title: MCF7_H3K27ac-ChIP-seq_10 pM E2 30 min_set 3

description:
Library name: MCF7_E2dose_10pM_H3K27ac_set3_S12_R1_001.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.

value: epithelial cells


title: PerturbPair lane13 GEX

status: Public on Apr 18 2026

type: SRA

city: San Francisco

first: Romain

last: Lopez

state: California

address: 1396 Sanchez St

country: USA

institute: New York University

description: Library name: LIB6253096_SAM24474585_lane13

library_source: transcriptomic

data_processing:
Raw reads were processed using Cell Ranger v7.0.0 with default parameters.
Reads were aligned to the mm10 reference genome.
Perturbation assignment was performed by demultiplexing gRNA barcodes with kallisto/bustools/kite.
Assembly: Mus musculus mm10 reference genome.
Supplementary files format and content: Processed data files are provided in Matrix Market (.mtx) format with accompanying feature and barcode annotation files (.tsv) for single-cell counts. In addition, perturbation assignment tables and processed gene expression matrices are provided as .csv and .h5ad (AnnData) formats for downstream analysis.
Library strategy: CITE-seq

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: Bone marrow cells were isolated from tibias and femurs of 6–12 week old Cas9 transgenic mice. Cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum, GlutaMAX, penicillin/streptomycin, and 100 ng/ml recombinant mouse M-CSF to differentiate into bone marrow–derived macrophages (BMDMs).

extract_protocol:
Following stimulation, cells were dissociated with Accutase and AccuMAX, washed, and prepared for single-cell encapsulation. Cellular RNA was extracted in droplet format using the 10x Genomics Chromium GEM-X chemistry according to manufacturer’s instructions.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Single Cell 3’ GEM-X kit. Libraries were indexed and sequenced on an Illumina NextSeq 2000 platform with 100 bp paired-end reads.

treatment_protocol: On day 10 of differentiation, cells were stimulated with lipopolysaccharide (LPS, 100 ng/ml) for 9 hours prior to collection for scRNA-seq.

tag: tissue

value: bone marrow

tag: cell line

value: BMDMs

tag: cell type


title: PerturbPair lane11 GEX

description: Library name: LIB6253094_SAM24474583_lane11


title: MCF7_ER-ChIP-seq_10 nM E2 30 min_set 3

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Library name: MCF7_E2dose_10nM_ER_set3_S30_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.

library_source: genomic

data_processing:
The Chip-seq reads were aligned to the hg38 human reference genome using bowtie2.
Mapped reads were sorted and captured in bam files for further downstream analysis of peak calling and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

molecule: genomic DNA

organism: Homo sapiens

source_name: ER+ breast adenocarcinoma

growth_protocol: MCF-7 human epithelia cells from breast adenocarsinoma cells from American Type Cell Culture (ATCC) were maintained in MEM supplemented with 5% calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin. MCF-7 cells were maintained in phenol red-free MEM supplimented with 5% charcoal-dextrantreated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin for at least 3 days prior to experimentation.

extract_protocol:
Nuclei were first extracted by inclubation in Farmham lysis buffer followed by centrifugation. Nuclei were then lysed in lysis buffer containing SDS, and sonicated for 8 cycles (30on/off) in a Dyagenode pico sonication device. Shear chromatin was cleared by incubation in dynabeads, protein concnetration measured, and at least 0.5 mg of material used for ChIP assays using the indicated antibody as described. Final ChIP'ed DNA was purified by phenol chloroform extraction followed by ethanol precipitation.
ChIP-seq libraries were generated as previously described (Judd J, et al., BioRxiv 2020). Libraries were generated from ChIP'ed DNA or input as described, and subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, adapter cleanup by SPRI-bead purification, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described using Illumina indexed barcodes and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded such that cells will bet at 70 to 80% confluency at the time of experimentation. Cells were treated with the indicated concentrations of E2 for 30 min., after which they were fixed with 1% formaldahyde for 10 mins at 37C before quencing with glycine at a final concentration of 125 mM. Fixed cells were snap frozen and stored at -80C until use.

value: ER+ breast adenocarcinoma

tag: treatment

value: 10 nM E2 for 30 min.


title: ATAC_shMed4 #1 biol rep 3

city: New York

first: Seongyeon

last: Bae

state: NY

institute: Columbia University

data_processing:
Reads were trimmed for both quality and Illumina adapter sequences using ‘trim_galore’ then aligned to mouse assembly mm10 with BWA using the default parameters.
Enriched regions were discovered using MACS2 and scored against matched input libraries (|fold change| > 2 and p-value < 0.005).
Raw read counts were tabulated over this peak atlas using featureCounts (http://subread.sourceforge.net).
Assembly: Genome_build: mm10 (GRCm38)
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: Breast

growth_protocol: D2A1-d breast cancer cell lines were maintained in DMED supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
5x10e4 D2A1-d cells were prepared and collected. Cells were then washed once with cold 1xPBS and spinned down at 500g for 5min at 4C. Cells were kept on ice and subsequently resuspended in 25ul 2xTD buffer (Illumina Nextera kit), 2.5ul Transposase enzyme (Illumina Nextera kit, 15028252) and 22.5ul Nuclease-free water in total of 50ul reaction for 1hr at 37C. DNA was then purified using Qiangen MinElute PCR purification kit (28004) in a final volume of 10ul.
ATAC-seq Libraries were prepared following the Buenrostro protocol (http://www.ncbi.nlm.gov/pmc/articles/PMC4374986/)

treatment_protocol: D2A1-d cells were transduced either non targeting control (NTC) or shRNAs targeting Med4.

value: Breast

value: Murine breast carcinoma

tag: genotype

value: Med4 Knockdown

value: Untreated


title: PerturbPair lane12 GEX

description: Library name: LIB6253095_SAM24474584_lane12


title: MCF7_H3K27ac-ChIP-seq_DMSO 30 min_set 3

description:
Library name: MCF7_E2dose_Veh_H3K27ac_set3_S11_R1_001.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with DMSO for 30 min.

value: DMSO for 30 min.


title: MCF7_ChIP-seq input_10 nM E2 30 min_set 3

description:
Library name: MCF7_E2dose_10nM_input_set3_S25_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 10 nM E2 for 30 min.


title: ATAC_shMed4 #1 biol rep 1


title: ATAC_shMed4 #4 biol rep 1


title: MCF7_H3K27ac-ChIP-seq_DMSO 30 min_set 2

description:
Library name: MCF7_E2dose_Veh_H3K27ac_set2_S3_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: MCF7_H3K27ac-ChIP-seq_DMSO 30 min_set 1

description:
Library name: MCF7_E2dose_Veh_H3K27ac_set1_S6_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: MCF7_ChIP-seq input_10 nM E2 30 min_set 2

description:
Library name: MCF7_E2dose_10nM_input_set2_S15_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 10 nM E2 for 30 min.


title: ATAC_shMed4 #1 biol rep 2


title: MCF7_ER-ChIP-seq_10 nM E2 30 min_set 1

description:
Library name: MCF7_E2dose_10nM_ER_set1_S10_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: PerturbPair lane9 GEX

description: Library name: LIB6253092_SAM24474581_lane9


title: MCF7_H3K27ac-ChIP-seq_10 pM E2 30 min_set 1

description:
Library name: MCF7_E2dose_10pM_H3K27ac_set1_S7_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.

value: 10 pM E2 for 30 min.


title: MCF7_ER-ChIP-seq_10 nM E2 30 min_set 2

description:
Library name: MCF7_E2dose_10nM_ER_set2_S20_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: MCF7_ChIP-seq input_10 nM E2 30 min_set 1

description:
Library name: MCF7_E2dose_10nM_input_set1_S5_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 10 nM E2 for 30 min.


title: PerturbPair lane8 GEX

description: Library name: LIB6253091_SAM24474580_lane8


title: PerturbPair lane10 GEX

description: Library name: LIB6253093_SAM24474582_lane10


title: ATAC_NTC biol rep 3

value: WT


title: MCF7_ER-ChIP-seq_1 nM E2 30 min_set 1

description:
Library name: MCF7_E2dose_1nM_ER_set1_S9_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 1 nM E2 for 30 min.

value: 1 nM E2 for 30 min.


title: ATAC_NTC biol rep 1


title: PerturbPair lane6 GEX

description: Library name: LIB6253089_SAM24474578_lane6


title: MCF7_ER-ChIP-seq_1 nM E2 30 min_set 3

description:
Library name: MCF7_E2dose_1nM_ER_set3_S29_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 1 nM E2 for 30 min.


title: MCF7_ChIP-seq input_1 nM E2 30 min_set 3

description:
Library name: MCF7_E2dose_1nM_input_set3_S24_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 1 nM E2 for 30 min.


title: ATAC_NTC biol rep 2


title: PerturbPair lane7 GEX

description: Library name: LIB6253090_SAM24474579_lane7


title: MCF7_ER-ChIP-seq_1 nM E2 30 min_set 2

description:
Library name: MCF7_E2dose_1nM_ER_set2_S19_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 1 nM E2 for 30 min.


title: MCF7_ER-ChIP-seq_100 pM E2 30 min_set 3

description:
Library name: MCF7_E2dose_100pM_ER_set3_S28_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 100 pM E2 for 30 min.

value: 100 pM E2 for 30 min.


title: MCF7_ER-ChIP-seq_100 pM E2 30 min_set 2

description:
Library name: MCF7_E2dose_100pM_ER_set2_S18_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 100 pM E2 for 30 min.


title: MCF7_ER-ChIP-seq_100 pM E2 30 min_set 1

description:
Library name: MCF7_E2dose_100pM_ER_set1_S8_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 100 pM E2 for 30 min.


title: PerturbPair lane5 GEX

description: Library name: LIB6253088_SAM24474577_lane5


title: PerturbPair lane4 GEX

description: Library name: LIB6253087_SAM24474576_lane4


title: MCF7_ChIP-seq input_100 pM E2 30 min_set 3

description:
Library name: MCF7_E2dose_100pM_input_set3_S23_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 100 pM E2 for 30 min.


title: MCF7_ChIP-seq input_1 nM E2 30 min_set 2

description:
Library name: MCF7_E2dose_1nM_input_set2_S14_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 1 nM E2 for 30 min.


title: PerturbPair lane2 GEX

description: Library name: LIB6251824_SAM24472316_lane2


title: MCF7_ER-ChIP-seq_10 pM E2 30 min_set 3

description:
Library name: MCF7_E2dose_10pM_ER_set3_S27_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: MCF7_ChIP-seq input_1 nM E2 30 min_set 1

description:
Library name: MCF7_E2dose_1nM_input_set1_S4_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 1 nM E2 for 30 min.


