title: GeoMx-DSP-1001660022457-B-E01

description: Library name: GeoMx-DSP-1001660022457-B-E01

value: liver


title: GeoMx-DSP-1001660022457-B-D11

status: Public on Aug 05 2026

type: SRA

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

country: USA

institute: Mayo Clinic

description: Library name: GeoMx-DSP-1001660022457-B-D11

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: tissue

tag: condition

tag: segment

tag: zone

tag: batch


title: PVA80N_T2/GDM

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

description:
Library name: PVA80N_T2
Urine_counts_T1nT2.txt

data_processing:
Raw reads obtained from sequencing were aligned to the human reference genome (hg38) using the STAR (v2.5.2b) software which retained unique alignments and those with up to 4 mismatches.
Read counts were obtained using featurecounts toll from subread package. Differential gene expressions were analyzed using DESeq2 (version v1.20.0) package in R.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file includes raw counts for each samples

source_name: cell free RNA from Urine

growth_protocol: Urine samples were collected   in-person at three study visits during pregnancy and again at delivery

extract_protocol:
Urine samples were centrifuged immediately after collection at 16,000Xg for 10 min at 4°C to remove any residual debris and cells, aliquoted and stored at -80°C. Cell-free RNA was extracted from 4 ml of urine using the QIAmp MiniElute Virus Spin kit (Qiagen). Total RNA was quantified using the Qubit RNA HS Assay kit (Thermofisher Scientific) and RNA integrity verified using the Agilent High sensitivity RNA Screen Tape System (Agilent) on a 2200 TapeStation System (Agilent)
Ten µl of the extracted RNA (ranging from 2-4 ng of total RNA) was used to construct RNA-seq libraries with the NuGen Ovation SoLo RNA-Seq kit, along with the Human rRNA AnyDeplete kit (NuGen), following the manufacturer's instructions. The libraries were sequenced using 100 bp single-end reads on the HiSeq4000 System (Illumina).

value: cell free RNA from Urine

tag: trimester

value: Second

tag: study group

value: GDM


title: GeoMx-DSP-1001660022457-B-D09

description: Library name: GeoMx-DSP-1001660022457-B-D09


title: RPMI-8226, H3K36me3, rep2

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

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

molecule: genomic DNA

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).

tag: cell line

tag: cell type

value: Multiple myeloma

tag: chip antibody


title: GeoMx-DSP-1001660022457-B-D07

description: Library name: GeoMx-DSP-1001660022457-B-D07


title: PSU85W_T2/GDM

description:
Library name: PSU85W_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-D06

description: Library name: GeoMx-DSP-1001660022457-B-D06


title: SK-MEL-2, H3K36me3, rep2

value: Melanoma


title: GeoMx-DSP-1001660022457-B-D05

description: Library name: GeoMx-DSP-1001660022457-B-D05


title: PSN79O_T2/GDM

description:
Library name: PSN79O_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-D03

description: Library name: GeoMx-DSP-1001660022457-B-D03


title: SK-OV-3, H3K36me3, rep2

value: Ovarian serous cystadenocarcinoma


title: GeoMx-DSP-1001660022457-B-D02

description: Library name: GeoMx-DSP-1001660022457-B-D02


title: PRN85I_T2/GDM

description:
Library name: PRN85I_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-D01

description: Library name: GeoMx-DSP-1001660022457-B-D01


title: HCT116, H3K36me3, rep2

value: Colon carcinoma


title: GeoMx-DSP-1001660022457-B-C11

description: Library name: GeoMx-DSP-1001660022457-B-C11


title: GeoMx-DSP-1001660022457-B-C09

description: Library name: GeoMx-DSP-1001660022457-B-C09


title: PRL80T_T2/GDM

description:
Library name: PRL80T_T2
Urine_counts_T1nT2.txt


title: NCI-H522, H3K36me3, rep2

value: Lung adenocarcinoma


title: GeoMx-DSP-1001660022457-B-C08

description: Library name: GeoMx-DSP-1001660022457-B-C08


title: PRA77U_T2/GDM

description:
Library name: PRA77U_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-C07

description: Library name: GeoMx-DSP-1001660022457-B-C07


title: GeoMx-DSP-1001660022457-B-E05

description: Library name: GeoMx-DSP-1001660022457-B-E05


title: NCI-H226, H3K36me3, rep2

value: Pleural epithelioid mesothelioma


title: GeoMx-DSP-1001660022457-B-C06

description: Library name: GeoMx-DSP-1001660022457-B-C06


title: PCP81G_T1/PE

description:
Library name: PCP81G_T1
Urine_counts_T1nT2.txt

value: First

value: PE


title: PPR84F_T2/GDM

description:
Library name: PPR84F_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-C05

description: Library name: GeoMx-DSP-1001660022457-B-C05


title: MDA-MB-468, H3K36me3, rep2

value: Breast adenocarcinoma


title: GeoMx-DSP-1001660022457-B-C04

description: Library name: GeoMx-DSP-1001660022457-B-C04


title: K562, H3K36me3, rep2

value: Chronic myeloid leukemia


title: PLJ81T_T2/GDM

description:
Library name: PLJ81T_T2
Urine_counts_T1nT2.txt


title: EMS404 cells, SR9011-treated rep3

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

description: Library name: SR9011_veh_3

data_processing:
After initial QCs (OD260/280, RIN), oligo dT selection, random (N6) primed reverse transcription, end repair and adaptator ligation, cDNAs samples were paired-end sequenced (100 b) on the DNBSEQ BGI platform.
Sequence data filtering was performed using BGI SOAPnuke (v 1.5.2)(parameters: -I 15 -q 0.2 -n 0.05) and cleaned data were store as a Fastq file.  HISAT [v 2.0.4, (Kim et al, 2015)] was used to align valid reads on the mouse genome (mm10)(parameters:--sensitive –no-discordant –no mixed -I 1 -X 1000 -p8 –rnastrandness RF).  Bowtie2 [v2.2.5, (Langmead & Salzberg, 2012)](parameters: -q –phred64 –sensitive –dpad0 –gbar99999999 –mp1,1 -np 1 –score-min L,0,-0.1 -p 16 -k 200) was used to map reads of the reference transcriptome.  RSEM was used to determine gene expression levels [v1.2.8, (Li & Dewey, 2011)].  DEseq2 was used to identify differentially expressed genes [q value < 0.05, (Love et al, 2014)].
Assembly: mm10
Supplementary files format and content: Is a csv file, contains FPKM values fro each sample

organism: Mus musculus

growth_protocol: Cells were tretaed with the indicated compound for 24 hours then treated for an additional 24 hours with the compound + TGFb

extract_protocol:
Cellular RNAs were extracted from cells using the Macherey-Nagel™ Nucleospin™ Mini kit (#872061) or Qiagen RNeasy Micro kit (#74004), depending on sample abundance, following the manufacturers’ protocols. RNA concentration and purity were assessed with a Nanodrop One (ThermoFisher Scientific) or Qubit fluorometer and RNA HS Assay kit (#Q32852). RNA integrity was evaluated using a Bioanalyzer 2100 (Agilent). Samples with RIN <6.0 were discarded.
RNA libraries were built at BGI

treatment_protocol: Treatment was 24 hours with indicated compounds then 24 hours with the indicated compounds + TGFb

value: hepatic stellate cells

tag: genotype

value: Express human TLR4, from C57Bl6 mouse liver, SV40 immortalized

tag: treatment


title: T47D, H3K36me3, rep2

value: Invasive breast carcinoma


title: GeoMx-DSP-1001660022457-B-C03

description: Library name: GeoMx-DSP-1001660022457-B-C03

value: liver


title: PLC79F_T2/GDM

description:
Library name: PLC79F_T2
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: EMS404 cells, SR9011-treated rep2

description: Library name: SR9011_veh_2


title: GeoMx-DSP-1001660022457-B-C01

description: Library name: GeoMx-DSP-1001660022457-B-C01


title: NCI-H460, H3K36me3, rep2

value: Lung large cell carcinoma


title: PFP80Z_T2/GDM

description:
Library name: PFP80Z_T2
Urine_counts_T1nT2.txt

value: Second

value: GDM


title: EMS404 cells, SR9011-treated rep1

description: Library name: SR9011_veh_1


title: 786-O, H3K36me3, rep2

value: Renal cell carcinoma


title: GeoMx-DSP-1001660022457-B-B12

description: Library name: GeoMx-DSP-1001660022457-B-B12


title: PCJ88V_T2/GDM

description:
Library name: PCJ88V_T2
Urine_counts_T1nT2.txt


title: EMS404 cells, SR9011 and TGFb-treated rep3

description: Library name: SR9011_TGF_3


title: A549, H3K36me3, rep2


title: GeoMx-DSP-1001660022457-B-B11

description: Library name: GeoMx-DSP-1001660022457-B-B11


title: PVA80N_T1/GDM

description:
Library name: PVA80N_T1
Urine_counts_T1nT2.txt


title: EMS404 cells, SR9011 and TGFb-treated rep2

description: Library name: SR9011_TGF_2


title: GeoMx-DSP-1001660022457-B-B09

description: Library name: GeoMx-DSP-1001660022457-B-B09


title: PSU85W_T1/GDM

description:
Library name: PSU85W_T1
Urine_counts_T1nT2.txt


title: NCI-H23, H3K36me3, rep2


title: EMS404 cells, SR9011 and TGFb-treated rep1

description: Library name: SR9011_TGF_1


title: GeoMx-DSP-1001660022457-B-H03

description: Library name: GeoMx-DSP-1001660022457-B-H03


title: SNB19, H3K36me3, rep2

value: Astrocytoma


title: GeoMx-DSP-1001660022457-B-H04

description: Library name: GeoMx-DSP-1001660022457-B-H04


title: GeoMx-DSP-1001660022457-B-B08

description: Library name: GeoMx-DSP-1001660022457-B-B08


title: GeoMx-DSP-1001660022457-B-H01

description: Library name: GeoMx-DSP-1001660022457-B-H01


title: EMS404 cells, SB431542-treated rep3

description: Library name: SB43_veh_3


title: PSN79O_T1/GDM

description:
Library name: PSN79O_T1
Urine_counts_T1nT2.txt


title: NCI-H23, H3K36me3, rep3


title: U251, H3K36me3, rep2

value: Prostate carcinoma


title: SNB19, H3K36me3, rep3


title: PRN85I_T1/GDM

description:
Library name: PRN85I_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-B05

description: Library name: GeoMx-DSP-1001660022457-B-B05


title: EMS404 cells, SB431542-treated rep2

description: Library name: SB43_veh_2


title: A498, H3K36me3, rep2


title: GeoMx-DSP-1001660022457-B-G05

description: Library name: GeoMx-DSP-1001660022457-B-G05


title: U251, H3K36me3, rep3


title: GeoMx-DSP-1001660022457-B-B03

description: Library name: GeoMx-DSP-1001660022457-B-B03


title: PRL80T_T1/GDM

description:
Library name: PRL80T_T1
Urine_counts_T1nT2.txt


title: EMS404 cells, SB431542-treated rep1

description: Library name: SB43_veh_1


title: GeoMx-DSP-1001660022457-B-G01

description: Library name: GeoMx-DSP-1001660022457-B-G01


title: A498, H3K36me3, rep3


title: DU145, H3K36me3, rep2


title: PRA77U_T1/GDM

description:
Library name: PRA77U_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-B01

description: Library name: GeoMx-DSP-1001660022457-B-B01


title: HL-60, H3K36me3, rep2

value: Adult acute myeloid leukemia


title: DU145, H3K36me3, rep3


title: GeoMx-DSP-1001660022457-B-A12

description: Library name: GeoMx-DSP-1001660022457-B-A12


title: EMS404 cells, SB431542 and TGFb-treated rep2

description: Library name: SB43_TGF_2


title: EMS404 cells, SB431542 and TGFb-treated rep3

description: Library name: SB43_TGF_3


title: PPR84F_T1/GDM

description:
Library name: PPR84F_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-A11

