endothelial cells

source_name: Endothelial cells

value: Endothelial cells


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-F19


title: Patient 957; ATAC-Seq - normal

description: Library name: xR957N1AT

source_name: Normal Kidney

value: Normal Kidney


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-E8

value: M


title: 6w - Beta-cell Hnf1a fl/wt- islet cells 1

description:
QNS30010_Expression Browser-6w-HTZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6htz-30010-015


title: Patient 1014; H3K27ac ChIP-Seq - normal

description: Library name: K271014N


title: Pure, Neutrophils

source_name: Neutrophils

value: Neutrophils


title: In vitro mixture, 9 cell-types, mix30

value: 9 cell-types mixture


title: WT noTx 10

source_name: Epidermis

value: Epidermis

value: WT

value: noTx


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-E7

value: 9 months


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 8

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-006

source_name: Pancreatic islet cells

value: hmz

value: 6 weeks old


title: In vitro mixture, 9 cell-types, mix28

description: genomic DNA part of double extraction (RNA/DNA)


title: Patient 716; ATAC-Seq - local tumor

description: Library name: xR716T1AT


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 7

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-012


title: Patient 1058; H3K27ac ChIP-Seq - normal

description: Library name: K271058N

value: H3K27ac anitbody, Diagenode C15410196


title: Patient 716; ATAC-Seq - normal

description: Library name: xR716N1AT


title: Patient 716; ATAC-Seq - mets

description: Library name: xR716M2AT

source_name: Metastasis; adrenal

value: Metastasis; adrenal


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-E20

value: FC


title: In vitro mixture, 9 cell-types, mix29


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-E19


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 5

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-008

value: mixed background


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-D8


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 6

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-007

value: hyperglyceamia


title: In vitro mixture, 9 cell-types, mix27


title: Patient 638; ATAC-Seq - local tumor

description: Library name: xR638T1AT

value: Primary; Kidney tumor


title: In vitro mixture, 9 cell-types, mix26


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 4

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-011


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-D7


title: In vitro mixture, 9 cell-types, mix25


title: Patient 638; ATAC-Seq - normal

description: Library name: xR638N1AT


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 3

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-013


title: In vitro mixture, 9 cell-types, mix8


title: Patient 962; ATAC-Seq - normal

description: Library name: xK962N1AT


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-D20


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-D19


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 2

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-009


title: In vitro mixture, 9 cell-types, mix7


title: Patient 1226 ATAC-Seq - local tumor

description: Library name: x1226T2AT


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-C8


title: 6w - Beta-cell Hnf1a fl/fl - islet cells 1

description:
QNS30010_Expression Browser-6w-HMZvsWT.xlsx
QNS30010_Expression Browser-6w-HMZvsHTZ.xlsx
6hmz-30010-010


title: Patient 1226; ATAC-Seq - normal

description: Library name: x1226N1AT


title: In vitro mixture, 9 cell-types, mix6


title: 24w - WT - islet cells 4

description:
24wt-20633-002
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HTZvsWT.xlsx

value: normal

value: wt

value: 24 weeks old


title: Patient 1226; ATAC-Seq - mets

description: Library name: x1226M1AT


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-C7

value: M


title: 24w - WT - islet cells 3

description:
24wt-20633-011
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HTZvsWT.xlsx


title: In vitro mixture, 9 cell-types, mix5

value: 9 cell-types mixture


title: In vitro mixture, 9 cell-types, mix4


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-C20


title: Patient 1058 (Sample no 1189); ATAC-Seq - mets

description: Library name: x1189M1AT

source_name: Metastasis; Spine

value: Metastasis; Spine


title: 24w - WT - islet cells 2

description:
24wt-20633-014
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HTZvsWT.xlsx


title: 24w - WT - islet cells 1

description:
24wt-20633-020
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HTZvsWT.xlsx


title: In vitro mixture, 9 cell-types, mix3


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-B8


title: Patient 957 (sample no 1131); ATAC-Seq - mets

description: Library name: x1131M1AT

source_name: Metastasis; Lung

value: Metastasis; Lung


title: In vitro mixture, 9 cell-types, mix2

source_name: 9 cell-types mixture


title: Patient 1058; ATAC-Seq - local tumor

description: Library name: x1058T1AT


title: 24w - Beta-cell Hnf1a fl/wt - islet cells 3

description:
24htz-20633-024
20633_Expression Browser_24w_HTZvsWT.xlsx
20633_Expression Browser_24w_HMZvsHTZ.xlsx

value: htz


title: In vitro mixture, 9 cell-types, mix1


title: Patient 1058; ATAC-Seq - normal

description: Library name: x1058N2AT

value: Normal Kidney


title: 24w - Beta-cell Hnf1a fl/wt - islet cells 4

description:
24htz-20633-010
20633_Expression Browser_24w_HTZvsWT.xlsx
20633_Expression Browser_24w_HMZvsHTZ.xlsx


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-B20

value: 9 months


title: Patient 957; ATAC-Seq - local tumor

description: Library name: R0957TAT


title: 24w - Beta-cell Hnf1a fl/wt - islet cells 2

description:
24htz-20633-023
20633_Expression Browser_24w_HTZvsWT.xlsx
20633_Expression Browser_24w_HMZvsHTZ.xlsx


title: R2

city: Changsha

first: Jingchao

last: Hong

address: Xiangya Street

country: China

institute: Central South University

description: Library name: R2

data_processing:
Raw sequencing reads containing adapter contaminants or low-quality bases were processed to ensure data integrity for downstream analyses. Quality filtering was performed using fastp (v0.18.0) with the following parameters: (1) Removal of adapter-containing reads; (2) Exclusion of reads with >10% undefined nucleotides (N); (3) Discarding reads where >50% of bases exhibited Q-scores ≤20. Subsequently, Bowtie2 (v2.2.8) aligned reads to a ribosomal RNA (rRNA) reference database, with rRNA-mapped reads eliminated. The resulting high-quality clean reads were utilized for transcriptome assembly and quantification. A HISAT2 (v2.1.0) index was constructed from the reference genome Ensembl_release111, and filtered paired-end reads were mapped using default parameters. Transcript assembly was conducted with StringTie (v1.3.1) in reference-guided mode. Expression abundance of each transcript was quantified as TPM (Transcripts Per Kilobase Million) values through RSEM (v1.2.19), reflecting normalized read counts relative to gene length and sequencing depth. It is critical to note that TPM values were generated for visualization and within-sample comparison only.
Raw reads containing adapter contaminants and low-quality bases were filtered using fastp (v0.22.0) to obtain high-quality clean data18. Paired-end clean reads were aligned to the Ensembl_release_111 reference genome using Bowtie2 (v2.4.1) with default parameters25. Peak calling was performed with MACS3 (v3.0.0a7) in narrowPeak mode (adjusted p-value < 0.05)26. Signal distributions across genomic regions were visualized using deepTools (v3.5.1)
Assembly: Ensembl_release_111 reference genome
Supplementary files format and content: ATAC peak differential expression.zip

source_name: Marrow

growth_protocol: SH-SY5Y cells (ATCC) were cultured in DMEM/F12 (1:1) medium (Gibco, MA, USA) supplemented with 10% fetal bovine serum (Gibco, MA, USA). Cells were plated in 6-well plates at a density of 5 × 105 cells/mL and incubated overnight at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from experimental samples using TRIzol reagent (Thermo Fisher Scientific, San Diego, USA) according to the manufacturer's protocol.
mRNA was enriched using poly(A) capture beads and purified. The enriched mRNA was fragmented by incubation at elevated temperature. First-strand cDNA synthesis was performed using fragmented mRNA as template in a reverse transcription system (Thermo Fisher Scientific, San Diego, USA). During second-strand synthesis, end repair and 3'-adenylation (A-tailing) were simultaneously completed. Illumina adapters were ligated to the cDNA fragments, followed by purification with Hieff NGS® DNA Selection Beads (Yeasen, Shanghai, China) for size selection. Libraries were amplified by PCR and quality-controlled.  ATAC-seq was performed according to established protocols. Briefly, 50,000 cells per sample were lysed to isolate nuclei. The nuclei were then extracted and incubated with Tn5 transposase (37°C, 30 min) for tagmentation. Illumina TruSeq adapters (N5 and N7) were ligated at a final concentration of 0.5 μM, followed by library amplification via PCR. Amplified libraries were purified using Novoprotein DNA Clean Beads (Novoprotein, Soochow, China). DNA concentration was quantified with a Qubit 2.0 Fluorometer (Thermo Fisher, MA, USA), and fragment size distribution was assessed using an Agilent 2100 Bioanalyzer. After quality control, 150-bp paired-end sequencing was conducted on an Illumina NovaSeq 6000 platform (PersonalBio, Shanghai, China).

