title: JH-2-002-CL-AZA-2

description: Library name: UMGC-Lar-170-JH-2-002-CL-AZA-2

value: tumor

value: MPNST

value: treated with AZA for 4 days


title: HepG2 H3K4me1 replicate 2

status: Public on Aug 05 2026

type: SRA

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

country: USA

institute: Children's Hospital of Philadelphia

library_source: genomic

data_processing:
fastq files were processed using the Encode pipeline (https://www.encodeproject.org/chip-seq/histone/), with reads aligned to hg19 and peaks called with macs2
Assembly: hg19
Supplementary files format and content: narrowPeak_files

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

growth_protocol: HepG2 Cells ([HEPG2 (ATCC, HB8065TM)) were maintained in Eagle's Minimum Essential Medium (ATCC, 30 2003) supplemented with 10% heat inactivated fetal bovine serum (Gibco,16000044) and 1X Antibiotic-Antimycotic (Gibco, 15240096) at standard tissue culture conditions; 37C and 5% CO2.

extract_protocol:
Fixed cells were subjected to sonication following the NEXSON procedure. Briefly, nuclei were isolated by sonication using a Q Sonica Sonicator with settings of 15 seconds On, 30 seconds Off for 8 cycles at 20% power (2 minutes total sonication time).  Nuclei were centrifuged at 1250 RCF and resuspended in CHIP Buffer.  DNA was sheared using sonicator settings of 30 seconds On, 30 seconds Off at 80% power for 4 cycles of 5 minutes each (20min. total sonication time). Samples were centrifuged at 18,000 RCF and supernatant was collected and tested on an agarose gel to check for size, phenol extracted, precipitated, and resuspended.  ChIP was carried out with 300ng sheared DNA and the Chip-IT High Sensitivity Kit (Active Motif, 53040) according to kit instructions with the following antibodies from Active Motif: H3K27ac (39685), H3K4me1 (39297), H3K4me3 (61379), and anti-mouse IgG (53017).
Libraries were generated from the resulting material using the ThruPLEX Tag-seq Library Kit (Takara, 030520), PCR amplified for 10-16 cycles then purified and size selected using AMPure XP Beads.  Completed libraries were checked for quality and quantity on a BioAnalyzer 2100 and Qubit respectively.  Libraries passing QC were pooled at 1nM and sequenced on a Novaseq 6000 using an S1 flow cell (51bp paired end read length, dual indexed).

tag: tissue

value: Liver

tag: cell line

tag: cell type

value: Hepatocellular carcinoma

tag: chip antibody

value: H3K4me1 (Active Motif:39297)

tag: treatment


title: Lung,UninvolvedIBA5

city: Mountain View

first: Lester

last: Kobzik

state: California

address: 320 Logue Avenue

institute: Cellecta, Inc

description: Library name: UninvolvedIBA5

library_source: transcriptomic

data_processing:
To obtain raw counts, raw sequencing files were converted to .DCC files via Nanostring geomxngspipeline function. The DCC files were uploaded to the DSP instrument and automatically associated with individual scans.  Sequencing and Probe QC was performed using default parameters.
Assembly: GRCm38.p6
Supplementary files format and content: RawCountTablePaucibacillaryvsMultibacillary.txt: Count table for paucibacillary and multibacillary lesions with gene names and probe details
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Formalin-fixed paraffin-embedded lung sections were prepared for spatial analysis.
Spatial transcriptomics libraries were prepared using samples corresponding to ROI (regions of interest) of paucibacillary and multibacillary lesions as per manufacturer’s instructions.

treatment_protocol: Mice were injected into their hocks with 10E6 M. Tb Erdman strain, followed by euthanasia 14 weeks later with harvesting and fixation of lungs.

value: Lung

tag: genotype

value: Tuberculosis infection

tag: batch

tag: sample group

value: UninvolvedIBA


title: JH-2-002-CL-AZA-1

city: Minneapolis

first: David

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description: Library name: UMGC-Lar-170-JH-2-002-CL-AZA-1

data_processing:
Data were processed using the CHURP (v. 0.2.2) pipeline
Assembly: hg38
Supplementary files format and content: text file contains raw counts for all samples

source_name: tumor

growth_protocol: Cell lines were maintained in DMEM or RPMI + 10% or 20% FBS + P/S at 37C with 5% CO2

extract_protocol:
RNA was extracted with the RNEasy mini purification kit (Qiagen) and TURBO DNase (Invitrogen) was added to remove genomic DNA contamination
Libraries were prepped using the TruSeq Stranded mRNA kit


title: Lung,UninvolvedIBA4

description: Library name: UninvolvedIBA4


title: NTS_7d_CO2_4

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

description: Library name: R2024.899

data_processing:
Filtered reads were obtained by running fastp v0.24.0 with default parameters.
Filtered reads were aligned to the goat reference (ARS1) using STAR v2.7.10b with gene-level counts generated by FeatureCounts v2.0.6.
Differential expression analysis was performed by EdgeR v4.6
Assembly: ARS1
Supplementary files format and content: gene name, log2 fold change, log2CPM, and FDR per comparison are included for all differentially expressed genes.

organism: Capra hircus

source_name: NTS

growth_protocol: Five groups (n = 6) of adult (≥ 2 years) outbred (Alpine, Saanen, Toggenburg, etc.) female goats were assigned to the protocol.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Lipid Tissue Kit per the manufacturer’s recommendations, including on-column DNase digestion
RNA-seq libraries were constructed using the SMART-SEQ v4 Ultra Low Input RNA Kit for Sequencing and the Nextera XT DNA Library Preparation Kit. Sequencing produced 100-bp paired end reads across up to two lanes.

treatment_protocol: The five groups were randomly assigned to different environmental CO2 exposures, either 24 hr of control (room air), 3 hours of 6% CO2, 24 hours of 6% CO2, 7 days of 6% CO2, or 7 days of control (room air).

value: NTS


title: Whole blood, patient 13, visit #9

city: MONTREAL

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: Sample_01-13_v9_2-3513009

data_processing:
Low quality bases and adaptor sequences were removed with the Trimmomatic v.0.36 tool (PMID: 24695404) using the following arguments: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:TRUE HEADCROP:4 LEADING:5 TRAILING: 3 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned to the human GRCh38 (hg38) reference genome using HISAT2 v2.2.1 (PMID: 25751142) and raw gene expression counts were quantified by counting the number of strand-specific reads aligning to gene exon features using featureCounts (Subread package v2.0.3) (PMID: 24227677). Reads mapped to rRNAs were removed to resolve any biases from incomplete depletion. Reads mapped to hemoglobin-related genes (HBA1, HBA2, HBB, HBG1, and HBG2) were also removed to exclude contamination from residual red blood cell RNA before extraction.
Assembly: hg38
Supplementary files format and content: count_matrix_unfiltered_unnormalized.csv: CSV file where columns represents individual samples and lines represents each genes (as Gene Symbol / geneNAME)

source_name: Whole blood

extract_protocol:
RNA was isolated with the PAXgene Blood RNA Kit (Qiagen, Canada) according to the manufacturer’s protocol.
Bulk RNA-seq was performed as previously described (PMID: 27001747) Briefly, total RNA was depleted of rRNA, and cDNA libraries were prepared using the NEBNextUltra Express Directional RNA kit (New England Biolabs, Canada) for paired-end 150 bp sequencing on a 25B flowcell of the Illumina NovaSeq X Plus. An average of 59.7 million reads were obtained per library.

treatment_protocol: Blood was drawn in PAXgene RNA tubes before initiation of nintedanib and at each study visit thereafter. Whole blood was stored at -80°C until RNA isolation.

value: Whole blood

value: Immune cells

value: Nintedanib


title: Lung,UninvolvedIBA3

description: Library name: UninvolvedIBA3


title: NTS_7d_CO2_3

description: Library name: R2024.898


title: Whole blood, patient 13, visit #8

description: Library name: Sample_01-13_v8_2-3513008


title: HepG2 H3K27ac replicate 2

value: H3K27ac (Active Motif:39685)


title: NTS_7d_CO2_2

description: Library name: R2024.897


title: Whole blood, patient 13, visit #7

description: Library name: Sample_01-13_v7_2-3513007


title: NTS_7d_CO2_1

description: Library name: R2024.896


title: Lung,UninvolvedIBA1

description: Library name: UninvolvedIBA1


title: Whole blood, patient 13, visit #6

description: Library name: Sample_01-13_v6_2-3513006


title: iPSC_Hepatocytes_37

description: chromatin accessibility measured by ATAC-seq for IPS derived Hepatocytes

data_processing:
ATAC-seq peaks were called using the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). Peaks called from the pooled read files across biological replicates were checked for reproducibility across individual biological replicates
Assembly: hg19
Supplementary files format and content: narrowpeak_calls

growth_protocol: IPS hepatocytes (iHEPs) were produced by differentiating three biological replicates of iPSCs, which in turn were generated from peripheral blood mononuclear cells using a previously published protocol (Pashos et al 2017.)

extract_protocol:
A total of 50,000 to 100,000 cells were centrifuged at 550g for 5min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50μL cold lysis buffer (10mM Tris-HCl, pH7.4, 10mM  NaCl, 3mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550g for 10min at 4°C. Nuclei were resuspended in the Nextera transposition reaction mix (25μL 2x TD Buffer, 2.5μL Nextera Tn5 transposase (Illumina Cat #FC-121-1030), and 22.5μL nuclease free H2O) on ice, then incubated for 45min at 37°C.
The tagmented DNA was then purified using the Qiagen MinElute kit eluted with 10.5μL Elution Buffer (EB). Ten microliters of purified tagmented DNA was PCR amplified using Nextera primers for 12cycles to generate each library. PCR reaction was subsequently cleaned up using 1.5x AMPureXP beads (Agencourt) and concentrations were measured by Qubit. Libraries were paired-end sequenced on the Illumina Libraries were paired-end sequenced on the Illumina Novaseq 6000 platform (100bp read length).


title: Lung,MultibacillaryIBA11

description: Library name: MultibacillaryIBA11

value: MultibacillaryIBA


title: NTS_7d_Control_6

description: Library name: R2024.895


title: Whole blood, patient 13, visit #5

description: Library name: Sample_01-13_v5_2-3513005


title: Whole blood, patient 13, visit #4

description: Library name: Sample_01-13_v4_2-3513004


title: iPSC_Hepatocytes_233


title: Lung,MultibacillaryIBA8

description: Library name: MultibacillaryIBA8


title: NTS_7d_Control_3

description: Library name: R2024.892


title: Lung,PaucibacillaryIBA30

description: Library name: PaucibacillaryIBA30

value: PaucibacillaryIBA


title: Whole blood, patient 13, visit #2

description: Library name: Sample_01-13_v2_2-3513002


title: Whole blood, patient 13, visit #1

description: Library name: Sample_01-13_v1_2-3513001


title: Lung,PaucibacillaryIBA29

description: Library name: PaucibacillaryIBA29


title: Whole blood, patient 12, visit #9

description: Library name: Sample_01-12_v9_2-3513000


title: NTS_7d_Control_1

description: Library name: R2024.890


title: DNA from Older adults 5

type: genomic

city: Bunkyo-ku

first: Hiroshi

last: Mutoh

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

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

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

data_processing: GenomeStudio software v1.9.0

label: Cy5 and Cy3

source_name: naïve CD4+ T cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from naïve CD4+ T cells using Allprep DNA/RNA Micro Kit (Qiagen) according to standard instructions