title: RNA_shMed4 #4 biol rep 3

data_processing:
Raw reads were quality-checked and subsequently mapped to the mouse genome (mm10_UCSC) through the Spliced Transcripts Alignment to a Reference (STAR)(Bioinformatics 29, 15-21), which outputs a BAM file containing both the sequence and its genomic coordinate.
Total number of reads per transcript was determined using the HTSeq Count program (Bioinformatics 31, 166-169).
Assembly: Genome_build: mm10 (GRCm38)
Supplementary files format and content: tab-delimited text file include raw counts for each sample

molecule: total RNA

extract_protocol:
Total RNA was extracted using the Maxwell® RSC simplyRNA Cells and RNase-free DNase Kit (Promega; AS1390) using an automated RNA/DNA isolation instrument (Maxwell, Promega).
Libraries were prepared by using the standard methodology and run on a BGISEQ-500 platform.


title: RNA_shMed4 #4 biol rep 1


title: RNA_shMed4 #1 biol rep 3


title: PerturbPair lane3 GEX

description: Library name: LIB6253086_SAM24474575_lane3


title: PerturbPair lane1 GEX

description: Library name: LIB6251823_SAM24472315_lane1


title: MCF7_ChIP-seq input_100 pM E2 30 min_set 2

description:
Library name: MCF7_E2dose_100pM_input_set2_S13_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 100 pM E2 for 30 min.


title: MCF7_ChIP-seq input_100 pM E2 30 min_set 1

description:
Library name: MCF7_E2dose_100pM_input_set1_S3_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 100 pM E2 for 30 min.


title: MCF7_ER-ChIP-seq_10 pM E2 30 min_set 2

description:
Library name: MCF7_E2dose_10pM_ER_set2_S17_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: RNA_shMed4 #1 biol rep 2


title: MCF7_ER-ChIP-seq_10 pM E2 30 min_set 1

description:
Library name: MCF7_E2dose_10pM_ER_set1_S7_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: RNA_shMed4 #1 biol rep 1


title: PerturbPair lane15 HTO

description: Library name: LIB6253085_SAM24474587_lane15


title: MCF7_ChIP-seq input_10 pM E2 30 min_set 3

description:
Library name: MCF7_E2dose_10pM_input_set3_S22_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 10 pM E2 for 30 min.


title: MCF7_ChIP-seq input_10 pM E2 30 min_set 2

description:
Library name: MCF7_E2dose_10pM_input_set2_S12_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 10 pM E2 for 30 min.


title: PerturbPair lane14 HTO

description: Library name: LIB6253084_SAM24474586_lane14


title: MCF7_ER-ChIP-seq_DMSO 30 min_set 2

description:
Library name: MCF7_E2dose_Veh_ER_set2_S16_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with DMSO for 30min.


title: MCF7_ChIP-seq input_10 pM E2 30 min_set 1

description:
Library name: MCF7_E2dose_10pM_input_set1_S2_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated with 10 pM E2 for 30 min.


title: PerturbPair lane13 HTO

description: Library name: LIB6253083_SAM24474585_lane13


title: MCF7_ER-ChIP-seq_DMSO 30 min_set 3

description:
Library name: MCF7_E2dose_Veh_ER_set3_S26_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with DMSO for 30min.


title: RNA_NTC biol rep 3


title: PerturbPair lane12 HTO

description: Library name: LIB6253082_SAM24474584_lane12


title: MCF7_ER-ChIP-seq_DMSO 30 min_set 1

description:
Library name: MCF7_E2dose_Veh_ER_set1_S6_R1_001.fastq.gz
Genomic DNA library derived from ERa enriched ChIP'ed DNA of cells treated with DMSO for 30min.


title: MCF7_ChIP-seq input_DMSO 30 min_set 3

description:
Library name: MCF7_E2dose_Veh_input_set3_S21_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated  with DMSO for 30min.


title: PerturbPair lane11 HTO

description: Library name: LIB6253081_SAM24474583_lane11


title: shMed1 #4 biol rep 3

treatment_protocol: D2A1-d cells were transduced either non targeting control (NTC) or shRNAs targeting Med1.

value: Med1 Knockdown


title: PerturbPair lane10 HTO

description: Library name: LIB6253080_SAM24474582_lane10


title: shMed1 #4 biol rep 2


title: RNA_NTC biol rep 1


title: C3_1.fq.gz

city: Jilin

first: chen

last: shaopeng

address: 77 Hanlin Road, Economic and Technological Development Zone, Jilin City, Jilin Province

country: China

institute: Jilin Agricultural Science and Technology College

description: Library name: Sample7

data_processing:
Raw sequencing data were processed using fastp software to remove adapters, poly-N, and low-quality reads to obtain high-quality clean data. The clean reads were aligned to the blueberry reference genome using HISAT2 software. Gene expression levels were estimated and normalized by calculating FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values using DESeq2/StringTie.
Assembly: Vaccinium corymbosum cv. 'Draper' v1.0
Supplementary files format and content: The feature-counts software (version 1.5.0) was employed to conduct quantitative statistics on the aligned reads corresponding to each gene, and fragments per kilobase of exon per million fragments mapped (FPKM) was used as the standard quantitative unit to measure the expression level of genes. With the help of the professional analysis tool DESeq2, differentially expressed genes (DEGs) were screened out. The specific screening criteria were as follows: genes with a false discovery rate (FDR) lower than 0.01 and an absolute value of log2 (fold change) not less than 1.2 were identified as DEGs
Supplementary files format and content: Tab-delimited text file containing the normalized gene expression values (FPKM) for all samples.

organism: Vaccinium corymbosum

source_name: fruit

growth_protocol: Blueberry plants (cultivar 'Bluecrop') were grown under standard agricultural conditions in the orchard. No specific controlled environmental conditions or artificial growth interventions were applied.

extract_protocol:
Total RNA was extracted from ground blueberry fruit samples using the TRIzol reagent following the manufacturer's instructions. The total RNA quantity and purity were evaluated using a NanoDrop 2000 spectrophotometer and an Agilent 2100 Bioanalyzer. High-quality RNA samples with an RNA Integrity Number (RIN) ≥ 7.0 were used for subsequent cDNA library construction .
The mRNA libraries were constructed for each sample of Populus simonii × P. nigra under alkaline stress, and sequencing work was carried out using the Illumina Novaseq platform to obtain the corresponding sequencing data. After sequencing was completed, quality assessment of the raw data was conducted.

treatment_protocol: No specific external biological or abiotic treatment was applied. Fruits were sampled at three distinct natural developmental stages: early green fruit stage (stage 1), color-break stage (stage 2), and mature stage (stage 3).

value: fruit

tag: developmental stage

value: mature stage (stage 3)

value: Bluecrop

value: None (natural development)


title: C3_3.fq.gz

description: Library name: Sample9


title: MCF7_ChIP-seq input_DMSO 30 min_set 1

description:
Library name: MCF7_E2dose_Veh_input_set1_S1_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated  with DMSO for 30min.

value: epithelial cells


title: MCF7_ChIP-seq input_DMSO 30 min_set 2

description:
Library name: MCF7_E2dose_Veh_input_set2_S11_R1_001.fastq.gz
Genomic DNA library derived from ChIP input DNA of cells treated  with DMSO for 30min.

value: ER+ breast adenocarcinoma


title: RNA_NTC biol rep 2


title: C3_2.fq.gz

description: Library name: Sample8


title: RNA_shMed4 #4 biol rep 2


title: C2_3.fq.gz

description: Library name: Sample6

value: color-break stage (stage 2)


title: PerturbPair lane8 HTO

description: Library name: LIB6253078_SAM24474580_lane8

value: bone marrow

value: BMDMs


title: C2_2.fq.gz

description: Library name: Sample5


title: shMed1 #2 biol rep 3

value: Breast

value: Murine breast carcinoma


title: C1_1.fq.gz

description: Library name: Sample1

value: early green fruit stage (stage 1)


title: PerturbPair lane7 HTO

description: Library name: LIB6253077_SAM24474579_lane7


title: PerturbPair lane9 HTO

description: Library name: LIB6253079_SAM24474581_lane9


title: shMed1 #2 biol rep 2


title: shMed1 #4 biol rep 1


title: C1_2.fq.gz

description: Library name: Sample2


title: MCF-7_HiC_10nM E2 30min_rep1

description:
Library name: MCF-7_10nM_HiC_rep1
Ligated genomic DNA purified after treatment with 10 nM E2 for 30 mins.

data_processing:
For alignment, theoretical fragments were first generated by in silico digestion of the hg19 reference genome using cut sites provided by Arima Genomics. UMI sequences were trimmed before alignment and processing using the HiC-Pro pipeline (Servant N. et al Genome Biol 2015).
Resulting paired .bam files from hic data alignment were converted to .validpair contact readmap files using the HiC-Pro pipeline. These files were then converted to .hic contact map files (which are compatible with most HiC data analysis software) using the Juicebox toolkit. TADs boundries were determined using the Arrowhead function in the Juicer toolkit as .bedpe files. These two file types were used for most downstream analysis. These were visualized using either HiCExplorer or UCSC genome browser.
Assembly: hg19
Supplementary files format and content: hic - Contact maps showing KR normalized and binned read counts, visualization on Galaxy HiCExplorer or UCSC geneome browser

extract_protocol:
The Arima High Coverage HiC Kit (Arima, A410110) was used as the manufacturer's protocol. In short, cells were treated as indicated, and fixed with 2% formaldehyde before quencing. Cells were counted using the BioRad TC20 cell counter and 0.4x10^6 cells were used per assay. Digestion was performed using the Arima HiC 2.0 RE cocktail mix, disgested ends were biotinylated, and proximity ligation was performed. Samples were confirmed to be >15% biotinylated.
Paired-ed sequencing libraries were prepared using the Arima Library Prep Module (Arima, A101030) as the manufacturer's protocol. In short, biotinylated DNA was sheared to ~550 to 600 bp usinig the Corvis E220 sonicator. 200 ng of resulting material was subjected to end repair, dA tailing, and adapter ligation as the protocol. Resulting libraries were amplified for 12 cycles before sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded such that cells will bet at 70 to 80% confluency at the time of experimentation. Cells were treated with the indicated concentrations of E2 for 30 min., after which cells were fixed in 2% formaldehyde and quenced with glycine before flash freezing and storing at -80C before HiC library preparation. Two biological replicates were used for each experimental condition.

