title: ZD034_KIRneg

description: Library name: ZD034_KIRneg

data_processing:
Fasta sequence files were analysed for quality using FastQC v0.11.9. Remaining adaptor sequences and low-quality sequence fragments were removed using fastp v0.20.1 with the parameters –length_required 25, –cut_tail, –cut_tail_window_size 4, –cut_tail_mean_quality 20, –disable_quality_filtering. Filtered reads were aligned to the human hg38 genome using STAR v2.7.5a without gene annotation GTF file, with the parameters –alignIntronMax 1, –alignEndsType Extend5pOfReads12 –alignMatesGapMax 2000, –outFilterMatchNminOverLread 0.50, –outFilterScoreMinOverLread 0.50, and filtering for properly paired mates with a mapq score of 40 or above and duplicates were marked using Picard.
deepTools AlignmentSieve with parameter –ATACshift was used to adjust sequencing pairs by +5 and −4 base pairs to account for the 9 bp shift introduced at Tn5 insert sites. Genome-wide sequencing coverage was calculated using deepTools v3.5.0 bamCoverage function using the --offset 1 option to consider only the transposase insertion sites, normalized by counts per million (CPM) in each sample, and saved as bigWig (bw) files
Assembly: hg38
Supplementary files format and content: ATAC-seq signal as density of read 5' ends (transposase insertion sites) in bigWig format

extract_protocol:
Libraries were prepared from 50,000 cells.
The OMNI-ATAC protocol of Corces et al. was followed (PMID 28846090)


title: ZD038_KIRneg

status: Public on Mar 24 2026

type: SRA

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

description: Library name: ZD038_KIRneg

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Gamma-delta T cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using Hypaque density gradient centrifugation and cryopreserved in FBS with 10% DMSO. After thawing, cells were rested overnight in RPMI supplemented with 10% FBS. Total γδ T cells were purified by negative magnetic selection, and KIR⁻ and KIR⁺ subsets were subsequently sorted by flow cytometry.

treatment_protocol: Cells were not treated.

tag: cell type

value: Gamma-delta T cells

tag: donor id

tag: kir status

value: KIRneg


title: ZD034_KIRpos

description: Library name: ZD034_KIRpos

value: KIRpos


title: ZD038_KIRpos

description: Library name: ZD038_KIRpos


title: ZD022_KIRneg

description: Library name: ZD022_KIRneg


title: ZD021_KIRneg

description: Library name: ZD021_KIRneg


title: ZD022_KIRpos

description: Library name: ZD022_KIRpos


title: ZD026_KIRneg

description: Library name: ZD026_KIRneg

library_source: transcriptomic

data_processing:
Raw reads processed using fastp v0.20.1 to remove low quality sections and trim adapter sequences
Trimmed reads aligned to the hg38 genome using STAR v.2.7.8a, retaining reads aligning uniquely on the genome
Aligned reads counted for overlap with exons and summarized to genes using Subread featureCounts v2.0.1 with -s2 option for reverse-stranded library and using ENSEMBL Homo_sapiens.GRCh38.104 GTF file
Assembly: hg38
Supplementary files format and content: Individual tab-delimited text files produced by Subread featureCounts giving the number of reads aligning to exons, and summarized over genes

molecule: total RNA

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen)
NEBNext Ultra II Directional RNA-Poly(A) Library Prep


title: ZD008_KIRpos

description: Library name: ZD008_KIRpos


title: ZD030_KIRneg

description: Library name: ZD030_KIRneg


title: ZD026_KIRneg

description: Library name: ZD026_KIRneg


title: SU-DIPGXVII_FB232_RNAseq_Rep3

city: Sydney

first: Samuel

middle: Ernest

last: Ross

state: NSW

address: The University of Sydney

country: Australia

institute: The University of Sydney

data_processing:
RNA-seq reads were trimmed using Trimmomatic  and aligned to the GRCh38 genome using STAR. Quantification of transcript and gene abundance was then performed using RSEM.
Direct RNA-seq libraries were mapped to the GRCh38 Ensembl annotations release version 91  using minimap2 (-ax map-ont -uf  --secondary=no). m6A site probabilities were calculated using nanopolish and m6anet (--num_iterations 1000)
Assembly: hg38
Supplementary files format and content: tab-delimited text files provide TPM counts for RNAseq experiments
Supplementary files format and content: csv files provide m6A site scores from m6Anet for direct-RNAseq experiments

molecule: polyA RNA

source_name: SU-DIPGXVII

extract_protocol:
total RNA was extracted using the ISOLATE II RNA Mini Kit from Bioline
cDNA libraries were prepared at the Ramaciotti Centre for Genomics using the Illumina Stranded mRNA prep kit. Direct RNA-seq libraries were prepared by the Garvan Sequencing Platform using the SQK-RNA002 kit and sequences on PromethION using FLO-PRO002 flow cells
RNA-seq and directRNA-seq

tag: cell line

value: SU-DIPGXVII

value: H3K27 altered DMG

tag: treatment


title: SU-DIPGXVII_FB232_RNAseq_Rep1


title: ZD026_KIRpos

description: Library name: ZD026_KIRpos


title: ZD030_KIRpos

description: Library name: ZD030_KIRpos


title: ZD008_KIRneg

description: Library name: ZD008_KIRneg


title: ZD030_KIRneg

description: Library name: ZD030_KIRneg


title: ZD021_KIRpos

description: Library name: ZD021_KIRpos


title: SU-DIPGXVII_DMSO_RNAseq_Rep3

value: DMSO


title: Kidney, DKD class III, rep2

type: RNA

city: Calgary

first: Justin

last: Chun

state: Alberta

address: 3330 Hospital Drive NW

institute: University of Calgary

description:
Run5830_Slide2A-polygons.csv
Run5830_Slide2A_exprMat_file.csv
Run5830_Slide2A_fov_positions_file.csv
Run5830_Slide2A_metadata_file.csv
Run5830_Slide2A_tx_file.csv
CellComposite_slide2A.tar
CellLabels_slide2A.tar
CellOverlay_slide2A.tar
CompartmentLabels_slide2A.tar
RawMorphologyImages_slide2A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide2A file package. Slide2A FOVs 2-10 correspond to this sample

hyb_protocol: NanoString CosMx spatial transcriptomics slides were prepared with NanoString 1000-plex human RNA probe assay according to manufacturer protocols.

scan_protocol: Spatial probe hybridization was measured on the NanoString CosMx Spatial Molecular Imager.

data_processing:
Raw data files were assembled including cell segmentation assembled by NanoString AtoMx software.
Cells having fewer than 20 total transcripts counts were excluded from downstream analyses.

source_name: kidney biopsy, DKD class III

extract_protocol: Paraffin embedded kidney biopsies from control and patients with diabetic kidney diseases were obtained from the Biobank for the Molecular Classification of Kidney Disease, Calgary, AB, Canada. Tissue was sectioned at 5 µm thickness with a microtome.

tag: tissue

value: Kidney cortex

tag: disease state

value: Class III


title: SU-DIPGXVII_FB232_RNAseq_Rep2


title: SU-DIPGXVII_DMSO_RNAseq_Rep1


title: SU-DIPGXVII_DMSO_RNAseq_Rep2


title: ZNF281_ChIP_Tumor_Parental_3

city: Edmonton

first: Maria Areli

last: Lorenzana Carillo

institute: University of Alberta

description: Library name: Tum_9

data_processing:
Raw sequencing reads were quality-checked, trimmed, and aligned to mm10 (mouse) or hg38 (human) reference genomes using STAR (RNA-seq) or Bowtie2 (ChIP-seq). Gene counts were generated using HTSeq-count, followed by TMM normalization and differential expression analysis using limma–voom. ChIP-seq peaks were identified using MACS2 and annotated using BEDtools. Analyses were performed using the Galaxy platform.
Assembly: mm10 (Mus musculus) and hg38 (Homo sapiens)
Supplementary files format and content: Processed RNA-seq data include raw gene count matrices generated using HTSeq-count and normalized expression values (log2 CPM) for A549 human cells and mouse cardiomyocytes analyzed as separate experimental systems. Differential expression results are also provided. ChIP-seq data include peak files in BED format and peak annotation files mapping peaks to the nearest transcription start site.

source_name: A549 Cells

growth_protocol: A549 human lung carcinoma cells were maintained under standard culture conditions. Primary mouse cardiomyocytes were isolated and cultured as described in the Methods section.

extract_protocol:
Total RNA was isolated using QIAzol reagent according to the manufacturer’s instructions.
RNA-seq libraries were prepared using standard library preparation protocols. ChIP-seq libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations.

treatment_protocol: A549 cells were genetically modified to generate ZNF281 knockout (KO) cells alongside parental controls. Mouse cardiomyocytes were genetically modified to induce ZNF281 overexpression (OE) and compared with control cells.

value: A549 Cells

value: Parental


title: Early OA 1

status: Public on Mar 25 2026

city: Chandigarh

first: Jyotdeep

last: Kaur

state: Chandigarh

address: PGIMER, Sector 12

department: Department of Biochemistry

country: India

institute: Postgraduate Institute of Medical Education and Research (PGIMER)

description: miRNA expression

hyb_protocol: Labelled miRNAs were then hybridized using a Microarray Hybridization Chamber Kit. Blocking agents and hybridization samples were prepared following kit protocol.The hybridization chamber was assembled and loaded into the oven rotator rack set at 20 rpm.Samples were hybridized at 55°C for 20-24 h.

scan_protocol: Following hybridization, arr×ays were washed using wash buffers containing 0.005% Triton X-102 (10%) at 37°C for 5 min and scanned on a SureScan microarray scanner using 1 color scan setting for 8×60k platform

data_processing: Data was extracted using Agilent Feature Extraction software using default parameters and was analyzed using Genespring GX software.

source_name: KL-grade II Early OA patient 1

label_protocol: 100ng of total RNA was used. Fluorescently-labeled miRNAs were generated with a miRNA complete labeling and hybridization kit( Agilent p/n 5190-04-56) following the manufacturer's instructions.Thus Cyanine 3-pCp molecules were ligated to the 3'end of RNA molecule

extract_protocol: For cellular miRNA isolation, the synovial fluid cell pellet was immediately processed for RNA isolation using RNeasy cells/tissue kit, Qiagen Inc.,USA following the manufacturer’s protocol.

treatment_protocol: Synovial fluid was aseptically aspirated from the affected knee of subjects. Samples were collected in sterile vial on ice. To reduce viscosity of the synovial fluids, samples were diluted with nuclease free water (1:1 dilution) and were centrifuged at 10,000 g for 15 minutes.