description: Library name: GeoMx-DSP-1001660022457-B-A11


title: PLJ81T_T1/GDM

description:
Library name: PLJ81T_T1
Urine_counts_T1nT2.txt


title: EMS404 cells, SB431542 and TGFb-treated rep1

description: Library name: SB43_TGF_1


title: PLC79F_T1/GDM

description:
Library name: PLC79F_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-A10

description: Library name: GeoMx-DSP-1001660022457-B-A10


title: PC-3, H3K36me3, rep2


title: PFP80Z_T1/GDM

description:
Library name: PFP80Z_T1
Urine_counts_T1nT2.txt


title: SW620, H3K36me3, rep2

value: Colon adenocarcinoma


title: EMS404 cells, untreated (control) rep3

description: Library name: DMSO_veh_3

value: No treatment


title: EMS404 cells, untreated (control) rep2

description: Library name: DMSO_veh_2


title: GeoMx-DSP-1001660022457-B-A05

description: Library name: GeoMx-DSP-1001660022457-B-A05


title: CCRF-CEM, H3K27me3, rep3

source_name: CCRF-CEM

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: EMS404 cells, untreated (control) rep1

description: Library name: DMSO_veh_1


title: GeoMx-DSP-1001660022457-B-A04

description: Library name: GeoMx-DSP-1001660022457-B-A04


title: SK-MEL-28, H3K27me3, rep3

value: Cutaneous melanoma


title: EMS404 cells, TGFb-treated rep3

description: Library name: DMSO_TGF_3

value: hepatic stellate cells

value: TGFb


title: PTG80IT2/NORM

description:
Library name: PTG80IT2
Urine_counts_T1nT2.txt

value: Normal pregnancy


title: PCJ88V_T1/GDM

description:
Library name: PCJ88V_T1
Urine_counts_T1nT2.txt

value: First


title: MOLT-4, H3K27me3, rep3

value: Adult T acute lymphoblastic leukemia


title: GeoMx-DSP-1001660022457-B-A03

description: Library name: GeoMx-DSP-1001660022457-B-A03

value: liver


title: EMS404 cells, TGFb-treated rep2

description: Library name: DMSO_TGF_2

value: Express human TLR4, from C57Bl6 mouse liver, SV40 immortalized


title: GeoMx-DSP-1001660022456-E-H12

description: Library name: GeoMx-DSP-1001660022456-E-H12


title: PPF87IT2/NORM

description:
Library name: PPF87IT2
Urine_counts_T1nT2.txt

value: cell free RNA from Urine

value: Second


title: RPMI-8226, H3K27me3, rep3

value: Multiple myeloma


title: EMS404 cells, TGFb-treated rep1

description: Library name: DMSO_TGF_1


title: BC119 5hmC_Seal

city: Chicago

first: Zhou

last: Zhang

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

data_processing:
Library strategy: 5hmC-Seal
Raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Genome_build: hg19

source_name: Plasma

extract_protocol:
Briefly, circulating cfDNA was extracted from ~2-3 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany) according to manufacturer’s protocols. DNA concentration was quantified using a Qubit fluorometer (Thermo Fisher Scientific Inc.).
The cfDNA samples were randomized for constructing 5hmC-Seal libraries and subsequent sequencing. First, the Illumina-compatible adaptors were ligated onto the cfDNA samples per our published protocols. Next, T4 bacteriophage β-glucosyltransferase was used to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5hmC-modified fragments. The azide group was then reacted with a biotin-conjugated strained alkyne DBCO-PEG4-biotin (Sigma) via click chemistry to biotinylated the DNA fragments. Streptavidin beads (Thermo) were used for affinity enrichment of 5hmC-containing DNA fragments. The 5hmC-Seal libraries were subsequently constructed through PCR amplification using KAPA HyperPlus library construction kit (Roche) and paired-end sequenced (PE60) using the Illumina NextSeq500 platform (Illumina Inc., California, USA) at The University of Chicago Genomics Facility.

value: Plasma

tag: population

value: EA

tag: diagnosis

value: MM

tag: molecule

value: circulating cell-free DNA (cfDNA)


title: BC116 5hmC_Seal


title: PMY86E-T2/NORM

description:
Library name: PMY86E-T2
Urine_counts_T1nT2.txt


title: LTL331R-CL 5%FBS PIK5-33d 0.3µM 6h biol rep 2

city: Ann Arbor

first: Arul

middle: M

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description:
Library name: SI_36903
RiboErase

data_processing:
Xenograft FASTQs were processed using xengsort. Then, the human FASTQs were trimmed using BBDuk. Transcripts were quantified by kallisto with human reference genome (GRCh38/hg38) and then summarized to obtain gene level counts and TPM.
Assembly: hg38
Supplementary files format and content: counts.tsv: Gene-level TPM counts obtained from kallisto.
Supplementary files format and content: tpm.tsv: Gene-level TPM values obtained from kallisto.

growth_protocol: 1. LTL331R-CL cells were maintained in modified RPMI-1640, supplemented with 1X ITS-G, 10 nM hydrocortisone, 10 nM beta-estradiol, extra 2mM Glutamax, and 5% FBS or 0.1% FBS overnight before treatment. 2. AR+ and NEPC tumors were maintained in SCID male mice. 3. NEPC tumors were maintained in SCID male mice.

extract_protocol:
Total RNA was extracted from cultured cells or tumor tissues using the RNeasy mini kit, following the manufacturer’s instructions. 1 μg of total RNA was used to construct the sequencing libraries.
For tumor samples, ribosomal RNA was depleted using the RiboErase selection kit (Kapa Biosystems, KK8561). For cell lines and other samples, polyadenylated transcripts were enriched using Sera-Mag Oligo(dT)-Coated Magnetic Particles (GE Healthcare Life Sciences, 38152103010150). RNA libraries were constructed using the KAPA RNA HyperPrep Kit (Roche Sequencing, KK8541) from 800 ng of total RNA. Following rRNA depletion and RNA fragmentation (200-300 bp), double-stranded cDNA was synthesized, ligated with NEB adapters, and PCR-amplified using KAPA HiFi HotStart ReadyMix and NEB dual-index barcodes.

treatment_protocol: 1. NEPC cells were treated with DMSO, ESK981, Apilimod, or PIK5-33d for 6 hours. 2. No treatment for basaline comparison. 3. NEPC tumor-bearing mice were treated with Vehicle, ESK981, or Apilimod for 5 days, once per day.

value: NEPC cells


title: EMS404 cells, CLK8-treated rep3

description: Library name: CLK8_veh_3


title: GeoMx-DSP-1001660022456-E-H07

description: Library name: GeoMx-DSP-1001660022456-E-H07


title: GeoMx-DSP-1001660022456-E-H09

description: Library name: GeoMx-DSP-1001660022456-E-H09


title: PJP90YT2/NORM

description:
Library name: PJP90YT2
Urine_counts_T1nT2.txt


title: SK-OV-3, H3K27me3, rep3

value: Ovarian serous cystadenocarcinoma


title: SK-MEL-2, H3K27me3, rep3

value: Melanoma


title: EMS404 cells, CLK8-treated rep2

description: Library name: CLK8_veh_2

value: hepatic stellate cells


title: PJI85G-T2/NORM

description:
Library name: PJI85G-T2
Urine_counts_T1nT2.txt


title: HCT116, H3K27me3, rep3

value: Colon carcinoma


title: PGN82S-T2/NORM

description:
Library name: PGN82S-T2
Urine_counts_T1nT2.txt

value: Normal pregnancy


title: NCI-H522, H3K27me3, rep3

value: Lung adenocarcinoma


title: PEW85XT2/NORM

description:
Library name: PEW85XT2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022456-E-G11

description: Library name: GeoMx-DSP-1001660022456-E-G11


title: EMS404 cells, CLK8 and TGFb-treated rep2

description: Library name: CLK8_TGF_2


title: EMS404 cells, CLK8 and TGFb-treated rep3

description: Library name: CLK8_TGF_3


title: GeoMx-DSP-1001660022456-E-G10

description: Library name: GeoMx-DSP-1001660022456-E-G10


title: PET80MT2/NORM

description:
Library name: PET80MT2
Urine_counts_T1nT2.txt


title: NCI-H226, H3K27me3, rep3

value: Pleural epithelioid mesothelioma


title: MDA-MB-468, H3K27me3, rep3

value: Breast adenocarcinoma


title: GeoMx-DSP-1001660022456-E-G09

description: Library name: GeoMx-DSP-1001660022456-E-G09

value: liver


title: EMS404 cells, CLK8 and TGFb-treated rep1

description: Library name: CLK8_TGF_1

value: Express human TLR4, from C57Bl6 mouse liver, SV40 immortalized


title: EMS404 cells, transfected with scrambled siRNA and treated with vehicle rep3

description: Library name: siNtVeh3

data_processing:
After initial QCs (OD260/280, RIN), oligo dT selection, random (N6) primed reverse transcription, end repair and adaptator ligation, cDNAs samples were paired-end sequenced (100 b) on the DNBSEQ BGI platform.
Sequence data filtering was performed using BGI SOAPnuke (v 1.5.2)(parameters: -I 15 -q 0.2 -n 0.05) and cleaned data were store as a Fastq file.  HISAT [v 2.0.4, (Kim et al, 2015)] was used to align valid reads on the mouse genome (mm10)(parameters:--sensitive –no-discordant –no mixed -I 1 -X 1000 -p8 –rnastrandness RF).  Bowtie2 [v2.2.5, (Langmead & Salzberg, 2012)](parameters: -q –phred64 –sensitive –dpad0 –gbar99999999 –mp1,1 -np 1 –score-min L,0,-0.1 -p 16 -k 200) was used to map reads of the reference transcriptome.  RSEM was used to determine gene expression levels [v1.2.8, (Li & Dewey, 2011)].  DEseq2 was used to identify differentially expressed genes [q value < 0.05, (Love et al, 2014)].
Assembly: mm10
Supplementary files format and content: Is a csv file, contains FPKM values fro each sample
Supplementary files format and content: csv

growth_protocol: Cells were transfected with indicated siRNAs and then treated 48 hours later with TGFb for an additional 24 hours period

tag: strain

value: Express human TLR4, SV40 immortalized


title: T47D, H3K27me3, rep3

value: Invasive breast carcinoma


title: GeoMx-DSP-1001660022456-E-G08

description: Library name: GeoMx-DSP-1001660022456-E-G08


title: PBH84CT2/NORM

description:
Library name: PBH84CT2
Urine_counts_T1nT2.txt

value: cell free RNA from Urine

value: Second


title: NCI-H460, H3K27me3, rep3

value: Lung large cell carcinoma


title: EMS404 cells, transfected with scrambled siRNA and treated with vehicle rep2

description: Library name: siNtVeh2


title: PAV82HT2/NORM

description:
Library name: PAV82HT2
Urine_counts_T1nT2.txt


title: EMS404 cells, transfected with scrambled siRNA and treated with vehicle rep1