value: 10 nM E2 for 30 min.


title: PerturbPair lane6 HTO

description: Library name: LIB6253076_SAM24474578_lane6


title: C2_1.fq.gz

description: Library name: Sample4


title: PerturbPair lane5 HTO

description: Library name: LIB6253075_SAM24474577_lane5


title: MCF-7_HiC_10nMM E2 30min_rep2

description:
Library name: MCF-7_10nM_HiC_rep2
Ligated genomic DNA purified after treatment with 10 nM E2 for 30 mins.


title: NTC biol rep 2

value: WT


title: MCF-7_HiC_10pM E2 30min_rep2

description:
Library name: MCF-7_10pM_HiC_rep2
Ligated genomic DNA purified after treatment with 10 pM E2 for 30 mins.

value: 10 pM E2 for 30 min.


title: MCF-7_HiC_DMSO 30min_rep2

description:
Library name: MCF-7_Veh_HiC_rep2
Ligated genomic DNA purified after treatment with DMSO for 30 mins.

value: DMSO for 30 min.


title: MCF-7_HiC_10pM E2 30min_rep1

description:
Library name: MCF-7_10pM_HiC_rep1
Ligated genomic DNA purified after treatment with 10 pM E2 for 30 mins.


title: NTC biol rep 3


title: PerturbPair lane2 HTO

description: Library name: LIB6251822_SAM24472316_lane2


title: MCF-7_HiC_DMSO 30min_rep1

description:
Library name: MCF-7_Veh_HiC_rep1
Ligated genomic DNA purified after treatment with DMSO for 30 mins.


title: NTC biol rep 1


title: PerturbPair lane3 HTO

description: Library name: LIB6253073_SAM24474575_lane3


title: shMed1 #2 biol rep 1

value: Med1 Knockdown


title: HL-60, mir451a overexpressed, LPS 90 minutes, replicate 1

city: Fribourg

first: Pierre-Yves

last: Mantel

address: Route Albert Gockel 1

department: Department: Oncology, Microbiology and Immunology

country: Switzerland

institute: University of Fribourg

description:
Library name: mirLPS901
HL-60, mir451a overexpressed, LPS 90 minutes, sample 1
counts_HL60.csv
normalizecount_HL60.csv

data_processing:
The pipeline was developed on Linux and includes Conda environment setup with tools like FASTQC, Trimmomatic, STAR, and MultiQC.
It loops through sample directories to process paired-end reads: renaming, compressing, quality control, and trimming.
STAR was used for genome indexing and alignment; MultiQC aggregated results across all tools for summary reporting.
Assembly: hg38
Supplementary files format and content: cvs files for  raw counts
Supplementary files format and content: csv files for normalized counts as Log2CPM

extract_protocol:
5x106 neutrophils or 1x106 HL-60 cells using the RNeasy Mini Kit including a DNase digest according to the manufacturer’s instructions (QIAGEN)
Library preparation used Novogene’s property RNA Library Prep Kit (PT042) based on NEB Next® Ultra™ RNA Library Prep Kit and NEB Next®.

value: mir451a overexpressed

value: LPS 90 minutes


title: HL-60, mir451a overexpressed, LPS 90 minutes, replicate 2

description:
Library name: mirLPS902
HL-60, mir451a overexpressed, LPS 90 minutes, sample 2
counts_HL60.csv
normalizecount_HL60.csv


title: PerturbPair lane4 HTO

description: Library name: LIB6253074_SAM24474576_lane4


title: Leaf, 12

city: Guiyang

first: Qin

last: Tang

address: Jiaxiu South Road

institute: Guizhou university

description:
Library name: sample12
YOE_3
YOE_3=L1EIH1305586-G31_4.R1.raw.fastq.gz=overexpression

data_processing:
Salmon,fastx_toolkit,stringtie,goatools
Assembly: Nicotiana_tabacum
Supplementary files format and content: rawdata

organism: Nicotiana tabacum

source_name: leaf

extract_protocol:
Complete transcriptome analysis of 12 samples
Functional database annotation analysis was performed on the genes and transcripts expressed in this study (NR, Swiss pro, Pfam, EggNOG, GO, and KEGG)

value: leaf

value: YOE

value: overexpression


title: HL-60, mir451a overexpressed, LPS 180 minutes, replicate 3

description:
Library name: mirLPS1803
HL-60, mir451a overexpressed, LPS 180 minutes, sample 3
counts_HL60.csv
normalizecount_HL60.csv

value: LPS 180 minutes


title: Leaf, 10

description:
Library name: sample10
YOE_1
YOE_1=L1EIH1305584-G31_2.R1.raw.fastq.gz=overexpression


title: JNGR114, PEComa tumor sample, EPIC methylation array

type: genomic

city: Illkirch

first: Gabriel

last: Malouf

state: Grand Est

address: 1 rue Laurent Fries

country: France

institute: INSTITUT/GENETIQUE/BIOLOGIE MOLEC/CELL

hyb_protocol: Amplified and fragmented DNA was denatured and hybridized overnight to the Illumina Infinium HumanMethylation850 (EPIC) BeadChip, allowing annealing to locus-specific oligonucleotides attached to bead types.

scan_protocol: Following hybridization and washing, BeadChips were scanned using the Illumina iScan system according to the manufacturer's instructions. Signal intensities were extracted using Illumina GenomeStudio software.

data_processing:
Raw signal intensities were extracted from IDAT files using the R package ChAMP (v2.28.0).  Beta (β) values representing DNA methylation levels were calculated for each CpG probe.  Probes with detection P-value > 0.01 were removed.  Probes with fewer than 3 beads in at least 5% of samples were filtered out.  Non-CpG probes, SNP-associated probes, and multi-hit probes were removed.  Probes located on sex chromosomes (X and Y) were excluded.  Filtered beta values were used for downstream analyses.
Tab-delimited text file containing CpG-level DNA methylation beta (β) values. Rows correspond to CpG probes and columns correspond to samples.

label: Cy5 and Cy3

source_name: PEComa

label_protocol: Genomic DNA (250–500 ng) was subjected to bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research), optimized for FFPE-derived DNA. The completeness of bisulfite conversion was verified using a MethyLight-based real-time PCR assay. Converted DNA was then whole-genome amplified and enzymatically fragmented according to the Illumina Infinium HumanMethylation850 BeadChip protocol.

growth_protocol: Not applicable (clinical human tumor samples; no in vitro cell culture).

extract_protocol: Genomic DNA was extracted from tumor tissue samples. DNA integrity, quantity, and purity were assessed using capillary electrophoresis (Agilent High Sensitivity DNA Kit) and Qubit fluorometric quantification.

treatment_protocol: Not applicable.

value: PEComa


title: Leaf, 11

description:
Library name: sample11
YOE_2
YOE_2=L1EIH1305585-G31_3.R1.raw.fastq.gz=overexpression


title: Leaf, 9

description:
Library name: sample9
Q_3
Q_3=L1EIH1305583-Q18_3.R1.raw.fastq.gz=knockout

value: knockout


title: PerturbPair lane1 HTO

description: Library name: LIB6251821_SAM24472315_lane1

value: bone marrow

value: BMDMs


title: HL-60, mir451a overexpressed, LPS 180 minutes, replicate 1

description:
Library name: mirLPS1801
HL-60, mir451a overexpressed, LPS 180 minutes, sample 1
counts_HL60.csv
normalizecount_HL60.csv


title: HL-60, mir451a overexpressed, LPS 180 minutes, replicate 2

description:
Library name: mirLPS1802
HL-60, mir451a overexpressed, LPS 180 minutes, sample 2
counts_HL60.csv
normalizecount_HL60.csv


title: HL-60, mir451a overexpressed, control, replicate 3

description:
Library name: mirCTRL3
HL-60, mir451a overexpressed, control, sample 3
counts_HL60.csv
normalizecount_HL60.csv

value: Untreated


title: HL-60, mir451a overexpressed, control, replicate 2

description:
Library name: mirCTRL2
HL-60, mir451a overexpressed, control, sample 2
counts_HL60.csv
normalizecount_HL60.csv


title: JNGR98, PEComa tumor sample, EPIC methylation array


title: HL-60, mir451a overexpressed, control, replicate 1

description:
Library name: mirCTRL1
HL-60, mir451a overexpressed, control, sample 1
counts_HL60.csv
normalizecount_HL60.csv


title: HL-60, GFP, LPS 90 minutes, replicate 2

description:
Library name: GFPLPS902
HL-60, GFP, LPS 90 minutes, sample 2
counts_HL60.csv
normalizecount_HL60.csv

value: GFP scramble


title: HL-60, GFP, LPS 90 minutes, replicate 3

description:
Library name: GFPLPS903
HL-60, GFP, LPS 90 minutes, sample 3
counts_HL60.csv
normalizecount_HL60.csv


title: C1_3.fq.gz

description: Library name: Sample3

value: fruit

value: early green fruit stage (stage 1)

value: Bluecrop

value: None (natural development)


title: JNGR139, PEComa tumor sample, EPIC methylation array


title: JNGR132, PEComa tumor sample, EPIC methylation array


title: HL-60, GFP, control, replicate 2

description:
Library name: GFPCTRL2
HL-60, GFP, control, sample 2
counts_HL60.csv
normalizecount_HL60.csv


title: JNGR136, PEComa tumor sample, EPIC methylation array


title: HL-60, GFP, control, replicate 1

description:
Library name: GFPCTRL1
HL-60, GFP, control, sample 1
counts_HL60.csv
normalizecount_HL60.csv


title: Neutrophils, LPS+EVs, sample 2

description:
Library name: Neutro2LPSEV
Neutrophils, LPS+EVs, sample 2
counts_Neutro.csv
normalizecount_Neutro.csv

source_name: Blood

value: Blood

value: Neutrophils

value: LPS+Evs


title: Neutrophils, LPS+EVs, sample 1

description:
Library name: Neutro1LPSEV
Neutrophils, LPS+EVs, sample 1
counts_Neutro.csv
normalizecount_Neutro.csv


title: JNGR130, PEComa tumor sample, EPIC methylation array


title: Leaf, 3

description:
Library name: sample3
KY_3
KY_3=L1EIH1305577-KY_4.R1.raw.fastq.gz=wildtype

value: leaf

value: KY

value: wildtype


title: Leaf, 8

description:
Library name: sample8
Q_2
Q_2=L1EIH1305582-Q18_2.R1.raw.fastq.gz=knockout