value: KL-grade II Early OA

tag: age

tag: gender

value: F


title: ZNF281_ChIP_Tumor_Parental_1

description: Library name: Tum_7


title: RNA_A549_ZNF281 KO_1

description: Library name: Tum_2


title: ZNF281_ChIP_Tumor_Parental_2

description: Library name: Tum_8


title: RNA_A549_ZNF281 KO_2

description: Library name: Tum_3


title: RNA_A549_Parental_1

description: Library name: Tum_1


title: Blood, Control, S141

city: Madrid

first: Ana I

last: Fernandez-Avila

state: Madrid

address: C/ Doctor Esquerdo, 46

department: Cardiology

country: Spain

institute: Hospital GU Gregorio Marañon

description:
Library name: Control7
Column name in mature_counts-allSamples.csv: Control7

data_processing:
FASTQ files from sequencing were filtered, aligned to the reference genome (hg38) and mature microRNAs quantified with  miRDeep2
Assembly: The genome assembly was done on hg38
Supplementary files format and content: tab-delimited text includes samples, counts and miRNA
Supplementary files format and content: The file is a csv with counts, sample -columns, gene -rows

source_name: whole blood

growth_protocol: Whole blood in TempusTube, Frozen -80C

extract_protocol:
Tempus blood RNA isolation kit
Libraries for small RNA sequencing were constructed using the TruSeq Small RNA Library Prep Kit, following kit guide in MACROGEN company

value: whole blood

tag: Sex

value: Female

value: Control

tag: batch


title: Blood, Control, S140

description:
Library name: Control6
Column name in mature_counts-allSamples.csv: Control6


title: Blood, Control, S139

description:
Library name: Control5
Column name in mature_counts-allSamples.csv: Control5


title: Blood, Control, S138

description:
Library name: Control4
Column name in mature_counts-allSamples.csv: Control4

value: Male


title: Blood, Control, S137

description:
Library name: Control32
Column name in mature_counts-allSamples.csv: Control32


title: Blood, Control, S132

description:
Library name: Control28
Column name in mature_counts-allSamples.csv: Control28


title: Blood, Control, S135

description:
Library name: Control30
Column name in mature_counts-allSamples.csv: Control30


title: Blood, Control, S133

description:
Library name: Control29
Column name in mature_counts-allSamples.csv: Control29


title: Blood, Control, S136

description:
Library name: Control31
Column name in mature_counts-allSamples.csv: Control31


title: Blood, Control, S134

description:
Library name: Control3
Column name in mature_counts-allSamples.csv: Control3


title: Blood, Control, S129

description:
Library name: Control25
Column name in mature_counts-allSamples.csv: Control25


title: Blood, Control, S131

description:
Library name: Control27
Column name in mature_counts-allSamples.csv: Control27


title: Blood, Control, S142

description:
Library name: Control9
Column name in mature_counts-allSamples.csv: Control9


title: Blood, Control, S130

description:
Library name: Control26
Column name in mature_counts-allSamples.csv: Control26


title: Blood, Control, S127

description:
Library name: Control23
Column name in mature_counts-allSamples.csv: Control23


title: Blood, Control, S128

description:
Library name: Control24
Column name in mature_counts-allSamples.csv: Control24


title: Blood, Control, S126

description:
Library name: Control21
Column name in mature_counts-allSamples.csv: Control21


title: Blood, Control, S125

description:
Library name: Control20
Column name in mature_counts-allSamples.csv: Control20


title: Blood, Control, S122

description:
Library name: Control18
Column name in mature_counts-allSamples.csv: Control18


title: Blood, Control, S121

description:
Library name: Control17
Column name in mature_counts-allSamples.csv: Control17


title: Blood, Control, S118

description:
Library name: Control14
Column name in mature_counts-allSamples.csv: Control14


title: Blood, Control, S123

description:
Library name: Control19
Column name in mature_counts-allSamples.csv: Control19


title: Blood, Control, S117

description:
Library name: Control13
Column name in mature_counts-allSamples.csv: Control13


title: Blood, Control, S124

description:
Library name: Control2
Column name in mature_counts-allSamples.csv: Control2


title: Blood, Control, S115

description:
Library name: Control11
Column name in mature_counts-allSamples.csv: Control11


title: Blood, Control, S119

description:
Library name: Control15
Column name in mature_counts-allSamples.csv: Control15


title: Blood, Control, S114

description:
Library name: Control10
Column name in mature_counts-allSamples.csv: Control10


title: Blood, Control, S112

description:
Library name: 8A-454
Column name in mature_counts-allSamples.csv: 8A-454

value: HTP


title: Blood, Control, S120

description:
Library name: Control16
Column name in mature_counts-allSamples.csv: Control16


title: Blood, HTP_II, S107

description:
Library name: 8A-003
Column name in mature_counts-allSamples.csv: 8A-003


title: Blood, HTP_II, S109

description:
Library name: 8A-007
Column name in mature_counts-allSamples.csv: 8A-007


title: Blood, HTP_II, S108

description:
Library name: 8A-004
Column name in mature_counts-allSamples.csv: 8A-004


title: Blood, HTP_II, S111

description:
Library name: 8A-010
Column name in mature_counts-allSamples.csv: 8A-010


title: Blood, HTP_II, S104

description:
Library name: 7A-009
Column name in mature_counts-allSamples.csv: 7A-009


title: Blood, HTP_II, S102

description:
Library name: 7A-007
Column name in mature_counts-allSamples.csv: 7A-007


title: Blood, Control, S116

description:
Library name: Control12
Column name in mature_counts-allSamples.csv: Control12


title: Blood, HTP_II, S103

description:
Library name: 7A-008
Column name in mature_counts-allSamples.csv: 7A-008


title: Blood, HTP_II, S100

description:
Library name: 7A-005
Column name in mature_counts-allSamples.csv: 7A-005


title: Blood, HTP_II, S96

description:
Library name: 5A-013
Column name in mature_counts-allSamples.csv: 5A-013


title: Blood, HTP_II, S110

description:
Library name: 8A-008
Column name in mature_counts-allSamples.csv: 8A-008


title: Blood, HTP_II, S98

description:
Library name: 5A-015
Column name in mature_counts-allSamples.csv: 5A-015


title: Blood, Control, S113

description:
Library name: Control1
Column name in mature_counts-allSamples.csv: Control1


title: Blood, HTP_II, S105

description:
Library name: 8A-001
Column name in mature_counts-allSamples.csv: 8A-001


title: Blood, HTP_II, S106

description:
Library name: 8A-002
Column name in mature_counts-allSamples.csv: 8A-002


title: Blood, HTP_II, S101

description:
Library name: 7A-006
Column name in mature_counts-allSamples.csv: 7A-006


title: Blood, HTP_II, S91

description:
Library name: 5A-008
Column name in mature_counts-allSamples.csv: 5A-008


title: Blood, HTP_II, S93

description:
Library name: 5A-010
Column name in mature_counts-allSamples.csv: 5A-010


title: Blood, HTP_II, S94

description:
Library name: 5A-011
Column name in mature_counts-allSamples.csv: 5A-011


title: Blood, HTP_II, S92

description:
Library name: 5A-009
Column name in mature_counts-allSamples.csv: 5A-009


title: Blood, HTP_II, S87

description:
Library name: 1A-100
Column name in mature_counts-allSamples.csv: 1A-100


title: Blood, HTP_II, S95

description:
Library name: 5A-012c
Column name in mature_counts-allSamples.csv: 5A-012c


title: Blood, HTP_II, S85

description:
Library name: 1A-098
Column name in mature_counts-allSamples.csv: 1A-098


title: Blood, HTP_II, S99

description:
Library name: 7A-002
Column name in mature_counts-allSamples.csv: 7A-002


title: Blood, HTP_II, S86

description:
Library name: 1A-099
Column name in mature_counts-allSamples.csv: 1A-099


title: Blood, HTP_II, S97

description:
Library name: 5A-014
Column name in mature_counts-allSamples.csv: 5A-014


title: Blood, HTP_II, S84

description:
Library name: 1A-097
Column name in mature_counts-allSamples.csv: 1A-097


title: Blood, HTP_II, S88

description:
Library name: 1A-101
Column name in mature_counts-allSamples.csv: 1A-101


title: Blood, HTP_II, S83

description:
Library name: 1A-096
Column name in mature_counts-allSamples.csv: 1A-096


title: Blood, HTP_II, S90

description:
Library name: 1A-103
Column name in mature_counts-allSamples.csv: 1A-103


title: Blood, HTP_II, S80

description:
Library name: 1A-093
Column name in mature_counts-allSamples.csv: 1A-093


title: Blood, HTP_II, S82

description:
Library name: 1A-095
Column name in mature_counts-allSamples.csv: 1A-095


title: Blood, HTP_II, S89

description:
Library name: 1A-102
Column name in mature_counts-allSamples.csv: 1A-102


title: Blood, HTP_II, S81

description:
Library name: 1A-094
Column name in mature_counts-allSamples.csv: 1A-094


title: Blood, HTP_II, S75

description:
Library name: 1A-087
Column name in mature_counts-allSamples.csv: 1A-087


title: Blood, HTP_II, S77

description:
Library name: 1A-090
Column name in mature_counts-allSamples.csv: 1A-090


title: Blood, HTP_II, S76

description:
Library name: 1A-088
Column name in mature_counts-allSamples.csv: 1A-088


title: Blood, HTP_II, S78

description:
Library name: 1A-091
Column name in mature_counts-allSamples.csv: 1A-091


title: Blood, HTP_II, S71

description:
Library name: 1A-083
Column name in mature_counts-allSamples.csv: 1A-083


title: Blood, HTP_II, S79

description:
Library name: 1A-092
Column name in mature_counts-allSamples.csv: 1A-092


title: Blood, HTP_II, S73

description:
Library name: 1A-085
Column name in mature_counts-allSamples.csv: 1A-085


title: Blood, HTP_II, S69

description:
Library name: 1A-081c
Column name in mature_counts-allSamples.csv: 1A-081c


title: Blood, HTP_II, S70

description:
Library name: 1A-082c
Column name in mature_counts-allSamples.csv: 1A-082c


title: Blood, HTP_II, S67

description:
Library name: 1A-079
Column name in mature_counts-allSamples.csv: 1A-079


title: Blood, HTP_II, S64

description:
Library name: 1A-076
Column name in mature_counts-allSamples.csv: 1A-076


title: Blood, HTP_II, S68

description:
Library name: 1A-080
Column name in mature_counts-allSamples.csv: 1A-080


title: Blood, HTP_II, S72

description:
Library name: 1A-084
Column name in mature_counts-allSamples.csv: 1A-084


title: Blood, HTP_II, S74

description:
Library name: 1A-086
Column name in mature_counts-allSamples.csv: 1A-086


title: Blood, HTP_II, S66

description:
Library name: 1A-078
Column name in mature_counts-allSamples.csv: 1A-078


title: Blood, HTP_II, S61

description:
Library name: 1A-073
Column name in mature_counts-allSamples.csv: 1A-073


title: Blood, HTP_II, S58

description:
Library name: 1A-070
Column name in mature_counts-allSamples.csv: 1A-070


title: Blood, HTP_II, S62

description:
Library name: 1A-074
Column name in mature_counts-allSamples.csv: 1A-074


title: Blood, HTP_II, S60

description:
Library name: 1A-072
Column name in mature_counts-allSamples.csv: 1A-072


title: Blood, HTP_II, S63

description:
Library name: 1A-075
Column name in mature_counts-allSamples.csv: 1A-075


title: Blood, HTP_II, S59

description:
Library name: 1A-071
Column name in mature_counts-allSamples.csv: 1A-071


title: Blood, HTP_II, S56

description:
Library name: 1A-068
Column name in mature_counts-allSamples.csv: 1A-068


title: Blood, HTP_II, S57

description:
Library name: 1A-069
Column name in mature_counts-allSamples.csv: 1A-069


title: Blood, HTP_II, S65

description:
Library name: 1A-077
Column name in mature_counts-allSamples.csv: 1A-077


title: Blood, HTP_II, S55

description:
Library name: 1A-067
Column name in mature_counts-allSamples.csv: 1A-067


title: Blood, HTP_II, S52

description:
Library name: 1A-064
Column name in mature_counts-allSamples.csv: 1A-064


title: Blood, HTP_II, S54

description:
Library name: 1A-066
Column name in mature_counts-allSamples.csv: 1A-066


title: Blood, HTP_II, S53

description:
Library name: 1A-065
Column name in mature_counts-allSamples.csv: 1A-065


title: Blood, HTP_II, S51

description:
Library name: 1A-063
Column name in mature_counts-allSamples.csv: 1A-063