description: Library name: siNtVeh1


title: EMS404 cells, transfected with scrambled siRNA and treated with TGFb rep3

description: Library name: siNtTGF3


title: A549, H3K27me3, rep3


title: PAP91E-T2/NORM

description:
Library name: PAP91E-T2
Urine_counts_T1nT2.txt


title: 786-O, H3K27me3, rep3

value: Renal cell carcinoma


title: GeoMx-DSP-1001660022456-E-G03

description: Library name: GeoMx-DSP-1001660022456-E-G03


title: GeoMx-DSP-1001660022456-E-F11

description: Library name: GeoMx-DSP-1001660022456-E-F11

value: Portal-Periportal


title: PAA85ET2/NORM

description:
Library name: PAA85ET2
Urine_counts_T1nT2.txt


title: NCI-H23, H3K27me3, rep3


title: PTG80I-T1/NORM

description:
Library name: PTG80I-T1
Urine_counts_T1nT2.txt

value: First


title: SNB19, H3K27me3, rep3

value: Astrocytoma


title: EMS404 cells, transfected with scrambled siRNA and treated with TGFb rep1

description: Library name: siNtTGF1

value: hepatic stellate cells


title: GeoMx-DSP-1001660022456-E-F08

description: Library name: GeoMx-DSP-1001660022456-E-F08


title: PTA81A-T1/NORM

description:
Library name: PTA81A-T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022456-E-F07

description: Library name: GeoMx-DSP-1001660022456-E-F07


title: PPF87IT1/NORM

description:
Library name: PPF87IT1
Urine_counts_T1nT2.txt


title: EMS404 cells, transfected with Bmal1 siRNA and treated with vehicle rep2

description: Library name: siBmalVeh2


title: A498, H3K27me3, rep3


title: PMY86ET1/NORM

description:
Library name: PMY86ET1
Urine_counts_T1nT2.txt


title: EMS404 cells, transfected with Bmal1 siRNA and treated with vehicle rep1

description: Library name: siBmalVeh1


title: GeoMx-DSP-1001660022456-E-F03

description: Library name: GeoMx-DSP-1001660022456-E-F03


title: PJP90YT1/NORM

description:
Library name: PJP90YT1
Urine_counts_T1nT2.txt


title: DU145, H3K27me3, rep3

value: Prostate carcinoma


title: EMS404 cells, transfected with Bmal1 siRNA and treated with TGFb rep3

description: Library name: siBmalTGF3


title: GeoMx-DSP-1001660022456-E-F01

description: Library name: GeoMx-DSP-1001660022456-E-F01


title: OVCAR-8, H3K27me3, rep3

value: High grade ovarian serous adenocarcinoma


title: PJI85GT1/NORM

description:
Library name: PJI85GT1
Urine_counts_T1nT2.txt

value: Normal pregnancy


title: GeoMx-DSP-1001660022456-E-E11

description: Library name: GeoMx-DSP-1001660022456-E-E11


title: EMS404 cells, transfected with Bmal1 siRNA and treated with TGFb rep2

description: Library name: siBmalTGF2


title: PGN82ST1/NORM

description:
Library name: PGN82ST1
Urine_counts_T1nT2.txt


title: EMS404 cells, transfected with Bmal1 siRNA and treated with TGFb rep1

description: Library name: siBmalTGF1


title: PC-3, H3K27me3, rep3


title: PEW85XT1/NORM

description:
Library name: PEW85XT1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022456-E-E08

description: Library name: GeoMx-DSP-1001660022456-E-E08


title: Prelim_control-bio rep 2

city: Urbana

first: Lauriebeth

last: Leonelli

state: Illinois

address: 1206 W Gregory Dr.

department: Department of Agricultural and Biological Engineering

institute: University of Illinois Urbana-Champaign

description:
Library name: Apr24005
Apr24005

data_processing:
Sequence reads were trimmed using the JGI BBDuk shellscript with parameters k=23 ktrim=r mink=11 qtrim=r trimq=14 minlength=20 hdist=1.
Trimmed reads were aligned to the T. versicolor reference genome using HISAT2.
Reads mapping to exons were counted using the featureCounts program.
Assembly: Trametes versicolor FP-101664 SS1 v1.0; NCBI:txid717944
Supplementary files format and content: Tab-separated values file including the raw read counts for each sample.

molecule: polyA RNA

organism: Trametes versicolor

source_name: Mycelial pellet

growth_protocol: Fungal pellets were grown in 2% malt extract media (control) or HTL-AP supplemented media (treatment) for 3 days (main) or 7 days (preliminary) at 28 °C and 135 rpm.

extract_protocol:
RNA was extracted from frozen fungal pellet tissue was homogenized using TRIzol™ (Invitrogen™), and RNA was purified using a Qiagen RNeasy Plant Mini Kit (Qiagen).
The total RNAs (200 ng) were converted into individually barcoded polyadenylated mRNAseq libraries with the Watchmaker mRNA library prep kit following the manufacturer’s protocol.

treatment_protocol: Controls consisted of liquid 2% (w/v) malt extract culture media. Treatments were comprised of culture media supplemented with 5% HTL-AP.

value: Mycelial pellet

value: 7d no AP exposure rep 2

value: preliminary


title: SW620, H3K27me3, rep3

value: Colon adenocarcinoma


title: Prelim_AB-AP-bio rep 3

description:
Library name: Apr24004
Apr24004

value: 7d exposure to 5% AB AP rep 3


title: GeoMx-DSP-1001660022456-E-E07

description: Library name: GeoMx-DSP-1001660022456-E-E07

value: liver


title: CCRF-CEM, H3K27me3, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: PEH80CT1/NORM

description:
Library name: PEH80CT1
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: Prelim_AB-AP-bio rep 2

description:
Library name: Apr24003
Apr24003

value: 7d exposure to 5% AB AP rep 2


title: SK-MEL-28, H3K27me3, rep2

value: Cutaneous melanoma


title: GeoMx-DSP-1001660022456-E-E06

description: Library name: GeoMx-DSP-1001660022456-E-E06


title: PBH84CT1/NORM

description:
Library name: PBH84CT1
Urine_counts_T1nT2.txt

value: First


title: MOLT-4, H3K27me3, rep2

value: Adult T acute lymphoblastic leukemia


title: Prelim_control-bio rep 1

description:
Library name: Apr24002
Apr24002

value: 7d no AP exposure rep 1


title: PAV82HT1/NORM

description:
Library name: PAV82HT1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022456-E-E05

description: Library name: GeoMx-DSP-1001660022456-E-E05


title: Prelim_AB-AP-bio rep 1

description:
Library name: Apr24001
Apr24001

value: 7d exposure to 5% AB AP rep 1


title: GeoMx-DSP-1001660022456-E-E03

description: Library name: GeoMx-DSP-1001660022456-E-E03


title: K562, H3K27me3, rep2

value: Chronic myeloid leukemia


title: PAP91E-T1/NORM

description:
Library name: PAP91E-T1
Urine_counts_T1nT2.txt

value: Normal pregnancy


title: RPMI-8226, H3K27me3, rep2

value: Multiple myeloma


title: AB-AP-bio rep 3

description:
Library name: Mar25017
Mar25017

value: Mycelial pellet

value: 72h exposure to 5% AB AP rep 3

value: main


title: GeoMx-DSP-1001660022456-E-E02

description: Library name: GeoMx-DSP-1001660022456-E-E02


title: PAD84L-T1/NORM

description:
Library name: PAD84L-T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022456-E-E10

description: Library name: GeoMx-DSP-1001660022456-E-E10


title: PET80MT1/NORM

description:
Library name: PET80MT1
Urine_counts_T1nT2.txt


title: AB-AP-bio rep 2

description:
Library name: Mar25016
Mar25016

value: 72h exposure to 5% AB AP rep 2


title: SK-MEL-2, H3K27me3, rep2

value: Melanoma


title: GeoMx-DSP-1001660022456-E-D11

description: Library name: GeoMx-DSP-1001660022456-E-D11

value: liver


title: PAA85E-T1/NORM

description:
Library name: PAA85E-T1
Urine_counts_T1nT2.txt


title: AB-AP-bio rep 1

description:
Library name: Mar25015
Mar25015

value: 72h exposure to 5% AB AP rep 1


title: SK-OV-3, H3K27me3, rep2

value: Ovarian serous cystadenocarcinoma


title: GeoMx-DSP-1001660022456-E-D10

description: Library name: GeoMx-DSP-1001660022456-E-D10


title: NP_I/NP

description:
Library name: NP_I
Urine_counts_T1nT2.txt

value: cell free RNA from Urine

value: Non Pregnant


title: HCT116, H3K27me3, rep2

value: Colon carcinoma


title: SD-AP-bio rep 3

description:
Library name: Mar25014
Mar25014

value: 72h exposure to 5% SD AP rep 3


title: GeoMx-DSP-1001660022456-E-D09

description: Library name: GeoMx-DSP-1001660022456-E-D09


title: NP_H/NP

description:
Library name: NP_H
Urine_counts_T1nT2.txt


title: OVCAR-8, H3K36me3, rep2

value: High grade ovarian serous adenocarcinoma


title: GeoMx-DSP-1001660022456-E-D08

description: Library name: GeoMx-DSP-1001660022456-E-D08


title: SD-AP-bio rep 2

description:
Library name: Mar25013
Mar25013

value: 72h exposure to 5% SD AP rep 2


title: NP_G/NP

description:
Library name: NP_G
Urine_counts_T1nT2.txt


title: NCI-H522, H3K27me3, rep2

value: Lung adenocarcinoma


title: SD-AP-bio rep 1

description:
Library name: Mar25012
Mar25012

value: 72h exposure to 5% SD AP rep 1


title: GeoMx-DSP-1001660022456-E-D07

description: Library name: GeoMx-DSP-1001660022456-E-D07


title: NCI-H226, H3K27me3, rep2

value: Pleural epithelioid mesothelioma


title: GeoMx-DSP-1001660022457-B-A09

description: Library name: GeoMx-DSP-1001660022457-B-A09


title: NP_F/NP

description:
Library name: NP_F
Urine_counts_T1nT2.txt


title: K562, H3K27me3, rep3

value: Chronic myeloid leukemia


title: GeoMx-DSP-1001660022456-E-D05

description: Library name: GeoMx-DSP-1001660022456-E-D05


title: FW-AP-bio rep 3

description:
Library name: Mar25011
Mar25011

value: Mycelial pellet

value: 72h exposure to 5% FW AP rep 3


title: FW-AP-bio rep 2

description:
Library name: Mar25010
Mar25010

value: 72h exposure to 5% FW AP rep 2

value: main


title: T47D, H3K27me3, rep2

value: Invasive breast carcinoma


title: GeoMx-DSP-1001660022456-E-D04

description: Library name: GeoMx-DSP-1001660022456-E-D04

value: liver


title: BC37 5hmC_Seal

value: Plasma

value: AA

value: MM

value: circulating cell-free DNA (cfDNA)


title: SK-OV-3, H3K4me1, rep2

value: Ovarian serous cystadenocarcinoma


title: PTA81AT2/NORM

description:
Library name: PTA81AT2
Urine_counts_T1nT2.txt

value: cell free RNA from Urine

value: Second

value: Normal pregnancy


title: MDA-MB-468, H3K27me3, rep2

value: Breast adenocarcinoma


title: NP_B/NP

description:
Library name: NP_B
Urine_counts_T1nT2.txt

value: Non Pregnant


title: NP9/NP

description:
Library name: NP9
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022456-E-H05