value: naïve CD4+ T cells

tag: developmental stage/age

value: Older adults


title: Lung,PaucibacillaryIBA28

description: Library name: PaucibacillaryIBA28


title: DNA from Older adults 4


title: Whole blood, patient 12, visit #8

description: Library name: Sample_01-12_v8_2-3512984


title: DNA from Older adults 2


title: Whole blood, patient 12, visit #7

description: Library name: Sample_01-12_v7_2-3512999


title: Lung,MultibacillaryIBA6

description: Library name: MultibacillaryIBA6


title: S9,HP_High_NoAr; OptimalPhosphorus_OptimalFood_NoArsenic (Control),rep2

city: Keene

first: Priyanka

last: Roy Chowdhury

state: New Hampshire

address: 229 Main Street

institute: Keene State College

description:
Library name: Sample 9
S9

data_processing:
Reads were trimmed using Trimmomatic (v 0.27) with the following specifications: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8 TRUE LEADING:20 TRAILING:20 MINLEN:40).
Transcriptomic index was created with NCBI GTF file for KAP4 Daphnia pulex using Salmon (v 1.9.0). Both the mapping based mode and quantification were completed by Salmon software. Transcript level abundances to gene level through using tximport.
Assembly: GTF from the following NCBI genome assembly: ASM2113471v1
Supplementary files format and content: text file of raw counts for each sample (based on library name)

molecule: polyA RNA

organism: Daphnia pulex

source_name: whole body

extract_protocol:
total RNA was extracted using the Qiagen RNeasy MiniKit and QIAshredder following the manufacturer’s protocol
RNA-seq libraries were constructed following a polyA selection approach using Illumina compatible Nextera DNA Flex Library Prep Kit following manufacturer's protocol

value: whole body


title: RTN_24hr_CO2_4

description: Library name: R2023.1492

source_name: RTN

value: RTN


title: Whole blood, patient 12, visit #6

description: Library name: Sample_01-12_v6_2-3512998


title: DNA from Younger adults 5

value: Younger adults


title: Lung,MultibacillaryIBA5

description: Library name: MultibacillaryIBA5


title: RTN_24hr_CO2_3

description: Library name: R2023.1491


title: Whole blood, patient 12, visit #5

description: Library name: Sample_01-12_v5_2-3512997


title: Lung,MultibacillaryIBA4

description: Library name: MultibacillaryIBA4


title: GeoMx-DSP-1001660022456-E-A03

city: Rochester

first: Alexandra

last: Krivonos

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: GeoMx-DSP-1001660022456-E-A03

data_processing:
The samples were sequenced on an Illumina NextSeq 2000 P3 instrument at PE50. Sequencing depth was calculated based on a total area of 9,002,857 μm2 and 900 million read pairs determined from the GeoMx GeoMx-DSP generated Lab Worksheet.
Sequencing-generated FASTQ files were processed using the NanoString GeoMx NGS pipeline to generate DCC files used in downstream data analysis.
Assembly: mm10
Supplementary files format and content: GeoMx_sample_metadata.csv includes the samples metadata
Supplementary files format and content: vwf+_VWF+_DE_analysis.xlsx Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: cd68+_CD68+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: ela2+_ELA+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: else_ELSE_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Library strategy: Spatial Transcriptomics

source_name: liver

growth_protocol: human liver FFPE

extract_protocol:
Fresh tissues from surgery were processed for FFPE embedding, 5um section were cut.
Slides were flourensently labeled with  endothelial cell marker Von Willebrand Factor (VWF), macrophage and monocyte marker CD68, and neutrophil marker Elastase (ELA2). Regions of interest (ROIs) were manually draw based on their zonal location within the liver lobule: periportal zone 1, midzonal zone 2, and pericentral zone 3. Each ROI consisted of four segments: segment 4 for VWF+ area, segment 1 for CD68+ area, segment 2 for ELA2+ area, and segment 3 was called ‘else’ to refer to non-stained areas within the ROI. Photo-cleaved oligonucleotide tags were collected from 377 AOI. PCR amplification and liabrary pprepareation were done using GeoMx Human Whole Transcriptome Atlas (WTA) accorrding to manufacture's instruction.

treatment_protocol: 3 patients with normal, 3 patients with steatosis and 4 patients with MASH

value: liver

tag: condition

tag: segment

tag: zone


title: DNA from Younger adults 3


title: RTN_24hr_CO2_2

description: Library name: R2023.1490


title: Whole blood, patient 12, visit #4

description: Library name: Sample_01-12_v4_2-3512996


title: Lung,MultibacillaryIBA3

description: Library name: MultibacillaryIBA3


title: RTN_24hr_CO2_1

description: Library name: R2023.1489


title: Whole blood, patient 12, visit #3

description: Library name: Sample_01-12_v3_2-3512995


title: HepG2 H3K4me1 replicate 1

value: Liver

value: Hepatocellular carcinoma

value: H3K4me1 (Active Motif:39297)


title: NTS_7d_CO2_5

description: Library name: R2024.900


title: HepG2 H3K27ac replicate 3


title: DNA from Younger adults 2


title: HepG2 H3K27ac replicate 1


title: Lung,UninvolvedIBA2

description: Library name: UninvolvedIBA2

value: Lung

value: Tuberculosis infection

value: UninvolvedIBA


title: DNA from Younger adults 4


title: Lung,MultibacillaryIBA2

description: Library name: MultibacillaryIBA2


title: NTS_7d_Control_5

description: Library name: R2024.894

value: NTS


title: iPSC_Hepatocytes_334


title: Lung,MultibacillaryIBA10

description: Library name: MultibacillaryIBA10


title: Whole blood, patient 12, visit #2

description: Library name: Sample_01-12_v2_2-3512994

value: Whole blood

value: Immune cells

value: Nintedanib


title: RTN_3hr_CO2_6

description: Library name: R2023.1488


title: Lung,MultibacillaryIBA1

description: Library name: MultibacillaryIBA1

value: MultibacillaryIBA


title: RTN_3hr_CO2_5

description: Library name: R2023.1487


title: Whole blood, patient 12, visit #1

description: Library name: Sample_01-12_v1_2-3512993


title: Lung,MultibacillaryIBA9

description: Library name: MultibacillaryIBA9


title: NTS_7d_Control_4

description: Library name: R2024.893


title: Whole blood, patient 13, visit #3

description: Library name: Sample_01-13_v3_2-3513003


title: DNA from Younger adults 1

value: naïve CD4+ T cells


title: Whole blood, patient 11, visit #9

description: Library name: Sample_01-11_v9_2-3512983


title: Lung,PaucibacillaryIBA27

description: Library name: PaucibacillaryIBA27

value: PaucibacillaryIBA


title: RTN_3hr_CO2_4

description: Library name: R2023.1486


title: RTN_3hr_CO2_3

description: Library name: R2023.1485


title: NTS_7d_Control_2

description: Library name: R2024.891


title: Lung,PaucibacillaryIBA26

description: Library name: PaucibacillaryIBA26


title: Whole blood, patient 11, visit #8

description: Library name: Sample_01-11_v8_2-3512992


title: NCI-H460, H3K18ac, rep1

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequencing reads from mChIP-seq were demultiplexed to samples by the barcodes in the 5’ end of Read2 using fastq-multx (version 1.4.2) (https://github.com/brwnj/fastq-multx) with a mismatch setting of 0. Then, reads of each sample with adapter contamination and low quality were trimmed and filtered using fastp with parameters as -f 10 -t 5 -F 30 -T 5 --complexity_threshold=30 –n_base_limit=5  --length_required 60 (version 0.23.2) and aligned to the human reference genomes hg38, mouse reference genome mm10, or budding yeast genome sacCer3 using bowtie2 (version 2.2.5) with default parameters. Uniquely mapping reads with mapping quality more than 30 were kept using samtools (version 1.9) and duplicates were removed using picard MarkDuplicates (v2.26.10, http://broadinstitute.github.io/picard).
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched by glycine with 0.125 M final concentration. sonicated using Covaris SE220 (75 W, 20% Duty factor, 1,000 cycles per burst) for 5 min at 4°C to obtain fragments with the peak size around 200 bp.
The tailing and ssDNA ligation method used to label sample chromatin, and then multiple barcoded samples were pooled and split for immunoprecipitation with relevant antibodies as standard ChIP-seq. After immunoprecipitation, the purified ChIPed DNA was resuspended in 18 µl of water and extended in an 40 µl reaction containing 1 × KAPA HiFi HotStart ReadyMix and 0.25 µM P7TruSeqHTRev at 98 for 30 sec and 63 °C for 5 min followed by purification with 1.2 × volume of SPRIselect™ beads. Then, the purified DNA was ligated to the second adapter in a 40 µl reaction (1× T4 DNA ligase buffer, 0.5 µM P5TruSeqHT/P5SPlint mixture (1:1), and 10 Weiss units of T4 DNA ligase) at 25 °C for 30 minutes and purified with 1.0 × volume of SPRIselect™ beads. Lastly, library was amplified in 50 μl of PCR reaction Mix containing eluted DNA, 0.5 μM of P5 index primer, 0.5 μM P7 index primers, and 25 μl of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems) for 12-16 cycles (each cycle with 20 s at 98°C, 30 s at 58°C, 1 min at 68°C). DNA of 200–700 bp was isolated using a double SPRIselect bead cleanup (0.6 × and 0.85 × volume).

value: Lung large cell carcinoma

value: H3K18ac (Abcam:#ab1191)