title: Blood, HTP_II, S49

description:
Library name: 1A-061
Column name in mature_counts-allSamples.csv: 1A-061


title: Blood, HTP_II, S47

description:
Library name: 1A-059
Column name in mature_counts-allSamples.csv: 1A-059


title: Blood, HTP_II, S48

description:
Library name: 1A-060
Column name in mature_counts-allSamples.csv: 1A-060


title: Blood, HTP_II, S45

description:
Library name: 1A-057
Column name in mature_counts-allSamples.csv: 1A-057


title: Blood, HTP_II, S50

description:
Library name: 1A-062
Column name in mature_counts-allSamples.csv: 1A-062


title: Blood, HTP_II, S44

description:
Library name: 1A-056
Column name in mature_counts-allSamples.csv: 1A-056


title: Blood, HTP_II, S46

description:
Library name: 1A-058
Column name in mature_counts-allSamples.csv: 1A-058


title: Blood, HTP_II, S39

description:
Library name: 1A-051
Column name in mature_counts-allSamples.csv: 1A-051


title: Blood, HTP_II, S38

description:
Library name: 1A-050
Column name in mature_counts-allSamples.csv: 1A-050


title: Blood, HTP_II, S43

description:
Library name: 1A-055
Column name in mature_counts-allSamples.csv: 1A-055


title: Blood, HTP_II, S40

description:
Library name: 1A-052
Column name in mature_counts-allSamples.csv: 1A-052


title: Blood, HTP_II, S41

description:
Library name: 1A-053
Column name in mature_counts-allSamples.csv: 1A-053


title: Blood, HTP_II, S42

description:
Library name: 1A-054
Column name in mature_counts-allSamples.csv: 1A-054


title: Blood, HTP_II, S37

description:
Library name: 1A-049
Column name in mature_counts-allSamples.csv: 1A-049


title: Blood, HTP_II, S36

description:
Library name: 1A-048
Column name in mature_counts-allSamples.csv: 1A-048


title: Blood, HTP_II, S34

description:
Library name: 1A-046
Column name in mature_counts-allSamples.csv: 1A-046


title: Blood, HTP_II, S35

description:
Library name: 1A-047
Column name in mature_counts-allSamples.csv: 1A-047


title: Blood, HTP_II, S32

description:
Library name: 1A-044
Column name in mature_counts-allSamples.csv: 1A-044


title: Blood, HTP_II, S31

description:
Library name: 1A-043
Column name in mature_counts-allSamples.csv: 1A-043


title: Blood, HTP_II, S30

description:
Library name: 1A-042
Column name in mature_counts-allSamples.csv: 1A-042


title: Blood, HTP_II, S33

description:
Library name: 1A-045
Column name in mature_counts-allSamples.csv: 1A-045


title: Blood, HTP_II, S27

description:
Library name: 1A-039
Column name in mature_counts-allSamples.csv: 1A-039


title: Blood, HTP_II, S25

description:
Library name: 1A-036
Column name in mature_counts-allSamples.csv: 1A-036


title: Blood, HTP_II, S29

description:
Library name: 1A-041
Column name in mature_counts-allSamples.csv: 1A-041


title: Blood, HTP_II, S28

description:
Library name: 1A-040
Column name in mature_counts-allSamples.csv: 1A-040


title: Blood, HTP_II, S26

description:
Library name: 1A-038
Column name in mature_counts-allSamples.csv: 1A-038


title: Blood, HTP_II, S23

description:
Library name: 1A-021
Column name in mature_counts-allSamples.csv: 1A-021


title: Blood, HTP_II, S24

description:
Library name: 1A-031
Column name in mature_counts-allSamples.csv: 1A-031


title: Blood, HTP_II, S22

description:
Library name: 1A-020
Column name in mature_counts-allSamples.csv: 1A-020


title: Blood, HTP_II, S21

description:
Library name: 1A-019
Column name in mature_counts-allSamples.csv: 1A-019


title: Blood, HTP_II, S18

description:
Library name: 1A-016
Column name in mature_counts-allSamples.csv: 1A-016


title: Blood, HTP_II, S19

description:
Library name: 1A-017
Column name in mature_counts-allSamples.csv: 1A-017


title: Blood, HTP_II, S17

description:
Library name: 1A-015
Column name in mature_counts-allSamples.csv: 1A-015


title: Blood, HTP_II, S16

description:
Library name: 1A-013
Column name in mature_counts-allSamples.csv: 1A-013


title: Blood, HTP_II, S15

description:
Library name: 1A-012
Column name in mature_counts-allSamples.csv: 1A-012


title: Blood, HTP_II, S13

description:
Library name: 1A-007
Column name in mature_counts-allSamples.csv: 1A-007


title: Blood, HTP_II, S10

description:
Library name: 1A-003
Column name in mature_counts-allSamples.csv: 1A-003


title: Blood, HTP_II, S11

description:
Library name: 1A-005
Column name in mature_counts-allSamples.csv: 1A-005


title: Blood, HTP_II, S9

description:
Library name: 1A-001
Column name in mature_counts-allSamples.csv: 1A-001


title: Blood, HTP_II, S12

description:
Library name: 1A-006
Column name in mature_counts-allSamples.csv: 1A-006


title: Blood, HTP_II, S14

description:
Library name: 1A-011
Column name in mature_counts-allSamples.csv: 1A-011


title: Blood, HTP_II, S6

description:
Library name: 14A-001
Column name in mature_counts-allSamples.csv: 14A-001


title: Blood, HTP_II, S7

description:
Library name: 19A-001
Column name in mature_counts-allSamples.csv: 19A-001


title: Blood, HTP_II, S4

description:
Library name: 11A-006
Column name in mature_counts-allSamples.csv: 11A-006


title: Blood, HTP_II, S5

description:
Library name: 11A-08R
Column name in mature_counts-allSamples.csv: 11A-08R


title: Blood, HTP_II, S20

description:
Library name: 1A-018
Column name in mature_counts-allSamples.csv: 1A-018


title: Blood, HTP_II, S2

description:
Library name: 10A-012
Column name in mature_counts-allSamples.csv: 10A-012


title: LPC_Drop

city: Guangzhou

first: Yin

middle: Jia

last: Xiang

address: Building B, Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

country: China

institute: Guangzhou Laboratory

description:
Library name: Sample 2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: GRCh38
Supplementary files format and content: gene expression matrices of 10X format

source_name: lung organoids

extract_protocol:
The organoid samples were washed with PBS solution and then resuspended in 0.25% pancreatic enzyme digestion solution at 37 ° C for 5 minutes.    Then digestion was terminated with 10% serum and centrifuged at 500g for 5 min. After removal of the supernatant, the cell particles were re-suspended in a wash buffer (0.04% bovine serum albumin [BSA] in Dulbecco's phosphate buffered saline [DPBS]).   The final cell concentration was adjusted to 1,000 cells/μL (viability≥80%) in all samples by using  Luna Dual Fluorescence Cell Counter
Libraries were prepared with the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10x Genomics) following the manufacturer's protocol. Briefly, single-cell suspensions were loaded into a Chromium Controller to produce Gel Bead-in-Emulsions (GEMs). Following reverse transcription, cDNA amplification, and library construction, sequencing was performed on an Illumina NovaSeq 6000 platform (PE150; Annoroad Gene Technology).

value: lung organoids

tag: genotype

value: LPC differentiation

value: uninfected


title: Blood, HTP_II, S1

description:
Library name: 10A-002
Column name in mature_counts-allSamples.csv: 10A-002


title: oxLDL-NIM-3

city: Hengyang

first: chaochao

last: he

address: 28 West Changsheng Road

institute: University of South China

description:
Library name: oxLDL-NIM-3
Nimbolide group, replicate biosample 3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: macrophage foam cells

extract_protocol:
Total RNA was extracted from cultured CAFs using TRIzol reagent. Subsequently, small RNA fragments (18-30 nt) were enriched and purified via denaturing polyacrylamide gel electrophoresis to isolate high-quality miRNAs for sequencing.
Purified miRNAs were sequentially ligated to 3' and 5' adapters. The ligated products were reverse-transcribed into cDNA and amplified by PCR. The final cDNA library was purified and validated for quality prior to sequencing.

value: macrophage foam cells

value: Nimbolide


title: DRAO_Cuboid

description:
Library name: Sample 3
10x Genomics

value: DRAO differentiation


title: oxLDL-NIM-2

description:
Library name: oxLDL-NIM-2
Nimbolide group, replicate biosample 2


title: AO_Cub

description:
Library name: Sample 4
10x Genomics

value: alveolar differentiation


title: oxLDL-NIM-1

description:
Library name: oxLDL-NIM-1
Nimbolide group, replicate biosample 1


title: LPC_Cub

description:
Library name: Sample 1
10x Genomics


title: Blood, HTP_II, S8

description:
Library name: 19A-003
Column name in mature_counts-allSamples.csv: 19A-003


title: oxLDL-3

description:
Library name: oxLDL-3
control group, replicate biosample 3

value: control


title: oxLDL-2

description:
Library name: oxLDL-2
control group, replicate biosample 2


title: oxLDL-1

description:
Library name: oxLDL-1
control group, replicate biosample 1


title: Melanoma, C-G08

city: ANN ARBOR

first: Ziyin

last: Huang

state: MI

address: 3003 S. STATE STREET

country: USA

institute: University of Michigan

description: Library name: DSP-1001250002574-C-G08

data_processing:
The GeoMx DSP Analysis Pipeline version 2.3.3.10 performed trimming, alignment, and deduplication of UV-cleaved probe barcodes
Assembly: GRCh38
Supplementary files format and content: csv files include TPM for each sample

source_name: Melanoma

extract_protocol:
The TMA underwent staining for CD20 (B cells), CD3 (T cells), and DNA to guide region of interest (ROI) selection. ROIs were drawn to maximize tumor content within each tissue spot on the TMA. Full ROIs were profiled without the use of segmentation to avoid inadequate cell counts.
DSP-derived oligos were dried down and rehydrated in 10 µL nuclease-free water. Libraries were prepared and pooled according to the NanoString GeoMx DSP protocol for Human Whole Transcriptome Atlas (WTA) RNA samples. Final pooled libraries were assessed for quality and quantity using the Agilent TapeStation D1000 assay and Qubit prior to sequencing.