description: Library name: GeoMx-DSP-1001660022456-E-H05


title: EMS404 cells, CLK8-treated rep1

description: Library name: CLK8_veh_1

value: hepatic stellate cells

value: Express human TLR4, from C57Bl6 mouse liver, SV40 immortalized


title: NCI-H460, H3K27me3, rep2

value: Lung large cell carcinoma


title: GeoMx-DSP-1001660022456-E-D03

description: Library name: GeoMx-DSP-1001660022456-E-D03


title: NP8/NP

description:
Library name: NP8
Urine_counts_T1nT2.txt


title: Control-bio rep 3

description:
Library name: Mar25008
Mar25008

value: Mycelial pellet

value: 72h no AP exposure rep 3


title: GeoMx-DSP-1001660022456-E-H01

description: Library name: GeoMx-DSP-1001660022456-E-H01


title: NP7/NP

description:
Library name: NP7
Urine_counts_T1nT2.txt


title: 786-O, H3K27me3, rep2

value: Renal cell carcinoma


title: GeoMx-DSP-1001660022456-E-D02

description: Library name: GeoMx-DSP-1001660022456-E-D02

value: liver


title: NP6/NP

description:
Library name: NP6
Urine_counts_T1nT2.txt


title: Control-bio rep 1

description:
Library name: Mar25006
Mar25006

value: 72h no AP exposure rep 1

value: main


title: A549, H3K27me3, rep2

value: Lung adenocarcinoma


title: Control-bio rep 2

description:
Library name: Mar25007
Mar25007

value: 72h no AP exposure rep 2


title: GeoMx-DSP-1001660022456-E-C12

description: Library name: GeoMx-DSP-1001660022456-E-C12


title: FW-AP-bio rep 1

description:
Library name: Mar25009
Mar25009

value: 72h exposure to 5% FW AP rep 1


title: NCI-H23, H3K27me3, rep2


title: PEH80CT2/NORM

description:
Library name: PEH80CT2
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: GeoMx-DSP-1001660022456-E-C10

description: Library name: GeoMx-DSP-1001660022456-E-C10


title: NP5/NP

description:
Library name: NP5
Urine_counts_T1nT2.txt


title: SNB19, H3K27me3, rep2

value: Astrocytoma


title: GeoMx-DSP-1001660022456-E-C09

description: Library name: GeoMx-DSP-1001660022456-E-C09


title: S57,HP_High_NoAr;HighPhosphorus_HighFood_NoArsenic (Control),rep3

city: Keene

first: Priyanka

last: Roy Chowdhury

state: New Hampshire

address: 229 Main Street

institute: Keene State College

description:
Library name: Sample 57
S57

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)

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: NP4/NP

description:
Library name: NP4
Urine_counts_T1nT2.txt


title: U251, H3K27me3, rep2

value: Prostate carcinoma


title: S52,LP_High_NoAr;LowPhosphorus_HighFood_NoArsenic,rep3

description:
Library name: Sample 52
S52


title: S51,LP_Low_NoAr;LowPhosphorus_LowFood_NoArsenic,rep3

description:
Library name: Sample 51
S51


title: GeoMx-DSP-1001660022456-E-C07

description: Library name: GeoMx-DSP-1001660022456-E-C07


title: NP3/NP

description:
Library name: NP3
Urine_counts_T1nT2.txt

value: Non Pregnant


title: A498, H3K27me3, rep2


title: GeoMx-DSP-1001660022456-E-C05

description: Library name: GeoMx-DSP-1001660022456-E-C05


title: NP2/NP

description:
Library name: NP2
Urine_counts_T1nT2.txt


title: BC14 5hmC_Seal

value: Plasma

value: AA

value: MM

value: circulating cell-free DNA (cfDNA)


title: S50,LP_Low_Ar;LowPhosphorus_LowFood_Arsenic,rep3

description:
Library name: Sample 50
S50


title: GeoMx-DSP-1001660022456-E-C03

description: Library name: GeoMx-DSP-1001660022456-E-C03


title: NCI-H522, H3K4me1, rep2


title: S49,LP_High_NoAr;LowPhosphorus_HighFood_NoArsenic,rep2

description:
Library name: Sample 49
S49


title: HL-60, H3K27me3, rep2

value: Adult acute myeloid leukemia


title: Tconvs, Day 25, ATAC

city: San Francsico

first: Qizhi

last: Tang

address: 513 Parnassus Ave

department: Diabetes Center

institute: University of California, San Francsico

description: 10X Genomics Multiome (ATAC + GEX)

library_source: genomic single cell

data_processing:
The demulitplexing, barcode processing, fragment (ATAC) or gene (GEX) counting were done via the Cell Ranger ARC v2.0.0 using default settings.
Assembly: hg38
Supplementary files format and content: File formats: filtered feature barcode matrix (filtered_feature_bc_matrix.h5) includes gene and peak features in rows and barcodes from CellRanger-identified cells in columns; ATAC fragments (atac_fragments.tsv.gz) includes count and barcode data for each ATAC fragment; GEX molecule info (gex_molecule_info.h5) in hdf5 file format includes count and barcode details for each GEX molecule observed; GEX files (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz) also provided in tab-separated value (TSV)  and matrix file format.

source_name: peripheral blood

growth_protocol: Freshly isolated primary human regulatory T cells (CD4+CD25+CD127dim/low) were stimulated or re-stimulated with CD3/CD28 Dynabeads at 1:1 cell:bead ratio on Days 0, 9, and 16. Cultures were maintained in RPMI-1640 plus recombinant human IL-2 (300 units/mL until Day 9, then reduced to 100 units/mL from Day 9 onward).

extract_protocol:
Nuclei were isolated according to 10X Genomics instructions for scMultiome (ATAC + Gene Expression) nuclei isolation. Briefly, cells were pelleted and washed with PBS + 0.04% BSA prior to cell lysis with Lysis Buffer (10 mM Tric-HCl, pH7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20; 0.1% NP-40 Substitute; 0.01% Digitonin; 1% BSA; 1 mM DTT; 1 U/uL RNase inhibitor) for 5 min on ice. The resulting nuclei were washed 3 times with pre-chilled Wash Buffer (10 mM Tric-HCl, pH7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20; 1% BSA; 1 mM DTT; 1 U/uL RNase inhibitor) and resuspended in Diluted Nuclei Buffer (10X Genomics Nuclei Buffer; 1 mM DTT; 1 U/uL RNase inhibitor).
Library was constructed according to manufacturer instructions for scMultiome (ATAC + Gene Expression). Briefly, the nuclei suspensions were incubated with Transposition Mix to fragment and append accesible chromatin regions with adapter sequences. The transposed nuclei are then combined with the master mix and loaded with barcoded Gel Beads and Partition Oil into a Chromium Next GEM Chip J to generate the gel bead-in-emulsion (GEM). Following retrotranscription of poly-A mRNA to cDNA, each GEM produces transposed DNA (for ATAC) and full-length cDNA (for gene expression), each with Illumina R1 primer sequences, 10X barcodes, and unique molecular identifiers (UMIs). Pooled fractions are recovered from each GEM with silane magnetic beads, and the barcoded transposed DNA and full-length cDNA are PCR-amplified to generate the input for library construction. For ATAC library construction, Illumina P7 and sample indexes are added via PCR to generate paired-end libraries with P5 and P7 sequences. For gene expression (GEX) libraries, cDNA amplicons are enzymatically fragmented and selected for appropriate size prior to addition of P5, P7, sample indexes, and TruSeq Read 2 primer sequences via end repair, A-tailing, adaptor ligation, and PCR.
snATAC-seq plus snRNA-seq

treatment_protocol: For the inflammatory cytokine-exposed samples, the culture media was supplemented with 25 ng/mL recombinant human IL-6, 20 ng/mL recombinant human IL-1beta, 20 ng/mL recombinant human IL-23 every 2-3 days.

value: peripheral blood

value: primary

value: CD4 Tconv

value: WT

value: IL-2 only


title: S46,HP_Low_NoAr;OptimalPhosphorus_LowFood_NoArsenic,rep3

description:
Library name: Sample 46
S46


title: OVCAR-8, H3K27me3, rep2

value: High grade ovarian serous adenocarcinoma


title: PC-3, H3K27me3, rep2


title: GeoMx-DSP-1001660022456-E-C02

description: Library name: GeoMx-DSP-1001660022456-E-C02

value: liver


title: GeoMx-DSP-1001660022456-E-C01

description: Library name: GeoMx-DSP-1001660022456-E-C01


title: GeoMx-DSP-1001660022456-E-B12

description: Library name: GeoMx-DSP-1001660022456-E-B12


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 25 rep3, ATAC

description: 10X Genomics Multiome (ATAC + GEX)

value: Treg

value: IL-2 plus IL-6, IL-1beta, IL-23


title: Tconvs, Day 25, GEX

description: 10X Genomics Multiome (ATAC + GEX)

library_source: transcriptomic single cell

molecule: nuclear RNA


title: GeoMx-DSP-1001660022456-E-B11

description: Library name: GeoMx-DSP-1001660022456-E-B11


title: SW620, H3K27me3, rep2

value: Colon adenocarcinoma


title: S38,HP_High_Ar; OptimalPhosphorus_OptimalFood_Arsenic,rep3

description:
Library name: Sample 38
S38

value: whole body


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 25 rep3, GEX

description: 10X Genomics Multiome (ATAC + GEX)


title: GeoMx-DSP-1001660022456-E-B10

description: Library name: GeoMx-DSP-1001660022456-E-B10


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 25 rep2, ATAC

description: 10X Genomics Multiome (ATAC + GEX)


title: MDA-MB-468, H3K4me2, rep2

value: Breast adenocarcinoma


title: SK-MEL-28, H3K4me2, rep2

value: Cutaneous melanoma


title: S36,HP_Low_NoAr; OptimalPhosphorus_LowFood_NoArsenic, rep2

description:
Library name: Sample 36
S36


title: GeoMx-DSP-1001660022456-E-B09

description: Library name: GeoMx-DSP-1001660022456-E-B09


title: GeoMx-DSP-1001660022456-E-B08

description: Library name: GeoMx-DSP-1001660022456-E-B08


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 25 rep1, ATAC

description: 10X Genomics Multiome (ATAC + GEX)


title: RPMI-8226, H3K4me2, rep2

value: Multiple myeloma


title: SK-MEL-2, H3K4me2, rep2

value: Melanoma


title: GeoMx-DSP-1001660022456-E-B07

description: Library name: GeoMx-DSP-1001660022456-E-B07


title: DU145, H3K4me1, rep2

value: Prostate carcinoma


title: BC6 5hmC_Seal

value: Plasma

value: AA

value: MM

value: circulating cell-free DNA (cfDNA)


title: PLJ81T_T4/GDM

description:
Library name: PLJ81T_T4
Urine_countsT3nT4.txt

value: cell free RNA from Urine

value: Delivery

value: GDM


title: S33,LP_High_Ar: LowPhosphorus_OptimalFood_Arsenic,rep2

description:
Library name: Sample 33
S33


title: Tregs, IL-2 only, Day 25, ATAC

description: 10X Genomics Multiome (ATAC + GEX)

value: peripheral blood

value: primary

value: WT

value: IL-2 only


title: GeoMx-DSP-1001660022456-E-B03

description: Library name: GeoMx-DSP-1001660022456-E-B03

value: liver


title: CCRF-CEM, H3K4me2, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: Tregs, IL-2 only, Day 25, GEX

description: 10X Genomics Multiome (ATAC + GEX)

value: Treg


title: GeoMx-DSP-1001660022456-E-B05

description: Library name: GeoMx-DSP-1001660022456-E-B05


title: T47D, H3K4me2, rep2

value: Invasive breast carcinoma


title: S31,LP_High_NoAr; LowPhosphorus_HighFood_NoArsenic,rep1

description:
Library name: Sample 31
S31

value: whole body


title: PC-3, H3K4me2, rep2

value: Prostate carcinoma


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 16 rep2, ATAC

description: 10X Genomics Multiome (ATAC + GEX)