title: Lung,PaucibacillaryIBA25

description: Library name: PaucibacillaryIBA25


title: RTN_3hr_CO2_2

description: Library name: R2023.1484

value: RTN


title: Whole blood, patient 11, visit #7

description: Library name: Sample_01-11_v7_2-3512991


title: Lung,PaucibacillaryIBA24

description: Library name: PaucibacillaryIBA24


title: Whole blood, patient 11, visit #6

description: Library name: Sample_01-11_v6_2-3512990


title: RTN_3hr_CO2_1

description: Library name: R2023.1483


title: RTN_24hr_Control_6

description: Library name: R2023.1482


title: Whole blood, patient 11, visit #5

description: Library name: Sample_01-11_v5_2-3512989


title: RTN_24hr_Control_5

description: Library name: R2023.1481


title: Whole blood, patient 11, visit #4

description: Library name: Sample_01-11_v4_2-3512988


title: Lung,PaucibacillaryIBA21

description: Library name: PaucibacillaryIBA21


title: RTN_24hr_Control_4

description: Library name: R2023.1480


title: Lung,PaucibacillaryIBA20

description: Library name: PaucibacillaryIBA20


title: Whole blood, patient 11, visit #3

description: Library name: Sample_01-11_v3_2-3512987


title: DNA from Children 4

value: Children


title: RTN_24hr_Control_3

description: Library name: R2023.1479


title: Whole blood, patient 11, visit #2

description: Library name: Sample_01-11_v2_2-3512986


title: DNA from Children 5


title: Lung,PaucibacillaryIBA19

description: Library name: PaucibacillaryIBA19


title: DNA from Older adults 3

value: Older adults


title: Whole blood, patient 11, visit #1

description: Library name: Sample_01-11_v1_2-3512985


title: RTN_24hr_Control_2

description: Library name: R2023.1478


title: DNA from Children 2


title: Lung,PaucibacillaryIBA18

description: Library name: PaucibacillaryIBA18


title: DNA from Children 3


title: Whole blood, patient 10, visit #9

description: Library name: Sample_01-10_v9_2-3512982


title: Lung,PaucibacillaryIBA17

description: Library name: PaucibacillaryIBA17


title: VRC_24hr_CO2_6

description: Library name: R2023.1476

source_name: VRC

value: VRC


title: DNA from Infants 5

value: Infants


title: Whole blood, patient 10, visit #7

description: Library name: Sample_01-10_v7_2-3512981


title: DNA from Children 1


title: Lung,PaucibacillaryIBA16

description: Library name: PaucibacillaryIBA16

value: Lung


title: Lung,PaucibacillaryIBA23

description: Library name: PaucibacillaryIBA23

value: Tuberculosis infection


title: VRC_24hr_CO2_5

description: Library name: R2023.1475


title: DNA from Infants 4


title: Lung,PaucibacillaryIBA22

description: Library name: PaucibacillaryIBA22


title: DNA from Infants 3


title: RTN_24hr_Control_1

description: Library name: R2023.1477


title: DNA from Infants 2


title: Whole blood, patient 10, visit #6

description: Library name: Sample_01-10_v6_2-3512980


title: VRC_24hr_CO2_4

description: Library name: R2023.1474


title: Lung,PaucibacillaryIBA14

description: Library name: PaucibacillaryIBA14


title: Whole blood, patient 10, visit #5

description: Library name: Sample_01-10_v5_2-3512979


title: Lung,PaucibacillaryIBA13

description: Library name: PaucibacillaryIBA13


title: VRC_24hr_CO2_3

description: Library name: R2023.1473


title: Whole blood, patient 10, visit #4

description: Library name: Sample_01-10_v4_2-3512978


title: VRC_24hr_CO2_2

description: Library name: R2023.1472


title: Lung,PaucibacillaryIBA12

description: Library name: PaucibacillaryIBA12


title: Whole blood, patient 10, visit #3

description: Library name: Sample_01-10_v3_2-3512977


title: Whole blood, patient 10, visit #2

description: Library name: Sample_01-10_v2_2-3512976


title: Lung,PaucibacillaryIBA11

description: Library name: PaucibacillaryIBA11


title: VRC_24hr_CO2_1

description: Library name: R2023.1471


title: Lung,PaucibacillaryIBA10

description: Library name: PaucibacillaryIBA10


title: DNA from Term neonates 5

value: Term neonates


title: DNA from Term neonates 3


title: VRC_3hr_CO2_6

description: Library name: R2023.1470


title: DNA from Term neonates 4


title: Whole blood, patient 10, visit #1

description: Library name: Sample_01-10_v1_2-3512975


title: Lung,PaucibacillaryIBA9

description: Library name: PaucibacillaryIBA9


title: VRC_3hr_CO2_5

description: Library name: R2023.1469


title: Whole blood, patient 09, visit #9

description: Library name: Sample_01-09_v9_2-3512974


title: Lung,PaucibacillaryIBA8

description: Library name: PaucibacillaryIBA8


title: VRC_3hr_CO2_4

description: Library name: R2023.1468


title: Whole blood, patient 09, visit #8

description: Library name: Sample_01-09_v8_2-3512973


title: Lung,PaucibacillaryIBA7

description: Library name: PaucibacillaryIBA7


title: DNA from Term neonates 2


title: VRC_3hr_CO2_3

description: Library name: R2023.1467


title: Whole blood, patient 09, visit #7

description: Library name: Sample_01-09_v7_2-3513010


title: Lung,PaucibacillaryIBA6

description: Library name: PaucibacillaryIBA6


title: DNA from Term neonates 1


title: VRC_3hr_CO2_2

description: Library name: R2023.1466


title: Whole blood, patient 09, visit #5

description: Library name: Sample_01-09_v5_2-3512972


title: DNA from Infants 1


title: L7851

city: Leiden

first: Sara

last: Cardoso

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

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

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

data_processing: minfi package using R environment

label: Cy3 and Cy5

source_name: Bulk Tumour

extract_protocol: DNA was isolated from fresh-frozen tissue using the Wizard Genomic DNA purification kit (A1125, Promega, Madison, WI, USA), according to manufacturer’s instructions.

value: Bulk Tumour

tag: diagnosis

value: Central Conventional Chondrosarcoma

tag: progression status

value: Primary

tag: grade

tag: age

tag: Sex

value: Male

tag: idh status

value: WT

tag: chrome

value: High

tag: idhmut vaf

tag: bone marrow content


title: Lung,PaucibacillaryIBA5

description: Library name: PaucibacillaryIBA5

tag: tissue

tag: treatment

value: PaucibacillaryIBA


title: DNA from Preterm neonates 7

value: naïve CD4+ T cells

value: Preterm neonates


title: VRC_3hr_CO2_1

description: Library name: R2023.1465


title: Whole blood, patient 09, visit #4

description: Library name: Sample_01-09_v4_2-3512971

value: Whole blood

tag: cell type

value: Immune cells

value: Nintedanib


title: L7754

value: Female

value: IDH1 MUT


title: DNA from Preterm neonates 6


title: Lung,PaucibacillaryIBA3

description: Library name: PaucibacillaryIBA3

value: Lung

tag: genotype

tag: batch

tag: sample group


title: Whole blood, patient 09, visit #3

description: Library name: Sample_01-09_v3_2-3512970


title: VRC_24hr_Control_6

description: Library name: R2023.1464

value: VRC


title: L7714


title: DNA from Preterm neonates 5

tag: developmental stage/age


title: Lung,PaucibacillaryIBA2

description: Library name: PaucibacillaryIBA2

value: Tuberculosis infection


title: VRC_24hr_Control_5

description: Library name: R2023.1463


title: Whole blood, patient 09, visit #2

description: Library name: Sample_01-09_v2_2-3512969


title: DNA from Preterm neonates 4


title: L7570

value: Bulk Tumour


title: Lung,PaucibacillaryIBA1

description: Library name: PaucibacillaryIBA1


title: L7262

value: Central Conventional Chondrosarcoma


title: Whole blood, patient 09, visit #1

description: Library name: Sample_01-09_v1_2-3512968


title: VRC_24hr_Control_4

description: Library name: R2023.1462


title: Lung,MultibacillaryCK15

description: Library name: MultibacillaryCK15

value: MultibacillaryCK


title: Whole blood, patient 08, visit #5

description: Library name: Sample_01-08_v5_2-3512967


title: L7172

value: Primary

value: Low


title: DNA from Preterm neonates 3


title: VRC_24hr_Control_2

description: Library name: R2023.1460


title: Lung,MultibacillaryCK14

description: Library name: MultibacillaryCK14


title: Whole blood, patient 08, visit #4

description: Library name: Sample_01-08_v4_2-3512966


title: DNA from Preterm neonates 2


title: VRC_24hr_Control_3

description: Library name: R2023.1461


title: L7147

value: Male

value: High


title: DNA from Preterm neonates 1

value: naïve CD4+ T cells


title: VRC_24hr_Control_1

description: Library name: R2023.1459


title: Lung,MultibacillaryCK13

description: Library name: MultibacillaryCK13


title: Whole blood, patient 08, visit #3

description: Library name: Sample_01-08_v3_2-3512965


title: L6991

value: WT


title: Whole blood, patient 08, visit #2

description: Library name: Sample_01-08_v2_2-3512964

value: Whole blood


title: NTS_24hr_CO2_6

description: Library name: R2023.1458

value: NTS


title: L6807


title: Lung,MultibacillaryCK11

description: Library name: MultibacillaryCK11


title: Whole blood, patient 08, visit #1

description: Library name: Sample_01-08_v1_2-3512963

value: Immune cells

value: Nintedanib


title: NTS_24hr_CO2_4

description: Library name: R2023.1456


title: Whole blood, patient 07, visit #9

description: Library name: Sample_01-07_v9_2-3512962


title: Lung,MultibacillaryCK10

description: Library name: MultibacillaryCK10


title: L6544


title: L6648

value: IDH1 MUT


title: Lung,MultibacillaryCK12

description: Library name: MultibacillaryCK12

value: Lung


title: Lung,MultibacillaryCK9

description: Library name: MultibacillaryCK9


title: NTS_24hr_CO2_5

description: Library name: R2023.1457


title: NTS_24hr_CO2_3

description: Library name: R2023.1455


title: L6541

value: Female


title: Whole blood, patient 07, visit #8

description: Library name: Sample_01-07_v8_2-3513011


title: NTS_24hr_CO2_2

description: Library name: R2023.1454


title: Lung,MultibacillaryCK8

description: Library name: MultibacillaryCK8

value: Tuberculosis infection


title: Whole blood, patient 07, visit #7

description: Library name: Sample_01-07_v7_2-3512961


title: L6502

value: Bulk Tumour


title: Whole blood, patient 07, visit #6

description: Library name: Sample_01-07_v6_2-3512960


title: NTS_24hr_CO2_1

description: Library name: R2023.1453


title: L6479

value: Central Conventional Chondrosarcoma


title: Whole blood, patient 07, visit #5

description: Library name: Sample_01-07_v5_2-3512959


title: Lung,MultibacillaryCK6

description: Library name: MultibacillaryCK6

value: MultibacillaryCK


title: L6431

value: Primary


title: Lung,MultibacillaryCK5

description: Library name: MultibacillaryCK5


title: Whole blood, patient 07, visit #4

description: Library name: Sample_01-07_v4_2-3512958


title: NTS_3hr_CO2_5

description: Library name: R2023.1451


title: NTS_3hr_CO2_6

description: Library name: R2023.1452


title: Lung,MultibacillaryCK7

description: Library name: MultibacillaryCK7


title: L6255

value: IDH2 MUT


title: Lung,MultibacillaryCK4

description: Library name: MultibacillaryCK4


title: NTS_3hr_CO2_4

description: Library name: R2023.1450


title: L6203

value: Low


title: Whole blood, patient 07, visit #3

description: Library name: Sample_01-07_v3_2-3512957


title: NTS_3hr_CO2_3

description: Library name: R2023.1449


title: Whole blood, patient 07, visit #2

description: Library name: Sample_01-07_v2_2-3512956


title: L6065

value: High


title: Lung,MultibacillaryCK3

description: Library name: MultibacillaryCK3


title: Lung,MultibacillaryCK2

description: Library name: MultibacillaryCK2


title: NTS_3hr_CO2_2

description: Library name: R2023.1448


title: Whole blood, patient 07, visit #1

description: Library name: Sample_01-07_v1_2-3512955


title: NTS_3hr_CO2_1

description: Library name: R2023.1447


title: Lung,MultibacillaryCK1

description: Library name: MultibacillaryCK1


title: L5976

value: Male


title: Lung,PaucibacillaryCK19

description: Library name: PaucibacillaryCK19

value: PaucibacillaryCK


title: NTS_24hr_Control_6

description: Library name: R2023.1446


title: L5837

value: WT


title: MDA-MB-231, JTE-607-treated 3 (JTE-607 3)

city: Boston

first: Claire

last: Moore

state: MA

address: 150 harrison Ave

institute: Tufts university school of medicine

description: Library name: Sample 6

data_processing:
For differential gene expression and generation of normalized_abundance_DESeq2.csv file, the read 1 data of the samples was first trimmed using the BBtools to remove adapters and polyA sequence, and then mapped to the human hg38 genome using STAR (v2.7.7a). The number of reads mapped to each gene was then quantified using featureCounts (v1.6.3), and only genes with more than five reads per sample were included in further analyses. Read counts were normalized to the total mapped reads to the genome. PseudoCount of 1 was applied to prevent infinity values in the ratio calculation. The significance of expression difference was assessed by DESeq2.
APA analysis was conducted using a polyA_DB-based pipeline for APA analysis as described in our previous study. Briefly, adapter and poly(T) sequences from QuantSeq FWD raw read 2 data were trimmed and aligned to the human (hg38) polyA_DB reference (-100nt, polyA_DB-annotated-PolyA Site (PAS), +25nt) using STAR (v2.7.7a), and only uniquely mapped reads were kept. The last aligned position of each mapped read was compared to polyA_DB-annotated PASs, allowing ± 24 nt flexibility. Matched reads were considered as pA site-supporting (PASS) reads and were used for further APA analysis.
Assembly: UCSC Genome Browser on Human (GRCh38/hg38)
Supplementary files format and content: txt file includes raw count for each sample
Supplementary files format and content: Excel worksheet includes RED values representing intronic polyA site usage in genes following JTE-607 treatment
Supplementary files format and content: Excel worksheet includes RED values representing polyA site usage in 3'-UTR of genes following JTE-607 treatment