treatment_protocol: Experimental groups were treated with 5 mM MPP⁺ (Selleck, Houston, USA) and 10 μM rotenone (Sigma, Saint Louis, USA). Negative control (NC) wells received equivalent volumes of dimethyl sulfoxide (DMSO) vehicle (Sigma, Saint Louis, USA). After 24-hour exposure, cells were harvested for RNA sequencing and ATAC-seq analyses.

value: Marrow

value: neuroblastoma cell line

value: Rot

value: 10 μM rotenone (Selleck, Houston, USA) treatment 24h.


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-B19

value: FC


title: R1

description: Library name: R1


title: 24w - Beta-cell Hnf1a fl/fl - islet cells 4

description:
24hmz-20633-004
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HMZvsHTZ.xlsx

value: mixed background

value: hyperglyceamia

value: hmz


title: Patient 962; ATAC-Seq - mets

description: Library name: K962M1AT


title: Patient K962; ATAC-Seq - local tumor

description: Library name: K962T2AT

value: Primary; Kidney tumor


title: M2

description: Library name: M2

value: MPP

value: 5 mM MPP⁺ (Selleck, Houston, USA) treatment 24h.


title: 24w - Beta-cell Hnf1a fl/fl - islet cells 3

description:
24hmz-20633-009
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HMZvsHTZ.xlsx

value: 24 weeks old


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-C19

value: M


title: M1

description: Library name: M1


title: 24w - Beta-cell Hnf1a fl/fl - islet cells 2

description:
24hmz-20633-013
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HMZvsHTZ.xlsx


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-A20


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-A7


title: N2

description: Library name: N2

value: NC

value: Negative control (NC) wells received equivalent volumes of dimethyl sulfoxide (DMSO) vehicle (Sigma, Saint Louis, USA).


title: 24w - Beta-cell Hnf1a fl/fl - islet cells 1

description:
24hmz-20633-012
20633_Expression Browser_24w_HMZvsWT.xlsx
20633_Expression Browser_24w_HMZvsHTZ.xlsx


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-A8


title: N1

description: Library name: N1


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-A19


title: 12w - WT - islet cells 3

description:
12wt-20633-030
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HTZvsWT.xlsx

value: normal

value: wt

value: 12 weeks old


title: Rot3

description: Library name: Rot 3

data_processing:
Raw sequencing reads containing adapter contaminants or low-quality bases were processed to ensure data integrity for downstream analyses. Quality filtering was performed using fastp (v0.18.0) with the following parameters: (1) Removal of adapter-containing reads; (2) Exclusion of reads with >10% undefined nucleotides (N); (3) Discarding reads where >50% of bases exhibited Q-scores ≤20. Subsequently, Bowtie2 (v2.2.8) aligned reads to a ribosomal RNA (rRNA) reference database, with rRNA-mapped reads eliminated. The resulting high-quality clean reads were utilized for transcriptome assembly and quantification. A HISAT2 (v2.1.0) index was constructed from the reference genome Ensembl_release111, and filtered paired-end reads were mapped using default parameters. Transcript assembly was conducted with StringTie (v1.3.1) in reference-guided mode. Expression abundance of each transcript was quantified as TPM (Transcripts Per Kilobase Million) values through RSEM (v1.2.19), reflecting normalized read counts relative to gene length and sequencing depth. It is critical to note that TPM values were generated for visualization and within-sample comparison only.
Raw reads containing adapter contaminants and low-quality bases were filtered using fastp (v0.22.0) to obtain high-quality clean data18. Paired-end clean reads were aligned to the Ensembl_release_111 reference genome using Bowtie2 (v2.4.1) with default parameters25. Peak calling was performed with MACS3 (v3.0.0a7) in narrowPeak mode (adjusted p-value < 0.05)26. Signal distributions across genomic regions were visualized using deepTools (v3.5.1)
Assembly: Ensembl_release_111 reference genome
Supplementary files format and content: RNA-seq differential expression.zip

value: Marrow

value: neuroblastoma cell line


title: Patient 573; ATAC-Seq - mets

description: Library name: AT573M2

source_name: Metastasis; Soft Tissue

value: Metastasis; Soft Tissue


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-P6

value: FC

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-4-M16-B7


title: Patient 964; ATAC-Seq - mets

description: Library name: AT964M1

source_name: Metastasis; Pancreas

value: Metastasis; Pancreas


title: Rot2

description: Library name: Rot 2

value: Rot

value: 10 μM rotenone (Selleck, Houston, USA) treatment 24h.


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-P18


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-P5


title: 12w - Beta-cell Hnf1a fl/wt - islet cells 3

description:
12htz-20633-008
20633_Expression Browser_12w_HTZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx

value: mixed background

value: hyperglyceamia

value: htz


title: Patient 968; ATAC-Seq - mets

description: Library name: AT968M1

value: Metastasis; Diaphragm


title: Patient 344; ATAC-Seq - mets

description: Library name: AT344M2

source_name: Metastasis; Brain

value: Metastasis; Brain


title: MPP3

description: Library name: MPP 3

value: MPP

value: 5 mM MPP⁺ (Selleck, Houston, USA) treatment 24h.


title: Patient 256; ATAC-Seq - mets

description: Library name: AT256M2


title: 12w - Beta-cell Hnf1a fl/wt - islet cells 1

description:
12htz-20633-019
20633_Expression Browser_12w_HTZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx


title: Patient 951; ATAC-Seq - mets

description: Library name: K951M2AT

value: Metastasis; Lung


title: 12w - WT - islet cells 1

description:
12wt-20633-028
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HTZvsWT.xlsx

value: normal

value: wt

value: 12 weeks old


title: 12w - WT - islet cells 2

description:
12wt-20633-029
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HTZvsWT.xlsx


title: Rot1

description: Library name: Rot 1

value: Marrow

value: neuroblastoma cell line


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-O5

value: FC

value: M

value: 9 months


title: Patient 354; ATAC-Seq - mets

description: Library name: AT354M1

source_name: Metastasis; Bone

value: Metastasis; Bone


title: Patient 1350; ATAC-Seq - mets

description: Library name: AT1350M1

source_name: Metastasis; Bladder

value: Metastasis; Bladder


title: 12w - Beta-cell Hnf1a fl/wt - islet cells 2

description:
12htz-20633-005
20633_Expression Browser_12w_HTZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx

value: mixed background

value: hyperglyceamia


title: MPP1

description: Library name: MPP 1


title: 12w - Beta-cell Hnf1a fl/fl - islet cells 5

description:
12hmz-20633-015
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx

value: hmz


title: Patient 1301; ATAC-Seq - mets

description: Library name: AT1301M1

source_name: Metastasis; Adrenal

value: Metastasis; Adrenal


title: Patient 1174; ATAC-Seq - mets

description: Library name: AT1174M2

value: Metastasis; Pancreas


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-O6


title: 12w - Beta-cell Hnf1a fl/fl - islet cells 4

description:
12hmz-20633-021
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx


title: Patient 1169; ATAC-Seq - mets

description: Library name: AT1169M1

value: Metastasis; Brain


title: NC2

description: Library name: NC 2

value: NC

value: Negative control (NC) wells received equivalent volumes of dimethyl sulfoxide (DMSO) vehicle (Sigma, Saint Louis, USA).