tag: aoi

value: Melanoma

tag: patient

tag: has replicate_(1=yes,_0=no)

tag: replicate (1=yes,_0=no)

tag: included in_analysis_(1=yes,0=no)

tag: lymph node_status_(1=yes,_0=no)

tag: distant metastasis_(1=yes,_0=no)

tag: acral melanoma_(1=yes,_0=no)

tag: vital status

tag: overall survival(years)


title: Blood, HTP_II, S3

description:
Library name: 10A-015
Column name in mature_counts-allSamples.csv: 10A-015

tag: tissue

tag: cell type


title: Melanoma, C-G07

description: Library name: DSP-1001250002574-C-G07


title: Melanoma, C-G05

description: Library name: DSP-1001250002574-C-G05


title: Melanoma, C-G03

description: Library name: DSP-1001250002574-C-G03


title: Melanoma, C-G06

description: Library name: DSP-1001250002574-C-G06


title: Melanoma, C-F09

description: Library name: DSP-1001250002574-C-F09


title: Melanoma, C-F11

description: Library name: DSP-1001250002574-C-F11


title: Melanoma, C-F12

description: Library name: DSP-1001250002574-C-F12


title: Melanoma, C-G02

description: Library name: DSP-1001250002574-C-G02


title: Melanoma, C-F07

description: Library name: DSP-1001250002574-C-F07


title: Melanoma, C-F10

description: Library name: DSP-1001250002574-C-F10


title: Melanoma, C-F04

description: Library name: DSP-1001250002574-C-F04


title: Melanoma, C-F06

description: Library name: DSP-1001250002574-C-F06


title: Melanoma, C-F02

description: Library name: DSP-1001250002574-C-F02


title: Melanoma, C-G04

description: Library name: DSP-1001250002574-C-G04


title: Melanoma, C-F01

description: Library name: DSP-1001250002574-C-F01


title: Melanoma, C-E12

description: Library name: DSP-1001250002574-C-E12


title: Melanoma, C-G01

description: Library name: DSP-1001250002574-C-G01


title: Melanoma, C-E10

description: Library name: DSP-1001250002574-C-E10


title: Melanoma, C-E06

description: Library name: DSP-1001250002574-C-E06


title: Melanoma, C-E05

description: Library name: DSP-1001250002574-C-E05


title: Melanoma, C-E08

description: Library name: DSP-1001250002574-C-E08


title: Melanoma, C-E11

description: Library name: DSP-1001250002574-C-E11


title: Melanoma, C-E07

description: Library name: DSP-1001250002574-C-E07


title: Melanoma, C-E02

description: Library name: DSP-1001250002574-C-E02


title: Melanoma, C-E09

description: Library name: DSP-1001250002574-C-E09


title: Melanoma, C-E04

description: Library name: DSP-1001250002574-C-E04


title: Melanoma, C-E03

description: Library name: DSP-1001250002574-C-E03


title: Melanoma, C-F03

description: Library name: DSP-1001250002574-C-F03


title: Melanoma, C-F05

description: Library name: DSP-1001250002574-C-F05


title: Melanoma, C-E01

description: Library name: DSP-1001250002574-C-E01


title: Melanoma, C-D07

description: Library name: DSP-1001250002574-C-D07


title: Melanoma, C-D09

description: Library name: DSP-1001250002574-C-D09


title: Melanoma, C-D08

description: Library name: DSP-1001250002574-C-D08


title: Melanoma, C-D11

description: Library name: DSP-1001250002574-C-D11


title: Melanoma, C-D06

description: Library name: DSP-1001250002574-C-D06


title: Melanoma, C-D04

description: Library name: DSP-1001250002574-C-D04


title: Melanoma, C-D10

description: Library name: DSP-1001250002574-C-D10


title: Melanoma, C-D12

description: Library name: DSP-1001250002574-C-D12


title: Melanoma, C-D02

description: Library name: DSP-1001250002574-C-D02


title: Melanoma, C-D03

description: Library name: DSP-1001250002574-C-D03


title: Melanoma, C-D01

description: Library name: DSP-1001250002574-C-D01


title: Melanoma, C-F08

description: Library name: DSP-1001250002574-C-F08


title: Melanoma, C-D05

description: Library name: DSP-1001250002574-C-D05


title: Melanoma, C-C02

description: Library name: DSP-1001250002574-C-C02


title: Melanoma, C-C03

description: Library name: DSP-1001250002574-C-C03


title: Melanoma, C-C10

description: Library name: DSP-1001250002574-C-C10


title: Melanoma, C-C06

description: Library name: DSP-1001250002574-C-C06


title: Melanoma, C-B10

description: Library name: DSP-1001250002574-C-B10


title: Melanoma, C-C07

description: Library name: DSP-1001250002574-C-C07


title: Melanoma, C-B08

description: Library name: DSP-1001250002574-C-B08


title: Melanoma, C-C01

description: Library name: DSP-1001250002574-C-C01


title: Melanoma, C-B12

description: Library name: DSP-1001250002574-C-B12


title: Melanoma, C-C08

description: Library name: DSP-1001250002574-C-C08


title: Melanoma, C-C12

description: Library name: DSP-1001250002574-C-C12


title: Melanoma, C-B06

description: Library name: DSP-1001250002574-C-B06


title: Melanoma, C-C11

description: Library name: DSP-1001250002574-C-C11


title: Melanoma, C-C09

description: Library name: DSP-1001250002574-C-C09


title: Melanoma, C-C04

description: Library name: DSP-1001250002574-C-C04


title: Melanoma, C-B09

description: Library name: DSP-1001250002574-C-B09


title: Melanoma, C-B03

description: Library name: DSP-1001250002574-C-B03


title: Melanoma, C-B07

description: Library name: DSP-1001250002574-C-B07


title: Melanoma, C-B05

description: Library name: DSP-1001250002574-C-B05


title: Melanoma, C-B04

description: Library name: DSP-1001250002574-C-B04


title: Melanoma, C-B02

description: Library name: DSP-1001250002574-C-B02


title: Melanoma, C-B01

description: Library name: DSP-1001250002574-C-B01


title: Melanoma, C-C05

description: Library name: DSP-1001250002574-C-C05


title: Melanoma, C-B11

description: Library name: DSP-1001250002574-C-B11


title: Melanoma, C-A10

description: Library name: DSP-1001250002574-C-A10


title: Melanoma, C-A11

description: Library name: DSP-1001250002574-C-A11


title: Melanoma, C-A12

description: Library name: DSP-1001250002574-C-A12


title: Melanoma, C-A09

description: Library name: DSP-1001250002574-C-A09


title: Melanoma, C-A07

description: Library name: DSP-1001250002574-C-A07


title: Melanoma, C-A06

description: Library name: DSP-1001250002574-C-A06


title: Melanoma, C-A08

description: Library name: DSP-1001250002574-C-A08


title: Melanoma, C-A05

description: Library name: DSP-1001250002574-C-A05


title: Melanoma, C-A03

description: Library name: DSP-1001250002574-C-A03


title: Melanoma, C-A01

description: Library name: DSP-1001250002574-C-A01


title: Melanoma, C-A02

description: Library name: DSP-1001250002574-C-A02


title: Melanoma, B-H10

description: Library name: DSP-1001250002573-B-H10


title: Melanoma, B-H12

description: Library name: DSP-1001250002573-B-H12


title: Melanoma, B-H09

description: Library name: DSP-1001250002573-B-H09


title: Melanoma, B-H07

description: Library name: DSP-1001250002573-B-H07


title: Melanoma, B-H08

description: Library name: DSP-1001250002573-B-H08


title: Melanoma, B-H04

description: Library name: DSP-1001250002573-B-H04


title: Melanoma, B-H05

description: Library name: DSP-1001250002573-B-H05


title: Melanoma, B-H06

description: Library name: DSP-1001250002573-B-H06


title: Melanoma, B-H02

description: Library name: DSP-1001250002573-B-H02


title: Melanoma, B-H11

description: Library name: DSP-1001250002573-B-H11


title: Melanoma, B-H03

description: Library name: DSP-1001250002573-B-H03


title: Melanoma, C-A04

description: Library name: DSP-1001250002574-C-A04


title: Melanoma, B-G12

description: Library name: DSP-1001250002573-B-G12


title: Melanoma, B-H01

description: Library name: DSP-1001250002573-B-H01


title: Melanoma, B-G09

description: Library name: DSP-1001250002573-B-G09


title: Melanoma, B-G08

description: Library name: DSP-1001250002573-B-G08


title: Melanoma, B-G11

description: Library name: DSP-1001250002573-B-G11


title: Melanoma, B-G10

description: Library name: DSP-1001250002573-B-G10


title: Melanoma, B-G07

description: Library name: DSP-1001250002573-B-G07


title: Melanoma, B-G05

description: Library name: DSP-1001250002573-B-G05


title: Melanoma, B-G06

description: Library name: DSP-1001250002573-B-G06


title: Melanoma, B-G03

description: Library name: DSP-1001250002573-B-G03


title: Melanoma, B-F12

description: Library name: DSP-1001250002573-B-F12


title: Melanoma, B-G02

description: Library name: DSP-1001250002573-B-G02


title: Melanoma, B-F09

description: Library name: DSP-1001250002573-B-F09


title: Melanoma, B-F11

description: Library name: DSP-1001250002573-B-F11


title: Melanoma, B-F07

description: Library name: DSP-1001250002573-B-F07


title: Melanoma, B-F06

description: Library name: DSP-1001250002573-B-F06


title: Melanoma, B-F01

description: Library name: DSP-1001250002573-B-F01


title: Melanoma, B-G04

description: Library name: DSP-1001250002573-B-G04


title: Melanoma, B-F08

description: Library name: DSP-1001250002573-B-F08


title: Melanoma, B-E10

description: Library name: DSP-1001250002573-B-E10


title: Melanoma, B-E08

description: Library name: DSP-1001250002573-B-E08


title: Melanoma, B-E07

description: Library name: DSP-1001250002573-B-E07


title: Melanoma, B-F04

description: Library name: DSP-1001250002573-B-F04


title: Melanoma, B-E04

description: Library name: DSP-1001250002573-B-E04


title: Melanoma, B-E06

description: Library name: DSP-1001250002573-B-E06


title: Melanoma, B-G01

description: Library name: DSP-1001250002573-B-G01


title: Melanoma, B-F10

description: Library name: DSP-1001250002573-B-F10


title: Melanoma, B-E12

description: Library name: DSP-1001250002573-B-E12


title: MHH-CALL4, FHD-286, 37 degree C, 24 hours, 2

city: Loma Linda

first: V. S. S. Abhinav

last: Ayyadevara

state: CA

address: 11085 Campus St

department: Basic Sciences

institute: Loma Linda University

description:
Library name: MC4_FHD2
MC4_FHD2

data_processing:
Quality control (QC) of raw sequencing data, alignment to a reference genome, quantification of gene expression, differential expression analysis, and functional analysis.
Quality control and preprocessing of the raw FASTQ files is handled using Fastp, an ultra-fasta all-in-one FASTQ preprocessor.
Following this, HiSat2 is utilized to map the reads to the reference genome.
Differential expression and functional analyses are then performed using tools like FeatureCounts and DESeq2.
Assembly: Homo sapiens Ensemble 94, GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: cell line

growth_protocol: Cell lines were grown in RPMI complete media i.e. RPMI 1640 + L-Glutamine + Penicillin/Streptomycin + 20% FBS in humidified atmosphere with 5% CO2 at 37c.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Cells were treated with either vehicle or 100nM FHD-286 (MedChem Express) for 24 hours.