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/high glucose supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, 15596018) and the Direct-zolTM RNA Miniprep Kit (Zymo Research, R2050), followed by DNase I treatment (Zymo Research, E1011A) to eliminate genomic DNA contamination according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using Quant-Seq FWD library kit following manufacturer's protocols

treatment_protocol: During the exponential growth phase (70-80% confluency), cells were detached using 0.05% trypsin/EDTA and seeded at 30% confluency. The following day, cells were treated with JTE-607 (10 μM) (Tocris, 5185) for 72 hours before harvest for total RNA extraction.

tag: cell line

value: breast cancer cell


title: MDA-MB-231, JTE-607-treated 2 (JTE-607 2)

description: Library name: Sample 5


title: L5850

tag: diagnosis


title: Lung,PaucibacillaryCK18

description: Library name: PaucibacillaryCK18


title: NTS_24hr_Control_5

description: Library name: R2023.1445

value: NTS


title: L5812

tag: progression status


title: Lung,PaucibacillaryCK17

description: Library name: PaucibacillaryCK17


title: MDA-MB-231, JTE-607-treated 1 (JTE-607 1)

description: Library name: Sample 4


title: NTS_24hr_Control_4

description: Library name: R2023.1444


title: Lung,PaucibacillaryCK16

description: Library name: PaucibacillaryCK16


title: L5717

tag: grade


title: L5692

tag: age


title: NTS_24hr_Control_3

description: Library name: R2023.1443


title: MDA-MB-231, untreated 2 (control 2)

description: Library name: Sample 2


title: NTS_24hr_Control_2

description: Library name: R2023.1442


title: L5688

tag: Sex


title: MDA-MB-231, untreated 3 (control 3)

description: Library name: Sample 3


title: MDA-MB-231, untreated 1 (control 1)

description: Library name: Sample 1


title: Lung,PaucibacillaryCK14

description: Library name: PaucibacillaryCK14


title: NTS_24hr_Control_1

description: Library name: R2023.1441


title: Lung,PaucibacillaryCK15

description: Library name: PaucibacillaryCK15


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, Hi-C, Rep2

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Dr

institute: Carnegie Institution of Washington

description: Library name: Nkx2-5Cre_Lmnb1Flox/-_P0_5_HiC_Rep2

data_processing:
We used the 4DN Hi-C processing pipeline (https://github.com/4dn-dcic/docker-4dn-hic) for read alignment and filtering. Quality control of individual Hi-C libraries was performed separately using the HiCUP pipeline to evaluate the proportion of valid read pairs and overall library complexity. Compartment scores were generated using the previously described C-score tool. The raw deduplicated contact pairs generated by the 4DN processing pipeline for each genotype were used as input to the tool, and scores were calculated at 5 kb resolution. Interactions spanning less than 1Mb were excluded to remove contacts more strongly associated with TAD-level interaction dynamics. C-score tracks were then compared with our LAD maps to identify A and B compartment regions. To ensure consistency with LAD assignments, chromosome-wide scores were multiplied by -1 to invert the C-scores, such that B compartments corresponded to positive values and A compartments corresponded to negative values across the genome.
Assembly: GRCm38
Supplementary files format and content: Processed Hi-C files are included as .mcool files. Tracks for cScore are included as .bedgraph files.

source_name: Heart

extract_protocol:
Hearts from P0.5 hearts were dissociated using the Pierce Primary Cardiomyocyte Isolation Kit from ThermoFisher Scientific. Cardiomyocytes were then purified with neonate cardiomyocyte isolation beads from Miltenyi Biotec.
10,000 cardiomyocytes were processed through an optimized low-input Hi-C protocol utilizing carriers. A comprehensive account of the methodology will be published elsewhere and is available upon request. Cardiomyocytes were fixed with 2% PFA for 10 minutes at room temperature. PFA was then neutralized by adding glycine to a final concentration of 125mM for 5 minutes at room temperature, followed by an additional incubation of 15 minutes on ice. Cells were pelleted at 300g for 5 minutes at 4°C and washed with 1ml of ice-cold PBS. 2. Cell lysis and enzyme digestion Cells were pelleted again in the same conditions as previous and resuspended in 1.0ml Hi-C lysis buffer (10mM Tris, pH8.0/ 10mM NaCl/ 0.2% IGEPAL CA-630 (NP-40)) with protease inhibitors. Cells were allowed to rotate for 30 minutes at 4°C and then spun down at 2000g for 8 minutes at 4oC. Pellets were then washed with 500μl ice cold 1.2X NEB3 buffer, spun down as previous, and resuspended in 40μL 1.2X NEB3.1.2μL of 10% SDS was added to each sample and incubated at 65°C for 10 minutes. Afterwards, samples were placed on ice and 4μl of 20% Triton X-100 was mixed, which was followed by an incubation at 37°C for 1 hour with no agitation. 2.5μL (25units; NEB R0543S, 10units/μl) was added to each sample and incubated for 90 minutes, with gentle mixing every 30 minutes. After, an additional 2.5 μL of DpnII was added and incubated for an additional 90 minutes as before. 3. Fill 5’overhang with biotin and proximity ligation  The 5’ overhand was filled with biotin by adding to each sample 0.5 μl mix of 10mM dCTP, dGTP, dTTP (Qiagen 201912), 1.0 μl 1mM biotin-14-dATP (JenaBioScience, NU-835-BIO14-S), and 1.5 μl 5units/μl Klenow (NEB M0210L, 5units/μl).  Samples were incubated for 60 minutes at 37°C and then put on ice. This was followed by ligation of the blunted DNA, which was done by adding 50.0 ul 10x T4 ligase buffer (NEB B0202S), 5.0 ul 100x BSA (NEB, B9000S), 390.8 ul water, and 1.0 ul NEB T4 Ligase (NEB M0202S, 400units/μl). Once added, samples were incubated overnight at 16°C with no agitation. 4. Reversal of crosslinking and DNA purification  Crosslinking was reversed by adding 2.5μl of 20mg/ml proteinase K (ThermoFisher, 25530049) and incubating overnight at 65°C. The following day an additional 2.5 of 20mg/ml proteinase K was added and incubated for another 2 hours at 65°C. DNA was then extracted by adding 500μl of P/C/I (25:24:1, Sigma P2069) and vortexing. The supernatant was taken and P/C/I extraction was performed one more time, with the supernatant being transferred to a 2ml eppendorf tube. DNA was further purified using a silica bead DNA extraction kit (ThermoFisher, k0513), as per the manufacturer’s protocol. Briefly, 500μl of the supernatant was mixed with 1.5ml of silica bead binding buffer and 10μl of silica bead suspension. The samples were then incubated at 55°C for 15 minutes with occasional mixing. Silica beads were then washed 3 times by spinning the beads down and resuspending in 500μl of the provided ice-cold washing buffer. Washing buffer was removed and pellets were completely air-dried. DNA was then eluted by resuspending the beads in 45μl of 10mM Tris (pH8.0). DNA and incubated at 55°C for 5 minutes. The beads were spun down again and the supernatant was transferred to Spin-X tube filters (Sigma, CLS8162-24EA or Costar, 8160) to remove residual beads. The tubes were spun at 16,000 g for 5 minutes at 4°C and 40μl of the filtered DNA solution was used for the de-biotinylation reaction. 5. Removal of biotin from unligated ends To remove biotin from unligated ends, 1.0μl 10mg/ml BSA, 10.0μl 10X NEB2 (B7002S), 12.5μl 10 mM dNTP (Qiagen, 201912), 34.9μl of distilled water, and 1.6μl T4 DNA polymerase (NEB, 3units/μl) was added to each sample. DNA was incubated in this solution at 20°C for 2 hours and 2μl of 0.5M without agitation and EDTA was then added to each sample to stop the reaction. DNA was purified as before with the silica bead extraction kit using the same buffer to sample ratios but instead eluting in 50μl. 6. DNA sonication and end repair  50μl of the DNA suspension was transferred to a microTUBE AFA Fiber Screw-Cap (Covaris, 520166) and sonicated with the Covaris M220 instrument with M220 Holder-XTU holder (500488). Hi-C DNA was sheared for 90 seconds at 20°C with 200 cycles per burst, at a peak incident power of 50 Watts and duty cycle of 20%. Sheared DNA was then transferred to PCR tubes. End repair was performed by adding 10μl of 10x Phosphorylation Reaction buffer (NEB, B0201S), 0.5μl T4 DNA Polymerase (NEB, M0203S), 0.5μl T4 Polynucleotide Kinase (NEB, M0201S), 5μl 10 mM dNTPs (Qiagen, 201912), 15μl 10 mM dATP  (NEB, N0440S), 2μl 10x dil DNA Pol I, Large(Klenow)(NEB, M0210L), and 17μl distilled water. Samples were then incubated at 37°C for 30 minutes with no agitation. 7. Streptavidin capture  100μl end repaired Hi-C DNA was mixed with 100 ul 2x BW in preparation for streptavidin capture. 20μl of Dynabeads M-280 Streptavidin (ThermoFisher, 11205D, 2ml) was transferred to a non-sticky 0.5ml PCR tube (Sigma CLS6530, polypropylene PCR tube). Streptavidin beads were then washed with 100 ul 2x BW (10mM Tris, pH7.5/1mM EDTA/2M NaCl). End repaired DNA was then transferred to the tube with streptavidin beads and mixed by mild pipetting. Samples were then rotated at room temperature for 60 minutes. Afterwards, samples were placed on a magnetic stand and beads were allowed to settle. The supernatant was then removed and beads were resuspended in 1X BWT buffer (5mM Tris, pH7.5/0.5mM EDTA/1M NaCl/0.1% Triton X-100) and placed on a magnetic stand to allow separation, after which the supernatant was removed; this wash step was repeated once without changing tubes. The beads were then resuspended in 10 mM Tris (pH 8.0, Qiagen EB), separated on a magnetic stand, and the supernatant was removed, with this wash step also repeated once. Finally, the beads were resuspended in 16 µl of 10 mM Tris (pH 8.0). 8. Library preparation and sequencing  A-tailing was performed on 16µl of Hi-C DNA by adding 2.5µl 10x NEB2 buffer, 5.0µl 1mM dATP (NEB Seq kit, N0440S), and 1.5µl 5units/μl Klenow 3’->5’Exonuclease (NEB, M0212L) and incubating at 37°C for 30 minutes with no agitation in a PCR machine. Samples were then placed on a magnetic stand, and beads were allowed to settle. Supernatant was removed and beads were washed with 100µl 1X BWT. The beads were again placed on a magnetic stand to allow separation, then resuspended in 100 µl of EB (10 mM Tris, pH 8.0). This wash step was repeated for a total of two washes. After the last wash, the supernatant was removed, and the beads were resuspended in 6.5 µl of elution buffer. After A-tailing adaptors were ligated on by adding 12.5µl quick ligation reaction buffer (NEB, M2200L), 5.0µl of 1/4 diluted NEBNext Adaptor (NEB, E7500S), and 1.0µl Quick T4 ligase (NEB, M2200L). Reaction mixes were incubated at 20°C for 15 minutes. Afterwards, 1.5µl of USER enzyme mix was added and mixed in by mild pipetting. The reaction mix was then incubated at 37°C for 15 minutes. Beads were magnetized and washed with 100µl 1x BWT three times, changing tubes between each wash. Beads were then again magnetized and washed two times with 100µl elution buffer without changing tubes, before being resuspended in 10µl elution buffer. PCR amplification reactions were set by adding 1.25µl Universal PCR primer (NEB, E7500S), 1.25µl of a chosen index primer (NEB, E7500S), and 12.5µl of NEBNext Ultra II Q5 Master Mix (NEB, M0544S). The PCR was performed with an initial denaturation at 98 °C for 1 min, followed by 12 cycles of 98 °C for 10 s, 62 °C for 75 s, and 72 °C for 20 s. This was followed by a final extension at 65 °C for 5 min, after which the reaction was held at 10 °C. Beads were magnetized and the supernatant containing the PCR products recovered. Finally, the 25µl of PCR products were purified by adding 20µl of SPRIselect beads (Beckman Coulter) and incubating for 15 minutes at room temperature. Beads were settled on the magnetic stand and washed twice with 200µl 80% ethanol while attached on the magnetic stand. Beads were then air-dried and resuspended in 12µl of elution buffer. The beads were magnetized and the supernatant was collected.  Libraries were quantified with the Qubit dsDNA Quantification Assay Kit and library quality was verified on the 2100 Bioanalyzer System with High Sensitivity DNA Kit. Sequencing was conducted on the Illumina NextSeq1000 using 50x50 bp length paired-end reads.