title: NC3

description: Library name: NC 3


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-N6


title: 12w - Beta-cell Hnf1a fl/fl - islet cells 3

description:
12hmz-20633-035
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx


title: Patient 1168; ATAC-Seq - mets

description: Library name: AT1168M2

source_name: Metastasis; Omentum

value: Metastasis; Omentum


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-P17


title: 12w - Beta-cell Hnf1a fl/fl - islet cells 2

description:
12hmz-20633-034
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx

value: 12 weeks old


title: 12w - Beta-cell Hnf1a fl/fl - islet cells 1

description:
12hmz-20633-031
20633_Expression Browser_12w_HMZvsWT.xlsx
20633_Expression Browser_12w_HMZvsHTZ.xlsx


title: siRNA3

city: suzhou

first: yán

last: hu

address: No. 58 Changsheng South Road, Taicang 215400, Jiangsu, China

department: Central Laboratory

institute: The First People's Hospital of Taicang

description:
Library name: siRNA3
siRNA group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

source_name: cell culture

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).


title: Patient 1164; ATAC-Seq - mets

description: Library name: AT1164M1


title: NC1

description: Library name: NC 1

value: Marrow


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-N18


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-N5


title: Patient 1166; ATAC-Seq - mets

description: Library name: AT1166M1


title: siRNA2

description:
Library name: siRNA2
siRNA group, replicate biosample 2


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-O18


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-N17


title: pTr-48h-Arg 3

description: Library name: pTr-48h-Arg 3

organism: Sus scrofa

source_name: pTr2 Cells

value: pTr2 Cells

value: porcine trophectoderm cells

value: wildtype

value: 0.2 mM Arginine


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-M6

value: FC

value: M

value: 9 months


title: pTr-48h-Arg 2

description: Library name: pTr-48h-Arg 2


title: Patient 1136; ATAC-Seq - mets

description: Library name: AT1136M2


title: pTr-48h-Arg 1

description: Library name: pTr-48h-Arg 1


title: NC3

description:
Library name: NC3
NC group, replicate biosample 3


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-M5


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-O17


title: Patient 1091 (sample no 1320); ATAC-Seq - mets

description: Library name: a1320M1

source_name: Metastasis; Ovary

value: Metastasis; Ovary


title: pTr-48h-Ctrl 3

description: Library name: pTr-48h-Ctrl 3

value: 0 mM Arginine


title: NC1

description:
Library name: NC1
NC group, replicate biosample 1


title: NC2

description:
Library name: NC2
NC group, replicate biosample 2


title: pTr-48h-Ctrl 2

description: Library name: pTr-48h-Ctrl 2


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-M18


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-M17


title: Patient 1091; ATAC-Seq - local tumor

description: Library name: a1091T1

source_name: Primary; Kidney tumor

value: Primary; Kidney tumor


title: Patient 1091; ATAC-Seq - normal

description: Library name: a1091N1

source_name: Normal Kidney

value: Normal Kidney


title: pTr-48h-Ctrl 1

description: Library name: pTr-48h-Ctrl 1


title: shCDK9_K56A_S2

city: Seoul

first: Yugyeong

last: KIM

address: 84, Heukseok-ro

department: Life science

country: South Korea

institute: Chung-Ang University

description:
Library name: shCDK9_K56A_S2
shCDK9_K56A

data_processing:
High-throughput sequencing was performed on a Novaseq 6000 platform (Illumina, Inc., USA) using paired-end 101-bp reads.
Post-sequencing, aAdapter sequence and low-quality bases sequences were trimmed removed from RNA-seq data using Trim Galore (v0.6.6).
The trimmed reads were aligned to GRCh38 using STAR-2.7.1a (version 2.7.1a). The alignment files were used to assemble transcripts, estimating their abundances, and detecting differential expression of genes.
Read feature counting was performed with RSEM (v.1.3.3), and FPKM values were calculated. Differential isoform and gene expression analysis was performed using DESeq2 (v1.32.0).
Assembly: GRCh38
Supplementary files format and content: txt files include FPKM values for each samples

source_name: colon

growth_protocol: HCT116 cells were maintained in RPMI 1640 with 10% fetal bivine serum (FBS) and 1% penicillin-streptomycin

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 150ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq mRNA sample preparation kit (Illumina).

treatment_protocol: 10 µM EPZ-5676 treated in HCT116 cells for 72h.

value: colon

value: Colorectal carcinoma

value: CDK9 knockdown


title: siRNA1

description:
Library name: siRNA1
siRNA group, replicate biosample 1


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-L6


title: pTr-0h-Ctrl 3

description: Library name: pTr-0h-Ctrl 3


title: shCDK9_K56A_S1

description:
Library name: shCDK9_K56A_S1
shCDK9_K56A


title: Patient 1014; ATAC-Seq - local tumor

description: Library name: a1014T1


title: pTr-0h-Ctrl 2

description: Library name: pTr-0h-Ctrl 2


title: Patient 1014; ATAC-Seq - normal

description: Library name: a1014N1


title: shCDK9_WT_S2

description:
Library name: shCDK9_WT_S2
shCDK9_WT


title: Patient 1022; ATAC-Seq - mets

description: Library name: AT1022M1

source_name: Metastasis; Diaphragm

value: Metastasis; Diaphragm


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-L18


title: shCDK9_WT_S1

description:
Library name: shCDK9_WT_S1
shCDK9_WT


title: pTr-0h-Ctrl 1

description: Library name: pTr-0h-Ctrl 1


title: Patient 951; ATAC-Seq - local tumor

description: Library name: a_R951T1AT


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-L17


title: Patient 951; ATAC-Seq - normal

description: Library name: a_R951N2AT


title: siUBE2I, replicate 3

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

description: Library name: siUBE2I_rep3

data_processing:
Clean reads were mapped to mouse genome (UCSC hg19) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: primary human endometrial stromal cells

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Primary human endometrial stromal cells (hESCs) were treated with siUBE2I or siNC, 6 h before decidualization induction.

value: primary human endometrial stromal cells


title: shCDK9_EV_S2

description:
Library name: shCDK9_EV_S2
shCDK9_EV


title: Patient 233 (sample no 338); ATAC-Seq - mets

description: Library name: a_R338M2AT

source_name: Metastasis; lung

value: Metastasis; lung


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-K6


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-K5


title: Patient 233; ATAC-Seq - local tumor

description: Library name: a_R233T1AT


title: EPZ_S2

description:
Library name: HCT116_EPZ_S2
EPZ-5676

value: Control


title: shCDK9_EV_S1

description:
Library name: shCDK9_EV_S1
shCDK9_EV


title: siUBE2I, replicate 2

description: Library name: siUBE2I_rep2


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-L5


title: Patient 233; ATAC-Seq - normal

description: Library name: a_R233N1AT


title: siNC, replicate_3

description: Library name: siNC_rep3


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-K17


title: siNC, replicate_2

description: Library name: siNC_rep2


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-K18


title: DMSO_S2

description:
Library name: HCT116_DMSO_S2
DMSO

value: DMSO


title: Patient 1077/1284/1308; ATAC-Seq - mets 3

description: Library name: a_1308M1AT

source_name: Metastasis; abdominal wall

value: Metastasis; abdominal wall


title: EPZ_S1

description:
Library name: HCT116_EPZ_S1
EPZ-5676


title: Patient 1077/1284/1308; ATAC-Seq - mets 2

description: Library name: a_1284M1AT

source_name: Metastasis; soft tissue

value: Metastasis; soft tissue


title: DMSO_S1

description:
Library name: HCT116_DMSO_S1
DMSO


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-J5

value: FC


title: siNC, replicate_1

description: Library name: siNC_rep1


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-J6

value: M


title: Patient 1247; ATAC-Seq - mets 2

description: Library name: a_1247B2AT

source_name: Metastasis; lymph node

value: Metastasis; lymph node


title: Panc1 with 1uM Brigatinib replicate 2

city: Seattle

first: Mehlam

middle: M

last: Saifudeen

state: WA

address: 1100 Fairview Ave North

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
Library name: Panc1 Brigatinib 2
Column Name in Control_Brigatinib_raw_all_counts.csv: Panc1 with 1uM Brigatinib 2