title: JNGR133, PEComa tumor sample, EPIC methylation array


title: HL-60, GFP, LPS 180 minutes, replicate 3

description:
Library name: GFPLPS1803
HL-60, GFP, LPS 180 minutes, sample 3
counts_HL60.csv
normalizecount_HL60.csv

value: LPS 180 minutes


title: HL-60, GFP, LPS 180 minutes, replicate 2

description:
Library name: GFPLPS1802
HL-60, GFP, LPS 180 minutes, sample 2
counts_HL60.csv
normalizecount_HL60.csv


title: Leaf, 7

description:
Library name: sample7
Q_1
Q_1=L1EIH1305581-Q18_1.R1.raw.fastq.gz=knockout


title: Neutrophils, LPS, sample 2

description:
Library name: Neutro2LPS
Neutrophils, LPS, sample 2
counts_Neutro.csv
normalizecount_Neutro.csv

value: LPS


title: Leaf, 1

description:
Library name: sample1
KY_1
KY_1=L1EIH1305575-KY_1.R1.raw.fastq.gz=wildtype


title: Leaf, 6

description:
Library name: sample6
K_3
K_3=L1EIH1305580-K326_3.R1.raw.fastq.gz=wildtype


title: Leaf, 5

description:
Library name: sample5
K_2
K_2=L1EIH1305579-K326_2.R1.raw.fastq.gz=wildtype


title: HL-60, GFP, control, replicate 3

description:
Library name: GFPCTRL3
HL-60, GFP, control, sample 3
counts_HL60.csv
normalizecount_HL60.csv


title: JNGR127, PEComa tumor sample, EPIC methylation array

value: PEComa


title: Leaf, 2

description:
Library name: sample2
KY_2
KY_2=L1EIH1305576-KY_2.R1.raw.fastq.gz=wildtype


title: Neutrophils, LPS+EVs, sample 3

description:
Library name: Neutro3LPSEV
Neutrophils, LPS+EVs, sample 3
counts_Neutro.csv
normalizecount_Neutro.csv


title: HL-60, mir451a overexpressed, LPS 90 minutes, replicate 3

description:
Library name: mirLPS903
HL-60, mir451a overexpressed, LPS 90 minutes, sample 3
counts_HL60.csv
normalizecount_HL60.csv

value: mir451a overexpressed

value: LPS 90 minutes


title: JNGR131, PEComa tumor sample, EPIC methylation array


title: Leaf, 4

description:
Library name: sample4
K_1
K_1=L1EIH1305578-K326_1.R1.raw.fastq.gz=wildtype


title: JNGR129, PEComa tumor sample, EPIC methylation array


title: Neutrophils, EVs, sample 3

description:
Library name: Neutro3EVs
Neutrophils, EVs, sample 3
counts_Neutro.csv
normalizecount_Neutro.csv

value: EVs


title: CD45_KOMI

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

institute: Xiamen University

description: Library name: scRNA 4

library_source: transcriptomic single cell

data_processing:
For RNA-seq, Raw sequencing reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2 (v2.2.1) 23. Gene-level counts were obtained using featureCounts (v2.0.1); For scRNA-seq, Gene expression count matrices were produced using MobiVision v3.2 software.
Assembly: mm10
Supplementary files format and content: table-delimitted txt files containing raw counts; and Tab-separted values files and matix files

source_name: Heart

growth_protocol: Male mice (C57BL/6J) at 8 weeks old were used to minimize variability associated with hormonal cycles in females. Cd163-/- mice on a C57BL/6 genetic background were used alongside their wild-type littermates as experimental controls following our previous reports 17,18. Given that CD163 is highly and exclusively expressed by cells of the monocytic–macrophage lineage 19, its genetic deletion primarily disrupts macrophage function. All animals were maintained under specific pathogen-free conditions with a 12-hour light/dark cycle and ambient temperature controlled at 22–23 °C at the animal facility of Xiamen University. For tissue collection, mice were deeply anesthetized using 5% isoflurane delivered via inhalation, followed by euthanasia through exsanguination and heart excision. Hearts were perfused through the left ventricle with phosphate-buffered saline and 10% potassium chloride (KCl) before collection. All procedures were approved by the Xiamen University Animal Ethics Committee (Protocol No. XMULAC20200150) and adhered to the standards set by Directive 2010/63/EU of the European Parliament and the U.S. National Institutes of Health guidelines on animal welfare.

extract_protocol:
Left ventricular tissues were dissected from the infarct zone (anterior wall) and remote zone (posterior wall) of each heart. One sample contains 2 to 3 mice. Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol; For scRNA-seq, Whole hearts were enzymatically digested as previously described, and CD45+ immune cells were isolated by fluorescence-activated cell sorting (FACS) using a BD FACSAria III.
Approximately 30,000 sorted cells were processed for single-cell suspension preparation and library construction using a 5′ transcriptome library kit according to the manufacturer’s protocol. Polyadenylated RNA was enriched and converted into cDNA libraries using a commercial library preparation kit. Libraries were multiplexed and sequenced to produce 150-base pair paired-end reads.

treatment_protocol: MI was induced in male mice by permanent ligation of the left anterior descending (LAD) coronary artery as reports . One day prior to surgery, chest hair was removed with depilatory cream. Mice were anesthetized with 2% isoflurane and placed on a heating pad to maintain body temperature. After disinfecting the skin with povidone-iodine, a 1.2 cm left thoracic incision was made to expose the fourth intercostal space. The pleura and pericardium were opened, and the heart was gently exteriorized. The left coronary artery (LCA) was ligated approximately 3 mm from its origin using a 6-0 silk suture, and successful ligation was confirmed by pallor of the anterior left ventricular wall. The heart was then returned to the thoracic cavity, residual air was evacuated, and the chest was closed. Mice typically recovered within 3–5 minutes under observation. Sham-operated mice underwent the same procedure without LCA ligation. Recombinant osteopontin (OPN) was dissolved in sterile phosphate-buffered saline (PBS) at 5 ng/μL. A total of 200 ng OPN (40 μL) or an equal volume of PBS was injected at three sites along the infarct border zone immediately after LAD ligation using a Hamilton syringe with a 30-gauge, 4 mm needle.

value: Heart

value: CD45+ cells

value: MI


title: HL-60, GFP, LPS 180 minutes, replicate 1

description:
Library name: GFPLPS1801
HL-60, GFP, LPS 180 minutes, sample 1
counts_HL60.csv
normalizecount_HL60.csv

value: GFP scramble


title: Neutrophils, EVs, sample 2

description:
Library name: Neutro2EVs
Neutrophils, EVs, sample 2
counts_Neutro.csv
normalizecount_Neutro.csv


title: Neutrophils, EVs, sample 1

description:
Library name: Neutro1EVs
Neutrophils, EVs, sample 1
counts_Neutro.csv
normalizecount_Neutro.csv


title: JNGR128, PEComa tumor sample, EPIC methylation array


title: CD45_KOsham

description: Library name: scRNA 3

value: Sham


title: Neutrophils, LPS, sample 3

description:
Library name: Neutro3LPS
Neutrophils, LPS, sample 3
counts_Neutro.csv
normalizecount_Neutro.csv

value: Blood


title: Neutrophils, LPS, sample 1

description:
Library name: Neutro1LPS
Neutrophils, LPS, sample 1
counts_Neutro.csv
normalizecount_Neutro.csv

value: Neutrophils


title: Glc_LPS_IFNg_3

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: Library name: Glc_LPS_IFNg_3

data_processing:
Sequenced libraries were processed with deepTools (Ramírez et al., 2016), using STAR (Dobin et al., 2013), for trimming and mapping, and featureCounts (Liao et al., 2014) to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 (Love et al., 2014) to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) or Prism 10.1.2 software (GraphPad) and determine differentially expressed genes with greater than 2-fold change and lower than 0.05 adjusted p-value.
Assembly: hg38
Supplementary files format and content: matrix of raw gene counts per sample

source_name: PBMC

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen)
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina) by the Deep-sequencing Facility at the Max-Planck-Institute for Immunobiology and Epigenetics.

value: Monocyte-derived Macrophage

value: IFNg+LPS

tag: donor

tag: media

value: RPMI with 10mM Glucose

value: PBMC


title: JNGR126, PEComa tumor sample, EPIC methylation array


title: JNGR125, PEComa tumor sample, EPIC methylation array


title: CD45_WTMI

description: Library name: scRNA 2

value: WT


title: Glc_LPS_IFNg_5

description: Library name: Glc_LPS_IFNg_5


title: Neutrophils, control, sample 2

description:
Library name: Neutro2
Neutrophils, control, sample 2
counts_Neutro.csv
normalizecount_Neutro.csv

value: Untreated


title: JNGR122, PEComa tumor sample, EPIC methylation array

value: PEComa


title: Glc_LPS_IFNg_6

description: Library name: Glc_LPS_IFNg_6


title: Neutrophils, control, sample 3

description:
Library name: Neutro3
Neutrophils, control, sample 3
counts_Neutro.csv
normalizecount_Neutro.csv


title: Neutrophils, control, sample 1

description:
Library name: Neutro1
Neutrophils, control, sample 1
counts_Neutro.csv
normalizecount_Neutro.csv


title: NO + low iron, biological replicate 3

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

description: Library name: Sample 12

data_processing:
Geneious program version 2023.2.1
In the Geneious program, raw data were trimmed using BBDuk with the following parameters: trim adapters (All Truseq), Kmer lengh 27, trim low quality on both ends with minimum quality 30, discard short reads with minimum length 36 bp, minimum entropy 0.1, entropy window size 4 and entropy Kmer size 5
In the Geneious program, trimmed sequences were assembled onto the CDC1551 genome (GenBank AE000516.2) using the Bowtie2 mapper with end-to-end alignment.
Gene expression levels were then calculated and excluded ambiguously mapped reads from calculation, with comparison of expression levels performed via DEseq2, all within the Geneious program.
Assembly: M. tuberculosis CDC1551 genome (GCA_000008585.1) (NCBI accession AE000516).
Supplementary files format and content: The file is presented in the .csv file format. It contains gene expression analysis from 3 biological replicates for each condition.