value: IL-2 plus IL-6, IL-1beta, IL-23


title: 29,HP_Low_Ar; OptimalPhosphorus_LowFood_Arsenic,rep3

description:
Library name: Sample 29
S29


title: K562, H3K4me2, rep2

value: Chronic myeloid leukemia


title: GeoMx-DSP-1001660022456-E-B01

description: Library name: GeoMx-DSP-1001660022456-E-B01


title: S28,LP_High_Ar; LowPhosphorus_OptimalFood_Arsenic,rep1

description:
Library name: Sample 28
S28


title: GeoMx-DSP-1001660022456-E-A11

description: Library name: GeoMx-DSP-1001660022456-E-A11


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 16 rep1, ATAC

description: 10X Genomics Multiome (ATAC + GEX)


title: S25,LP_Low_Ar; LowPhosphorus_LowFood_Arsenic,rep1

description:
Library name: Sample 25
S25


title: GeoMx-DSP-1001660022456-E-A10

description: Library name: GeoMx-DSP-1001660022456-E-A10


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 16 rep1, GEX

description: 10X Genomics Multiome (ATAC + GEX)


title: S20,HP_Low_Ar; OptimalPhosphorus_LowFood_Arsenic,rep2

description:
Library name: Sample 20
S20


title: HCT116, H3K4me2, rep2

value: Colon carcinoma


title: GeoMx-DSP-1001660022456-E-A09

description: Library name: GeoMx-DSP-1001660022456-E-A09


title: HL-60, H3K4me2, rep2

value: Adult acute myeloid leukemia


title: GeoMx-DSP-1001660022456-E-A08

description: Library name: GeoMx-DSP-1001660022456-E-A08


title: S14,HP_High_Ar; OptimalPhosphorus_OptimalFood_Arsenic,rep1

description:
Library name: Sample 14
S14


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 16 rep2, GEX

description: 10X Genomics Multiome (ATAC + GEX)


title: GeoMx-DSP-1001660022456-E-A07

description: Library name: GeoMx-DSP-1001660022456-E-A07


title: MOLT-4, H3K4me2, rep2

value: Adult T acute lymphoblastic leukemia


title: SK-MEL-28-Input, rep1

value: Cutaneous melanoma


title: S8,HP_High_NoAr; OptimalPhosphorus_OptimalFood_NoArsenic (Control),rep1

description:
Library name: Sample 8
S8


title: GeoMx-DSP-1001660022456-E-A06

description: Library name: GeoMx-DSP-1001660022456-E-A06


title: S3,HP_Low_Ar; OptimalPhosphorus_LowFood_Arsenic,rep1

description:
Library name: Sample 3
S3


title: NCI-H522, H3K4me2, rep2

value: Lung adenocarcinoma


title: RPMI-8226-Input, rep1

value: Multiple myeloma


title: GeoMx-DSP-1001660022456-E-A05

description: Library name: GeoMx-DSP-1001660022456-E-A05


title: S1,HP_High_Ar; OptimalPhosphorus_OptimalFood_Arsenic,rep1

description:
Library name: Sample 1
S1


title: GeoMx-DSP-1001660022456-E-A04

description: Library name: GeoMx-DSP-1001660022456-E-A04


title: OVCAR-8, H3K4me2, rep2

value: High grade ovarian serous adenocarcinoma


title: SK-MEL-2-Input, rep1

value: Melanoma


title: ovary_NC_3

city: Xi'an

first: Song

last: Yan

state: Shaanxi Province

address: Xinsi Road, Baqiao District, Xi’an City

department: Department of Gynecology and Obstetrics, Tangdu Hospital

institute: Air Force Medical University

description:
Library name: sample9
NC_3

data_processing:
Raw data quality control: Raw reads in FASTQ format were processed using fastp (v0.23.4) to remove adapter sequences and low-quality reads. Reads with uncertain nucleotides (N) > 10% or low-quality bases (Q < 5) > 50% were discarded.
Assembly: GRCm39/mm39
Supplementary files format and content: Matrix tables with FPKM values for all detected genes across all samples (.txtx format).

source_name: ovary

extract_protocol:
Total RNA was extracted from mouse ovarian tissues using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's instructions. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed using the Agilent Fragment Analyzer 5400 system (Agilent Technologies, CA, USA).
RNA-seq libraries were constructed using the VAHTS® mRNA-seq v3 Library Prep Kit for Illumina (Vazyme, Nanjing, China) following the manufacturer's instructions. Briefly, mRNA was enriched by oligo(dT) magnetic beads, fragmented, and reverse-transcribed into cDNA. The cDNA underwent end-repair, A-tailing, adapter ligation, and PCR amplification. Library quality was assessed using the Agilent Fragment Analyzer 5400 system and quantified by Qubit® 2.0 Fluorometer.

value: ovary

value: NC


title: NCI-H23, H3K4me2, rep2


title: CCRF-CEM-Input, rep1

source_name: CCRF-CEM-Input

value: CCRF-CEM-Input

value: Childhood T acute lymphoblastic leukemia


title: ovary_NC_2

description:
Library name: sample8
NC_2


title: A498, H3K4me2, rep2

value: Renal cell carcinoma


title: GeoMx-DSP-1001660022456-E-A02

description: Library name: GeoMx-DSP-1001660022456-E-A02

value: liver


title: T47D-Input, rep1

value: Invasive breast carcinoma


title: DU145, H3K4me2, rep2

value: Prostate carcinoma


title: ovary_NC_1

description:
Library name: sample7
NC_1


title: GeoMx-DSP-1001660022455-C-H10

description: Library name: GeoMx-DSP-1001660022455-C-H10


title: U251, H3K4me2, rep2

value: Astrocytoma


title: K562-Input, rep1

value: Chronic myeloid leukemia


title: ovary_HBOT_2

description:
Library name: sample5
HBO_2

value: HBOT


title: A549, H3K4me2, rep2


title: DU145, H3K27me3, rep2


title: GeoMx-DSP-1001660022455-C-H06

description: Library name: GeoMx-DSP-1001660022455-C-H06


title: NP1/NP

description:
Library name: NP1
Urine_counts_T1nT2.txt

value: cell free RNA from Urine

value: Non Pregnant


title: S43,LP_Low_NoAr; LowPhosphorus_LowFood_NoArsenic,rep2

description:
Library name: Sample 43
S43

value: whole body


title: S48,LP_High_Ar;LowPhosphorus_OptimalFood_Arsenic,rep2

description:
Library name: Sample 48
S48


title: PC-3-Input, rep1


title: ovary_HBOT_1

description:
Library name: sample4
HBO_1


title: ovary_HBOT_3

description:
Library name: sample6
HBO_3


title: SK-OV-3-Input, rep1

value: Ovarian serous cystadenocarcinoma


title: 786-O, H3K4me2, rep2


title: S37,LP_Low_NoAr; LowPhosphorus_LowFood_NoArsenic,rep1

description:
Library name: Sample 37
S37


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 25 rep2, GEX

description: 10X Genomics Multiome (ATAC + GEX)

value: peripheral blood

value: primary

value: Treg

value: WT

value: IL-2 plus IL-6, IL-1beta, IL-23


title: GeoMx-DSP-1001660022455-C-H02

description: Library name: GeoMx-DSP-1001660022455-C-H02


title: GeoMx-DSP-1001660022455-C-H09

description: Library name: GeoMx-DSP-1001660022455-C-H09


title: SW620-Input, rep1

value: Colon adenocarcinoma


title: ovary_CTX_3

description:
Library name: sample3
CTX_3

value: ovary

value: CTX


title: S35,HP_High_Ar; OptimalPhosphorus_OptimalFood_Arsenic,rep2

description:
Library name: Sample 35
S35


title: GeoMx-DSP-1001660022455-C-G10

description: Library name: GeoMx-DSP-1001660022455-C-G10

value: liver


title: NCI-H460, H3K4me2, rep2

value: Lung large cell carcinoma


title: HCT116-Input, rep1

value: Colon carcinoma


title: ovary_CTX_2

description:
Library name: sample2
CTX_2


title: SNB19, H3K4me2, rep2

value: Astrocytoma


title: GeoMx-DSP-1001660022455-C-G09

description: Library name: GeoMx-DSP-1001660022455-C-G09


title: HL-60-Input, rep1

value: Adult acute myeloid leukemia


title: ovary_CTX_1

description:
Library name: sample1
CTX_1


title: SK-MEL-28, H3K36me2, rep2

value: Cutaneous melanoma


title: S34,LP_Low_Ar; LowPhosphorus_LowFood_Arsenic,rep2

description:
Library name: Sample 34
S34


title: Tregs, IL-2 + IL-6, IL-1beta, IL-23, Day 25 rep1, GEX

description: 10X Genomics Multiome (ATAC + GEX)


title: GeoMx-DSP-1001660022455-C-G06

description: Library name: GeoMx-DSP-1001660022455-C-G06


title: MOLT-4-Input, rep1

value: Adult T acute lymphoblastic leukemia


title: dep2_sal_8

city: Novosibirsk

first: Natalya

last: Bondar

address: 10, Ac. Lavrentieva ave.

country: Russia

institute: Institute of Cytology and Genetics SB RAS

description: Library name: dep2_sal_8

data_processing:
Raw sequencing reads were processed using fastp v0.20.1 for adapter trimming and quality filtering.
Filtered paired-end reads were aligned to the Mus musculus reference genome GRCm38 (mm10) using HISAT2 v2.2.1.
Gene-level read counts were generated using featureCounts from the Subread v2.0 package with GENCODE vM22 gene annotation.
Sequencing quality control metrics were assessed using FastQC and Picard tools.
Differential gene expression analysis was performed using DESeq2 v1.36.0 in R. Genes with at least 10 aligned reads in each sample were retained for analysis. P-values were adjusted using the Benjamini-Hochberg method.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data files contain normalized gene expression counts generated with DESeq2 for all analyzed samples.
Supplementary files format and content: Processed data files also include differential expression analysis results for glucocorticoid stimulation effects, chronic stress effects, and stress*dexamethasone interaction effects. Files contain gene identifiers, log2 fold changes, raw p-values, and adjusted p-values.

source_name: dorsal raphe nuclei

growth_protocol: Male C57BL/6 mice were housed under standard laboratory conditions with food and water available ad libitum. Animals were maintained under a 12 h light/dark cycle.

extract_protocol:
Total RNA was isolated from frozen dorsal raphe nuclei tissue using PureZOL reagent (Bio-Rad) according to the manufacturer’s instructions. RNA samples were purified using Agencourt RNAClean XP magnetic beads (Beckman Coulter). RNA quantity and quality were assessed using NanoDrop 2000 and Agilent 2100 Bioanalyzer. Only samples with RIN > 8.0 were used for RNA sequencing.
Strand-specific cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Poly(A)+ RNA was enriched using oligo-dT magnetic beads. Libraries were size-selected using Agencourt AMPure XP beads and amplified by PCR. Paired-end sequencing was performed on the Illumina XTen platform.

treatment_protocol: Mice were exposed to chronic social stress for 30 days. Transcriptomic responses were analyzed in basal conditions (6h after saline injection) and 6h following dexamethasone stimulation (2 mg/kg).