data_processing:
Raw RNA-seq reads were aligned to the hg38 reference genome using STAR v2.7.7a with two-pass mode and gene-level quantification enabled (--quantMode GeneCounts). BAM files were sorted and indexed using SAMtools. Gene expression counts were obtained using featureCounts (Subread package) with GENCODE v40 GTF, allowing multimapping reads (-M) and paired-end assignment (-p). The resulting raw gene count matrix was used for downstream analysis.
Assembly: hg38_149
Supplementary files format and content: comma separated file includes raw counts for each sample

source_name: Pancreas

extract_protocol:
Total cellular RNA was extracted using the GenCatch Total RNA Mini Prep Kit (Epoch Life Science, Missouri City, TX, USA) following the manufacturer’s protocol. The extracted RNA was assessed for quality and quantity using a NanoDrop spectrophotometer (Thermo Fisher Scientific) and Qubit Fluorometer (Invitrogen). RNA integrity was verified using an Agilent Bioanalyzer or TapeStation. 1 μg of total RNA was used for downstream applications, including library preparation.
RNA libraries for RNA sequencing were prepared using Novogene and following the Illumina manufacturer’s protocol.

value: Pancreas

value: Pancreatic cancer cells

value: Brigatinib

value: Treatment with Brigatinib

tag: batch


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-J18

value: 9 months


title: Patient 1247; ATAC-Seq - mets 1

description: Library name: a_1247A2AT


title: Panc1 with 1uM Brigatinib replicate 1

description:
Library name: Panc1 Brigatinib 1
Column Name in Control_Brigatinib_raw_all_counts.csv: Panc1 with 1uM Brigatinib 1


title: siUBE2I, replicate 1

description: Library name: siUBE2I_rep1


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-J17


title: Patient 1120 (sample no 1124); ATAC-Seq - mets

description: Library name: a_1124M2AT


title: Panc1 DMSO replicate 2

description:
Library name: Panc1 DMSO 2
Column Name in Control_Brigatinib_raw_all_counts.csv: Panc1 CTL RNA 2


title: EHH_2

city: TianJin

first: Yan

last: Li

address: NO.23 PingJiang street

department: Family Planning

institute: The second hospital of Tianjin medical university

description:
Library name: EHH_2
essential high-altitude hypertension (EHH)

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes miRNA count for each sample

source_name: blood

extract_protocol:
Cell Harvesting & Lysis: Culture cells are pelleted and lysed using a phenol-based reagent (e.g., TRIzol™) or a specialized column-based buffer system designed to efficiently capture small RNAs. Separation & Binding: For column-based kits, lysate is mixed with ethanol and passed through a silica membrane. The miRNA binds to the membrane while contaminants are washed away. Elution: Pure, concentrated miRNA is eluted in a low-volume RNase-free buffer or water. Quality Control: RNA integrity and concentration are verified using a spectrophotometer (e.g., NanoDrop) and/or a bioanalyzer.
The miRNA library construction process begins with RNA extraction, followed by size selection to enrich small RNAs. Adapters are then ligated to the 3' and 5' ends of the miRNAs. This is followed by reverse transcription to create cDNA. The cDNA is then amplified using PCR with specific primers. Finally, the amplified library is purified and its quality and concentration are checked before sequencing. This process prepares the miRNA sample for high-throughput sequencing analysis.

value: blood


title: Patient 1120; ATAC-Seq - local tumor

description: Library name: a_1120T2AT

value: Primary; Kidney tumor


title: ARH_3

description:
Library name: ARH_3
altitude-related hypertension (ARH)


title: EHH_1

description:
Library name: EHH_1
essential high-altitude hypertension (EHH)


title: Panc1 DMSO replicate 1

description:
Library name: Panc1 DMSO 1
Column Name in Control_Brigatinib_raw_all_counts.csv: Panc1 CTL RNA 1


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-I5


title: Patient 1120; ATAC-Seq - normal

description: Library name: a_1120N1AT

value: Normal Kidney


title: ARH_2

description:
Library name: ARH_2
altitude-related hypertension (ARH)


title: ARH_1

description:
Library name: ARH_1
altitude-related hypertension (ARH)


title: N_3

description:
Library name: N_3
high-altitude cohort including normotensive entrants (N)


title: EHH_3

description:
Library name: EHH_3
essential high-altitude hypertension (EHH)


title: MDA-MB-231 with 1uM Gilteritinib replicate 1

description:
Library name: MDA-MB 231 Gilteritinib 1
Column Name in Control_Gliteritinib_raw_all_counts.csv: MDA-MB-231 Glit 1uM Day 3 RNA duplicate 1

source_name: Breast

value: Breast

value: Triple-negative breast cancer cells

value: Giltertinib

value: Treatment with Giltertinib


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-I17


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-I18


title: Patient 1077/1284/1308; ATAC-Seq - mets 1

description: Library name: a_1077M1AT

source_name: Metastasis; bone

value: Metastasis; bone


title: MDA-MB-231 DMSO duplicate 2

description:
Library name: MDA-MB-231 DMSO 2
Column Name in Control_Gliteritinib_raw_all_counts.csv: MDA-MB-231 CTL Day 3 RNA duplicate 2

value: DMSO


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-H6

value: FC


title: MDA-MB-231 with 1uM Gilteritinib replicate 2

description:
Library name: MDA-MB 231 Gilteritinib 2
Column Name in Control_Gliteritinib_raw_all_counts.csv: MDA-MB-231 Glit 1uM Day 3 RNA duplicate 2


title: Test 3

city: Changde

first: Ming

last: Lei

state: Hunan

address: No. 818 Renmin Road, Wuling District

institute: The First People’s Hospital of Changde City

description: Library name: Sample 6

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequencing quality are examined by FastQC (pass Illumina quality filter),  and reads were trimmed 5 ,3-adaptor bases by cutadapt.
The expression profiling of tRF & tiRNA  were calculated based on counts of reads mapped.
Reads were aligned allowing for 1 mismatch only to the mature tRNA sequences,  then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
Differential expression analysis of tRF&tiRNAs between groups was performed using edgeR. For differentially expressed tRF&tiRNAs were screened with the significant threshold to 1.5-fold difference, p-value ≤ 0.05 and the mean CPM within the group ≥ 1
Assembly: HG38
Supplementary files format and content: .xlsx file containing the CPM value of detected tRF&tiRNA for each sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Agarose electrophoresis was used to check the integrality of total RNA samples, and then the samples werequantified on the NanoDrop ND-1000 instrument.
Total RNA samples were first pretreated as following to remove some RNA  modifications that interfere with small RNA-seq library construction: 3-aminoacyl (charged) deacylation to 3-OHfor 3-adaptor ligation, 3-cP (2 ,3-cyclic phosphate) removal to 3-OH for 3-adaptor ligation,5-OH(hydroxyl group) phosphorylation to 5-P for 5-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Then pretreated total RNA was used to prepare the sequencing library in the following steps: 1) 3-adapter ligation; 2) 5-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5)  size selection of 134～160bp PCR amplified fragments (corresponding to 14～40nt small RNA size range). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq 500 system per the manufacturers instructions