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: M. tuberculosis CDC1551 wild type was grown to an OD600 of ~0.6 (mid-log phase) in aerated cultures, originally seeded at an OD600 = 0.05.

extract_protocol:
RNA was extracted as previously described by Rohde, Abramovitch, and Russell (Cell Host and Microbe 2:352-364, 2007). In brief, RNA was stabilized with guanidine-thiocyanate lysis buffer prior to a freeze-thaw step. Once thawed, bacteria were lysed with 5 µg/ml lysozyme, followed by hot Trizol and physical disruption through silica bead agitation in a Beadbeater.  A chloroform extraction was used to further isolate the RNA before purification with an RNAeasy kit (Qiagen). DNA was degraded with Turbo DNAfree DNAse (Ambion). RNA quality was assessed with an Aligent Bioanalyzer.
The cDNA library was constructed with an Illumina Stranded Total RNA with Ribo-Zero Plus kit.

treatment_protocol: M. tuberculosis CDC1551 wild type at mid-log phase were subcultured in 12 ml of media to an OD600 of 0.3 in filter-capped T-75 flasks laid flat, containing: (i) iron-depleted minimal medium + 150 µM FeNO3 (control condition), (ii) iron-depleted minimal medium + 150 µM FeNO3 + 100 µM DETA NONOate (NO condition), (iii) iron-depleted minimal medium + 100 µM 2’2’-dipyridyl (low iron condition), or (iv) iron-depleted minimal medium + 100 µM 2’2’-dipyridyl + 100 µM DETA NONOate (NO + low iron condition). Exposure was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted.

value: Bacterial cell

value: CDC1551 wild type

value: Iron-depleted minimal medium + 100 µM 2’2’-dipyridyl + 100 µM DETA NONOate (NO + low iron condition)


title: Glc_LPS_IFNg_1

description: Library name: Glc_LPS_IFNg_1


title: Monocytes_Rep2_LPS_LPS

city: Moscow

first: Svetlana

last: Verkhova

address: 8 Baltiyskaya Street

country: Russia

institute: Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology

description: Library name: SAMPLE 57

data_processing:
Read quality was assessed using FastQC v0.11.9. Reads were aligned (STAR v2.7.10b) to the human genome (GRCh38/hg38), and gene expression was quantified (featureCounts/Salmon). Gene-level quantification was carried out during alignment using STAR with the --quantMode GeneCounts parameter enabled.
Assembly: hg38
Supplementary files format and content: csv. the file contains counts data for each sample

source_name: monocytes from PBMC

growth_protocol: Primary monocytes were isolated from healthy male donors after informed consent. The leukocyte fraction was isolated using a Ficoll density gradient. Monocytes were cultured at a density of 3×10⁵ cells in serum-free X-Vivo 10 medium (Lonza, Switzerland). THP-1 cells were cultured at a density of 3×10⁵ cells in RPMI-1640 (Paneco, Russia) supplemented with 10% FBS, L-glutamine, and antibiotics. Fibro (977hTERT) and EC (EA.hy926) were cultured at a density of 2×10⁵ cells in low-glucose DMEM (Paneco, Russia) containing 10% FBS, L-glutamine, and antibiotics. Primary human aortic intimal smooth muscle cells (SMC) were obtained from V.A. Almazov National Medical Research Center, a federal state budgetary institution under the Ministry of Health of the Russian Federation. SMCs were cultured at a density of 2×10⁵ cells in DMEM  containing 4.5 g/L glucose, L-glutamine, 15% FBS, and antibiotics.

extract_protocol:
The cell pellet was lysed, followed by RNA extraction using ExtractRNA (Eurogen, Russia) and the phenol-chloroform method. It was then treated with DNase (NEB, US) according to the manufacturer’s protocol. RNA was precipitated with sodium acetate/ethanol and resuspended in RNase-free water. RNA concentration was measured on a Qubit 4 (Thermo Fisher Scientific, USA), and quality was assessed on an Agilent 2100 Bioanalyzer (RNA 6000 Nano; Agilent Technologies, USA). Only samples with RIN > 7 were used for library preparation.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, USA) with poly(A)-mRNA isolation (NEBNext Poly(A) mRNA Magnetic Isolation Module). Following mRNA fragmentation, double-stranded cDNA synthesis, end processing, A-tailing, and adapter ligation were performed. Enrichment was carried out by PCR using unique dual-indexed primers (NEBNext Multiplex Oligos, UK). Library quality was assessed on an Agilent 2100 Bioanalyzer (DNA 1000).

treatment_protocol: Cells were exposed to control medium or LPS (1 μg/mL) for 4 h (priming). After medium change, cells were exposed to control medium or LPS (1 μg/mL) for 20 h (second exposure), yielding four conditions: C_C, C_LPS, LPS_C, and LPS_LPS.

value: monocytes from PBMC

value: monocytes

value: primary monocytes

value: repeated LPS exposure


title: JNGR124, PEComa tumor sample, EPIC methylation array


title: Low iron, biological replicate 3

description: Library name: Sample 9

value: Iron-depleted minimal medium + 100 µM 2’2’-dipyridyl (low iron condition)


title: JNGR123, PEComa tumor sample, EPIC methylation array


title: JNGR119, PEComa tumor sample, EPIC methylation array


title: CD45_WTsham

description: Library name: scRNA 1

value: Heart

value: CD45+ cells

value: Sham


title: SMC_Rep3_LPS_LPS

description: Library name: SAMPLE 56

source_name: smooth muscle cells of the intima and media of the aorta

value: smooth muscle cells

value: primary smooth muscle cells


title: Glc_LPS_IFNg_4

description: Library name: Glc_LPS_IFNg_4

value: Monocyte-derived Macrophage

value: IFNg+LPS

value: RPMI with 10mM Glucose

value: PBMC


title: Glc_LPS_6

description: Library name: Glc_LPS_6

value: LPS


title: Monocytes_Rep3_C_C

description: Library name: SAMPLE 58

value: WT

value: untreated control


title: NO + low iron, biological replicate 2

description: Library name: Sample 11

value: Bacterial cell

value: CDC1551 wild type

value: Iron-depleted minimal medium + 100 µM 2’2’-dipyridyl + 100 µM DETA NONOate (NO + low iron condition)


title: Glc_LPS_IFNg_2

description: Library name: Glc_LPS_IFNg_2


title: JNGR118, PEComa tumor sample, EPIC methylation array

value: PEComa


title: JNGR120, PEComa tumor sample, EPIC methylation array


title: NO + low iron, biological replicate 1

description: Library name: Sample 10


title: Low iron, biological replicate 2

description: Library name: Sample 8

value: Iron-depleted minimal medium + 100 µM 2’2’-dipyridyl (low iron condition)


title: JNGR117, PEComa tumor sample, EPIC methylation array


title: SMC_Rep3_LPS_C

description: Library name: SAMPLE 55

value: smooth muscle cells of the intima and media of the aorta

value: first LPS exposure


title: SMC_Rep3_C_LPS

description: Library name: SAMPLE 54

value: second LPS exposure


title: Glc_LPS_5

description: Library name: Glc_LPS_5


title: Monocytes_Rep2_LPS_C

description: Library name: SAMPLE 53

value: monocytes from PBMC

value: monocytes

value: primary monocytes


title: JNGR116, PEComa tumor sample, EPIC methylation array


title: SMC_Rep3_C_C

description: Library name: SAMPLE 52

value: smooth muscle cells

value: primary smooth muscle cells


title: Low iron, biological replicate 1

description: Library name: Sample 7


title: Glc_LPS_3

description: Library name: Glc_LPS_3

value: Monocyte-derived Macrophage

value: RPMI with 10mM Glucose

value: PBMC


title: JNGR115, PEComa tumor sample, EPIC methylation array


title: Glc_LPS_2

description: Library name: Glc_LPS_2

value: LPS


title: NO, biological replicate 2

description: Library name: Sample 5

value: Bacterial cell

value: Iron-depleted minimal medium + 150 µM FeNO3 + 100 µM DETA NONOate (NO condition)


title: Glc_LPS_4

description: Library name: Glc_LPS_4


title: SMC_Rep2_LPS_LPS

description: Library name: SAMPLE 51

value: WT

value: repeated LPS exposure


title: JNGR113, PEComa tumor sample, EPIC methylation array

value: PEComa


title: Glc_IFNg_5

description: Library name: Glc_IFNg_5

value: IFNg


title: JNGR109, PEComa tumor sample, EPIC methylation array


title: Glc_LPS_1

description: Library name: Glc_LPS_1


title: Glc_IFNg_3

description: Library name: Glc_IFNg_3


title: Control, biological replicate 3

description: Library name: Sample 3

value: CDC1551 wild type

value: Iron-depleted minimal medium + 150 µM FeNO3 (control condition)


title: JNGR110, PEComa tumor sample, EPIC methylation array


title: NO, biological replicate 3

description: Library name: Sample 6


title: JNGR108, PEComa tumor sample, EPIC methylation array


title: NO, biological replicate 1

description: Library name: Sample 4


title: JNGR107, PEComa tumor sample, EPIC methylation array


title: SMC_Rep1_LPS_LPS

description: Library name: SAMPLE 47

value: smooth muscle cells of the intima and media of the aorta


title: Control, biological replicate 1

description: Library name: Sample 1


title: SMC_Rep2_C_LPS

description: Library name: SAMPLE 49

value: second LPS exposure


title: SMC_Rep2_LPS_C

description: Library name: SAMPLE 50

value: first LPS exposure


title: Glc_IFNg_4

description: Library name: Glc_IFNg_4


title: JNGR105, PEComa tumor sample, EPIC methylation array


title: Control, biological replicate 2

description: Library name: Sample 2


title: SMC_Rep2_C_C

description: Library name: SAMPLE 48

value: smooth muscle cells

value: untreated control


title: Glc_IFNg_2

description: Library name: Glc_IFNg_2

value: Monocyte-derived Macrophage


title: SMC_Rep1_LPS_C

description: Library name: SAMPLE 46

value: primary smooth muscle cells


title: H7-d15-2

city: Shanghai

first: ZHUO

last: LIU

address: Road Dongan NO.130

institute: Fudan University

data_processing:
Data processing, splitting, quality control, filtering.
A reference transcriptome library was constructed.
After the library was checked, Illumina sequencing platform was used for high-throughput sequencing. The sequencing read length was PE150
FastQC was used to analyze the sequencing results. hisat2 and samtools were used for localization matching and transformation of reads. Quantitative analysis was performed using featureCounts.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: H7 hESC

growth_protocol: Differentiated cells were treated with CDM3 containing RPMI 1640(Corning,10-040-CV),BSA (Sigma-Aldrich,A7906) and Ascobic Acid(Sigma-Aldrich,50-81-7), which was replaced every other day.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
A cDNA library was constructed based on TrueLib mRNA Library Preparation kit (ExCell Bio) using 1 μg of total RNA from the cardiomyocytes on day 15 of differentiation.