value: Heart

value: Isolated Cardiomyocyte

value: Nkx2-5Cre;Lmnb1 Flox/-

tag: timepoint


title: L5670

tag: idh status

tag: chrome


title: Lung,PaucibacillaryCK13

description: Library name: PaucibacillaryCK13

value: Lung


title: L5574

value: Female

value: IDH1 MUT

tag: idhmut vaf

tag: bone marrow content


title: shCtrl2

city: Wuhan

first: jianhong

last: zhao

state: Hubei

address: Donghu Road, No. 115

institute: Wuhan University

hyb_protocol: Amplified and fragmented bisulfite-converted DNA was hybridized to the Infinium MethylationEPIC BeadChip according to the manufacturer’s instructions. Following hybridization, the BeadChips were washed, subjected to single-base extension and staining, and prepared for scanning.

scan_protocol: BeadChips were scanned by Shanghai Biotechnology Corporation using an Illumina-compatible array scanner according to the manufacturer’s instructions. Raw signal-intensity data were exported as IDAT files.

data_processing:
BeadStudio software v3.2
average beta

source_name: lymph node metastasis of colorectal adenocarcinoma

label_protocol: Bisulfite-converted genomic DNA was subjected to whole-genome amplification, enzymatic fragmentation, precipitation, resuspension, single-base extension, and fluorescent staining according to the Infinium MethylationEPIC BeadChip protocol supplied by Illumina.

extract_protocol: Genomic DNA was extracted from shCtrl and shDNMT3A SW620 cells using the DNeasy Blood & Tissue Kit (QIAGEN, catalog no. 69504) according to the manufacturer’s instructions. Purified genomic DNA was subjected to bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, catalog no. D5007).

tag: tissue

value: SW620 cells

value: colorectal adenocarcinoma cell


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, Hi-C, Rep1

description: Library name: Nkx2-5Cre_Lmnb1Flox/-_P0_5_HiC_Rep1

tag: cell type


title: shCtrl1

value: lymph node metastasis of colorectal adenocarcinoma


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, Hi-C, Rep2

description: Library name: Nkx2-5Cre_Lmnb1Flox/+_P0_5_HiC_Rep2

tag: genotype

value: Nkx2-5Cre;Lmnb1 Flox/+


title: Lung,PaucibacillaryCK12

description: Library name: PaucibacillaryCK12

tag: treatment

value: Tuberculosis infection

tag: batch


title: L5546

value: Bulk Tumour

value: Central Conventional Chondrosarcoma

value: Primary

value: High


title: shDNMT3A2


title: Lung,PaucibacillaryCK11

description: Library name: PaucibacillaryCK11

tag: sample group

value: PaucibacillaryCK


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, Hi-C, Rep1

description: Library name: Nkx2-5Cre_Lmnb1Flox/+_P0_5_HiC_Rep1


title: shDNMT3A1

tag: cell line


title: Lung,PaucibacillaryCK10

description: Library name: PaucibacillaryCK10


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, IgG CUT&RUN, Rep2

description: Library name: Nkx2-5Cre_Lmnb1Flox/minus_P0_5_IgG_Rep2

data_processing:
Samples were processed using the nf-core/cutandrun pipeline v3.2.2 with Nextflow v23.10.0. Reads were aligned to the mm10 mouse reference genome, and mitochondrial reads were removed by including the --remove_mitochondrial_reads flag during pipeline execution. The pipeline performed adapter trimming, quality control, alignment, duplicate marking, and filtering. For Hidden Markov Modeling (HMM), outputted replicate bam files were merged using samtools merge and converted to bigwig files in CPM normalized with 5kb bins. Histone and lamin CUT&RUN samples were then normalized to their corresponding IgG control by running bigwigCompare with the --operation log2 and --pseudocount 1 flags applied. Genome-wide signal tracks at 5 kb resolution for H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me1, H3K4me3, ATAC-seq, and lamin-associated domains (LADs) were compiled and processed, as discussed previously. ATAC-seq signals were log2-transformed with a small pseudocount, while all other datasets were used as provided. Signal values across all tracks were capped to the range of -3 to 3 to limit the influence of outliers. Analyses were restricted to autosomal chromosomes, and the first and last 3 Mb of each chromosome were excluded to reduce edge effects. Regions overlapping a combined blacklist (mm10 ENCODE blacklist v2 and low-signal regions) were removed. All datasets were then merged by genomic coordinates, and missing values were set to zero. Principal component analysis (PCA) was performed on z-score-scaled signals from all tracks. The first three principal components were retained, and their scores were appended to the genomic coordinates for downstream analyses. We then applied HMM to infer chromatin states and define HiLands domains as previously described, with emission probabilities modeled using a multivariate normal inverse Gaussian distribution. A six-state model was used throughout the analysis to capture chromatin variation across the seven markers. Model parameters were estimated using the expectation-maximization (Baum-Welch) algorithm, with 20 random initializations to reduce convergence to local optima and selection of the highest-likelihood solution. Chromatin states were assigned using the Viterbi algorithm, and adjacent genomic windows sharing the same state were merged to generate continuous HiLands regions. For lamin CUT&RUNs, additional z-score normalization was performed on the generated bigwig files to enable comparison between samples. We then identified LAD regions with the depmixS4 v1.4-0 R package was used to call a two-state HMM.
Assembly: GRCm38
Supplementary files format and content: CUT&RUN tracks for histone markers and lamins are included as bigwigs. Lamin HMM calling and HiLands calling are included as .bed files.
Library strategy: CUT&Run

extract_protocol:
Hearts from P0.5 hearts were dissociated using the Pierce Primary Cardiomyocyte Isolation Kit from ThermoFisher Scientific. Cardiomyocytes were then purified with neonate cardiomyocyte isolation beads from Miltenyi Biotec.
CUT&RUN was performed with the CUTANA ChIC/CUT&RUN Kit as per manufacturer instructions using 100,000 P0.5 cardiomyocytes. Sequencing libraries were prepared with the Takara ThruPLEX DNA-seq kit according to the manufacturer’s protocol utilizing 10 cycles of PCR amplification. Libraries were quantified with the Qubit dsDNA Quantification Assay Kit and library quality was verified on the 2100 Bioanalyzer System with High Sensitivity DNA Kit. Sequencing was conducted on the Illumina NextSeq1000 using 50x50 bp length paired-end reads.

value: Wildtype

tag: cut&run antibody

value: IgG


title: L5540

tag: diagnosis

tag: progression status

value: WT

value: Low


title: L5432

tag: grade

tag: age


title: Lung,PaucibacillaryCK9

description: Library name: PaucibacillaryCK9

value: Lung


title: Lung,PaucibacillaryCK8

description: Library name: PaucibacillaryCK8


title: L5380

tag: Sex

value: Female


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, IgG CUT&RUN, Rep1

description: Library name: Nkx2-5Cre_Lmnb1Flox/minus_P0_5_IgG_Rep1

value: Heart

value: Isolated Cardiomyocyte

tag: timepoint


title: 4MOSC1 Tumor_CXCL10_Day10 4

type: RNA

city: San Diego

first: Cheyanne

middle: Kristen

last: Shinn

state: CA

address: 9500 Gilman Drive, MC 0684

institute: University of California, San Diego

hyb_protocol: Hybridization of samples was performed at The Next Generation Sequencing Core (Salk Institute for Biological Studies, La Jolla, CA) according to the NanoString Hybridization Protocol for nCounter XT CodeSet Gene Expression Assays.

scan_protocol: Samples were run on the nCounter SPRINT Profiler with the nCounter PanCancer Mouse Immune Profiling gene expression platform.

data_processing: Data was analyzed by ROSALIND® (https://rosalind.bio/) (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by NanoString. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalization probes from the same lane. Housekeeping probes used for normalization were selected based on the geNorm algorithm as implemented in the NormqPCR R library (Perkins et al., 2012). Abundance of various cell populations was calculated using the Nanostring Cell Type Profiling Module with ROSALIND software. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues were calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment was performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library (Hennig, 2024) that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The top GO R library was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro (Mitchell et al., 2019), NCBI (Geer et al., 2010), MSigDB (Subramanian et al., 2005; Liberzon et al., 2011), REACTOME (Jassal et al., 2020), WikiPathways (Slenter et al., 2018). Enrichment was calculated relative to a set of background genes relevant for the experiment. GraphPad Prism version 10 statistical analysis program (GraphPad Software, Boston, MA) was used to produce figures.

source_name: 4MOSC1 buccal tumor, day 17

extract_protocol: RNA was isolated by homogenization of whole tumors in TRIzol® (Invitrogen) followed by phenol:chloroform extraction and RNeasy Mini Kt based column purification with on-column DNase treatment (Qiagen).

treatment_protocol: 1 million cells were transplanted into the right buccal space of female C57BL/6N mice (4–6 weeks of age). When average tumor volumes reached 10-20 mm3 (around day 3), the mice were randomized into groups and treatment initiated. For IT treatment, 10 µg chemokine in 50 µl PBS or vehicle control (50 µl PBS) were injected directly into tumors. 4MOSC1 mice were treated on days 3, 6, and 9 post tumor cell implantation.