value: dorsal raphe nuclei

value: sal


title: GeoMx-DSP-1001660022455-C-G03

description: Library name: GeoMx-DSP-1001660022455-C-G03


title: MDA-MB-468, H3K36me2, rep2

value: Breast adenocarcinoma


title: NCI-H226-Input, rep1

value: Pleural epithelioid mesothelioma


title: dep2_sal_40

description: Library name: dep2_sal_40


title: RPMI-8226, H3K36me2, rep2

value: Multiple myeloma


title: GeoMx-DSP-1001660022455-C-G02

description: Library name: GeoMx-DSP-1001660022455-C-G02


title: NCI-H522-Input, rep1

value: Lung adenocarcinoma


title: SK-MEL-2, H3K36me2, rep2

value: Melanoma


title: GeoMx-DSP-1001660022456-E-B02

description: Library name: GeoMx-DSP-1001660022456-E-B02


title: dep2_sal_14

description: Library name: dep2_sal_14


title: GeoMx-DSP-1001660022455-C-G01

description: Library name: GeoMx-DSP-1001660022455-C-G01


title: SK-OV-3, H3K4me2, rep2

value: Ovarian serous cystadenocarcinoma


title: OVCAR-8-Input, rep1

value: High grade ovarian serous adenocarcinoma


title: dep2_dex_42

description: Library name: dep2_dex_42

value: dex


title: CCRF-CEM, H3K36me2, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: NCI-H23-Input, rep1


title: GeoMx-DSP-1001660022455-C-F10

description: Library name: GeoMx-DSP-1001660022455-C-F10

value: liver


title: T47D, H3K36me2, rep2

value: Invasive breast carcinoma


title: dep2_dex_38

description: Library name: dep2_dex_38


title: A498-Input, rep1

value: Renal cell carcinoma


title: GeoMx-DSP-1001660022455-C-F06

description: Library name: GeoMx-DSP-1001660022455-C-F06


title: dep1_sal_68

description: Library name: dep1_sal_68


title: GeoMx-DSP-1001660022455-C-F05

description: Library name: GeoMx-DSP-1001660022455-C-F05


title: DU145-Input, rep1

value: Prostate carcinoma


title: dep1_sal_62

description: Library name: dep1_sal_62


title: PC-3, H3K36me2, rep2


title: K562, H3K36me2, rep2

value: Chronic myeloid leukemia


title: GeoMx-DSP-1001660022455-C-F04

description: Library name: GeoMx-DSP-1001660022455-C-F04


title: SK-OV-3, H3K36me2, rep2


title: dep1_dex_64

description: Library name: dep1_dex_64

value: dorsal raphe nuclei


title: dep1_dex_6

description: Library name: dep1_dex_6


title: GeoMx-DSP-1001660022455-C-E12

description: Library name: GeoMx-DSP-1001660022455-C-E12


title: SW620, H3K36me2, rep2

value: Colon adenocarcinoma


title: 786-O-Input, rep1


title: dep1_dex_34

description: Library name: dep1_dex_34


title: GeoMx-DSP-1001660022455-C-E06

description: Library name: GeoMx-DSP-1001660022455-C-E06

value: Portal-Periportal


title: HCT116, H3K36me2, rep2

value: Colon carcinoma


title: con_sal_114

description: Library name: con_sal_114

value: sal


title: HL-60, H3K36me2, rep2

value: Adult acute myeloid leukemia


title: GeoMx-DSP-1001660022455-C-E05

description: Library name: GeoMx-DSP-1001660022455-C-E05


title: SNB19-Input, rep1

value: Astrocytoma


title: con_sal_104

description: Library name: con_sal_104


title: MOLT-4, H3K36me2, rep2

value: Adult T acute lymphoblastic leukemia


title: GeoMx-DSP-1001660022455-C-E03

description: Library name: GeoMx-DSP-1001660022455-C-E03


title: NCI-H226, H3K36me2, rep2

value: Pleural epithelioid mesothelioma


title: GeoMx-DSP-1001660022455-C-E02

description: Library name: GeoMx-DSP-1001660022455-C-E02


title: con_dex_122

description: Library name: con_dex_122

value: dex


title: NCI-H522, H3K36me2, rep2

value: Lung adenocarcinoma


title: MDA-MB-468, H3K9me3

value: Breast adenocarcinoma


title: GeoMx-DSP-1001660022455-C-D11

description: Library name: GeoMx-DSP-1001660022455-C-D11

value: liver


title: con_dex_116

description: Library name: con_dex_116


title: RPMI-8226, H3K9me3

value: Multiple myeloma


title: GeoMx-DSP-1001660022455-C-D10

description: Library name: GeoMx-DSP-1001660022455-C-D10


title: SK-MEL-2, H3K9me3

value: Melanoma


title: con_dex_101

description: Library name: con_dex_101


title: GeoMx-DSP-1001660022455-C-D09

description: Library name: GeoMx-DSP-1001660022455-C-D09


title: NCI-H23, H3K36me2, rep2


title: CCRF-CEM, H3K9me3

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: U251-Input, rep1


title: UTD-MM-001-2

city: Richardson

first: Marisol

last: Mancilla Moreno

address: 800 w. Campbell Road

department: Neuroscience

institute: University of Texas at Dallas

description:
Library name: UTD-MM-001-VIS2
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.

data_processing:
Raw data were processed with the 10X SpaceRanger pipeline
Assembly: Macaca_fascicularis_6.0 (GCA_011100615.1), Panubis1.0 GCA_008728515.1, Mmul_10 (GCA_003339765.3)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: lis of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifuing spots
Supplementary files format and content: spatial_enrichment.csv: list of gene enrishment in specific locations of the tissue
Library strategy: Spatial Transcriptomics

organism: Macaca mulatta

source_name: dorsal root ganglia

extract_protocol:
Fresh frozen non-human primate were collected from Worldwide Primates, inc.
Fresh frozen non-human primate dorsal root ganglia underwent Visium tissue optimization and spatial gene expression. Protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain.

value: dorsal root ganglia

tag: Sex


title: GeoMx-DSP-1001660022455-C-D08

description: Library name: GeoMx-DSP-1001660022455-C-D08

tag: tissue


title: T47D, H3K9me3

value: Invasive breast carcinoma


title: DU145, H3K36me2, rep2

value: Prostate carcinoma


title: UTD-MM-001-1

description:
Library name: UTD-MM-001-VIS1
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: PC-3, H3K9me3


title: U251, H3K36me2, rep2


title: GeoMx-DSP-1001660022455-C-D06

description: Library name: GeoMx-DSP-1001660022455-C-D06

tag: condition


title: K562, H3K9me3

value: Chronic myeloid leukemia


title: Mus musculus primary culture, sample WT2, Mthfd1l wildtype

city: Indianapolis

first: Gang

last: Peng

state: IN

address: 635 Barnhill Dr

department: Medical & Molecular Genetics

institute: Indiana University

description:
Library name: MTHWT-2
m6A levels

data_processing:
Basecalling with Dorado v0.5.1 using model rna004_130bps_sup@v3.0.1, with --modified-bases m6A_DRACH and --estimate-poly-a.
Base-called unaligned BAM converted to FASTQ using samtools fastq.
Reads aligned to mouse reference genome GRCm39 using minimap2 v2.26.
m6A modification sites detected using modkit 0.2.3 (pileup).
Splice junctions and isoforms identified with ESPRESSO; GENCODE vM34 annotation used.
Assembly: Mouse reference genome GRCm39 (GENCODE vM34 annotation).
Supplementary files format and content: .csv file includes m6A levels for each sample

source_name: primary culture

extract_protocol:
Total RNA was used as input; 1000ng for each sample
Direct RNA libraries prepared with ONT SQK-RNA004 per manufacturer’s instructions; 1,000 ng total RNA per sample; sequenced on PromethION R10 RNA flow cells (FLO-PRO004RA), one flow cell per sample; run up to 72 hours with MinKNOW on a PromethION 24.

value: primary culture

value: Mthfd1l wildtype


title: GeoMx-DSP-1001660022455-C-D03

description: Library name: GeoMx-DSP-1001660022455-C-D03

tag: segment


title: Mus musculus primary culture, sample WT1, Mthfd1l wildtype

description:
Library name: MTHWT-1
m6A levels


title: 786-O, H3K36me2, rep2

value: Renal cell carcinoma


title: GeoMx-DSP-1001660022455-C-D02

description: Library name: GeoMx-DSP-1001660022455-C-D02

tag: zone


title: SW620, H3K9me3

value: Colon adenocarcinoma


title: Mus musculus primary culture, sample KO3, Mthfd1l knockout

description:
Library name: MTHKO-3
m6A levels

value: Mthfd1l knockout

tag: batch


title: NCI-H460, H3K36me2, rep2

value: Lung large cell carcinoma


title: GeoMx-DSP-1001660022455-C-C11

description: Library name: GeoMx-DSP-1001660022455-C-C11


title: HCT116, H3K9me3

value: Colon carcinoma


title: Mus musculus primary culture, sample KO2, Mthfd1l knockout

description:
Library name: MTHKO-2
m6A levels


title: SNB19, H3K36me2, rep2

value: Astrocytoma


title: GeoMx-DSP-1001660022455-C-C10

description: Library name: GeoMx-DSP-1001660022455-C-C10

value: liver


title: HL-60, H3K9me3

value: Adult acute myeloid leukemia


title: Mus musculus primary culture, sample KO1, Mthfd1l knockout

description:
Library name: MTHKO-1
m6A levels


title: GeoMx-DSP-1001660022455-C-C07

description: Library name: GeoMx-DSP-1001660022455-C-C07


title: MOLT-4, H3K9me3

value: Adult T acute lymphoblastic leukemia


title: Xenium In situ Spatial Gene expression WE EDT-073-SV1_high_BFI

type: RNA

city: Pittsburgh

first: Fabio

last: Muniz De Oliveira

state: PA

address: 450 Technology Drive

institute: University of Pittsburgh

hyb_protocol: The probe hybridization, ligation, and rolling circle amplification were performed accordingly to the manufacturer’s protocol (CG000749 Rev B, 10x Genomics).

scan_protocol: Xenium In Situ Analyzer

data_processing: Data processed using Xenium Ranger software

label: Xenium custom 470-gene expression probe set

source_name: 5µm section High Biofilm-infected chronic wound skin

extract_protocol: total RNA

tag: disease state

value: chronic wound skin


title: MDA-MB-468, H3K36me1, rep2

value: Breast adenocarcinoma


title: GeoMx-DSP-1001660022455-C-C06

description: Library name: GeoMx-DSP-1001660022455-C-C06


title: SK-OV-3, H3K9me3

value: Ovarian serous cystadenocarcinoma


title: NCI-H226, H3K9me3

value: Pleural epithelioid mesothelioma


title: Xenium In situ Spatial Gene expression WE EDT-057-SV1_low_BFI

source_name: 5µm section Low Biofilm-infected chronic wound skin

label_protocol: Xenium custom 470-gene expression probe set


title: RPMI-8226, H3K36me1, rep2

value: Multiple myeloma


title: NCI-H522, H3K9me3

value: Lung adenocarcinoma


title: GeoMx-DSP-1001660022455-C-C02

description: Library name: GeoMx-DSP-1001660022455-C-C02


title: A_epidermis_rep3

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

hyb_protocol: GeneChip™ Hybridization, Wash, and Stain Kit Fluidics stations FS450-007

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Data processing and statistical data evaluation was performed in the R environment. The raw data were normalized and summarized using the RMA (robust multi-array average) algorithm from the R package oligo version 1.68.2. The genes were associated with vendor-provided annotation information (Release 36, Thermo Fisher Scientific, https://www.thermofisher.com/order/catalog/product/sec/assets?url=TFS-Assets/LSG/Support-Files/Clariom_S_Human.r1.na36.hg38.a1.transcript.csv.zip) and control genes were removed after background correction. Furthermore, irrelevant genes with low expression were removed so that 21,194 probes corresponding to 19,304 genes remained (intensity > 4 in at least 2 samples). After applying quality metrices to normalized data, it was determined that one biological replicate from control models at timepoint 4 was an outlier. Thus, that sample was further excluded from the microarray data analysis.   Differential gene expression (DGE) analysis was performed by the R package limma version 3.60.2: linear models were fit and moderated t-statistics computed by the eBayes function. The linear models were fitted, and moderated t-statistics were computed using the eBayes function. Subsequently, the Benjamini-Hochberg correction was applied to exclude false-positive results, and the differentially expressed genes were considered significant with an adjusted p-value<0.05 and a log2FC>0.5 as well as log2FC<-0.5.