value: cell line

tag: cell line

value: B-ALL

tag: treatment

value: 100nM FHD-286, BRG1/BRM inhibition


title: Melanoma, B-E11

description: Library name: DSP-1001250002573-B-E11


title: Melanoma, B-E09

description: Library name: DSP-1001250002573-B-E09


title: Melanoma, B-E03

description: Library name: DSP-1001250002573-B-E03


title: MHH-CALL4, FHD-286, 37 degree C, 24 hours, 1

description:
Library name: MC4_FHD1
MC4_FHD1


title: MHH-CALL4, control, 2

description:
Library name: MC4_Ctrl2
MC4_Ctrl2

value: Vehicle


title: MHH-CALL4, control, 1

description:
Library name: MC4_Ctrl1
MC4_Ctrl1


title: Melanoma, B-F03

description: Library name: DSP-1001250002573-B-F03


title: Melanoma, B-E02

description: Library name: DSP-1001250002573-B-E02


title: Melanoma, B-F05

description: Library name: DSP-1001250002573-B-F05


title: Melanoma, B-E01

description: Library name: DSP-1001250002573-B-E01


title: MUTZ5, FHD-286, 37 degree C, 24 hours, 2

description:
Library name: MUTZ5_FHD2
MUTZ5_FHD2


title: Melanoma, B-F02

description: Library name: DSP-1001250002573-B-F02


title: Melanoma, B-E05

description: Library name: DSP-1001250002573-B-E05


title: Melanoma, B-D11

description: Library name: DSP-1001250002573-B-D11


title: MUTZ5, FHD-286, 37 degree C, 24 hours, 1

description:
Library name: MUTZ5_FHD1
MUTZ5_FHD1


title: Melanoma, B-D12

description: Library name: DSP-1001250002573-B-D12


title: MUTZ5, control, 2

description:
Library name: MUTZ5_Ctrl2
MUTZ5_Ctrl2


title: RS4;11, FHD-286, 37 degree C, 24 hours, 2

description:
Library name: RS411_FHD2
RS411_FHD2


title: MUTZ5, control, 1

description:
Library name: MUTZ5_Ctrl1
MUTZ5_Ctrl1


title: Melanoma, B-D10

description: Library name: DSP-1001250002573-B-D10


title: RS4;11, control, 2

description:
Library name: RS411_Ctrl2
RS411_Ctrl2


title: Melanoma, B-D07

description: Library name: DSP-1001250002573-B-D07


title: Melanoma, B-D08

description: Library name: DSP-1001250002573-B-D08


title: Melanoma, B-D09

description: Library name: DSP-1001250002573-B-D09


title: RS4;11, FHD-286, 37 degree C, 24 hours, 1

description:
Library name: RS411_FHD1
RS411_FHD1


title: HB11;19, FHD-286, 37 degree C, 24 hours, 2

description:
Library name: HB1119_FHD2
HB1119_FHD2


title: Melanoma, B-D06

description: Library name: DSP-1001250002573-B-D06


title: Melanoma, B-D05

description: Library name: DSP-1001250002573-B-D05


title: HB11;19, FHD-286, 37 degree C, 24 hours, 1

description:
Library name: HB1119_FHD1
HB1119_FHD1


title: Melanoma, B-D04

description: Library name: DSP-1001250002573-B-D04


title: HB11;19, control, 1

description:
Library name: HB1119_Ctrl1
HB1119_Ctrl1


title: Melanoma, B-D03

description: Library name: DSP-1001250002573-B-D03


title: Melanoma, B-D02

description: Library name: DSP-1001250002573-B-D02


title: Line XIII scramble rep1

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: Library name: XIII_scramble_rep1

data_processing:
Samples were sequenced on the Illumina NovaSeq X Plus with 150 base paired-end sequencing.
Salmon was used to quantify transcripts.
EdgeR was used for differential expression analysis
Assembly: hg19
Supplementary files format and content: salmon_quant_table_new.txt  (table with quantification data)

source_name: DIPG Line XIII

growth_protocol: Cells were grown in Tumor Stem Medium, which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen) (27).

extract_protocol:
RNA was collected 72 hours after transfection for cells transfected with either scramble control siRNA or CTCF siRNA. There were 2 replicates of each transfection. RNA was extracted using the NucleoSpin RNA extraction kit (Machery Nagel 740955.50 ).
Poly-A + Non-Directional libraries were prepared

treatment_protocol: Cells were transfected with 90 nM of either scramble control or CTCF siRNA using the RNAi Max reagent (Invitrogen 13778075) and OptiMEM medium (Gibco 31985070). Samples were collected 72 hours after transfection.

value: DIPG Line XIII

value: pediatric glioma tumor cells

value: transfection with scramble control


title: Line XIII siCTCF rep2

description: Library name: XIII_siCTCF_rep2

value: transfection with CTCF siRNA


title: Melanoma, B-D01

description: Library name: DSP-1001250002573-B-D01


title: Line XIII scramble rep2

description: Library name: XIII_scramble_rep2


title: Melanoma, B-C10

description: Library name: DSP-1001250002573-B-C10


title: Melanoma, B-C12

description: Library name: DSP-1001250002573-B-C12


title: Melanoma, B-C11

description: Library name: DSP-1001250002573-B-C11


title: BIT#3 (bulk RNA)

city: Frederick

first: Biraj

last: Shrestha

state: MD

address: 8560 Progress Drive

institute: Frederick National Laboratory

description: Library name: 6_BIT_3

data_processing:
The instrument run was processed by using Real Time Analysis software (RTA 4.12.2). The Illumina bcl2fastq2.20 was used to demultiplex and convert binary base calls and quality scores to fastq format.
Adapters from the samples were trimmed using Cutadapt 1.18 software
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome GRCm39 and gencode vM38
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: GRCm39
Supplementary files format and content: gene count matrix in csv format

organism: Mus musculus

source_name: lymph nodes

extract_protocol:
CD8⁺ T cells were sorted from lymph nodes and spleens of WT and BIT mice (9–10weeks old, male, n = 3 individual mice per group, >98% purity).Total RNA was prepared from sorted cells with the RNeasy Kit (Qiagen). The quality of RNA was assessed by Bioanalyzer (Agilent).
The library was made by using the Stranded Total RNA Prep Ligation with Ribo-Zero Plus for sequencing (Illumina).

value: lymph nodes

value: TCRbhighCD4-CD8+ T cells


title: Melanoma, B-C09

description: Library name: DSP-1001250002573-B-C09


title: BIT#2 (bulk RNA)

description: Library name: 5_BIT_2


title: Line XIII siCTCF rep1

description: Library name: XIII_siCTCF_rep1


title: HB11;19, control, 2

description:
Library name: HB1119_Ctrl2
HB1119_Ctrl2


title: Melanoma, B-C08

description: Library name: DSP-1001250002573-B-C08


title: Melanoma, B-C07

description: Library name: DSP-1001250002573-B-C07


title: BIT#1 (bulk RNA)

description: Library name: 4_BIT_1


title: RS4;11, control, 1

description:
Library name: RS411_Ctrl1
RS411_Ctrl1


title: Melanoma, B-C05

description: Library name: DSP-1001250002573-B-C05


title: WT#3 (bulk RNA)

description: Library name: 3_WT_3


title: WT#1 (bulk RNA)

description: Library name: 1_WT_1


title: Melanoma, B-C04

description: Library name: DSP-1001250002573-B-C04


city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: 12_Parental_rep2_Hx_Pol2_pSer5_S12_combined

data_processing:
ChIP-seq reads were sequentially aligned to the Drosophila melanogaster BDGP6 genome and to the Human GRCh37 genome using BWA (0.7.5a-r405). The output SAM files were converted to BAM using SAMtools view (0.1.19) and the number of mapped reads were counted with SAMtools flagstat for later normalisation.
Reads mapping to both genomes and human reads mapping to the Duke Encode blacklist regions were excluded using Bedtools (2.17.0)34. Less than 0.001% of all reads mapped to both species.
The final normalised read counts for each ChIP-seq sample were calculated by dividing the total number of Human mapped reads by the total number of Drosophila mapped reads to provide a scaling factor for normalisation of each sample.
Assembly: Human GRCh37 and Drosophila melanogaster BDGP6 genomes.
Supplementary files format and content: BAM files were firstly indexed with SAMtools (0.1.19). Next, Bedtools genomecov (2.17.0) was used to assess genome-wide sequencing coverage. The bedGraph output files were then normalised using the scaling factors above and converted to BigWig using the bedGraphtoBigWig tool.

source_name: prostate cancer

growth_protocol: PC3 cells were grown in DMEM/Hams F12 medium. Cells were grown at 37oC in a humidified incubator with 5% CO2 with 100 U/mL penicillin, 100 mg/mL streptomycin, 2mM L-glutamine and 10% fetal bovine serum (Sigma-Aldrich) and regularly tested for mycoplasma infection.

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using anti-Rbp1 NTD (Cell Signaling, 14958), anti-Phospho-Rbp1 CTD Ser2 (Cell Signaling, 13499), or anti-Phospho-Rbp1 CTD Ser5 (Cell Signaling, 13523). In addition, 10ng of Drosophila melanogaster chromatin (Active Motif, 53083) and 1µg of Drosophila-specific histone variant H2Av antibody (Active Motif, 61686) were added to each reaction as a spike-in control for downstream normalisation.
All libraries were prepared and sequenced by the US NCI CCR Genomics Core.

treatment_protocol: Hypoxia incubations were performed at 0.5% O2 for 16 hours in a hypoxia chamber (In Vivo2 400 Hypoxia Work Station, Ruskinn Technology)

value: prostate cancer

value: hypoxia


description: Library name: 11_Parental_rep2_Nx_Pol2_pSer5_S11_combined

value: normoxia


title: Melanoma, B-B12

description: Library name: DSP-1001250002573-B-B12


title: Melanoma, B-C01

description: Library name: DSP-1001250002573-B-C01


title: Melanoma, B-C06

description: Library name: DSP-1001250002573-B-C06


title: 8_Parental_rep2_Hx_Pol2_NTD_S8_combined

description: Library name: 8_Parental_rep2_Hx_Pol2_NTD_S8_combined


title: Melanoma, B-B11

description: Library name: DSP-1001250002573-B-B11


title: Melanoma, B-B10

description: Library name: DSP-1001250002573-B-B10


title: Melanoma, B-B09

description: Library name: DSP-1001250002573-B-B09


description: Library name: 6_Parental_rep1_Hx_Pol2_pSer5_S6_combined


title: 7_Parental_rep2_Nx_Pol2_NTD_S7_combined

description: Library name: 7_Parental_rep2_Nx_Pol2_NTD_S7_combined


title: Melanoma, B-C03

description: Library name: DSP-1001250002573-B-C03


title: WT#2 (bulk RNA)

description: Library name: 2_WT_2


description: Library name: 5_Parental_rep1_Nx_Pol2_pSer5_S5_combined


title: Melanoma, B-B08

description: Library name: DSP-1001250002573-B-B08


title: Melanoma, B-B06

description: Library name: DSP-1001250002573-B-B06


title: Melanoma, B-C02

description: Library name: DSP-1001250002573-B-C02


description: Library name: 4_Parental_rep1_Hx_Pol2_pSer2_S4_combined


description: Library name: 3_Parental_rep1_Nx_Pol2_pSer2_S3_combined


title: 2_Parental_rep1_Hx_Pol2_NTD_S2_combined

description: Library name: 2_Parental_rep1_Hx_Pol2_NTD_S2_combined


title: Melanoma, B-B05

description: Library name: DSP-1001250002573-B-B05


title: 1_Parental_rep1_Nx_Pol2_NTD_S1_combined

description: Library name: 1_Parental_rep1_Nx_Pol2_NTD_S1_combined


title: Melanoma, B-B03

description: Library name: DSP-1001250002573-B-B03


description: Library name: 10_Parental_rep2_Hx_Pol2_pSer2_S10_combined


title: skin, hydrotic area in AIGA2

city: Hamamatsu

first: Tetsuya

last: Honda

address: 1-20-1 Handayama, Chuo-ku

country: Japan

institute: Hamamatsu University School of Medicine

description:
Library name: 4_AIGA2_post
10X Genomics

data_processing:
Preprocessing of the single-cell RNA sequencing data was performed using Cell Ranger version 7.2.0 (10x Genomics). Raw sequencing files were demultiplexed using the Cell Ranger command “mkfastq.” Each sample was aligned to the human reference genome assembly “refdata-cellranger-GRCh38-2020-A” using the Cell Ranger command “count.” Raw expression data were then loaded into R version 4.4.1.
Assembly: GRCh38 (10x Genomics reference: refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Tab-separated text files (.tsv.gz) and matrix files (.mtx.gz) including the raw gene-barcode count matrix, gene annotation, and cell barcode information.
Supplementary files format and content: matrix.mtx.gz: raw count matrix
Supplementary files format and content: barcodes.tsv.gz: cell barcode identifiers
Supplementary files format and content: features.tsv.gz: gene identifiers (feature annotation)