tag: gender

tag: strain


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, IgG CUT&RUN, Rep2

description:
Library name: Nkx2-5Cre_Lmnb1Flox/plus_P0_5_IgG_Rep2
P0_5_6_state_Hilands.bed


title: 4MOSC1 Tumor_CXCL10_Day10 3

source_name: 4MOSC1 buccal tumor, day 16


title: L5364

value: Male

tag: idh status

tag: chrome

tag: idhmut vaf

tag: bone marrow content


title: L5255

tag: tissue

value: ACT

value: IDH1 MUT


title: Lung,PaucibacillaryCK7

description: Library name: PaucibacillaryCK7

tag: genotype

tag: treatment

value: Tuberculosis infection

tag: batch


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, IgG CUT&RUN, Rep1

description:
Library name: Nkx2-5Cre_Lmnb1Flox/plus_P0_5_IgG_Rep1
P0_5_6_state_Hilands.bed

tag: cell type

tag: cut&run antibody


title: 4MOSC1 Tumor_CXCL10_Day10 2

source_name: 4MOSC1 buccal tumor, day 15


title: Lung,PaucibacillaryCK6

description: Library name: PaucibacillaryCK6

tag: sample group


title: WT, P0.5 Heart, IgG CUT&RUN, Rep4

description:
Library name: WT_P0_5_IgG_chrom_Rep4
P0_5_6_state_Hilands.bed


title: L5227

value: Bulk Tumour

tag: diagnosis

tag: progression status

tag: grade

value: IDH2 MUT


title: Lung,PaucibacillaryCK5

description: Library name: PaucibacillaryCK5


title: 4MOSC1 Tumor_Vehicle_Day10 4

source_name: 4MOSC1 buccal tumor, day 13


title: 4MOSC1 Tumor_CXCL10_Day10 1

source_name: 4MOSC1 buccal tumor, day 14


title: WT, P0.5 Heart, IgG CUT&RUN, Rep3

description:
Library name: WT_P0_5_IgG_chrom_Rep3
P0_5_6_state_Hilands.bed

tag: timepoint


title: Lung,PaucibacillaryCK4

description: Library name: PaucibacillaryCK4

source_name: Lung


title: L5213

value: Central Conventional Chondrosarcoma

value: Primary

tag: age

tag: Sex


title: WT, P0.5 Heart, IgG CUT&RUN, Rep2

description:
Library name: WT_P0_5_IgG_chrom_Rep2
P0_5_6_state_Hilands.bed


title: 4MOSC1 Tumor_Vehicle_Day10 3

source_name: 4MOSC1 buccal tumor, day 12

tag: gender

tag: strain


title: L5206

tag: idh status

tag: chrome

value: High

tag: idhmut vaf


title: Lung,PaucibacillaryCK3

description: Library name: PaucibacillaryCK3

tag: tissue

tag: genotype

value: PaucibacillaryCK


title: WT, P0.5 Heart, IgG CUT&RUN, Rep1

description:
Library name: WT_P0_5_IgG_chrom_Rep1
P0_5_6_state_Hilands.bed

value: Wildtype

value: IgG


title: L5205

value: WT

tag: bone marrow content


title: L5099

value: Low


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, Lamin-A CUT&RUN, Rep2

description:
Library name: Nkx2-5Cre_Lmnb1Flox/minus_P0_5_lamin_A_Rep2
Corresponding IgG is Nkx2-5Cre;Lmnb1Flox/- Rep2
Nkx2_5Cre_Lmnb1Fminus_lamin-A_zscore.bw
P0_5_6_state_Hilands.bed

tag: cell type

value: Nkx2-5Cre;Lmnb1 Flox/-

value: Lamin-A/C


title: 4MOSC1 Tumor_Vehicle_Day10 2

source_name: 4MOSC1 buccal tumor, day 11

value: Female


title: Lung,PaucibacillaryCK2

description: Library name: PaucibacillaryCK2

value: Lung

tag: treatment

tag: batch


title: 4MOSC1 Tumor_Vehicle_Day10 1

source_name: 4MOSC1 buccal tumor, day 10


title: PEDV_exo_3

city: nanjing

first: qiu

last: zhong

address: No. 1 Weigang, Xuanwu District

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description:
Library name: sample 9
PEDV group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Sscrofa11.1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

organism: Sus scrofa

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


title: Lung,PaucibacillaryCK1

description: Library name: PaucibacillaryCK1

tag: sample group


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, Lamin-A CUT&RUN, Rep1

description:
Library name: Nkx2-5Cre_Lmnb1Flox/minus_P0_5_lamin_A_Rep1
Corresponding IgG is Nkx2-5Cre;Lmnb1Flox/- Rep1
Nkx2_5Cre_Lmnb1Fminus_lamin-A_zscore.bw
P0_5_6_state_Hilands.bed

value: Heart

value: Isolated Cardiomyocyte

tag: cut&run antibody


title: L5076

tag: diagnosis

tag: progression status

tag: grade

value: ACT


title: Lung,UninvolvedCK5

description: Library name: UninvolvedCK5

value: Tuberculosis infection

value: UninvolvedCK


title: PEDV_exo_2

description:
Library name: sample 8
PEDV group, replicate biosample 2


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, Lamin-A CUT&RUN, Rep2

description:
Library name: Nkx2-5Cre_Lmnb1Flox/plus_P0_5_lamin_A_Rep2
Corresponding IgG is Nkx2-5Cre;Lmnb1Flox/+ Rep2
Nkx2_5Cre_Lmnb1Fplus_lamin-A_zscore.bw
P0_5_6_state_Hilands.bed

value: Nkx2-5Cre;Lmnb1 Flox/+

tag: timepoint


title: Lung,MultibacillaryIBA7

description: Library name: MultibacillaryIBA7

value: MultibacillaryIBA


title: PEDV_exo_1

description:
Library name: sample 7
PEDV group, replicate biosample 1


title: Lung,UninvolvedCK4

description: Library name: UninvolvedCK4


title: L5037

value: Bulk Tumour

value: Central Conventional Chondrosarcoma

value: Primary

tag: age

tag: Sex

value: IDH1 MUT


title: aged_B rep4

city: yunnan

first: wang

middle: yi

last: chao

address: Jingming South Road, Chenggong District, Kunming City, Yunnan Province

institute: Kunming University of Science and Technology

description: Library name: sample36

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.0 (https://www.10xgenomics.com/cn/support/software/cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: Testis

extract_protocol:
Following the 10x Genomics single-cell protocol for cell extraction
RNA libraries for RNA-seg were prepared using 10X Library Prep Kitfollowing manufacturer's protocols.

value: Testis


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, Lamin-A CUT&RUN, Rep1

description:
Library name: Nkx2-5Cre_Lmnb1Flox/plus_P0_5_lamin_A_Rep1
Corresponding IgG is Nkx2-5Cre;Lmnb1Flox/+ Rep1
Nkx2_5Cre_Lmnb1Fplus_lamin-A_zscore.bw
P0_5_6_state_Hilands.bed


title: L5017

tag: idh status

value: WT

value: High


title: Lung,UninvolvedCK3

description: Library name: UninvolvedCK3

data_processing:
To obtain raw counts, raw sequencing files were converted to .DCC files via Nanostring geomxngspipeline function. The DCC files were uploaded to the DSP instrument and automatically associated with individual scans.  Sequencing and Probe QC was performed using default parameters.
Assembly: GRCm38.p6
Supplementary files format and content: RawCountTablePaucibacillaryvsMultibacillary.txt: Count table for paucibacillary and multibacillary lesions with gene names and probe details
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed paraffin-embedded lung sections were prepared for spatial analysis.
Spatial transcriptomics libraries were prepared using samples corresponding to ROI (regions of interest) of paucibacillary and multibacillary lesions as per manufacturer’s instructions.


title: Col-0, 3-week-old, young true leaf, replicate2

city: Hefei

first: Wenjie

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

library_source: other

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 2 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw
Library strategy: DEtail-seq

molecule: other

organism: Arabidopsis thaliana

source_name: young true leaf

extract_protocol:
The chloroplasts were embedded in 0.5% low-melting-point agarose (Promega) and lysed in 1% sarkosyl, 0.45 M EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), and 2 mg/mL proteinase K at 48°C for 16 h with shaking. The agarose plugs were washed in TE buffer six times at 37°C, with the first two washes containing 1 mM PMSF. Cut agarose plug into 12 pieces and incubated in 1 ml TE with 10 μg/ml RNase A at 37°C overnight. The agarose pieces were washed five times with 1 ml TE buffer at 37°C for 6 min, then stored in plug storage solution (0.05 M EDTA pH 8.0, 60% glycerol) at -20°C until all samples were ready for the next step.
The DNA library was constructed with Scale ssDNA-seq Lib Prep Kit for Illumina V2 (ABclonal, RK20228). Five agarose pieces (~30 mg) were washed three times with 200 μl 1× CutSmart buffer (NEB) at 37°C for 6 min. The spike-in was performed by incubating the agarose pieces with 15 U I-CeuI (NEB) in 150 μl 1× CutSmart buffer at 37°C for 12 h. After digestion, the agarose pieces were washed three times with 500 μl TE buffer at 37°C for 6 min, followed by twice washes with 200 μl Low EDTA TE (ABclonal) at 37°C for 6 min. The agarose pieces were incubated in 80 μl T7 Tailing & Ligation buffer (ABclonal) at 37°C for 12 h. Then, heated the agarose pieces at 98°C for 2 min. The DNA in the agarose was recovered using a DNA purification kit (Magen, Catalog No D2111-02) and eluted with Low EDTA TE. The DNA was then sonicated to ~250 bp using Focused-ultrasonicator (Covaris S220). To finish the library preparation, the subsequent steps were performed according to the manufacturer's protocol exactly.

treatment_protocol: For tissue at different ages, the seeds were sown at the same time, while the tissues were collected every week as indicated for chloroplast isolation. For temperature treatment, the seedlings were grown on plates for 19 days, then transferred into growth chambers and grown under different temperatures with long-day conditions as indicated for 2 days. The aerial parts were harvested for chloroplast isolation. For photoperiod treatment, the seedlings were grown on plates for 16 days, then transferred into growth chambers and grown under different photoperiods as indicated for 5 days. The aerial parts were harvested for chloroplast isolation.

value: young true leaf

tag: developmental stage

value: 16 h light/8 h dark, 22°C/20°C


title: L4937

value: Female

tag: chrome

value: Low

tag: idhmut vaf


title: WT, P0.5 Heart, H3K27ac CUT&RUN, Rep2

description:
Library name: WT_P0_5_H3K27ac_Rep2
Corresponding IgG is WT Rep4
WT_H3K27ac_log2fc.bw
P0_5_6_state_Hilands.bed

tag: tissue

value: Heart

value: Isolated Cardiomyocyte

tag: genotype

value: Wildtype


title: iPEDV_exo_3

description:
Library name: sample 6
iPEDV group, replicate biosample 3

tag: cell type


title: WT, P0.5 Heart, H3K27ac CUT&RUN, Rep1

description:
Library name: WT_P0_5_H3K27ac_Rep1
Corresponding IgG is WT Rep3
WT_H3K27ac_log2fc.bw
P0_5_6_state_Hilands.bed


title: Lung,UninvolvedCK2

description: Library name: UninvolvedCK2

value: Lung

tag: treatment

value: Tuberculosis infection

value: UninvolvedCK


title: iPEDV_exo_2

description:
Library name: sample 5
iPEDV group, replicate biosample 2


title: Lung,UninvolvedCK1

description: Library name: UninvolvedCK1

tag: batch


title: L4893

value: Bulk Tumour

value: Male

value: IDH2 MUT

tag: bone marrow content


title: iPEDV_exo_1

description:
Library name: sample 4
iPEDV group, replicate biosample 1


title: WT, P0.5 Heart, H3K9me3 CUT&RUN, Rep2

description:
Library name: WT_P0_5_H3K9me3_Rep2
Corresponding IgG is WT Rep2
WT_H3K9me3_merged.bw
P0_5_6_state_Hilands.bed

tag: cut&run antibody


title: L4872

tag: diagnosis

value: Central Conventional Chondrosarcoma

value: Primary


title: mutant-4

city: Guangzhou

first: yan

middle: Zi

last: Wu

address: xiaoguwei

institute: South China university of technology

description: Library name: sample 4

data_processing:
Clean reads were mapped to the zebrafish genome (Danio rerio, GRCz11) with Hisat2 tools (v2.2.1). Differential expression analysis of two groups was performed using the DESeq2 R package (v1.26.0). Genes with FDR < 0.05 & |log2(foldchange)| ≥1 found by DESeq2 were assigned as differentially expressed. Clustering heat map of the differentially expressed genes (DEGs) was visualized by the pheatmap R packges (v1.0.12). Gene Ontology (GO) enrichment analysis of the DEGs was implemented by the GOseq R packages (v3.14.0).
genome build/assembly: Sequence read were mapped to Danio rerio Genomics GRCz11
processed data files format and content: tab-delimited text file includes raw counts for each Samples
processed data files format and content: csv files include FPKM values for each Samples

organism: Danio rerio

source_name: embryo

extract_protocol:
RNA was harvested using Trizol. 500ng of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using Hieff® NGS Ultima Dual-mode mRNA Library Prep Kit for illumina (Cat#12301, Yeason).