treatment_protocol: The myocardial cells on day 25 of differentiation were transfected with plasmid and infected with virus. After the treatment, the cardiomyocytes on day 30 of differentiation were used to detect the downstream mechanisms and functions.

value: H7 hESC

value: Human H7 embryonic stem cell line

value: cardiac differentiation

tag: time

value: Day 15


title: 7-18d15-2

value: HILPDA knockdown


title: Glc_Control_5

description: Library name: Glc_Control_5

value: Control

value: RPMI with 10mM Glucose

value: PBMC


title: H7d15

value: WT


title: Glc_IFNg_1

description: Library name: Glc_IFNg_1

value: IFNg


title: hTERT977_Rep3_LPS_LPS

description: Library name: SAMPLE 43

source_name: hybrid cell

value: hybrid cell

value: fibroblasts

value: telomerase-immortalized fibroblasts

value: repeated LPS exposure


title: Glc_Control_6

description: Library name: Glc_Control_6


title: SMC_Rep1_C_LPS

description: Library name: SAMPLE 45

value: smooth muscle cells of the intima and media of the aorta

value: smooth muscle cells

value: second LPS exposure


title: 7-18d15-1

value: H7 hESC


title: SMC_Rep1_C_C

description: Library name: SAMPLE 44

value: primary smooth muscle cells

value: untreated control


title: Glc_Control_4

description: Library name: Glc_Control_4

value: Monocyte-derived Macrophage


title: JNGR102, PEComa tumor sample, EPIC methylation array

value: PEComa


title: JNGR138, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR138

data_processing:
Base calling and demultiplexing were performed using RTA (v2.7.7) and either bcl2fastq (v2.20.0.422) or BCL Convert (v3.8.4).
For QuantSeq libraries, UMI sequences were extracted using UMI-tools (v1.1.2), and adapter trimming and quality filtering were performed using cutadapt (v1.10). Reads shorter than 40 bp were discarded.
Reads were aligned to rRNA sequences using Bowtie2 (v2.2.8), and rRNA-mapped reads were removed.
Filtered reads were aligned to the human reference genome (GRCh38/hg38) using STAR (v2.5.3a).
PCR duplicates (for QuantSeq data) were removed using UMI-tools dedup.
Gene-level read counts were generated using htseq-count (v0.6.1p1) with Ensembl annotation (v107) in “union” mode.
Expression values were normalized TPM for downstream analyses.
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited text file containing gene expression matrix. Rows correspond to genes and columns correspond to samples. Expression values are normalized as TPM (transcripts per million).
Supplementary files format and content: The file “TPMs_all_Samples.txt” contains TPM-normalized gene expression values for all samples across genes.

extract_protocol:
Total RNA was extracted from tissue samples using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA using either (i) the Illumina TruSeq RNA Exome kit (capture-based library preparation) or (ii) the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) following the manufacturers’ protocols. For TruSeq RNA Exome libraries, cDNA was generated by random priming, followed by adapter ligation, PCR amplification, and exome capture using sequence-specific probes. For QuantSeq libraries, first-strand synthesis was performed using oligo(dT) priming, followed by second-strand synthesis with UMI-containing primers, PCR amplification, and bead purification.


title: JNGR100, PEComa tumor sample, EPIC methylation array


title: hTERT977_Rep3_C_LPS

description: Library name: SAMPLE 41


title: Glc_Control_1

description: Library name: Glc_Control_1

value: Control


title: hTERT977_Rep3_C_C

description: Library name: SAMPLE 40


title: JNGR103, PEComa tumor sample, EPIC methylation array


title: JNGR133, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR133


title: JNGR97, PEComa tumor sample, EPIC methylation array


title: Glc_Control_3

description: Library name: Glc_Control_3

value: RPMI with 10mM Glucose


title: JNGR136, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR136


title: Gal_LPS_IFNg_6

description: Library name: Gal_LPS_IFNg_6

value: IFNg+LPS

value: RPMI with 10mM Galactose

value: PBMC


title: JNGR99, PEComa tumor sample, EPIC methylation array


title: Gal_LPS_IFNg_5

description: Library name: Gal_LPS_IFNg_5


title: JNGR135, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR135


title: JNGR95, PEComa tumor sample, EPIC methylation array


title: JNGR129, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR129


title: Gal_LPS_IFNg_4

description: Library name: Gal_LPS_IFNg_4


title: JNGR101, PEComa tumor sample, EPIC methylation array


title: JNGR24, PEComa tumor sample, EPIC methylation array


title: THP1_Rep3_C_LPS

description: Library name: SAMPLE 37

value: hybrid cell

value: monocytes

value: leukemia-derived cell line


title: hTERT977_Rep3_LPS_C

description: Library name: SAMPLE 42

value: fibroblasts

value: telomerase-immortalized fibroblasts

value: first LPS exposure


title: Glc_Control_2

description: Library name: Glc_Control_2


title: Gal_LPS_IFNg_3

description: Library name: Gal_LPS_IFNg_3


title: JNGR132, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR132


title: JNGR128, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR128


title: JNGR96, PEComa tumor sample, EPIC methylation array


title: THP1_Rep2_LPS_LPS

description: Library name: SAMPLE 35

value: repeated LPS exposure


title: JNGR131, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR131


title: JNGR22, PEComa tumor sample, EPIC methylation array


title: JNGR127, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR127


title: THP1_Rep3_LPS_LPS

description: Library name: SAMPLE 39


title: JNGR126, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR126


title: THP1_Rep3_LPS_C

description: Library name: SAMPLE 38


title: JNGR21, PEComa tumor sample, EPIC methylation array


title: JNGR125, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR125


title: JNGR20, PEComa tumor sample, EPIC methylation array


title: Gal_LPS_6

description: Library name: Gal_LPS_6

value: LPS


title: THP1_Rep3_C_C

description: Library name: SAMPLE 36


title: Monocytes_Rep2_C_C

description: Library name: SAMPLE 32

value: monocytes from PBMC

value: primary monocytes

value: WT


title: JNGR23, PEComa tumor sample, EPIC methylation array

value: PEComa


title: Gal_LPS_5

description: Library name: Gal_LPS_5

value: Monocyte-derived Macrophage


title: JNGR123, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR123


title: THP1_Rep2_LPS_C

description: Library name: SAMPLE 34


title: Gal_LPS_IFNg_2

description: Library name: Gal_LPS_IFNg_2


title: THP1_Rep1_LPS_LPS

description: Library name: SAMPLE 30


title: Gal_LPS_IFNg_1

description: Library name: Gal_LPS_IFNg_1


title: THP1_Rep1_LPS_C

description: Library name: SAMPLE 29


title: JNGR120, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR120


title: JNGR16, PEComa tumor sample, EPIC methylation array


title: JNGR19, PEComa tumor sample, EPIC methylation array


title: THP1_Rep2_C_LPS

description: Library name: SAMPLE 33

value: second LPS exposure


title: JNGR122, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR122


title: THP1_Rep1_C_LPS

description: Library name: SAMPLE 28


title: JNGR18, PEComa tumor sample, EPIC methylation array


title: JNGR119, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR119


title: Gal_LPS_4

description: Library name: Gal_LPS_4


title: THP1_Rep2_C_C

description: Library name: SAMPLE 31

value: untreated control


title: Gal_IFNg_5

description: Library name: Gal_IFNg_5

value: IFNg

value: RPMI with 10mM Galactose


title: hTERT977_Rep2_LPS_C

description: Library name: SAMPLE 25

value: hybrid cell


title: Wt_E2Fc_GFP_S6

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

institute: universite-paris-saclay

description:
Library name: Sample 3
WT

library_source: other

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.4.4 with the following setting "bowtie2 --very-sensitive" against the genome of TAIR10.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam -g 119481543 -p 0.05  -B -n --outdir "; Bigwig generation: read density was scored with s3norm with the default paramaters.
Assembly: TAIR10
Supplementary files format and content: bigWig files

molecule: protein

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis thaliana plantlets were grown to 10-day-old stage before harvest for ChIP-seq.

extract_protocol:
Samples were ground in liquid nitrogen and resuspended in extraction buffer 1 (0.4 M sucrose, 10 mM tris-HCl pH 8, 10 mM MgCl2, 5 mM β-mercaptoethanol, and cOmplete Mini EDTA-free protease inhibitor cocktail). After filtration through 100-μm filters and centrifugation at 1500g for 10 min, pellets were resuspended and washed twice in extraction buffer 2 (0.25 M sucrose, 10 mM tris-HCl pH 8, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol, protease inhibitors) for 5 min at 1000g. Nuclei were resuspended in nuclei lysis buffer (0.1% SDS, 50 mM tris-HCl pH 8, 10 mM EDTA pH 8). Chromatin was sonicated for 10 min using a Covaris S220 (peak power 175, cycles/burst 200, duty factor 20). Sonicated chromatin was immunoprecipitated overnight at 4°C with 2 μl anti-GFP antibody (Abcam ab290). Immunocomplexes were captured using 40 μl Dynabead protein A for 3 h at 4°C. Beads were washed nine times with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM tris-HCl pH 8, 167 mM NaCl, protease inhibitors). ChIP DNA was eluted with elution buffer (1% SDS, 0.1 M NaHCO3) at 65°C for 15 min (twice). Cross-links were reversed by addition of 5 M NaCl and overnight incubation at 65°C. Samples were treated with RNase A + T1 for 20 min and Proteinase K for 3 h at 50°C. DNA was extracted with phenol:chloroform:indole-3-acetic acid (25:24:1, pH 8) and precipitated with ethanol, NaOAc, and GlycoBlue. DNA was resuspended in nuclease-free water.
Sequencing libraries were generated using a minimum of 2 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). Library quality was assessed on an Agilent 2100 Bioanalyzer. Libraries were subjected to 75-bp high-throughput sequencing on an Illumina NextSeq 500.

treatment_protocol: Plantlets were cross-linked in 1% (v/v) formaldehyde for 15 min, and cross-linking was quenched by adding glycine to a final concentration of 125 mM and incubating under vacuum for 5 min.