value: peripheral blood mononuclear cells


title: Test 2

description: Library name: Sample 5


title: Test 1

description: Library name: Sample 4


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-H5

value: M


title: GSC923 with 1uM Tepotinib replicate 2

description:
Library name: GSC 923 Tepotinib 2
Column Name in GSC923_Tepotinib_raw_all_counts.csv: GSC923 with 1uM Tepotinib 2

source_name: Brain (Glioblastoma)

value: Brain (Glioblastoma)

value: Glioblastoma stem-like cells

value: Tepotinib

value: Tepotinib drug treatment


title: GSC923 with 1uM Tepotinib replicate 1

description:
Library name: GSC 923 Tepotinib 1
Column Name in GSC923_Tepotinib_raw_all_counts.csv: GSC923 with 1uM Tepotinib 1


title: MDA-MB-231 DMSO replicate 1

description:
Library name: MDA-MB-231 DMSO 1
Column Name in Control_Gliteritinib_raw_all_counts.csv: MDA-MB-231 CTL Day 3 RNA duplicate 1


title: N_1

description:
Library name: N_1
high-altitude cohort including normotensive entrants (N)


title: Con 3

description: Library name: Sample 3


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-H18

value: 9 months


title: 20250415_AMT017_hMSC_SMARCD2-SWIFT_SPI1_SPI1

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: Library name: Sample 184

data_processing:
ATAC-seq, CUT&RUN, and CUT*TAG reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project’s unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
RNAseq reads were aligned to the GRCh38 genome using STAR v2.5.2b, with GTF annotation from GENCODE v46. Gene counts were obtained using --quantMode "GeneCounts". Differential gene analysis was performed using DESeq2 v1.48.1 in R v4.5.1.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN, CUT&TAG, and ATAC-seq bigWig files give the normalized coverage of DNA fragments across the genome in RPM. In CUT&RUN samples of BRG1 profiling in hMSCs comparing truncations of PU.1, samples were normalized over all SMARCA4 peaks using the method described in DESeq2. In hMSCs expressing PU.1 and SMARCD2-SWIFT, IgG RPM was subtracted to obtain a reduced-background bigWig. Peaks were called using MACS3 and IgG peaks were subtracted when applicable. Gene counts are provided for RNA-seq read counts mapped to exons of given genes, produced using STAR geneCounts.
Library strategy: CUT&RUN

source_name: hMSC

extract_protocol:
CUT&RUN: Cells were pelleted by centrifugation (300 rcf, 5 minutes, room temperature) and were washed with PBS containing 200mM Glycine. Cells were resuspended with 100ul/sample of Nuclear Extraction Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) for 2 min on ice. Nuclei were pelleted by centrifugation (600 rcf, 3 minutes, 4C), and resuspended in 100ul/sample cold Wash150 Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) and incubated with activated ConA beads at room temperature for 15 minutes. Nuclei-ConA bead complexes were resuspended in 50 ul/sample cold Antibody Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS, 2mM EDTA supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), 0.01% Digitonin, and 0.5 ug primary antibody/sample, and incubated overnight nutating at 4C. Following removal of supernatant, ConA-nuclei complexes were washed twice with Digitonin Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), and 0.01% Digitonin. Samples were then resuspended in 50ul Digitonin Buffer and 2 ul of CUTANA pAG-MNase (Epicypher, Cat#: 15-1116) each and incubated at room temperature for 10 minutes. Samples were washed twice with Digitonin Buffer and resuspended in 50ul Digitonin Buffer and 1ul of 100mM CaCl2 per sample. Following incubation nutating at 4C for 2 hours, samples received 33ul of Stop Buffer containing 340 mM NaCl, 20 mM EDTA, 4 mM EGTA supplemented with fresh 50 ug/mL RNase A, 50 ug/ml Glycogen and incubated at 37C for 1 hour to release MNase digested DNA fragments. Supernatant was collected into fresh tubes and supplemented with 0.8uL 10% SDS and 1uL of 20mg/mL Proteinase K for overnight incubation at 55C. DNA was purified with Ampure XP (Beckman Coulter, Cat#: A63881) beads and 80% EtOH washes. DNA was eluted with 25uL of 0.1X TE buffer and transferred to new tubes. DNA fragments were prepared for next generation sequencing with CUTANA CUT&RUN Library Prep Kit (Epicypher, Cat#: 14-1001) according to manufacturer protocol. ATAC-seq: Nuclei were resuspended in transposition mix (1X TD Buffer, 2.5 ul TDE1 Nextera Tn5 Transposase (Illumina)) and incubated with mild rotation for 30 min at 37°C. Tagmented DNA was purified using MinElute PCR cleanup kit (Qiagen). RNA-seq: 2 X 106 live cells as were washed with PBS and RNA was extracted using QIAshredder and RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. CUT&TAG: Cells were processed for Cut & Tag as previously published and according to manufacturer’s CUTANA protocol (Epicypher) with the use of BioMag Plus Concanavalin A beads (Polysciences), CUTANA pAG-Tn5 (Epicypher), primary antibodies, and Guinea Pig anti-Rabbit IgG (Heavy & Light chain) antibody (Antibodies-Online). Tn5 transposed fragments were amplified between 14-18 cycles using NEB Next HF 2X PCR Master Mix (NEB) and custom primers originally designed for ATAC-seq library amplification to allow for multiplexing of 50+ samples. Amplified DNA was purified using 0.75X AMPpure Beads (Beckman Coulter) to remove primer-dimers.
CUT&RUN: Concanavalin A (ConA) beads (Polysciences, Cat#: 86057-10) were activated with Bead Activation Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were stored on ice until used. 500,000 cells per sample were harvested and resuspended in media at 1 million cells per mL. Cells were lightly crosslinked with 16% paraformaldehyde at a final concentration of 0.1% at room temperature for 2 minutes. Crosslinking was quenched with 2.5M Glycine at a final concentration of 200mM at room temperature for 5 minutes.  Cells were pelleted by centrifugation (300 rcf, 5 minutes, room temperature) and were washed with PBS containing 200mM Glycine. Cells were resuspended with 100ul/sample of Nuclear Extraction Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) for 2 min on ice. Nuclei were pelleted by centrifugation (600 rcf, 3 minutes, 4C), and resuspended in 100ul/sample cold Wash150 Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) and incubated with activated ConA beads at room temperature for 15 minutes. Nuclei-ConA bead complexes were resuspended in 50 ul/sample cold Antibody Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS, 2mM EDTA supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), 0.01% Digitonin, and 0.5 ug primary antibody/sample, and incubated overnight nutating at 4C. Following removal of supernatant, ConA-nuclei complexes were washed twice with Digitonin Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), and 0.01% Digitonin. Samples were then resuspended in 50ul Digitonin Buffer and 2 ul of CUTANA pAG-MNase (Epicypher, Cat#: 15-1116) each and incubated at room temperature for 10 minutes. Samples were washed twice with Digitonin Buffer and resuspended in 50ul Digitonin Buffer and 1ul of 100mM CaCl2 per sample. Following incubation nutating at 4C for 2 hours, samples received 33ul of Stop Buffer containing 340 mM NaCl, 20 mM EDTA, 4 mM EGTA supplemented with fresh 50 ug/mL RNase A, 50 ug/ml Glycogen and incubated at 37C for 1 hour to release MNase digested DNA fragments. Supernatant was collected into fresh tubes and supplemented with 0.8uL 10% SDS and 1uL of 20mg/mL Proteinase K for overnight incubation at 55C. DNA was purified with Ampure XP (Beckman Coulter, Cat#: A63881) beads and 80% EtOH washes. DNA was eluted with 25uL of 0.1X TE buffer and transferred to new tubes. DNA fragments were prepared for next generation sequencing with CUTANA CUT&RUN Library Prep Kit (Epicypher, Cat#: 14-1001) according to manufacturer protocol. CUT&RUN experiments were performed in one replicate but with antibodies for different mSWI/SNF subunits. Overlap between distinct subunit peaks were used for high confidence in results. ATAC-seq: ATAC-seq was performed as previously described with 100,000 cells per sample. Cells were dissociated and counted, as described above, 7-days post transduction with lentivirus. Cells were washed with cold PBS, resuspend in lysis buffer (10mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL) and centrifuged at 500 g for 10 min at 4°C. Nuclei were resuspended in transposition mix (1X TD Buffer, 2.5 ul TDE1 Nextera Tn5 Transposase (Illumina)) and incubated with mild rotation for 30 min at 37°C. Tagmented DNA was purified using MinElute PCR cleanup kit (Qiagen). Samples were amplified using 10 total PCR amplification cycles with custom PCR Primers using NEBNext HF PCR Master Mix (NEB). Samples were purified with 1.2X Agencourt AMPure XP beads (Beckman Coulter) and size distribution was determined using D5000 HS reagents and screentapes (Agilent) on 2200 TapeStation Instrument (Agilent). Samples were pooled in equimolar amounts and sequenced on Illumina Next-seq 500 with NextSeq 500/550 High Output Kit V2 75 cycles (Illumina) using 37bp paired-end sequencing parameters. ATAC-Seq experiments were performed in two replicates. RNA-seq: Cells were dissociated and counted, as described above, 7-days post transduction with lentivirus. 2 X 106 live cells as were washed with PBS and RNA was extracted using QIAshredder and RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. 1 µg of total RNA was used as input for library preparation and processed per the manufacturer’s instructions using NEBNext Poly(A) mRNA magnetic isolation module (NEB) followed by the NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB) with NEBNext Multiplex Oligos for Illumina (NEB). Samples were collected in biological replicate. ERCC synthetic RNA spike-in control (Thermo Fisher Scientific) was added at the beginning of library preparation per manufacturer’s recommendations to normalize samples across conditions. Libraries were quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and size distribution was verified using Tapestation D1000 HS reagents and screentapes (Agilent). Equimolar amounts of libraries were pooled, denatured, and sequenced on Illumina Next-seq 500 with NextSeq 500/550 High Output Kit V2 75 cycles (Illumina) according to standard Illumina protocols with single-end sequencing parameters. RNA-Seq were performed in two biological replicates. CUT&TAG: CUT&TAG was performed following published protocols (Epicypher). Cells were dissociated from culture plates using TrypLE Express (Thermo Fisher Scientific) and washed once with PBS pH 7.4 (Gibco). Cells were counted with Countess II (Invitrogen). 200,000-500,000 live cells were used per epitope as determined by Trypan Blue (Thermo Fisher Scientific) exclusion. Cells were processed for Cut & Tag as previously published and according to manufacturer’s CUTANA protocol (Epicypher) with the use of BioMag Plus Concanavalin A beads (Polysciences), CUTANA pAG-Tn5 (Epicypher), primary antibodies, and Guinea Pig anti-Rabbit IgG (Heavy & Light chain) antibody (Antibodies-Online). Tn5 transposed fragments were amplified between 14-18 cycles using NEB Next HF 2X PCR Master Mix (NEB) and custom primers originally designed for ATAC-seq library amplification to allow for multiplexing of 50+ samples. Amplified DNA was purified using 0.75X AMPpure Beads (Beckman Coulter) to remove primer-dimers. Libraries were quantified and QC’d as above. Samples were sequenced by the Dana Farber Cancer Institute Molecular Biology Core Facility using paired-end read parameters on an Illumina Nextseq 500 (Illumina) using Illumina NextSeq 500/550 High Output Kit V2 75 cycles (Illumina).