label: biotin

source_name: bacterial mixture A_epidermis

label_protocol: Terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin

growth_protocol: Tissues were cultivated at 37°C and 5% CO2 in antibiotic-free maintenance medium (EFT-400-ABF) obtained from MatTek.

extract_protocol: Total RNA of the epidermis and dermis was extracted using Trizol ® reagent (Ambion) following manufacturer´s protocol.

treatment_protocol: Tissues were inoculated with different bacterial mixtures, which were previously isolated from skin swabs. As vehicel control, PBS was used.

value: MatTek's EpiDermFT

value: human-derived epidermal keratinocytes

value: NHEK

value: bacterial inoculation, mixture A


title: SK-MEL-2, H3K36me1, rep2

value: Melanoma


title: GeoMx-DSP-1001660022455-C-B11

description: Library name: GeoMx-DSP-1001660022455-C-B11


title: OVCAR-8, H3K9me3

value: High grade ovarian serous adenocarcinoma


title: CCRF-CEM, H3K36me1, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: GeoMx-DSP-1001660022455-C-B10

description: Library name: GeoMx-DSP-1001660022455-C-B10

value: liver


title: A_dermis_rep3

source_name: bacterial mixture A_dermis

value: human-derived dermal fibroblasts

value: NHDF


title: NCI-H23, H3K9me3


title: SK-MEL-28, H3K36me1, rep2

value: Cutaneous melanoma


title: T47D, H3K36me1, rep2

value: Invasive breast carcinoma


title: A498, H3K9me3

value: Renal cell carcinoma


title: GeoMx-DSP-1001660022455-C-B07

description: Library name: GeoMx-DSP-1001660022455-C-B07


title: PC-3, H3K36me1, rep2

value: Prostate carcinoma


title: A549-Input, rep1


title: GeoMx-DSP-1001660022455-C-E10

description: Library name: GeoMx-DSP-1001660022455-C-E10

value: Portal-Periportal


title: A_dermis_rep2


title: NCI-H460-Input, rep1

value: Lung large cell carcinoma


title: GeoMx-DSP-1001660022455-C-B06

description: Library name: GeoMx-DSP-1001660022455-C-B06


title: DU145, H3K9me3


title: K562, H3K36me1, rep2

value: Chronic myeloid leukemia


title: GeoMx-DSP-1001660022455-C-B04

description: Library name: GeoMx-DSP-1001660022455-C-B04


title: A_epidermis_rep1

value: MatTek's EpiDermFT

value: human-derived epidermal keratinocytes


title: SK-MEL-28, H3K9me3


title: con_sal_102

description: Library name: con_sal_102

value: dorsal raphe nuclei

value: sal


title: SK-OV-3, H3K36me1, rep2

value: Ovarian serous cystadenocarcinoma


title: GeoMx-DSP-1001660022455-C-B03

description: Library name: GeoMx-DSP-1001660022455-C-B03


title: A_dermis_rep1

value: bacterial inoculation, mixture A


title: A549, H3K9me3

value: Lung adenocarcinoma


title: SW620, H3K36me1, rep2

value: Colon adenocarcinoma


title: GeoMx-DSP-1001660022455-C-B02

description: Library name: GeoMx-DSP-1001660022455-C-B02

value: liver


title: OVCAR-8, H3K36me2, rep2

value: High grade ovarian serous adenocarcinoma


title: 786-O, H3K9me3


title: U251, H3K9me3

value: Astrocytoma


title: HCT116, H3K36me1, rep2

value: Colon carcinoma


title: GeoMx-DSP-1001660022455-C-A12

description: Library name: GeoMx-DSP-1001660022455-C-A12


title: AP_epidermis_rep3

source_name: bacterial mixture AP_epidermis

value: NHEK

value: bacterial inoculation, mixture AP


title: NCI-H460, H3K9me3


title: AP_dermis_rep3

source_name: bacterial mixture AP_dermis

value: human-derived dermal fibroblasts

value: NHDF


title: HL-60, H3K36me1, rep2

value: Adult acute myeloid leukemia


title: AP_epidermis_rep2

value: MatTek's EpiDermFT


title: A498, H3K36me2, rep2

value: Renal cell carcinoma


title: SNB19, H3K9me3


title: MOLT-4, H3K36me1, rep2

value: Adult T acute lymphoblastic leukemia


title: GeoMx-DSP-1001660022455-C-A10

description: Library name: GeoMx-DSP-1001660022455-C-A10

source_name: liver


title: GeoMx-DSP-1001660022455-C-A11

description: Library name: GeoMx-DSP-1001660022455-C-A11


title: SW620, H3K4me2, rep2


title: SK-MEL-28, H3K4me3

value: Cutaneous melanoma


title: NCI-H226, H3K36me1, rep2

value: Pleural epithelioid mesothelioma


title: AP_dermis_rep2


title: AP_epidermis_rep1

value: human-derived epidermal keratinocytes


title: GeoMx-DSP-1001660022455-C-D07

description: Library name: GeoMx-DSP-1001660022455-C-D07


title: GeoMx-DSP-1001660022455-C-A07

description: Library name: GeoMx-DSP-1001660022455-C-A07


title: Mus musculus primary culture, sample WT3, Mthfd1l wildtype

description:
Library name: MTHWT-3
m6A levels

value: primary culture

value: Mthfd1l wildtype


title: MDA-MB-468, H3K4me3

value: Breast adenocarcinoma


title: NCI-H522, H3K36me1, rep2

value: Lung adenocarcinoma


title: GeoMx-DSP-1001660022455-C-A06

description: Library name: GeoMx-DSP-1001660022455-C-A06

value: liver


title: RPMI-8226, H3K4me3

value: Multiple myeloma


title: OVCAR-8, H3K36me1, rep2

value: High grade ovarian serous adenocarcinoma


title: AP_dermis_rep1

value: bacterial inoculation, mixture AP


title: GeoMx-DSP-1001660022455-C-A05

description: Library name: GeoMx-DSP-1001660022455-C-A05


title: SK-MEL-2, H3K4me3

value: Melanoma


title: NCI-H23, H3K36me1, rep2


title: CCRF-CEM, H3K4me3

source_name: CCRF-CEM

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: BP_epidermis_rep3

source_name: bacterial mixture BP_epidermis

value: MatTek's EpiDermFT

value: NHEK

value: bacterial inoculation, mixture BP


title: GeoMx-DSP-1001660010639-D-H09

description: Library name: GeoMx-DSP-1001660010639-D-H09


title: BP_dermis_rep3

source_name: bacterial mixture BP_dermis

value: human-derived dermal fibroblasts

value: NHDF


title: T47D, H3K4me3

value: Invasive breast carcinoma


title: A498, H3K36me1, rep2

value: Renal cell carcinoma


title: PC-3, H3K4me3

value: Prostate carcinoma


title: GeoMx-DSP-1001660010639-D-H06

description: Library name: GeoMx-DSP-1001660010639-D-H06


title: DU145, H3K36me1, rep2


title: BP_dermis_rep2


title: U251, H3K36me1, rep2

value: Astrocytoma


title: GeoMx-DSP-1001660010639-D-H05

description: Library name: GeoMx-DSP-1001660010639-D-H05

value: Portal-Periportal


title: K562, H3K4me3

value: Chronic myeloid leukemia


title: BP_epidermis_rep1

value: human-derived epidermal keratinocytes


title: GeoMx-DSP-1001660010639-D-H04

description: Library name: GeoMx-DSP-1001660010639-D-H04

value: liver


title: A549, H3K36me1, rep2

value: Lung adenocarcinoma


title: BP_dermis_rep1


title: SK-OV-3, H3K4me3

value: Ovarian serous cystadenocarcinoma


title: GeoMx-DSP-1001660010639-D-H02

description: Library name: GeoMx-DSP-1001660010639-D-H02


title: NCI-H460, H3K36me1, rep2

value: Lung large cell carcinoma


title: SW620, H3K4me3

value: Colon adenocarcinoma


title: GeoMx-DSP-1001660010639-D-H01

description: Library name: GeoMx-DSP-1001660010639-D-H01


title: BA_epidermis_rep3

source_name: bacterial mixture BA_epidermis

value: MatTek's EpiDermFT

value: bacterial inoculation, mixture BA


title: GeoMx-DSP-1001660010639-D-G12

description: Library name: GeoMx-DSP-1001660010639-D-G12


title: BA_dermis_rep3

source_name: bacterial mixture BA_dermis


title: BA_epidermis_rep2

value: NHEK


title: HL-60, H3K4me3

value: Adult acute myeloid leukemia


title: BA_dermis_rep2

value: human-derived dermal fibroblasts

value: NHDF


title: MOLT-4, H3K4me3

value: Adult T acute lymphoblastic leukemia


title: Sublibrary_8 from multiplexed Anableps retina samples

city: Baton Rouge

first: Patricia

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

description: Library name: Aa_sub8

data_processing:
Sequence reads were mapped to Anableps anableps Genome Assembly GCA_014839685.1. SnRNA-seq FASTQ files were processed using the TrailmakerTM pipeline module (https://app.trailmaker.parsebiosciences.com/; v1.4.0, Parse Biosciences, 2024)
Assembly: GCA_014839685.1
Supplementary files format and content: Anableps_retina.rds - RDS file from Trailmaker

organism: Anableps anableps

source_name: Whole retina

extract_protocol:
Nuclei were fixed and frozen using the Evercode Nuclei Fixation Kit v3 (#NF100, #NF200) from Parse Biosciences following the manufacturer’s protocol.
snRNA-seq libraries were generated using Parse Biosciences combinatorial barcoding technology.  Fixed and frozen nuclei from each sample were processed to generate barcoded libraries aiming for 7,000 nuclei per sample using the Evercode WT v3 Kit (#WT100A-D, #WT200) as per manufacturer’s instructions. Samples were multiplexed during barcoding and sequenced as multiple technical sublibraries at the depth of 20,000 reads per nuclei in an Illumina Novaseq Xplus platform (paired-end, 150bp).