value: whole seedlings

tag: antibody

value: Abcam ab290


title: JNGR116, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR116


title: Gal_IFNg_4

description: Library name: Gal_IFNg_4

value: PBMC


title: Gal_LPS_3

description: Library name: Gal_LPS_3


title: Gal_LPS_1

description: Library name: Gal_LPS_1


title: JNGR17, PEComa tumor sample, EPIC methylation array


title: JNGR117, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR117


title: JNGR124, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR124


title: Gal_IFNg_6

description: Library name: Gal_IFNg_6


title: hTERT977_Rep2_C_C

description: Library name: SAMPLE 23

value: fibroblasts

value: telomerase-immortalized fibroblasts


title: hTERT977_Rep2_LPS_LPS

description: Library name: SAMPLE 26

value: repeated LPS exposure


title: JNGR15, PEComa tumor sample, EPIC methylation array


title: Gal_IFNg_2

description: Library name: Gal_IFNg_2


title: JNGR115, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR115


title: THP1_Rep1_C_C

description: Library name: SAMPLE 27

value: monocytes

value: leukemia-derived cell line


title: cas5Δ/Δ, 0.2 M calcium, rep 2

first: JIHONG

last: liu

state: Shanghai

address: No. 320 Yueyang Road, Shanghai

institute: siii

description: Library name: sample 16

data_processing:
The RNA-seq data analysis pipeline begins with raw sequencing data processed by fastp for quality control, including adapter trimming, low-quality read removal, and base correction. Filtered reads are aligned to a reference genome using STAR, ensuring splice-aware mapping and generating BAM files and read counts per gene. These counts are imported into DESeq2 for differential expression analysis.
Assembly: Candida albicans SC5314
Supplementary files format and content: tab-separated reads counts file

organism: Candida albicans

source_name: Candida albicans

extract_protocol:
Each strain was cultured in three independent parallel groups for each condition at the same time. Take 2 OD C. albicans to remove the supernatant by rapid centrifugation at 4 ℃, frozen in liquid nitrogen, and then use the above total RNA extraction method for RNA extraction, extraction of RNA samples using 1.5% agarose gel electrophoresis identification. The total RNA samples were sent to Tianjin Novogene for quality control, and the subsequent sequencing of the samples was carried out
Each strain was cultured in three independent parallel groups for each condition at the same time. Take 2 OD C. albicans to remove the supernatant by rapid centrifugation at 4 ℃, frozen in liquid nitrogen, and then use the above total RNA extraction method for RNA extraction, extraction of RNA samples using 1.5% agarose gel electrophoresis identification. The total RNA samples were sent to Tianjin Novogene for quality control, and the subsequent sequencing of the samples was carried out

value: Candida albicans


title: fbl17_E2Fc_GFP_rep2

description:
Library name: Sample 2
Bioreplicate 2

value: E2Fc-GFP fbl17-/-


title: hTERT977_Rep1_LPS_LPS

description: Library name: SAMPLE 22


title: JNGR118, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR118

value: PEComa


title: cas5Δ/Δ , YPD, rep 2

description: Library name: sample 14


title: fbl17_E2Fc_GFP_S7

description:
Library name: Sample 1
Bioreplicate 1


title: JNGR108, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR108


title: hTERT977_Rep2_C_LPS

description: Library name: SAMPLE 24


title: JNGR113, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR113


title: Gal_Control_6

description: Library name: Gal_Control_6

value: Monocyte-derived Macrophage

value: Control


title: Monocytes_Rep1_LPS_LPS

description: Library name: SAMPLE 21

value: monocytes from PBMC

value: primary monocytes

value: WT


title: Gal_Control_5

description: Library name: Gal_Control_5

value: RPMI with 10mM Galactose


title: JNGR109, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR109


title: Gal_IFNg_1

description: Library name: Gal_IFNg_1

value: IFNg


title: cas5Δ/Δ, 0.2 M calcium, rep 1

description: Library name: sample 15


title: JNGR103, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR103


title: hTERT977_Rep1_C_LPS

description: Library name: SAMPLE 19

value: hybrid cell

value: HUVEC-A549 hybrid cell line

value: second LPS exposure


title: Gal_Control_4

description: Library name: Gal_Control_4

value: PBMC


title: hTERT977_Rep1_C_C

description: Library name: SAMPLE 18

value: fibroblasts

value: untreated control


title: Gal_Control_3

description: Library name: Gal_Control_3


title: Gal_IFNg_3

description: Library name: Gal_IFNg_3


title: cnb1Δ/Δ, 0.2 M calcium, rep 1

description: Library name: sample 11


title: JNGR107, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR107


title: cas5Δ/Δ, YPD, rep 1

description: Library name: sample 13


title: hTERT977_Rep1_LPS_C

description: Library name: SAMPLE 20

value: first LPS exposure


title: cnb1Δ/Δ, 0.2 M calcium, rep 2

description: Library name: sample 12

value: Candida albicans


title: JNGR102, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR102


title: Gal_Control_2

description: Library name: Gal_Control_2


title: JNGR101, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR101


title: crz1Δ/Δ , 0.2 M calcium, rep 2

description: Library name: sample 8


title: Gal_Control_1

description: Library name: Gal_Control_1


title: cnb1Δ/Δ , YPD, rep 2

description: Library name: sample 10


title: JNGR99, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR99


title: EA.hy926_Rep3_LPS_C

description: Library name: SAMPLE 16

value: endothelial cells


title: cnb1Δ/Δ, YPD, rep 1

description: Library name: sample 9


title: CAR3

city: Lishui

first: Yahong

last: Lu

state: Zhejiang

address: No.289, Kuocang Road, Liandu District, Lishui City, Zhejiang Province, China

institute: The Fifth Affiliated Hospital of Wenzhou Medical University

description: Library name: Sample 9

data_processing:
Software trim_galore (version 0.6.4): de-joining, low quality, short reads.  Software bowtie2 (version 2.4.2): compare rRNA databases of corresponding species, remove rRNA.  Software hisat2 (version 2.2.0): compare reference genome Human:GRCh38.104 ; Mouse: GRCm39.104 ; Rattus: Rnor_6.0.  Software htseq-count (version 0.13.5): for RNA quantification.  Software edgeR : for differential analysis.
Assembly: GRCm39.104
Supplementary files format and content: Supplementary file format content processed date.xlsx

source_name: muscle

extract_protocol:
Total RNA extraction of samples was performed using the RNeasy (Qiagen) RNA extraction kit and according to the standard procedure provided by the manufacturer.  The resulting RNA was subjected to electrophoretic QC by Agilent 4200 TapeStation (Cat#G2991A, Agilent) and quantitative QC by Qubit 3.0 Fluorometer (Cat#Q33216, Thermo Fisher Scientific)/NanoDrop One (ND-ONE, Thermo Fisher Scientific). (Cat#Q33216, Thermo Fisher Scientific)/NanoDrop One (ND-ONE, Thermo Fisher Scientific) for quantitative QC. Qualified RNA can be used for subsequent library construction.  Translated with DeepL.com (free version)
Experiments were performed using the VAHTS Stranded mRNA-seq Library Prep Kit (NR602, Vazyme) and according to the manufacturer's product instruction manual. The constructed mRNA libraries were quality checked by Qubit fluorometer (#Q33216, Thermo Fisher Scientific) and Agilent 4200 TapeStation (Cat#G2991A, Agilent). The libraries were uploaded using the illumina sequencing platform.

treatment_protocol: Nine-week-old C57BL/6J mice were assigned to three groups, and after two weeks of acclimatization, mice in the control group were fed a regular chow (10% kcal of fat, D12450J, Research Diets), and mice in the other groups were fed a high-fat diet (60% kcal of fat, D12492, Research Diets). Mice in the HFD+CAR group was given 100 mg/kg/day L-carnitine through their drinking water (MCE; Shanghai, China). All the mice were fed for 8 weeks. Before sacrifice, the mice were fasted for 6 h, and tissues were collected according to the appropriate preparation method for each experiment.

value: muscle

value: high-fat diet + carnitine


title: JNGR100, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR100

value: PEComa


title: EA.hy926_Rep3_C_LPS

description: Library name: SAMPLE 15


title: EA.hy926_Rep3_LPS_LPS

description: Library name: SAMPLE 17

value: repeated LPS exposure


title: CAR2

description: Library name: Sample 8


title: EA.hy926_Rep3_C_C

description: Library name: SAMPLE 14


title: JNGR97, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR97


title: EA.hy926_Rep2_LPS_LPS

description: Library name: SAMPLE 13


title: crz1Δ/Δ, 0.2 M calcium, rep 1

description: Library name: sample 7


title: CAR1

description: Library name: Sample 7


title: A3

description: Library name: Sample 6

value: high-fat diet


title: JNGR96, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR96


title: Monocytes_Rep1_C_LPS

description: Library name: SAMPLE 12

value: monocytes from PBMC

value: monocytes

value: primary monocytes

value: WT


title: crz1Δ/Δ, YPD, rep 1

description: Library name: sample 5


title: Gal_LPS_2

description: Library name: Gal_LPS_2

value: Monocyte-derived Macrophage

value: LPS

value: RPMI with 10mM Galactose


title: JNGR95, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR95


title: JNGR24, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR24


title: WT, 0.2 M calcium, rep 1

description: Library name: sample 3


title: A1

description: Library name: Sample 4


title: crz1Δ/Δ , YPD, rep 2

description: Library name: sample 6


title: A2

description: Library name: Sample 5


title: JNGR23, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR23


title: WT, 0.2 M calcium, rep 2

description: Library name: sample 4


title: WT, YPD, rep 2

description: Library name: sample 2


title: EA.hy926_Rep2_LPS_C

description: Library name: SAMPLE 11

value: hybrid cell

value: HUVEC-A549 hybrid cell line


title: JNGR22, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR22


title: JNGR21, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR21


title: WT, YPD, rep 1

description: Library name: sample 1


title: EA.hy926_Rep2_C_LPS

description: Library name: SAMPLE 10

value: second LPS exposure


title: CON2

description: Library name: Sample 2

value: control


title: EA.hy926_Rep1_LPS_LPS

description: Library name: SAMPLE 8

value: endothelial cells


title: JNGR20, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR20


title: EA.hy926_Rep2_C_C

description: Library name: SAMPLE 9

value: untreated control


title: 0.2 M calcium, Cas5, ChIP rep1

description: Library name: Cas5-200-1

data_processing:
Sequencing reads were aligned to the reference genome using Bowtie2. Post-alignment processing was carried out with SAMtools, including conversion to BAM format, name and coordinate sorting, mate information fixing, and duplicate removal. Peak calling was performed using MACS2 to identify enriched genomic regions.
Assembly: Candida albicans SC5314
Supplementary files format and content: bigwig

extract_protocol:
Briefly, cells were cultured in 50 mL of YPD medium until the optical density reached 0.6, in which the calcium ion-treated group was supplemented with 0.2 M calcium and continued to incubate for 1 h. Subsequently, cells were crosslinked with 1% formaldehyde for 15 min at 30°C with gentle shaking, and then quenched by adding 0.125 M glycine for 5 min. After three rounds of cold phosphate buffer (PBS) washing, fungal cells were lysed using glass beads in low-salt buffer with added protease inhibitors. After cell lysis, the lysate was sonicated on ice to fragment the chromatin into fragments of 200 to 500 bp size. After removal of the cellular debris, chromatin fragments were captured using protein A/G magnetic beads by the addition of anti-Myc-Tag monoclonal antibody(Abmart, M20002L) or Normal Rabbit IgG (Cell signaling technology, 2729S). The beads were subsequently washed using buffers of different salt concentrations ( in sequence, low salt buffer, high salt buffer, lithium chloride buffer and tri-ethylenediaminetetraacetic acid (TE) buffer). Subsequently, a buffer containing sodium dodecyl sulfate (SDS) and sodium chloride was added and heated overnight at 65°C to promote the release of DNA fragments. The beads were then treated with RNAase and proteinase K sequentially, the supernatant was centrifuged and purified using a DNA purification kit (Thermo Fisher Scientific, K0702).
After the DNA sample passes quality testing, chromatin co-precipitation technology is used to specifically enrich protein-bound DNA fragments. The library preparation process is completed through steps including end repair, A-tailing, sequencing adapter ligation, purification, and PCR amplification. Once the library is constructed, it is first quantified preliminarily using Qubit 2.0 and diluted. The Agilent 2100 system is then employed to detect the insert fragment size of the library. If the insert size meets the expected criteria, the Q-PCR method is applied to accurately quantify the effective concentration of the library, ensuring its quality.