value: hMSC

tag: chip antibody

value: SMARCD2-SWIFT and SPI1transduced


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-H17


title: Con 1

description: Library name: Sample 1


title: GSC923 DMSO replicate 2

description:
Library name: GSC923 DMSO 2
Column Name in GSC923_Tepotinib_raw_all_counts.csv: GSC923 CTL RNA 2


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-I6


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-G6


title: 20250415_AMT014_hMSC_SMARCD2-SWIFT_SPI1

description: Library name: Sample 182

value: SMARCD2-SWIFT transduced


title: EC_4

city: tianjin

first: Yu

last: kaiyuan

address: Meteorological Station Road 22

institute: Tianjin Medical University

data_processing:
The ranscriptome library was prepared  following TruSeq  TM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of  total RNA.
messenger RNA was isolated according to polyA selection method by  oligo(dT) beads and then fragmented by fragmentation buffer firstly.
Secondly double-stranded  cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA)  with random hexamer primers (Illumina).
Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra  Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles
After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the  Illumina NovaSeq 6000 sequencer (2 × 150bp read length).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and  quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample  (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct  sequencing library
RNA purification, reverse transcription, library construction and sequencing were performed at  Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the  manufacturer’s instructions (Illumina, San Diego, CA).

value: Intestinal epithelial cells

value: WT

value: LPS+EC supernatant stimulus


title: 20250415_AMT016_hMSC_EV_SPI1_SPI1

description: Library name: Sample 183

value: SPI1 transduced


title: N_2

description:
Library name: N_2
high-altitude cohort including normotensive entrants (N)

value: blood


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-G18

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-G5


title: 20210315_KWR055_MSC_+HA-OTX2_rep1

description: Library name: Sample 230

data_processing:
ATAC-seq, CUT&RUN, and CUT*TAG reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project’s unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
RNAseq reads were aligned to the GRCh38 genome using STAR v2.5.2b, with GTF annotation from GENCODE v46. Gene counts were obtained using --quantMode "GeneCounts". Differential gene analysis was performed using DESeq2 v1.48.1 in R v4.5.1.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN, CUT&TAG, and ATAC-seq bigWig files give the normalized coverage of DNA fragments across the genome in RPM. In CUT&RUN samples of BRG1 profiling in hMSCs comparing truncations of PU.1, samples were normalized over all SMARCA4 peaks using the method described in DESeq2. In hMSCs expressing PU.1 and SMARCD2-SWIFT, IgG RPM was subtracted to obtain a reduced-background bigWig. Peaks were called using MACS3 and IgG peaks were subtracted when applicable. Gene counts are provided for RNA-seq read counts mapped to exons of given genes, produced using STAR geneCounts.

value: HA-OTX2 transduced


title: GSC923 DMSO replicate 1

description:
Library name: GSC923 DMSO 1
Column Name in GSC923_Tepotinib_raw_all_counts.csv: GSC923 CTL RNA 1

value: DMSO


title: 20210315_KWR054_MSC_+HA-REST_rep2

description: Library name: Sample 229

value: HA-REST transduced


title: Con 2

description: Library name: Sample 2

value: peripheral blood mononuclear cells


title: 20250415_AMT013_hMSC_EV_SPI1

description: Library name: Sample 181


title: 20210315_KWR056_MSC_+HA-OTX2_rep2

description: Library name: Sample 231


title: 20250415_AMT010_hMSC_EV_SPI1_SMARCA4

description: Library name: Sample 179

value: SMARCA4 (CST, 49360S)


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-G17

value: FC

value: M


title: MPP2

description: Library name: MPP 2

source_name: Marrow

value: Marrow

value: neuroblastoma cell line

value: MPP

value: 5 mM MPP⁺ (Selleck, Houston, USA) treatment 24h.