source_name: skin

extract_protocol:
Biopsies were taken from anhidrotic skin areas before corticosteroid therapy and from adjacent sweat-recovered areas after therapy. For each skin sample, a 5 mm punch biopsy was obtained after local anesthesia and was placed immediately into 1 mL BAMBANKER freezing medium (Nippon Genetic Co.) on ice and stored at –80°C until analysis. Cryopreserved human skin tissues were thawed in a 37°C water bath and cut into small pieces using scissors. The tissues were then transferred to 0.5 mL of 0.25% Trypsin-EDTA (Gibco, Life Technologies) and incubated at 37°C for 20 minutes. After enzymatic digestion, the tissues were transferred to the dissociation solution provided in the Miltenyi Human Whole Skin Dissociation Kit (Miltenyi Biotec) and incubated for 2.5 hours, following the manufacturer’s instructions. Subsequently, the partially dissociated tissue was manually disaggregated by pipetting up and down 10 times through an 18G needle. The resulting cell suspension was filtered through a 70 μm cell strainer (Corning, 352340) and kept on ice. Cells were pelleted by centrifugation at 300 × g for 10 minutes and resuspended in 1 mL of RPMI medium. Viable cells were counted using 0.4% Trypan Blue solution (Gibco, Thermo Fisher Scientific; 15250061). Isolated single-cell suspensions were then subjected to droplet-based single-cell RNA sequencing.
Single-cell libraries were formed by using the Chromium Next GEM Single-Cell 5′ Reagent Kit v2 (Dual Index)(10x Genomics) in line with the manufacturer’s protocol  (https://www.10xgenomics.com/jp/support/single-cell-immune-profiling/documentation/steps/library-prep/chromium-single-cell-5-reagent-kits-user-guide-v-2-chemistry-dual-index). Sequencing was performed using Illumina NextSeq 2000.

treatment_protocol: Corticosteroid pulse therapy

value: skin

value: single-cell suspension of mixed skin cells

value: after corticosteroid pulse therapy


title: Melanoma, B-B07

description: Library name: DSP-1001250002573-B-B07

value: Melanoma


title: Melanoma, B-B04

description: Library name: DSP-1001250002573-B-B04


title: skin, anhydrotic area in AIGA2

description:
Library name: 3_AIGA2_pre
10X Genomics

value: before corticosteroid pulse therapy


description: Library name: 9_Parental_rep2_Nx_Pol2_pSer2_S9_combined


title: Melanoma, B-B02

description: Library name: DSP-1001250002573-B-B02


title: Melanoma, B-B01

description: Library name: DSP-1001250002573-B-B01


title: skin, hydrotic area in AIGA1

description:
Library name: 2_AIGA1_post
10X Genomics


title: Melanoma, B-A12

description: Library name: DSP-1001250002573-B-A12


title: HCT116_Hx_rep3_S14

description: Library name: HCT116_Hx_rep3_S14

data_processing:
RNA-seq reads were sequentially aligned to the ERCC sequence library (ERCC92.fa - https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) and to the Human GRCh37 genome using HISAT2 (2.05). The output SAM files were converted to BAM using SAMtools view (0.1.19) and the number of ERCC mapped reads were counted with SAMtools flagstat for later normalisation.
The final normalised read counts for each RNA-seq sample were calculated by dividing the total number of Human mapped reads by the total number of ERCC mapped reads to provide a scaling factor for normalisation of each sample.
HTSeq (0.5.4p3) set to “intersection-strict” mode was utilised to count the total number of reads mapping within each Refseq-defined gene. Finally, differential expression between normoxia and hypoxia conditions was quantified using DESeq2.
Assembly: Human GRCh37 genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: colon cancer

growth_protocol: PC3 cells were grown in DMEM/Hams F12 medium and HCT116 cells were grown in McCoy's 5a medium. Cells were grown at 37oC in a humidified incubator with 5% CO2 with 100 U/mL penicillin, 100 mg/mL streptomycin, 2mM L-glutamine and 10% fetal bovine serum (Sigma-Aldrich) and regularly tested for mycoplasma infection.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with an on-column Dnase-treatment (Qiagen). Poly-A mRNA was purified using NEBNext Poly-A mRNA Magnetic Isolation Module. 1-4 µl of 1:10 diluted ERCC RNA Spike-in Mix 1 (Ambion, 4456740) was added to each sample.
Messenger RNA (mRNA) isolation and library preparation was performed by the US NCI CCR Genomics Core using the NEB Ultra II RNA-seq kit and PolyA (mRNA) selection.

value: colon cancer

value: colon cancer cell line


title: HCT116_Nx_rep3_S13

description: Library name: HCT116_Nx_rep3_S13


title: skin, anhydrotic area in AIGA1

description:
Library name: 1_AIGA1_pre
10X Genomics


title: HCT116_Hx_rep2_S12

description: Library name: HCT116_Hx_rep2_S12


title: Melanoma, B-A09

description: Library name: DSP-1001250002573-B-A09


title: Melanoma, B-A11

description: Library name: DSP-1001250002573-B-A11


title: Melanoma, B-A08

description: Library name: DSP-1001250002573-B-A08


title: Melanoma, B-A10

description: Library name: DSP-1001250002573-B-A10


title: HCT116_Nx_rep2_S11

description: Library name: HCT116_Nx_rep2_S11


title: Melanoma, B-A07

description: Library name: DSP-1001250002573-B-A07


title: HCT116_Nx_rep1_S9

description: Library name: HCT116_Nx_rep1_S9


title: Melanoma, B-A05

description: Library name: DSP-1001250002573-B-A05


title: HCT116_Hx_rep1_S10

description: Library name: HCT116_Hx_rep1_S10


title: Melanoma, B-A06

description: Library name: DSP-1001250002573-B-A06


title: HCT116_24_Hxrep2_input_S24

description: Library name: HCT116_24_Hxrep2_input_S24

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using anti-H3K4me3 (Cell Signaling, 9751S), anti-H3K9me3 (Cell Signaling, 13969S), anti-H3K27me3 (Cell Signaling, 9733S), anti-H3K36me3 (Cell Signaling, 4909S), anti-H3 (Abcam, ab1791) antibodies. In addition, 10ng of Drosophila melanogaster chromatin (Active Motif, 53083) and 1µg of Drosophila-specific histone variant H2Av antibody (Active Motif, 61686) were added to each reaction as a spike-in control for downstream normalisation.
All libraries were prepared and sequenced by the US NCI CCR Genomics Core.


title: HCT116_23_Nxrep2_input_S23

description: Library name: HCT116_23_Nxrep2_input_S23


title: HCT116_21_Nxrep1_input_S21

description: Library name: HCT116_21_Nxrep1_input_S21


title: Melanoma, B-A04

description: Library name: DSP-1001250002573-B-A04


title: HCT116_20_Hxrep2_H3_S20

description: Library name: HCT116_20_Hxrep2_H3_S20


title: HCT116_18_Hxrep1_H3_S18

description: Library name: HCT116_18_Hxrep1_H3_S18


title: HCT116_19_Nxrep2_H3_S19

description: Library name: HCT116_19_Nxrep2_H3_S19


title: Melanoma, B-A01

description: Library name: DSP-1001250002573-B-A01


title: Melanoma, B-A02

description: Library name: DSP-1001250002573-B-A02


title: HCT116_22_Hxrep1_input_S22

description: Library name: HCT116_22_Hxrep1_input_S22


title: HCT116_17_Nxrep1_H3_S17

description: Library name: HCT116_17_Nxrep1_H3_S17


title: Melanoma, A-H12

description: Library name: DSP-1001250002572-A-H12


title: Melanoma, A-H11

description: Library name: DSP-1001250002572-A-H11


title: Melanoma, B-A03

description: Library name: DSP-1001250002573-B-A03


title: HCT116_16_Hxrep2_K36me3_S16

description: Library name: HCT116_16_Hxrep2_K36me3_S16


title: Melanoma, A-H10

description: Library name: DSP-1001250002572-A-H10


title: HCT116_13_Nxrep1_K36me3_S13

description: Library name: HCT116_13_Nxrep1_K36me3_S13


title: Melanoma, A-H08

description: Library name: DSP-1001250002572-A-H08


title: HCT116_14_Hxrep1_K36me3_S14

description: Library name: HCT116_14_Hxrep1_K36me3_S14


title: Melanoma, A-H07

description: Library name: DSP-1001250002572-A-H07


title: Melanoma, A-H09

description: Library name: DSP-1001250002572-A-H09


title: HCT116_11_Nxrep2_K27me3_S11

description: Library name: HCT116_11_Nxrep2_K27me3_S11


title: Melanoma, A-H06

description: Library name: DSP-1001250002572-A-H06


title: A549 cells, sgH2AC19-3

city: Jinan

first: xiaorui

last: liu

address: 107 Wenhua West Road

institute: Qilu hospital of Shandong University

description: Library name: Sample 6

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: FPKM

growth_protocol: A549 was maintained in RPMI-1640 with 10 % fetal bovine serum. Cell was incubated at 37 ℃ in a humidified atmosphere with 5 % CO2.

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

value: Epithelial

value: Human Non-Small Cell Lung Cancer Cells


title: HCT116_10_Hxrep1_K27me3_S10

description: Library name: HCT116_10_Hxrep1_K27me3_S10


title: HCT116_12_Hxrep2_K27me3_S12

description: Library name: HCT116_12_Hxrep2_K27me3_S12


title: A549 cells, sgH2AC19-1

description: Library name: Sample 4


title: A549 cells, sgControl-3

description: Library name: Sample 3

value: WT


title: HCT116_15_Nxrep2_K36me3_S15

description: Library name: HCT116_15_Nxrep2_K36me3_S15


title: A549 cells, sgH2AC19-2

description: Library name: Sample 5


title: Melanoma, A-H05

description: Library name: DSP-1001250002572-A-H05


title: HCT116_9_Nxrep1_K27me3_S9

description: Library name: HCT116_9_Nxrep1_K27me3_S9


title: HCT116_8_Hxrep2_K9me3_S8

description: Library name: HCT116_8_Hxrep2_K9me3_S8


title: HCT116_7_Nxrep2_K9me3_S7

description: Library name: HCT116_7_Nxrep2_K9me3_S7


title: Melanoma, A-H03

description: Library name: DSP-1001250002572-A-H03


title: HCT116_5_Nxrep1_K9me3_S5

description: Library name: HCT116_5_Nxrep1_K9me3_S5


title: Melanoma, A-H04

description: Library name: DSP-1001250002572-A-H04


title: A549 cells, sgControl-2

description: Library name: Sample 2


title: HCT116_6_Hxrep1_K9me3_S6

description: Library name: HCT116_6_Hxrep1_K9me3_S6


title: A549 cells, sgControl-1

description: Library name: Sample 1


title: HCT116_3_Nxrep2_K4me3_S3

description: Library name: HCT116_3_Nxrep2_K4me3_S3


title: Melanoma, A-H02

description: Library name: DSP-1001250002572-A-H02


title: HCT116_4_Hxrep2_K4me3_S4

description: Library name: HCT116_4_Hxrep2_K4me3_S4


title: HCT116_1_Nxrep1_K4me3_S1

description: Library name: HCT116_1_Nxrep1_K4me3_S1


title: HCT116_2_Hxrep1_K4me3_S2

description: Library name: HCT116_2_Hxrep1_K4me3_S2


title: Soybean roots infected with M. hapla strain VW9 bio rep 6

city: Raleigh

first: Dahlia

middle: M

last: Nielsen

state: NC

address: Campus Box 7566

department: Biological Sciences

institute: North Carolina State University

description: Library name: soybean_VW9_6

data_processing:
RNA-Sequencing reads were aligned to the appropriate genome using HISAT2 version 2-2.2.1 (Kim, Langmead, and Salzberg 2015; Pertea et al. 2016; Kim et al. 2019) with default settings.
Gene expression counts were generated from aligned sequence reads using HTSeq version 2.0.2 (Anders, Pyl, and Huber 2015; Putri et al. 2022).
Counts were normalized using edgeR (Robinson, McCarthy, and Smyth 2010; Y. Chen et al. 2025).
Assembly: Medicago truncatula Mt4.0v1 (Tang et al. 2014; Young et al. 2011; Goodstein et al. 2012).
Assembly: Glycine max Wm82.a4.v1 (Valliyodan et al. 2019; Schmutz et al. 2010; Goodstein et al. 2012).
Supplementary files format and content: medicago_raw_counts.dat is a matrix-formatted ascii text file containing the medicago raw counts derived from HTSeq-Count.
Supplementary files format and content: medicago_norm_counts.dat is a matrix-formatted ascii text file containing the medicago adjusted counts derived from edgeR.
Supplementary files format and content: soybean_raw_counts.dat is a matrix-formatted ascii text file containing the soybean raw counts derived from HTSeq-Count.
Supplementary files format and content: soybean_norm_counts.dat is a matrix-formatted ascii text file containing the soybean adjusted counts derived from edgeR.