value: Whole retina

value: multiple

tag: developmental stage

value: adult


title: Sublibrary_7 from multiplexed Anableps retina samples

description: Library name: Aa_sub7


title: BA_epidermis_rep1

tag: cell line


title: GeoMx-DSP-1001660010639-D-G09

description: Library name: GeoMx-DSP-1001660010639-D-G09

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


title: BA_dermis_rep1

tag: cell type


title: Sublibrary_6 from multiplexed Anableps retina samples

description: Library name: Aa_sub6


title: GeoMx-DSP-1001660010639-D-G08

description: Library name: GeoMx-DSP-1001660010639-D-G08


title: BAP_dermis_rep3

source_name: bacterial mixture BAP_dermis

value: bacterial inoculation, mixture BAP


title: BAP_epidermis_rep3

source_name: bacterial mixture BAP_epidermis

value: human-derived epidermal keratinocytes


title: Sublibrary_5 from multiplexed Anableps retina samples

description: Library name: Aa_sub5


title: GeoMx-DSP-1001660010639-D-G06

description: Library name: GeoMx-DSP-1001660010639-D-G06

value: liver


title: NCI-H23, H3K4me3

value: Lung adenocarcinoma

tag: chip antibody


title: GeoMx-DSP-1001660010639-D-G05

description: Library name: GeoMx-DSP-1001660010639-D-G05

value: Portal-Periportal


title: A498, H3K4me3

value: Renal cell carcinoma


title: Sublibrary_3 from multiplexed Anableps retina samples

description: Library name: Aa_sub3


title: BAP_dermis_rep2


title: GeoMx-DSP-1001660010639-D-G02

description: Library name: GeoMx-DSP-1001660010639-D-G02


title: DU145, H3K4me3

value: Prostate carcinoma


title: BAP_dermis_rep1

value: MatTek's EpiDermFT


title: GeoMx-DSP-1001660010639-D-F12

description: Library name: GeoMx-DSP-1001660010639-D-F12


title: U251, H3K4me3

value: Astrocytoma


title: BAP_epidermis_rep1

value: NHEK


title: GeoMx-DSP-1001660022455-C-A02

description: Library name: GeoMx-DSP-1001660022455-C-A02


title: Csrp3 KO P21 sample 3

city: Houston

first: Riham

middle: Raafat Elgharib

last: Abouleisa

state: Texas

address: 6519 Fannin Street

department: surgery

institute: Baylor College of Medicine

description:
Library name: C9
column  E in gene_fpkm.xlsx: C9

data_processing:
Following end-repair and adapter ligation, libraries were PCR-amplified for nine cycles. Library quality was assessed using a Bioanalyzer High-Sensitivity DNA chip (Agilent), and concentrations were determined by qPCR (KAPA). Sequencing was performed on an Illumina NovaSeq platform using a 50-cycle single-read format. RNA-seq data processing followed a previously described pipeline. Briefly, adapter sequences and low-quality bases were removed using Fastq-mcf (http://code.google.com/p/ea-utils), and read quality was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the GRCh38 (human) or mm10 (mouse) reference genomes using TopHat v2.0.13. Gene expression levels were quantified using Subread featureCounts based on Ensembl annotations. Differential gene expression was analyzed using edgeR. Genes were filtered to include only those with at least two samples having counts per million (CPM) between 0.5 and 5000; genes with CPM < 0.5 were considered undetectable, and genes with CPM > 5000 (typically mitochondrial) were excluded to prevent skewed normalization. Remaining genes were normalized using the calcNormFactor function in edgeR, and P-values for differential expression were computed based on the negative binomial distribution model.
Assembly: GRCm39
Supplementary files format and content: gene_fpkm.xlsx

source_name: heart

extract_protocol:
RNA was extracted following the miRNeasy micro kit protocol (Qiagen Cat# 217084).
the Ovation Ultralow V2 Kit (NuGEN)

value: heart

tag: genotype

value: Csrp3 ko


title: BP_epidermis_rep2

tag: treatment

value: bacterial inoculation, mixture BP


title: Sublibrary_10 from multiplexed Anableps retina samples

description: Library name: Aa_sub10


title: GeoMx-DSP-1001660010639-D-F10

city: Rochester

first: Alexandra

last: Krivonos

address: 200 1st St SW

institute: Mayo Clinic

description: Library name: GeoMx-DSP-1001660010639-D-F10

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.


title: A549, H3K4me3

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


title: Csrp3 KO P21 sample 2

description:
Library name: C8
column  L in gene_fpkm.xlsx: C8


title: control_epidermis_rep3

value: negative control


title: 786-O, H3K36me1, rep2


title: GeoMx-DSP-1001660010639-D-F09

description: Library name: GeoMx-DSP-1001660010639-D-F09


title: HCT116, H3K4me3

value: Colon carcinoma


title: SNB19, H3K36me1, rep2


title: 786-O, H3K4me3


title: Sublibrary_9 from multiplexed Anableps retina samples

description: Library name: Aa_sub9

value: Whole retina

value: multiple


title: GeoMx-DSP-1001660010639-D-F06

description: Library name: GeoMx-DSP-1001660010639-D-F06


title: Csrp3 KO P21 sample 1

description:
Library name: C7
column  K in gene_fpkm.xlsx: C7


title: control_dermis_rep3

value: human-derived dermal fibroblasts

value: NHDF


title: NCI-H460, H3K4me3

value: Lung large cell carcinoma


title: GeoMx-DSP-1001660010639-D-G11

description: Library name: GeoMx-DSP-1001660010639-D-G11

value: liver


title: WT P21 sample 3

description:
Library name: C3
column  J in gene_fpkm.xlsx: C3

value: wt


title: control_epidermis_rep2

value: human-derived epidermal keratinocytes


title: GeoMx-DSP-1001660010639-D-F05

description: Library name: GeoMx-DSP-1001660010639-D-F05

value: Portal-Periportal


title: NCI-H226, H3K4me3

value: Pleural epithelioid mesothelioma


title: GeoMx-DSP-1001660010639-D-G10

description: Library name: GeoMx-DSP-1001660010639-D-G10


title: SNB19, H3K4me3

value: Astrocytoma


title: GeoMx-DSP-1001660010639-D-F04

description: Library name: GeoMx-DSP-1001660010639-D-F04


title: WT P21 sample 2

description:
Library name: C2R
column  I in gene_fpkm.xlsx: C2R


title: NCI-H522, H3K4me3

value: Lung adenocarcinoma


title: SK-MEL-28, H3K4me2, rep1

value: Cutaneous melanoma


title: GeoMx-DSP-1001660010639-D-F01

description: Library name: GeoMx-DSP-1001660010639-D-F01


title: MDA-MB-468, H3K4me2, rep1

value: Breast adenocarcinoma


title: EMS404 cells, transfected with Bmal1 siRNA and treated with vehicle rep3

description: Library name: siBmalVeh3

value: hepatic stellate cells

value: Express human TLR4, SV40 immortalized


title: Csrp3 KO P1 sample 3

description:
Library name: A9
column  G in gene_fpkm.xlsx: A9

value: heart

value: Csrp3 ko


title: control_epidermis_rep1

value: MatTek's EpiDermFT

value: NHEK

value: negative control


title: GeoMx-DSP-1001660010639-D-E12

description: Library name: GeoMx-DSP-1001660010639-D-E12


title: RPMI-8226, H3K4me2, rep1

value: Multiple myeloma


title: WT P21 sample 1

description:
Library name: C1R
column  H in gene_fpkm.xlsx: C1R


title: atrnh1c_DRIP_rep2

city: Hefei

first: Wenjie

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

data_processing:
Reads were aligned to the TAIR10 genome with Bowtie 2 using default settings, with all duplicates removed by Picard tools (http://broadinstitute.github.io/picard). The total mapped reads (nonstrand R-loops) were divided into strand Watson and Crick strand by using samtools
For visualization, the aligned reads files (Binary Alignment Map [BAM]) were converted to normalized coverage files (bigWig) with 1-bp bins using bamCoverage from deepTools.
Snapshots of the data were constructed using the Integrative Genomics Viewer.
Assembly: TAIR10
Supplementary files format and content: bw

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
ChloroplastDNAwas fragmented using 1Uof DdeI, MseI, RsaI and AluI (New England Biolabs) each per 2  g of DNA at 37◦C for 12 h. RNaseHpretreated cpDNA of Col-0 was included as negative control. Then the DNA was purified with the phenol–chloroform method and precipitated with 1 volume of isopropyl alcohol at –20◦C overnight. 2  g of fragmentedDNAwas incubated with 10  g S9.6 antibody overnight at 4◦C. Samples were further incubated with 50  l Protein G beads (Invitrogen) for 4 h at 4◦C. DRIPed DNA was purified with phenol-chloroform.
The DRIPed DNA was sonicated to ;250 bp with an M220 Fcused-ultrasonicator (Covaris). The sonicated DNA was used to construct ssDRIP-seq library by using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences), following instructions from the manufacturer.

value: leaf


title: Csrp3 KO P1 sample 2

description:
Library name: A8
column  F in gene_fpkm.xlsx: A8


title: U251, H3K27me3, rep3

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

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: Prostate carcinoma


title: OVCAR-8, H3K4me3

value: High grade ovarian serous adenocarcinoma


title: control_dermis_rep1

value: human-derived dermal fibroblasts

value: NHDF


title: GeoMx-DSP-1001660010639-D-E09

description: Library name: GeoMx-DSP-1001660010639-D-E09

value: liver

value: Portal-Periportal


title: SK-MEL-2, H3K4me2, rep1

value: Melanoma


title: atrnh1c_DRIP_rep1


title: GeoMx-DSP-1001660010639-D-E08

description: Library name: GeoMx-DSP-1001660010639-D-E08


title: Col0_DRIP_rep2


title: GeoMx-DSP-1001660010639-D-E06

description: Library name: GeoMx-DSP-1001660010639-D-E06


title: CCRF-CEM, H3K4me2, rep1

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: WT P1 sample 3

description:
Library name: A3
column D in gene_fpkm.xlsx: A3

value: wt


title: Col0_DRIP_rep1


title: T47D, H3K4me2, rep1

value: Invasive breast carcinoma


title: WT P1 sample 2

description:
Library name: A2
column C in gene_fpkm.xlsx: A2

value: heart


title: PC-3, H3K4me2, rep1


title: Patient NR1, BMMCs, HR_MDS, Non-Responder, Post-AZA

city: Patras

first: Argyro

last: Sgourou

address: Parodos Aristotelous 18

country: Greece

institute: Hellenic Open University

description: Library name: TB8463B_S2_L001_R1_001

data_processing:
Quality control using FastQC.
Unique Molecular Identifiers using UMI-tools
Adapter trimming using Cutadapt.
Alignment to mirBase using BWA.
Assembly: Hg38
Supplementary files format and content: csv comma-delimited containg raw counts for each sample

source_name: BMMCs

extract_protocol:
Total RNA including microRNA species was purified from the HR-MDS patient BMMCs, pre- and post-AZA treatment. RNA quality and integrity was assessed using the QIAxcel RNA QC Kit v2.0 (Qiagen, 929104) on the QIAxcel® Advanced System following the manufacturer’s instructions. All RNA samples showed high Integrity Scores (RIS), ranging from 8.5 to 9.5, except for sample R4 pre-AZA treatment (low RIS<4.5).
Libraries were constructed (QIAseq miRNA library kit, QIAGEN GmbH, Hilden, Germany) and RNA sequencing reactions were performed in Illumina iSeq 100 instrument (Illumina, Inc., US).

value: BMMCs

value: Post-AZA


title: GeoMx-DSP-1001660010639-D-E04

description: Library name: GeoMx-DSP-1001660010639-D-E04


title: control_dermis_rep2

value: MatTek's EpiDermFT

value: negative control


title: GeoMx-DSP-1001660010639-D-E03

description: Library name: GeoMx-DSP-1001660010639-D-E03


title: Patient NR1, BMMCs, HR_MDS, Non-Responder, Pre-AZA

description: Library name: TB8463A_S1_L001_R1_001

value: Pre-AZA


title: SK-OV-3, H3K4me2, rep1

value: Ovarian serous cystadenocarcinoma


title: 1525-2 DOX- MAK rep2

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: 1525-2_DOX-MAK_rep2

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: LUAD cell line

growth_protocol: 1525-2, 1533, 1544-2 cell lines were cultured with RPMI-1640 with 10% FBS, 100 U/mL of penicillin, and 100 μg/mL of streptomycin and 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Quick-RNA™ Miniprep kit (Cat # R1055, Zymo Research, CA, USA) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed.
Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

treatment_protocol: In corresponding treatment group, cells were treated with doxycyclin at 1ug/ml and MAK-683 at 2 uM for 6 days.

value: LUAD cell line

value: LUAD

value: MAK


title: Patient R1, BMMCs, HR_MDS, Responder, Post-AZA

description: Library name: PA8066B_S4_L001_R1_001


title: 1525-2 DOX- DMSO rep2

description: Library name: 1525-2_DOX-DMSO_rep2

value: DMSO


title: GeoMx-DSP-1001660010639-D-E02

description: Library name: GeoMx-DSP-1001660010639-D-E02

value: liver


title: GeoMx-DSP-1001660010639-D-D10

description: Library name: GeoMx-DSP-1001660010639-D-D10