title: EC_1


title: 20210315_KWR053_MSC_+HA-REST_rep1

description: Library name: Sample 228

value: hMSC


title: pos4

value: Intestinal epithelial cells

value: LPS+BHI stimulus


title: 20210315_KWR052_MSC_+HA-PAX3_rep2

description: Library name: Sample 227

value: HA-PAX3 transduced


title: 20250415_AMT011_hMSC_SMARCD2-SWIFT_SPI1_SMARCA4

description: Library name: Sample 180

value: SMARCD2-SWIFT and SPI1transduced


title: EC_3

value: WT

value: LPS+EC supernatant stimulus


title: 20210315_KWR051_MSC_+HA-PAX3_rep1

description: Library name: Sample 226


title: 20250415_AMT007_hMSC_EV_SMARCA4

description: Library name: Sample 177


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-F18

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-F17


title: 20200616_KWR042_MSC_+HA-SOX2_rep2

description: Library name: Sample 225

value: HA-SOX2 transduced


title: pos3


title: neg4

value: BHI stimulus


title: 20250415_AMT005_hMSC_SMARCD2-SWIFT_SPI1_IgG

description: Library name: Sample 176

value: IgG (Epicypher, 13-0042)


title: 20250415_AMT002_hMSC_SMARCD2-SWIFT_IgG

description: Library name: Sample 174

value: SMARCD2-SWIFT transduced


title: 20200616_KWR041_MSC_+HA-SOX2_rep1

description: Library name: Sample 224


title: 20250415_AMT004_hMSC_EV_SPI1_IgG

description: Library name: Sample 175

value: SPI1 transduced


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-E6

value: FC

value: M


title: 20200616_KWR040_MSC_+HA-MYOD1_rep2

description: Library name: Sample 223

value: HA-MYOD1 transduced


title: 20250415_AMT001_hMSC_EV_IgG

description: Library name: Sample 173


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-E5


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-E18


title: 20200616_KWR039_MSC_+HA-MYOD1_rep1

description: Library name: Sample 222


title: ILA_3

data_processing:
Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly
Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).
Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.
After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).
To identify DEGs (differential expression genes) between two different samples/groups, the  expression level of each gene was calculated according to the transcripts per million reads (TPM)  method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  [4] was used to quantify gene abundances.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: SW480 cell

growth_protocol: SW480 cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the tissue using Trizol reagent according to the manufacturer’s instructions (Invitrogen), and genomic DNA was removed using DNase I (TaKara).
Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) performed RNA purification, reverse transcription, library construction and sequencing according to the manufacturer’s instructions (Illumina, San Diego, CA).

treatment_protocol: RNA-seq analysis of SW480 cells treated with PBS or LPS (6 μg/ml) in addition with DMSO or ILA (200 μM) for 6 h.

value: SW480 cell

value: ILA+LPS


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-F6

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: neg1

value: Intestinal epithelial cells


title: Decidua, A03, first trimester, replicate 3

city: Hangzhou

first: Hongliang

last: Xie

state: Zhejiang Province

address: 浙江省杭州市西湖区紫金港校区药学院

institute: Zhejiang University

description:
Library name: A03
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw base call (BCL) files were processed using Cell Ranger v7.1.0 (10x Genomics) with default parameters to perform demultiplexing, barcode assignment, and alignment to the human reference genome GRCh38. Cell quality control was performed by filtering out cells with fewer than 200 detected genes or greater than 20% mitochondrial gene content. Doublets were identified and removed using DoubletFinder v2.0.3 in R. Gene expression data were normalized using the SCTransform method, and batch correction was performed using Harmony v0.1.1. Downstream clustering, dimensionality reduction, differential expression analysis, and cell-type annotation were conducted using Seurat v4.3.0. Genes with |log2 fold change| > 0.25 and adjusted p-value < 0.05 (Wilcoxon rank-sum test) were considered differentially expressed. Functional enrichment analysis was performed using clusterProfiler v4.8.1. Cell trajectory analysis was performed using Monocle2, and cell-cell communication networks were inferred using CellChat v1.6.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Decidua

extract_protocol:
Human decidual tissues from first-trimester elective surgical terminations were collected and immediately processed. Tissues were enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec, 130-095-929) and the gentleMACS™ Octo Dissociator (Miltenyi Biotec, 130-096-427) following the manufacturer's instructions. The resulting cell suspension was filtered through a 70 μm cell strainer (Miltenyi Biotec, 130-101-262), followed by red blood cell lysis using RBC Lysis Buffer (Miltenyi Biotec, 130-094-183). Dead cells were removed and cell viability was assessed using trypan blue exclusion. Samples with cell viability above 85% were used for single-cell library preparation.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, 1000121) according to the manufacturer’s protocol. Briefly, viable single-cell suspensions were loaded onto the Chromium Controller to generate Gel Bead-in-Emulsions (GEMs), enabling barcoding of individual cells. Reverse transcription was performed within droplets, followed by cDNA amplification and library preparation steps including fragmentation, end repair, A-tailing, adaptor ligation, and sample indexing. The final libraries were quantified, pooled, and subjected to paired-end sequencing.

value: Decidua

tag: group

value: AMA group (35-49 years)

value: mixed decidual cell populations

value: wild type


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-F5


title: 20250415_AMT008_hMSC_SMARCD2-SWIFT_SMARCA4

description: Library name: Sample 178

value: hMSC

value: SMARCA4 (CST, 49360S)


title: 20200616_KWR038_MSC_+HA-FOS_rep2

description: Library name: Sample 221

value: HA-FOS transduced


title: pos1

value: WT

value: LPS+BHI stimulus


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-D6

value: 9 months


title: ILA_2


title: neg3

value: BHI stimulus


title: ILA_1


title: Decidua, A01, first trimester, replicate 1

address: 浙江省杭州市西湖区紫金港校区药学院

description:
Library name: A01
10x Genomics


title: 20200616_KWR036_MSC_+HA-FOXA1_rep2

description: Library name: Sample 219

value: HA-FOXA1 transduced


title: Decidua, C02, first trimester, replicate 2

address: 浙江省杭州市西湖区紫金港校区药学院

description:
Library name: C02
10x Genomics

value: control (CTR) group of women of optimal reproductive age (22-30 years)


title: LPS_2

value: LPS


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-D17

value: FC

value: M


title: 20200616_KWR037_MSC_+HA-FOS_rep1

description: Library name: Sample 220


title: 20200616_KWR035_MSC_+HA-FOXA1_rep1

description: Library name: Sample 218


title: LPS_3

value: SW480 cell

value: Intestinal epithelial cells


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-D5


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-D18


title: 20200616_KWR034_MSC_+HA-POU5F1_rep2

description: Library name: Sample 217

value: HA-POU5F1 transduced


title: LPS_1


title: Decidua, C01, first trimester, replicate 1

address: 浙江省杭州市西湖区紫金港校区药学院

description:
Library name: C01
10x Genomics

value: Decidua

value: mixed decidual cell populations


title: Decidua, C03, first trimester, replicate 3

address: 浙江省杭州市西湖区紫金港校区药学院

description:
Library name: C03
10x Genomics

value: wild type


title: 20200616_KWR033_MSC_+HA-POU5F1_rep1

description: Library name: Sample 216

value: hMSC


title: Decidua, A02, first trimester, replicate 2

address: 浙江省杭州市西湖区紫金港校区药学院

description:
Library name: A02
10x Genomics

value: AMA group (35-49 years)


title: DMSO_4

value: WT

value: DMSO


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-E17

value: 9 months


title: T24 cell,si-KNSTRN,2

city: nanchang

first: Yaoyi

last: Xiong

state: jiangxi

address: No. 17 Yongwai Zhengjie, Donghu District, Nanchang City, Jiangxi Province, China

institute: Nanchang University

description:
Library name: Sample 5
Column name in All_sample_counts.txt:S2

data_processing:
For raw data, use fastqc software (version: 0.11.5) for quality control processing.
Use the software fastp(version 0.20.0) with the parameters: –adapter_sequence R1_adpter –adapter_sequence_r2 R2_adpter.
For filtering data, use the software fastqc (version: 0.11.5) for quality control processing.
Align the clean reads data to the reference genome using the hisat2 software (version: 2.0.1-beta).
After obtaining valid reads, we used the featureCounts software (version: v1.6.0) to count the number of reads falling on genes based on the genome annotation file.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bladder

growth_protocol: T24 cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, and incubated at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA of cell was isolated with RNA extract (Servicebio, Wuhan, China) ,1.3ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: T24 cells were inoculated into 6 cm dishes and cultured for 24 hours until the cells were fully adherent to the wall, then treated with si-NC or si-KNSTRN for 24 h.