treatment_protocol: We collect the embryos from a pair of cpa1+/-cpa5+/- zebrafish, when they develop to 3 dpf, we removed the heads and tails, tails for RNA sample store in TRIzolTM Reagent (Invitrogen, 15596018) and heads for identification according to the method mentioned in genotyping above.

value: embryo

value: Cpa1 & Cpa5 konckout

value: 3 dpf


title: Ctrl_exo_3

description:
Library name: sample 3
ctrl group, replicate biosample 3


title: WT, P0.5 Heart, H3K9me2 CUT&RUN, Rep2

description:
Library name: WT_P0_5_H3K9me2_Rep2
Corresponding IgG is WT Rep4
WT_H3K9me2_log2fc.bw
P0_5_6_state_Hilands.bed


title: WT, P0.5 Heart, H3K9me3 CUT&RUN, Rep1

description:
Library name: WT_P0_5_H3K9me3_Rep1
Corresponding IgG is WT Rep1
WT_H3K9me3_merged.bw
P0_5_6_state_Hilands.bed


title: L4832

tag: progression status

value: ACT


title: Ctrl_exo_2

description:
Library name: sample 2
ctrl group, replicate biosample 2


title: Ctrl_exo_1

description:
Library name: sample 1
ctrl group, replicate biosample 1


title: L4840

tag: grade


title: L4714

value: IDH1 MUT


title: sibling-3

description: Library name: sample 1

value: WT


title: DNA from Older adults 1

source_name: naïve CD4+ T cells

value: naïve CD4+ T cells

tag: developmental stage/age

value: Older adults


title: sibling-4

description: Library name: sample 2


title: L4610

tag: age

value: Female

value: Low


title: midgut, mated 3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
A minimum of 20 million Paired End 100bp reads per sample were generated on a HiSeq2500 with single 6bp indexing
Data was processed using RTA version 1.18.64, with default filter and quality settings
The reads were demultiplexed with CASAVA 1.8.4 (allowing no mismatch)
Sequencing reads were mapped to dm6 genome using STAR aligner. Gene based counting was performed using the STAR aligner
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.42.0)
Assembly: Ensembl Drosophila genome reference sequence assembly (dm6)
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

organism: Drosophila melanogaster

source_name: midgut

growth_protocol: Flies were reared under standard conditions

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and quality was assessed using the Agilent 2100 Bioanalyser RNA 6000 Nano assay.
NGS libraries made using the Illumina TruSeq Stranded mRNA kit according to manufacturer’s instructions.

treatment_protocol: Flies were anestesised on ice and dissected in cold PBS.

value: midgut

value: wild-type (w1118)

value: mated


title: miRNA_PEDV_exo_2

description:
Library name: sample 17
PEDV group, miRNA-SEQ, replicate biosample 2

source_name: IPEC-DQ

value: IPEC-DQ


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, ATAC Rep1

description:
Library name: P0_5_ATAC_LB1Fplus_rep1
Nkx2_5Cre_LB1Fplus_merged_ATAC_5kb.bedgraph
Nkx2_5Cre_LB1Fplus_consensus_peaks.bed

data_processing:
Samples were processed using the nf-core/atacseq pipeline version 2.1.2 with Nextflow version 23.10.0. The pipeline performed adapter trimming, quality control, alignment, duplicate marking, filtering, broad peak calling, and generation of counts per million (CPM) normalized signal tracks. Reads were aligned to the Mus musculus reference genome (mm10) with the iGenomes GTF gene annotation file (iGenomes, UCSC) also provided during execution for peak annotation. A read length of 100 bp was specified, which was used to estimate fragment size and inform background modeling during broad peak calling with MACS2. Lastly, regions in the mm10 ENCODE blacklist (v2) were also excluded during execution with the --blacklist flag.
Assembly: GRCm38
Supplementary files format and content: Bedgraph file containing merged ATAC-seq profile and bed containing conensus peaks from broad peak calling.

source_name: Heart

extract_protocol:
Hearts from P0.5 hearts were dissociated using the Pierce Primary Cardiomyocyte Isolation Kit from ThermoFisher Scientific. Cardiomyocytes were then purified with neonate cardiomyocyte isolation beads from Miltenyi Biotec.
P0.5 cardiomyocytes were isolated and purified as previously described in the cardiomyocyte isolation and culture section of these methods and an aliquot of 50,000 cells per sample was taken for further processing. ATAC-seq was performed using the Zymo-Seq ATAC Library Prep Kit (Zymo, D5458-B) as per the manufacturer’s protocol. Briefly, live cells were lysed and nuclei isolated with the supplied reagents. Nuclei were then incubated with the provided transposition mix at 37°C for 30 minutes and DNA purified with the supplied Zymo-Spin IC Columns. Libraries were made with the provided library reagents and amplified with over 10 PCR cycles. Libraries were quantified with the Qubit dsDNA Quantification Assay Kit and library quality was verified on the 2100 Bioanalyzer System with High Sensitivity DNA Kit. Sequencing was conducted on the Illumina NextSeq1000 using 50x50 bp length paired-end reads.

value: Heart

value: Isolated Cardiomyocyte

value: Nkx2-5Cre; Lmnb1 Flox/+

tag: timepoint


title: L4595

source_name: Bulk Tumour

value: Bulk Tumour

value: Central Conventional Chondrosarcoma

value: Primary

tag: Sex

value: Male

tag: idh status


title: midgut, mated 2


title: Neurospora crassa, KTC, replicate3

city: Beijing

first: Shuting

last: Ye

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Library name: Sample12

data_processing:
Basecalling was performed using a software developed for DNBSEQ-T7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al.,  Genome Research, 1997.
Assembly: GCA_000182925.2
Supplementary files format and content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: Transcriptomic profiling of the WT, emp47(NCU00162)ko strains, with or without Ketoconazole treatment, were analyzed by high-throughput RNA sequencing (RNA-seq). Ketoconazole (Sigma) was added, with final concentration of 2 μg/mL.

value: mycelia

value: Ketoconazole


title: miRNA_iPEDV_exo_3

description:
Library name: sample 15
iPEDV group, miRNA-SEQ, replicate biosample 3


title: L4543

value: WT

tag: chrome

value: High


title: Neurospora crassa, KTC, replicate2

description: Library name: Sample11


title: L4540

value: ACT

value: Female

value: IDH2 MUT

tag: idhmut vaf


title: miRNA_iPEDV_exo_2

description:
Library name: sample 14
iPEDV group, miRNA-SEQ, replicate biosample 2


title: midgut, mated 1

tag: tissue

value: midgut

value: wild-type (w1118)


title: midgut, virgin 3

tag: genotype

value: virgin


title: L4532

value: Low


title: miRNA_iPEDV_exo_1

description:
Library name: sample 13
iPEDV group, miRNA-SEQ, replicate biosample 1

tag: cell type

value: IPEC-DQ


title: U251, H3K27ac

tag: cell line

value: Astrocytoma

tag: chip antibody

value: H3K27ac (Abcam:#ab4729)


title: Neurospora crassa, Control, replicate3

description: Library name: Sample9

tag: treatment

value: No treatment

tag: batch


title: L4485

value: Bulk Tumour

tag: diagnosis

value: Central Conventional Chondrosarcoma

value: Primary

tag: bone marrow content


title: L4348

tag: progression status

tag: grade

value: Male

value: IDH1 MUT


title: midgut, virgin 1


title: Y

city: Kunming

first: Ruixia

last: Tang

address: Jiaoling Road 935

institute: Chinese  Academy  of Medical Sciences & Peking Union Medical College

description: Library name: Sample18

data_processing:
Raw sequencing data (fastq format) were processed using Seqtk to remove adapter sequences, trim low-quality bases (Q < 20) from the 3' end, filter reads shorter than 25 nt, and remove rRNA-derived reads. Clean reads were aligned to the human reference genome (hg38) using BWA-MEM with default parameters. Circular RNAs were predicted and annotated using CIRI (v2.0). circRNA expression levels were quantified using SRPBM (Spliced Reads Per Billion Mapping) based on back-splicing junction reads. Differential expression analysis between groups was performed using edgeR (v3.32) with the following criteria: |Fold-change| ≥ 2 and p-value ≤ 0.05. Functional enrichment analyses (GO and KEGG) of parental genes of differentially expressed circRNAs were carried out using hypergeometric test with q-value ≤ 0.05 as significance threshold.
Assembly: GRCh38.p12 (hg38)
Supplementary files format and content: Format: xls; Content: circRNA_expression.xls

source_name: healthy control

extract_protocol:
Total RNA was extracted from whole-blood samples using TRIzol reagent (Invitrogen, Catalog No. 10296028CN) per the manufacturer’s protocol. RNA concentration/purity was assessed via NanoDrop 1000 (A260/A280 ≥ 1.8, A260/A230 ≥ 2.0), and integrity via Agilent 2100 Bioanalyzer (RNA Integrity Number (RIN) ≥ 8.0). Only qualified RNA was used for subsequent sequencing.
Total RNA was subjected to ribosomal RNA (rRNA) removal using Ribo-Zero rRNA Removal Kit (Epicentre), followed by fragmentation at 94°C for 8 minutes. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) with random primers and Actinomycin D. Second-strand cDNA was synthesized using Second Strand Marking Master Mix. The double-stranded cDNA products were purified using AMPure XP beads (Beckman). After end repair and adenylation at the 3' ends, Illumina RNA adapters were ligated. Libraries were amplified by PCR (98°C for 30 sec; 10 cycles of 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; final extension 72°C for 5 min). The final libraries were validated on an Agilent 2100 Bioanalyzer and quantified by Qubit 2.0 Fluorometer.

value: PBMC

tag: infected with


title: X3-1-1

description: Library name: Sample17

source_name: infected late mild


title: miRNA_Ctrl_exo_2

description:
Library name: sample 11
ctrl group, miRNA-SEQ, replicate biosample 2


title: L4213

value: ACT

tag: age


title: miRNA_Ctrl_exo_1

description:
Library name: sample 10
ctrl group, miRNA-SEQ, replicate biosample 1


title: L4265

tag: Sex

value: Female


title: X2-2-5

description: Library name: Sample16

source_name: infected early severe


title: lncRNA_PEDV_exo_3

description:
Library name: sample 9
PEDV group, lncRNA-SEQ, replicate biosample 3


title: L4165

tag: idh status


title: lncRNA_PEDV_exo_2

description:
Library name: sample 8
PEDV group, lncRNA-SEQ, replicate biosample 2


title: X2-2-3

description: Library name: Sample15


title: L4066

tag: chrome

value: High


title: lncRNA_PEDV_exo_1

description:
Library name: sample 7
PEDV group, lncRNA-SEQ, replicate biosample 1


title: X2-1-5

description: Library name: Sample14


title: Neurospora crassa emp47(NCU00162) mutant, Control, replicate3

description: Library name: Sample3

value: mycelia

value: emp47(NCU00162) knockout


title: L4057

value: IDH2 MUT

tag: idhmut vaf


title: X2-1-4

description: Library name: Sample13

source_name: infected early mild

tag: tissue


title: lncRNA_iPEDV_exo_3

description:
Library name: sample 6
iPEDV group, lncRNA-SEQ, replicate biosample 3


title: Neurospora crassa emp47(NCU00162) mutant, KTC, replicate1

description: Library name: Sample4

tag: genotype

value: Ketoconazole


title: Neurospora crassa emp47(NCU00162) mutant, Control, replicate2

description: Library name: Sample2


title: L4004

value: Low


title: lncRNA_iPEDV_exo_2

description:
Library name: sample 5
iPEDV group, lncRNA-SEQ, replicate biosample 2

tag: cell type

value: IPEC-DQ


title: L3691


title: X2-1-2

description: Library name: Sample11


title: Neurospora crassa emp47(NCU00162) mutant, Control, replicate1

description: Library name: Sample1


title: G6 - Lymph node, P toxin-induced, M#3

city: Suwon

first: Truc

middle: Do Thanh

last: Nguyen

state: All

address: 2066 Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University School of Medicine

description:
Library name: G6-Lymph Node-Mouse 3
10x Genomics

data_processing:
Libraries were processed according to the manufacturer’s instructions (10x Genomics) and sequenced on a Next-Seq 2000 platforms with 100-bp paired-end sequencing. Raw sequencing data were processed using CellRanger (version 7.0.0) (10x Genomics) with default setting.
Assembly: Mouse ref. package mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Mouse tissues were mechanically dissociated and enzymatically digested using Tumor Dissociation Kit, mouse (Miltenyi Biotech, Germany) according to the manufacturer’s instructions. Dead cells were removed using Ficoll-Paque PLUS (GE Healthcare).
We performed 10x Genomics scRNA-seq experiments according to the manufacturer’s instruction. The library preparation was performed using a Chromium Next GEM Single Cell 5’Kit v2 (10x Genomics, CA, USA), following the manufacturer’s protocols.