organism:
Glycine max
Meloidogyne hapla

source_name: root gall

growth_protocol: Plants were grown in a growth chamber for 16 hr under 200-300 µmol/m-2s-1 of light at 22° C and 60% humidity, and for 8 hr at 18° in the dark.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Valencia, CA). One sample (soybean-VW9 bio rep 7) did not produce sufficient RNA.
Libraries were prepared using a TruSeq RNA library prep kit.

treatment_protocol: After four weeks, plants were inoculated with 2,500 freshly hatched J2 per pot. At three weeks post inoculation, resected sections of plant root (galls or root knots) harboring feeding nematodes were collected for RNA-Seq.

value: root gall

tag: variety

value: Williams 82


title: IR + high Sodium butyrate HepG2 replicate 2

city: Xining

first: Yinan

last: Zhao

state: Qinghai

address: No. 251 Ningda Road

institute: Qinghai University

description:
Library name: IR_24h_HIGH_NAB_24h_R2
FPKM_ HNaB-2

data_processing:
Raw sequencing reads were quality-checked using FastQC and trimmed to remove adapters and low-quality bases. Clean reads were aligned to the reference genome using HISAT2. Gene expression levels were quantified using featureCounts and normalized as TPM values. Differential expression analysis was performed using DESeq2.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include gene expression matrices and differential expression results. Expression matrices are provided in tab-delimited text format, containing gene identifiers and normalized expression values (TPM) for each sample. Differential expression result files include gene ID, log2 fold change, p-value, and adjusted p-value (FDR). Functional enrichment results (GO and KEGG) are also provided, including term ID, description, gene count, and statistical significance.Expression matrices include both raw read counts and TPM-normalized values for each gene across all samples.

source_name: liver

growth_protocol: HepG2 cells (Wuhan Pricella Biotechnology Co., Ltd.) were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) and 1% penicillin–streptomycin (Pricella). Cells were maintained at 37°C in a humidified incubator with 5% CO₂. For routine experiments, cells were seeded and allowed to adhere overnight before drug treatment.

extract_protocol:
Total RNA was extracted from HepG2 cells using TRIzol reagent according to the manufacturer's instructions. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using agarose gel electrophoresis or an Agilent Bioanalyzer.
RNA-seq libraries were prepared using a standard Illumina library preparation protocol. Briefly, mRNA was enriched using poly(A) selection, followed by fragmentation, cDNA synthesis, end repair, adapter ligation, and PCR amplification. The libraries were sequenced on an DNBSEQ-T7 platform to generate paired-end reads.

treatment_protocol: To induce insulin resistance, HepG2 cells were treated with palmitate (200mM). For intervention groups, sodium butyrate (NaB) was added at low (0.5mM), medium (1mM), and high (1.5mM) concentrations. Cells were harvested at designated time points (48 h) after treatment.

value: liver

value: hepatocellular carcinoma cell line

value: wild type

value: palmitate + high sodium butyrate

tag: batch


title: Melanoma, A-H01

description: Library name: DSP-1001250002572-A-H01


title: Soybean roots infected with M. hapla strain VW9 bio rep 8

description: Library name: soybean_VW9_8


title: IR + high Sodium butyrate HepG2 replicate 3

description:
Library name: IR_24h_HIGH_NAB_24h_R3
FPKM_ HNaB-3

tag: genotype


title: IR + high Sodium butyrate HepG2 replicate 1

description:
Library name: IR_24h_HIGH_NAB_24h_R1
FPKM_ HNaB-1


title: Melanoma, A-G12

description: Library name: DSP-1001250002572-A-G12

tag: aoi


title: Soybean roots infected with M. hapla strain VW9 bio rep 3

description: Library name: soybean_VW9_3


title: IR + medium Sodium butyrate HepG2 replicate 3

description:
Library name: IR_24h_MID_NAB_24h_R3
FPKM_ MNaB-3

value: palmitate + medium sodium butyrate


title: Soybean roots infected with M. hapla strain VW9 bio rep 5

description: Library name: soybean_VW9_5


title: Melanoma, A-G11

description: Library name: DSP-1001250002572-A-G11

tag: patient


title: Soybean roots infected with M. hapla strain VW9 bio rep 4

description: Library name: soybean_VW9_4


title: Soybean roots infected with M. hapla strain VW9 bio rep 2

description: Library name: soybean_VW9_2


title: IR + medium Sodium butyrate HepG2 replicate 2

description:
Library name: IR_24h_MID_NAB_24h_R2
FPKM_ MNaB-2


title: Soybean roots infected with M. hapla strain VW9 bio rep 1

description: Library name: soybean_VW9_1


title: Melanoma, A-G10

description: Library name: DSP-1001250002572-A-G10

tag: has replicate_(1=yes,_0=no)


title: Soybean roots infected with M. hapla strain LM bio rep 8

description: Library name: soybean_LM_8


title: Soybean roots infected with M. hapla strain LM bio rep 7

description: Library name: soybean_LM_7


title: Melanoma, A-G08

description: Library name: DSP-1001250002572-A-G08

tag: replicate (1=yes,_0=no)


title: IR + medium Sodium butyrate HepG2 replicate 1

description:
Library name: IR_24h_MID_NAB_24h_R1
FPKM_ MNaB-1


title: IR + low Sodium butyrate HepG2 replicate 3

description:
Library name: IR_24h_LOW_NAB_24h_R3
FPKM_ LNaB-3

value: palmitate + low sodium butyrate


title: Soybean roots infected with M. hapla strain LM bio rep 6

description: Library name: soybean_LM_6


title: Soybean roots infected with M. hapla strain LM bio rep 4

description: Library name: soybean_LM_4


title: IR + low Sodium butyrate HepG2 replicate 2

description:
Library name: IR_24h_LOW_NAB_24h_R2
FPKM_ LNaB-2


title: Melanoma, A-G06

description: Library name: DSP-1001250002572-A-G06

tag: included in_analysis_(1=yes,0=no)


title: Soybean roots infected with M. hapla strain LM bio rep 5

description: Library name: soybean_LM_5


title: Soybean roots infected with M. hapla strain LM bio rep 1

description: Library name: soybean_LM_1


title: Soybean roots infected with M. hapla strain LM bio rep 2

description: Library name: soybean_LM_2


title: Melanoma, A-G09

description: Library name: DSP-1001250002572-A-G09

tag: lymph node_status_(1=yes,_0=no)


title: Desulfovibrio ferrophilus IS5, grown for 4 days in Fe-enriched EASW medium

city: Tsukuba

first: Xiao

last: Deng

state: Ibaraki

address: 1-1 Namiki

institute: National Institute for Materials Science

description:
Library name: Sample2
easw

data_processing:
Sequencing was performed on a NovaSeq X Plus platform (Illumina) using 150 bp paired-end reads, generating approximately 4 Gb of data per sample. Quality-controlled reads were mapped to the draft genome of D. ferrophilus IS5 using STAR with a minimum mapping identity of 97.53%. To compare relative expression patterns of IS5 cells under trace-Fe2+ and Fe2+-enriched growth conditions, gene expressions were normalized to cpm (counts per million).
Assembly: GCF_003966735.1
Supplementary files format and content: xlsx file includes cpm values for each Sample

organism: Desulfovibrio ferrophilus

source_name: bacterial cells

growth_protocol: IS5 cells grown for 4 days in DSMZ medium 195c or EASW were harvested by centrifugation at 7,800 × g inside a COY anaerobic chamber.

extract_protocol:
The cell pellets were immediately preserved in NucleoProtect RNA (TaKaRa Bio Inc., Japan) and processed for RNA extraction using the NucleoSpin RNA Plus kit (TaKaRa Bio Inc., Japan).
Ribosomal RNA (rRNA) was removed from total RNA using the TIANSeq rRNA Depletion Kit (TIANGEN Biotech, China), and RNA-seq libraries were prepared with the Fast RNA-seq Lib Prep Kit V2 (ABclonal, USA).

tag: strain

value: bacterial cells


title: Melanoma, A-G05

description: Library name: DSP-1001250002572-A-G05

tag: distant metastasis_(1=yes,_0=no)

tag: acral melanoma_(1=yes,_0=no)


title: Palmitate-treated HepG2 48h replicate 3

description:
Library name: IR_48h_R3
FPKM_ IR-3

value: palmitate


title: Desulfovibrio ferrophilus IS5, grown for 4 days in DSMZ medium 195c

description:
Library name: Sample1
195c


title: IR + low Sodium butyrate HepG2 replicate 1

description:
Library name: IR_24h_LOW_NAB_24h_R1
FPKM_ LNaB-1


title: Melanoma, A-G03

description: Library name: DSP-1001250002572-A-G03

value: Melanoma

tag: vital status

tag: overall survival(years)


title: Melanoma, A-G07

description: Library name: DSP-1001250002572-A-G07

tag: tissue


title: P10-Ctrl

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on HTA 2.0 Array(human, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: para-OSCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Normal clinical colon mucosa tissue samples from different colorectal cancer patients were collected immediately after surgical resection prior to any other therapeutic intervention

extract_protocol: Total RNA was extracted from tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) and purified with a RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: All tissue samples were stored at -80 °C.