value: bladder

value: tumor epithelial cells

value: KNSTRN knockdown


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-C6


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-C5


title: DMSO_2


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-C18


title: 20190523_KWR031_MSC_+HA-RUNX1_rep1

description: Library name: Sample 214

value: HA-RUNX1 transduced


title: T24 cell,si-KNSTRN,1

description:
Library name: Sample 4
Column name in All_sample_counts.txt:S1


title: DMSO_1


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-B6

value: FC


title: T24 cell,si-NC,2

description:
Library name: Sample 2
Column name in All_sample_counts.txt:N2

value: NC knockdown


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-B5

value: M


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-C17


title: 20190523_KWR029_MSC_+HA-NANOG_rep1

description: Library name: Sample 212

value: HA-NANOG transduced


title: 20190523_KWR030_MSC_+HA-NANOG_rep2

description: Library name: Sample 213


title: T24 cell,si-NC,3

description:
Library name: Sample 3
Column name in All_sample_counts.txt:N3


title: Human OFs derived from patient 3(C), with nimodipine pretreatment and without TGF-β [C_CCB]

first: Qian

last: Chen

state: Guangdong Province

address: No. 54 Xianlie South Rd

department: Zhongshan Ophthalmic Center

institute: Zhongshan Ophthalmic Center

description:
counts_anno
CCB-vs-blank-all.gene

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Orbital fibroblasts (OFs)

growth_protocol: Human orbital fibroblasts (OFs) were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
The total RNA was isolated from cultured cells using a RNeasy Mini Kit (QIAGEN, Valencia, CA)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Fibrotic phenotype switching of human orbital fibroblasts was induced by co-cultured with TGF-β for 24 hours, with or without nimodipine pretreatment

value: Orbital fibroblasts (OFs)


title: Human OFs derived from patient 3(C), with nimodipine pretreatment and co-cultured with TGF-β for 24 hours [C_treatment]

description:
counts_anno
treatment-vs-model-all.gene


title: Intestinal-organoids, J4Fut2-KI line, 5 day differentiated, media treated, 24h

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description: Library name: J4Fut2KI_media_INT_24h

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Raw count and Differentially expressed gene list

growth_protocol: HIOs were grown as multilobular 3-dimensional (3D) HIOs in Matrigel and maintained in L-WRN complete media. For HuNoV infection, the 3D HIOs were dissociated by trypsinization and pipetting and seeded onto collagen IV coated 96-well plates using a 1:1 ratio of IntestiCult™ Organoid Growth Medium Human Basal Medium (StemCell Technologies, 100-0190) and Organoid Supplement (StemCell Technologies, 100-0191) (referred to as OGM proliferation medium) supplemented with 10 µM ROCK inhibitor Y-27632 for 24 hours. The HIEs were then differentiated for 5 days using a 1:1 ratio of Intesticult™ OGM Human Basal Medium and complete medium without growth factors (CMGF (-) medium, advanced DMEM/F12 prepared with 1X GlutaMAX and 10 mM HEPES) with media changes every two days prior to inoculation with HuNoV.

extract_protocol:
Total cellular RNAs were extracted from intestinal organoids (HIOs) using RNeasy Mini Kit (Qiagen) according to the manufacture's instructions.
Libraries were amplified for 13 PCR cycles in 50 μl reactions containing 150 pmol of P1.1 (5'-AAT GAT ACG GCG ACC ACC GAGA) and P3 (5’-CAA GCA GAA GAC GGC ATA CGA GA) primers and Kapa HiFi Hot Start Library Amplification kit (Cat# KK2612, Roche Sequencing and Life Science). A set of 96 unique dual-index barcodes (Illumina TruSeq UD Indexes, # 20022370) were used for sample barcoding. Libraries were purified with Agencourt AMPure XP beads (Beckman Coulter, Cat # A63882) after each enzymatic reaction and PCR amplification, and were quantified using the Fragment Analyzer (Agilent Technologies, Inc.) electrophoresis system.

treatment_protocol: Five-day differentiated HIE monolayers were washed once with CMGF (−) medium and inoculated with gamma irradiated (g) GII.3 HuNoV, live GII.3 HuNoV or media in OGM differentiation medium containing 500 μM bile acid glycochenodeoxycholic acid (GCDCA) for 1–2 h at 37°C. The inoculum was removed, and monolayers were washed twice with CMGF (−) medium to remove unbound virus. OGM differentiation medium (100 μL containing 500 μM GCDCA) was then added, and the cultures were incubated at 37°C for 24hours.

tag: culture status

value: differentiated

value: media

tag: media

value: Intesticult™ OGM, 500 µM GCDCA

value: 24 hour


title: 20190523_KWR027_MSC_+HA-JUN_rep1

city: Boston

description: Library name: Sample 210

value: hMSC

value: HA-JUN transduced


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-B18

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute


title: 20190523_KWR028_MSC_+HA-JUN_rep2

description: Library name: Sample 211


title: 20190523_KWR024_MSC_+HA-HOXA9_rep2

description: Library name: Sample 209

value: HA-HOXA9 transduced


title: Intestinal-organoids, J4Fut2-KI line, 5 day differentiated, GII.3 treated, 24h

description: Library name: J4Fut2KI_GII3_INT_24h


title: Human OFs derived from patient 1(A) with nimodipine pretreatment and co-cultured with TGF-β for 24 hours [A_treatment]

description:
counts_anno
treatment-vs-model-all.gene

value: WT


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-A6

value: 9 months


title: T24 cell,si-KNSTRN,3

description:
Library name: Sample 6
Column name in All_sample_counts.txt:S3

tag: tissue

value: bladder

value: tumor epithelial cells


title: Human OFs derived from patient 3(C), co-cultured with TGF-β for 24 hours and without nimodipine pretreatment [C_model]

description:
counts_anno
model-vs-blank-all.gene
model-vs-blank-diff-q-val-0.05-FC-2.gene

tag: genotype


title: Human OFs derived from patient 2(B), with nimodipine pretreatment and co-cultured with TGF-β for 24 hours [B_treatment]

description:
counts_anno
treatment-vs-model-all.gene

tag: treatment


title: 20190523_KWR032_MSC_+HA-RUNX1_rep2

description: Library name: Sample 215

value: HA-RUNX1 transduced


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-B17

value: FC


title: Intestinal-organoids, J4Fut2-KI line, 5 daydifferentiated, gGII.3 treated, 24h

description: Library name: J4Fut2KI_gGII3_INT_24h


title: 20190523_KWR023_MSC_+HA-HOXA9_rep1

description: Library name: Sample 208


title: 20190523_KWR022_MSC_+HA-GATA3_rep2

description: Library name: Sample 207

value: HA-GATA3 transduced


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-A5

value: M


title: Human OFs derived from patient 1(A), with nimodipine pretreatment and without TGF-β [A_CCB]

description:
counts_anno
CCB-vs-blank-all.gene


title: Intestinal-organoids, J4 line, 5 day differentiated, media treated, 24h

description: Library name: J4_media_INT_24h


title: T24 cell,si-NC,1

description:
Library name: Sample 1
Column name in All_sample_counts.txt:N1

value: NC knockdown


title: Intestinal-organoids, J4 line, 5 day differentiated, GII.3 treated, 24h

description: Library name: J4_GII3_INT_24h


title: 20190523_KWR021_MSC_+HA-GATA3_rep1

description: Library name: Sample 206


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-A17