value: Lymph node

value: lymphocytes

value: Pertussis Toxin


title: L3522

value: Bulk Tumour

value: Central Conventional Chondrosarcoma

value: WT


title: X1-2-1

description: Library name: Sample10

source_name: infected late severe


title: lncRNA_Ctrl_exo_3

description:
Library name: sample 3
ctrl group, lncRNA-SEQ, replicate biosample 3


title: G6 - Lymph node, P toxin-induced, M#2

description:
Library name: G6-Lymph Node-Mouse 2
10x Genomics


title: L3349

value: Primary


title: L2814

value: Male

value: IDH1 MUT


title: W

description: Library name: Sample8

value: PBMC


title: X1-1-3

description: Library name: Sample9


title: lncRNA_Ctrl_exo_1

description:
Library name: sample 1
ctrl group, lncRNA-SEQ, replicate biosample 1


title: G6 - Lymph node, P toxin-induced, M#1

description:
Library name: G6-Lymph Node-Mouse 1
10x Genomics


title: lncRNA_Ctrl_exo_2

description:
Library name: sample 2
ctrl group, lncRNA-SEQ, replicate biosample 2


title: G6 - Tumor single cell, P toxin-induced, M#3

description:
Library name: G6-Tumor-Mouse 3
10x Genomics

source_name: Tumor

value: Tumor

value: cancer cells


title: L2788

value: High


title: L2375


title: G6 - Tumor single cell, P toxin-induced, M#2

description:
Library name: G6-Tumor-Mouse 2
10x Genomics


title: H

description: Library name: Sample6


title: Patient 5_Saliva

city: Bar Harbor

first: James

middle: Leonard

last: Miller

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Total RNA was derived from biofluid supernatant and analyzed by the Nanostring nCounter platform. 798 c-miRNAs were assessed in each sample.

hyb_protocol: Manufacturer's instructions via Human v3b miRNA CodeSet Kit (Nanostring)

data_processing: Normalization of code-set data was performed using linear standard curves from Positive Controls (Pos A-F) and Ligation Positive Control (A and B) via nSolver Analysis Software v4.0 (Nanostring). miRNAs with maximum normalized counts below 50 were excluded to minimize background noise Ahmed et al 2022 (Cancer (Baseline)), following manufacturer’s recommendations.

label: miRTag

extract_protocol:
Participants who consented to provide unstimulated whole saliva samples for the SUNY Upstate Medical University Biorepository Core were instructed to spit into a sterile container prior to performing a routine mouthwash. Collected saliva samples were immediately chilled on ice, transferred to cryogenic vials, and subsequently stored at -80ºC. For serum collection, whole blood was drawn into sterile Vacutainer Serum Tubes (BD, Franklin Lakes, NJ), allowed to clot for 30 min at room temperature (RT), and then centrifuged at 1250 x g for 10 min at 4ºC. The serum fraction was separated, aliquoted into individual freezer tubes, flash-frozen in liquid nitrogen, and stored at -80ºC. For plasma collection, whole blood was collected in sterile Vacutainer EDTA tubes (BD), centrifuged under the same conditions (1250 x g for 10 min at 4ºC), and the plasma layer was similarly aliquoted, frozen in liquid nitrogen, and stored at -80ºC.
Total RNA for Nanostring nCounter (Nanostring, Seattle WA) analysis was extracted using the Midi Plasma/Serum RNA Purification Kit (Norgen Biotek, Thorold, Ontario, Canada). Serum, plasma, and saliva samples were thawed on ice. To remove cell debris, saliva was centrifuged at 10,000 x g for 10 min, while serum and plasma samples were spun at 400 x g for 3 min. One mL of supernatant was collected from each sample and processed according to the manufacturer’s instructions, with RNA eluted at 100 µL volumes across all treatment groups. Following extraction, RNA samples were concentrated and purified using linear acrylamide. Each 100 mL RNA sample received 300 mL of ice cold 100% EtOH, 10 mL 3M sodium acetate (pH 5.5) (Invitrogen), 3 mL linear acrylamide (5mg/mL) (Invitrogen), and were incubated at -80ºC for 16 h. Samples were centrifuged at 13,000 x g for 30 min at 4ºC to pellet the RNA, followed by two washes with 75% ethanol. After air drying, RNA pellets were responded in 10 mL of nuclease-free water.

tag: patient id

tag: patient pathology

value: Benign urothelial issue. No history of cancer

tag: receptor expression

tag: tumor grade


title: Patient 6_Saliva

value: Invasive carcinoma, cribriform


title: L1763

data_processing: minfi package using R environment

extract_protocol: DNA was isolated from fresh-frozen tissue using the Wizard Genomic DNA purification kit (A1125, Promega, Madison, WI, USA), according to manufacturer’s instructions.

tag: diagnosis

value: ACT

value: Female

value: IDH2 MUT

value: Low


title: Patient 4_Saliva

value: Uterine-related pathology, No history of cancer


title: G5 - Lymph node, M#3

description:
Library name: G5-Lymph Node-Mouse 3
10x Genomics

value: Lymph node

value: lymphocytes

tag: treatment

value: non

tag: batch


title: L903

value: Bulk Tumour

value: Central Conventional Chondrosarcoma

tag: progression status

value: Primary

tag: grade

tag: bone marrow content


title: E

description: Library name: Sample4

value: PBMC

tag: infected with


title: Patient 3_Saliva

tag: age


title: G5 - Lymph node, M#2

description:
Library name: G5-Lymph Node-Mouse 2
10x Genomics


title: L795

tag: Sex

value: Male

tag: idh status

value: WT

tag: chrome


title: D

description: Library name: Sample3

tag: tissue


title: G5 - Lymph node, M#1

description:
Library name: G5-Lymph Node-Mouse 1
10x Genomics

tag: cell type

tag: genotype


title: Patient 2_Saliva

tag: patient id

tag: patient pathology


title: TNFko_24h_rep4

city: Milano

first: Stefano

last: Raffaele

state: -- Please Select (only U.S. / Can / Aus)

address: Via Balzaretti 9

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli Studi di Milano

description:
Gene expression data from brain of TNF knockout adult mouse 24 h post-stroke
Sample name: KL82_10

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: Arrays were scanned in a GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
Image analysis was performed using GeneChip® Operating Software (GCOS, Affymetrix). Expression data was normalized, background corrected and summarized using the GC-RMA algorithm implemented in the Partek Genomic Suite software.
Expression values are reported as log2 RMA-normalized signal intensities.

label: biotin

source_name: 24 h post-pMCAO TNF_KO

label_protocol: GeneChip® WT Terminal Labeling Kit (Affymetrix Inc, Santa Clara, CA, USA).

extract_protocol: Total RNA was extracted from frozen braines using Trizol reagent  (Invitrogen, Carlsbad, CA, USA) according to the manufacturers' instructions.

value: 8 weeks

value: TNFko

value: Brain

tag: surgery

value: pMCAO


title: Patient 1_Saliva

value: Invasive carcinoma of no special type (NST)

tag: receptor expression

tag: tumor grade


title: A

description: Library name: Sample1


title: TNFko_24h_rep3

description:
Gene expression data from brain of TNF knockout adult mouse 24 h post-stroke
Sample name: KL82_9


title: Patient 6_Serum

source_name: Serum

value: Serum

value: Invasive carcinoma, cribriform


title: G5 - Tumor single cell, M#2

description:
Library name: G5-Tumor-Mouse 2
10x Genomics

value: Tumor

value: cancer cells

tag: treatment

tag: batch


title: SD435C

city: La Jolla

first: Mark

last: Antkowiak

address: 3855 Health Sciences Dr

department: Surgery

description: Library name: Sample 6

data_processing:
Genome alignment was performed by STAR aligner with the human genome (hg38). The gene expression level were obtained by processing the RNA-sequencing reads through the BCBIO-nextGen pipeline, including alignment with STAR aligner and isoforms expression using Salmon and gene level expression using the featureCount script. The expression counts were then processed using DESeq including variance stabilization with rlog transformation.
Assembly: hg38
Supplementary files format and content: abundance.h5

source_name: mutant SDH-GIST

extract_protocol:
Total RNA was isolated from homogenized, snap-frozen human GISTs and from the corresponding cell cultures using the Qiagen RNeasy Kit. Libraries were generated from 1 µg of total RNA.
RNA libraries were prepared using Illumina's TruSeq Stranded mRNA Sample Prep Kit.

tag: cell line

value: mutant SDH-GIST

value: patient-derived SDH-mutant GIST cell line

value: SDHC mutant


title: TNFko_24h_rep2

description:
Gene expression data from brain of TNF knockout adult mouse 24 h post-stroke
Sample name: KL82_8


title: G6 - Tumor single cell, P toxin-induced, M#1

description:
Library name: G6-Tumor-Mouse 1
10x Genomics

value: Pertussis Toxin


title: Patient 5_Serum

value: Benign urothelial issue. No history of cancer


title: G5 - Tumor single cell, M#1

description:
Library name: G5-Tumor-Mouse 1
10x Genomics

value: non


title: F

description: Library name: Sample5

value: PBMC


title: SD424B

description: Library name: Sample 5

value: SDHB mutant


title: TNFko_24h_rep1

description:
Gene expression data from brain of TNF knockout adult mouse 24 h post-stroke
Sample name: KL76_22

value: Male

value: 8 weeks


title: G2 - Lymph node, P toxin-induced, M#3

description:
Library name: G2-Lymph Node-Mouse 3
10x Genomics

value: Lymph node

value: lymphocytes


title: Patient 4_Serum

value: Uterine-related pathology, No history of cancer


title: SD437A

description: Library name: Sample 4

value: SDHA mutant


title: mutant-3

description: Library name: sample 3

source_name: embryo

value: embryo

value: Cpa1 & Cpa5 konckout

value: 3 dpf


title: C57BL6_24h_rep4

description:
Gene expression data from brain of C57BL/6 adult mouse 24 h post-stroke
Sample name: KL42_5

source_name: 24 h post-pMCAO C57BL/6

value: Brain

value: pMCAO


title: G2 - Lymph node, P toxin-induced, M#2

description:
Library name: G2-Lymph Node-Mouse 2
10x Genomics