tag: gender

value: female

value: normal oral mucosae


title: Control HepG2 48h replicate 3

description:
Library name: CTRL_48h_R3
FPKM_ con-3

tag: cell line

tag: cell type

tag: treatment

value: Control


title: Palmitate-treated HepG2 48h replicate 1

description:
Library name: IR_48h_R1
FPKM_ IR-1

tag: genotype

tag: batch


title: P8-Ctrl

value: male


title: P7-Ctrl


title: Melanoma, A-G02

description: Library name: DSP-1001250002572-A-G02

tag: aoi

tag: patient


title: P9-Ctrl


title: Soybean roots infected with M. hapla strain LM bio rep 3

description: Library name: soybean_LM_3

tag: variety


title: Melanoma, A-G04

description: Library name: DSP-1001250002572-A-G04

tag: has replicate_(1=yes,_0=no)

tag: replicate (1=yes,_0=no)

tag: included in_analysis_(1=yes,0=no)


title: Control HepG2 48h replicate 2

description:
Library name: CTRL_48h_R2
FPKM_ con-2


title: Melanoma, A-F12

description: Library name: DSP-1001250002572-A-F12

tag: lymph node_status_(1=yes,_0=no)

tag: distant metastasis_(1=yes,_0=no)


title: Palmitate-treated HepG2 48h replicate 2

description:
Library name: IR_48h_R2
FPKM_ IR-2


title: Control HepG2 48h replicate 1

description:
Library name: CTRL_48h_R1
FPKM_ con-1


title: P4-Ctrl


title: Melanoma, A-F11

description: Library name: DSP-1001250002572-A-F11

tag: acral melanoma_(1=yes,_0=no)

tag: vital status


title: P1-Ctrl

tag: tissue


title: P2-Ctrl

tag: gender


title: P3-Ctrl


title: Melanoma, A-F10

description: Library name: DSP-1001250002572-A-F10

tag: overall survival(years)


title: S2, 1hr BrdU gradient, 0 to 12 uM

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

institute: Vanderbilt University

description:
Library name: Gradient Library
ONT PromethION sequencing performed on S2 cells treated with a BrdU gradient

data_processing:
Raw Oxford Nanopore sequencing data in POD5 format were processed using a custom pipeline utilizing DNAscent v4.0.3 and Dorado v0.9.1 basecaller. POD5 file were basecalled using Dorado (na_r10.4.1_e8.2_400bps_5khz_hac configuration, GPU-enabled). DNAscent index and detect steps were used with identical options as the other analysis (including production of a human readable DETECT file rather than the updated BAM file format). The DETECT file was split by read and the second column (first analogue probability value column) was removed in preparation for ori-ter_promethion_calls_server_TVDiff.R. Individual read files less than 300 lines in length were removed prior to gradient detection due to the ori-ter_promethion_calls_server_TVDiff.R script seeming to encounter errors in processing reads approaching the window size. The script was then run with a window size and step size of 250 bases, a probability threshold of 0.5, and a gradient threshold of 1. Origin calls were visually validated using the limited_plot_read.sh script from the fork_arrest repository.
Assembly: Drosophila dm6
Supplementary files format and content: BED files of origins identified by BrdU gradient labeling

organism: Drosophila melanogaster

growth_protocol: S2 cell stocks were maintained in T225 Flasks with room temperature Schneider S2 Media supplemented with 10% fetal bovine serum (FBS), 100 U/mL Penicillin, and 100 µg/mL Streptomycin. Cells were passaged 1:5 dilution (1-part old media: 5-part final volume) when flasks reached 90-100% confluency (fully confluent). New stocks were thawed and maintained after 30 passages.

extract_protocol:
uHMW gDNA extraction and library preparation was conducted as a variation on New England Biolab’s adaption for their T3050L Kit for Oxford Nanopore Sequencing. EB+ was prepared by supplementing 1mL of Monarch Elution Buffer 2 with 2µL of 10% Triton X-100. 100 million previously labeled and frozen cells were resuspended to a concentration of 50 million cells per 100uL 1x PBS and divided into two 1.5mL Eppendorf for parallel extraction. The cells were lysed using 100µL Nuclei Prep Buffer and 50µL of 10mg/mL RNase A and mixed at room temperature for two minutes. Nuclei Lysis Solution was prepared using 200µL Nuclei Lysis Buffer and 80µL 1mg/mL Proteinase K. The nuclei were then lysed using 150µL Nuclei Lysis Solution. The sample was inverted to mix, incubated at 56oC and 300rpm for 10 minutes, then incubated at room temperature for 20 minutes. The sample was precipitated using 150µL of Precipitation Enhancer, two DNA Capture Beads, and 700µL of isopropanol and incubated on a vertical rotating mixer at six rpm for eight minutes. The samples were then washed twice with 500µL each of Wash Buffer before incubating in 200µL 1mg/mL Proteinase K for 16 hours at room temperature. The following morning, the precipitation step was repeated with 75µL Precipitation Enhancer and 350µL isopropanol and incubated on a vertical rotating mixer at six rpm for eight minutes. The samples were washed twice more with 500µL each Wash Buffer, the beads with naked DNA were transferred to a spin column and quickly tapped on an absorbent pad to remove excess buffer, then transferred to 385µL of EB+ buffer. The DNA was allowed to solubilize at room temperature for 16 hours. The sample was poured into a bead retainer seated in a 1.5mL LoBind Eppendorf tube and spun at 16,000xg for one minute. The sample was examined and if DNA strands were visible between the flow through and the beads, the sample was spun again. The sample was mixed gently with a wide-bore pipette until maximally solubilized, pipetted roughly 10-20 times, then stored in the fridge.
Sample libraries were prepared using Oxford Nanopore’s Ultra-Long Sequencing Kit (Cat# SQK-ULK114, Batch #ULK114.20.0003). Dilute fragmentation mix was prepared using 6µL Fragmentation Mix (FRA) and 244µL Fragmentation dilution buffer (FDB) before the dilute fragmentation mix was mixed with the sample via gently pipetting with a wide-bore pipette for two minutes at room temperature. The sample was then incubated for eight more minutes at room temperature followed by 10 minutes at 75oC, five minutes on ice, and finally five minutes at room temperature. 5µL of Rapid Adaptor (RA) was added and mixed thoroughly via wide-bore pipetting and the sample was incubated at room temperature for 30 minutes. Precipitation and sample clean-up was carried out by adding a precipitation star sample followed by 500µL Precipitation Buffer (PTB). The sample was precipitated on a vertical rotating mixer for 20 minutes at 6 rpm. The sample was then spun briefly, and the supernatant was removed. The sample was eluted in 300µL Elution Buffer (EB) overnight at room temperature before being stored at 4oC.

treatment_protocol: 24-hours prior to labeling, a fully confluent flask was passaged 1:3 to achieve 60-80% confluency at the time of labeling to ensure cells were actively replicating. The two flasks of cells resulting from this split were labeled at the same time and combined during a later step. The day of labeling, old media was removed and immediately replaced with new media. The flasks were treated with a gradient of BrdU in 0.5µM steps to a maximum of 12µM over a period of an hour, with each step lasting for 2.5 minutes. Between each step, the cells were returned to the 25oC incubator. After the gradient, the flasks remained in the incubator for a further half hour at 12µM before being scraped and cells from pairs of flasks labeled at the same time were combined into a single 50mL conical and 200µL of cells were set aside on ice for later counting and labeling validation. The remaining cells were pelleted at 600xg for 5 minutes and the old media was removed. The cells were then washed via resuspending in 10mL 1x PBS and subsequent pelleting at 600xg for 5 minutes. This wash step was repeated once. After washing, the cells were resuspended into 1mL 1x PBS, transferred to a 1.5mL Eppendorf tube, and pelleted at 600xg for 5 minutes. The supernatant was discarded and the cells pellets were stored at -80 oC for up to two weeks until DNA extraction and sequencing.

tag: cell line

tag: cell type

value: Embryonic Cells

value: 1 hour BrdU gradient followed by a final incubation of 30 minutes. BrdU gradient was perfroed in 0.5uM steps every 2.5 minutes


title: P9

source_name: OSCC

value: oral squamous cell carcinoma


title: P6-Ctrl


title: P5-Ctrl


title: Melanoma, A-G01

description: Library name: DSP-1001250002572-A-G01


title: P8


title: P10


title: S2, 3minEdU 6minBrdU, rep4

description:
Library name: PromethION_4
ONT PromethION sequencing performed on S2 cells treated with EdU and BrdU pulses

data_processing:
Raw Oxford Nanopore sequencing data in POD5 format were processed using a custom DNAscent analysis pipeline. First, POD5 files were converted to FAST5 using the Oxford Nanopore pod5 utility. Basecalling was performed with Guppy v6.4.2 (dna_r10.4.1_e8.2_400bps_5khz_hac DNAscent indexing was used to generate searchable indices from the FAST5 files and sequencing summary data. Replication detection was performed with DNAscent (GPU-accelerated) using a minimum read length threshold of 15 kb. ForkSense analysis was conducted with all detection modes enabled, including forks, origins, terminations, analogues, and stress signatures, using EdU and BrdU as replication markers. Bedgraph files were generated using DNAscent utility scripts to visualize replication features across the genome.configuration, GPU-enabled). Reads were aligned to the Drosophila melanogaster dm6 reference genome using Minimap2 v2.24 with the map-ont preset, followed by conversion and indexing using Samtools v1.10.
Assembly: Drosophila dm6
Supplementary files format and content: BED files of EdU and BrdU labeled tracks identified as left forks, right forks, origins, or terminations

treatment_protocol: 24-hours prior to labeling, a fully confluent flask was passaged 1:2 or 1:3 to achieve 60-80% confluency at the time of labeling to ensure cells were actively replicating. The two flasks of cells resulting from this split were labeled at the same time and combined during a later step. The day of labeling, old media was removed and immediately replaced with 25 mL of new media supplemented with 10µM EdU. Cells were returned to the 25oC incubator for 3 or 7 minutes for labeling. After the appropriate time had passed, media was removed, and the cells were gently washed three times with 10mL of 1x Phosphate Buffer Saline (1x PBS). Cells were then incubated with 25mL of new media supplemented with 10µM BrdU. For HU treatment, 1mM was added to the BrdU media. Cells were returned to the 25 oC incubator for 6 or 15 minutes for labeling. After the appropriate time had passed, media was removed, and the cells were gently wash three times with 10mL of 1x Phosphate Buffer Saline (1x PBS). The cells were then incubated with 25mL of new media supplemented with 50µM thymidine. Cells were returned to the 25 oC incubator for 20 minutes before harvesting. Cells from pairs of flasks labeled at the same time were combined into a single 50mL conical and 200µL of cells were set aside on ice for later counting and labeling validation. The remaining cells were pelleted at 600xg for 5 minutes and the old media was removed. The cells were then washed via resuspending in 10mL 1x PBS and subsequent pelleting at 600xg for 5 minutes. This wash step was repeated once. After washing, the cells were resuspended into 1mL 1x PBS, transferred to a 1.5mL Eppendorf tube, and pelleted at 600xg for 5 minutes.

tag: treatment

value: 3 minutes EdU followed by 6 minutes BrdU


title: Melanoma, A-F09

description: Library name: DSP-1001250002572-A-F09


title: S2, 3minEdU 6minBrdU, rep3

description:
Library name: PromethION_3
ONT PromethION sequencing performed on S2 cells treated with EdU and BrdU pulses

tag: batch


title: Melanoma, A-F08

description: Library name: DSP-1001250002572-A-F08

tag: aoi


title: Melanoma, A-F07

description: Library name: DSP-1001250002572-A-F07

tag: patient


title: S2, 7minEdU 15minBrdU, rep2

description:
Library name: PromethION_2
ONT PromethION sequencing performed on S2 cells treated with EdU and BrdU pulses

value: 7 minutes EdU followed by 15 minutes BrdU


title: S2, 7minEdU 15minBrdU, rep1

description:
Library name: PromethION_1
ONT PromethION sequencing performed on S2 cells treated with EdU and BrdU pulses


title: P7


title: P6


title: S2W-CCL4-DOX-HSC-2

city: Shanghai

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

description: Library name: SAMPLES5

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
mm10
Assembly: hg38
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

source_name: primary hepatic stellate cells

growth_protocol: BucheKI/KI-Hep mice were housed in a room at 25℃ with a 12-hour lingh/dark cycle and understricted access to chow food and water

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

value: primary hepatic stellate cells

tag: genotype

value: BucheKI/KI-Hep

value: CCL4 treatment

tag: sample group


title: P4


title: S2W-CCL4-DOX-HSC-3

description: Library name: SAMPLES6


title: P2


title: P1


title: S2W-CCL4-DOX-HSC-1

description: Library name: SAMPLES4


title: P3