value: Candida albicans


title: YPD, Cas5, Input

description: Library name: input-Cas5-0


title: CON1

description: Library name: Sample 1

value: muscle


title: shJag1_3_3

city: London

first: Linxiang

last: Lan

address: 237 Fulham Rd

country: United Kingdom

institute: The Institute of Cancer Research

data_processing:
Raw reads were quality checked Trimmomatic v.0.3635 before alignment.
Reads were mapped to the mouse transcriptome using the STAR aligner v.2.5.2b using GRCm38 (Ensembl release 102) as the annotation source.
Normalisation of raw count data was performed with the DESeq2 package (version 1.32.0).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file including normalised counts for each sample.

growth_protocol: shCtrl and shJag1_3 PDAC organoids were cultured in advanced DMEM/F12 (Thermo Fisher Scientific) medium containing 100 µg/mL Primocin (InvivoGen), 1x B27 supplement (Thermo Fisher Scientific), 10 mM Nicotinamide (Sigma-Aldrich), 1.25 mM N-acetylcysteine (Sigma-Aldrich), 10 nM Gastrin (Sigma-Aldrich), 100 ng/mL hFGF-10 (Peprotech), 50 ng/mL EGF (Peprotech), 10% (v/v) R-Spondin-1 conditioned medium and 10% (v/v) mNoggin conditioned medium.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
cDNA libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's instructions.

value: Pancreatic cancer organoids

value: Jag1 knockdown


title: EA.hy926_Rep1_LPS_C

description: Library name: SAMPLE 7

value: first LPS exposure


title: CON3

description: Library name: Sample 3


title: Monocytes_Rep3_LPS_LPS

description: Library name: SAMPLE 4

value: monocytes from PBMC

value: monocytes

value: repeated LPS exposure


title: JNGR17, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR17

value: PEComa


title: YPD, Cas5, ChIP rep1

description: Library name: Cas5-0-1


title: JNGR16, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR16


title: EA.hy926_Rep1_C_LPS

description: Library name: SAMPLE 6


title: EA.hy926_Rep1_C_C

description: Library name: SAMPLE 5


title: shJag1_3_1


title: WT,YPD, Input

description: Library name: input-250


title: JNGR19, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR19


title: Monocytes_Rep3_LPS_C

description: Library name: SAMPLE 3

value: primary monocytes

value: WT


title: shJag1_3_2


title: YPD, Cas5, ChIP rep2

description: Library name: Cas5-0-2


title: Monocytes_Rep3_C_LPS

description: Library name: SAMPLE 2


title: shCtrl_3


title: shCtrl_2


title: 0.2 M calcium, Cas5, Input

description: Library name: input-Cas5-200


title: Monocytes_Rep1_C_C

description: Library name: SAMPLE 1


title: shCtrl_1


title: JNGR15, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR15


title: WT,YPD, ChIP

description: Library name: 250-1


title: 0.2 M calcium, Cas5, ChIP rep2

description: Library name: Cas5-200-2


title: Cd9 Hi Sorted, scRNASeq

first: Axel

last: Behrens

address: 123 Old Brompton Road

institute: Institute of Cancer Research

description: 10x Genomics

data_processing:
Preprocessing was performed using the Cell Ranger 7.0.0 software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39 mouse
Supplementary files format and content: Tab-separated values files and matrix fils

source_name: Pancreas

extract_protocol:
Mouse pancreatic tumours were dissected and placed into ice-cold DMEM/F-12 with 50 U/ml penicillin-streptomycin. Tissues were minced on ice and incubated in DMEM containing 1 mg/ml collagenase V  for 1 h at 37 °C. Digestion was stopped by adding ice cold G solution and cells were centrifuged (300 g, 5 min at 4 °C). Cells were further digested with TrypLE for 5 min at 37 °C, followed bystopping with ice-cold PBS with 2% FCS and centrifugation. Single cells were resuspended in PBS with 2% FCS and stained with fluorophore-conjugated antibody on ice in the dark when required. Cells were washed three times with PBS and filtered through a 40-μm nylon mesh and incubated in FACS buffer with 3 μM DAPI. Alive cells  were sorted with BD FACSymphony™ S6 (BD Biosciences) based on GFP or CD9 expression.
Libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to manufacturer's instructions.

value: Pancreas

tag: disease

value: Pancreatic Ductal Adenocarcinoma

tag: sub population

value: Cd9 Hi Sorted


title: whole tumour, scRNAseq

description: 10x Genomics

value: whole


title: Arsenite stressed (75min), polyA+ RNA, replicate 1

status: Public on Apr 17 2026

city: Ann Arbor

first: Stephanie

middle: L

last: Moon

state: MI

address: 3734 Med Sci II 1241 E. Catherine St

department: Human Genetics

institute: University of Michigan

description:
Library name: 75min_As_rep1
colname in Time_Course_Counts_File.csv: 75min_rep1

data_processing:
For Biostate (nuc/cyto): Adapter contaminants and low-quality reads trimmed with Cutadapt (v4.2) and aligned to hg38 using HISAT2 (v2.2.1). Gene expression quantified with featureCounts (v2.0.3) using exon level-first strand quantification. Final CPM in Nuc_Cyto_Total_Counts_File.csv.
For plasmidsaurus (time-course): FastQ generation and demux with BCL conver (v4.3.6) and fqtk (v0.3.1). Read-filtering using FastP (v0.24.0) including poly-X tail trimming, 3' quality-based tail trimming, minimum Phred quality of 15 and length of 50 bp. Aligned to hg38 with STAR (v2.7.11) with non-canonical splice junction removal and output of unmapped reads. Coordinate sorting of BAMs with samtools (v1.22.1) and UMI de-duplication with UMICollapse (v1.1.0). Gene-expression quantification using featureCounts (v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons, and 3'UTRs as feature identifeires. Final CPM in Time_Course_Counts_File.csv
Assembly: hg38
Supplementary files format and content: format: csv; content: counts tables

source_name: U-2 OS

growth_protocol: U-2 OS cells were maintained in Dulbecco's modified Eagle medium with 9% FetalGro Ex, 1% penicillin/streptomycin, and 1% Glutamax at 37 °C and 5% CO2

extract_protocol:
Nuc/Cyto fractionation was done as previously described as in Bhatt et al., 2012; Ji et al., 2021; and letswaart et al., 2022 and detailed in accompying manuscript for this submission (Helton et al., 2026). RNA was sent to Biostate.ai for rRNA depletion using Probes for Excess RNA depletion and RNAseq.  For time course RNAseq of PolyA+ RNA, cells were scraped into DNA/RNA Shield (Zymo research) and sent for bulk RNAseq by Plasmidsaurus.
For Biostate (nuc/cyto) library preparation: rRNA depleted RNA was reverse transcribed into cDNA and barcoded using Biostate's Barcode-Integrated Reverse Transcription technology.  For plasmidsaurus (time-course) library prepraration: PolyA+ RNA was converted into cDNA via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

treatment_protocol: Cells were treated with 250 µM arsenite in complete growth medium or untreated with a change in complete growth medium for unstressed conditions

value: U-2 OS

value: osteosarcoma

value: WT with endogenously tagged G3BP1 with eGFP

value: 250 µM arsenite


title: Patient 2 Tumor tissues

type: RNA

city: Nanchong

first: Zhen

last: Jiang

state: Sichuan Province

address: No. 234 Fujiang Road

institute: North Sichuan Medical College

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

hyb_protocol: The hybridization was carried out by using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) for 17hours at 65°C.

scan_protocol: The arrays were then scaned by Agilent Microarray Scanner (Agilent p/n G2565BA.

data_processing: The raw data were extracted by Agilent Feature Extraction software.Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: patients with gastric adenocarcinoma

label_protocol: The RNA was labeled by Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufactures guideline.

extract_protocol: Cryopulverization of tissue using the Biopulverizer. Homogenization using the Mini-Bead-Beater-16. After phase separation, remove the supernatant, wash the RNA pellet once with 75% ethanol, dissolve RNA in 85ul or less RNase-free water.

value: primary gastric  cancer

tag: histology

value: adenocarcinoma

tag: Sex

value: Male


title: Arsenite stressed (75min), polyA+ RNA, replicate 3

description:
Library name: 75min_As_rep3
colname in Time_Course_Counts_File.csv: 75min_rep3


title: Arsenite stressed (105min), polyA+ RNA, replicate 1

description:
Library name: 105min_As_rep1
colname in Time_Course_Counts_File.csv: 105min_rep1


title: Patient 2 Adjacent non-tumorous tissues


title: Arsenite stressed (75min), polyA+ RNA, replicate 2

description:
Library name: 75min_As_rep2
colname in Time_Course_Counts_File.csv: 75min_rep2


title: Patient 3 Adjacent non-tumorous tissues


title: Arsenite stressed (45min), polyA+ RNA, replicate 1

description:
Library name: 45min_As_rep1
colname in Time_Course_Counts_File.csv: 45min_rep1


title: Arsenite stressed (105min), polyA+ RNA, replicate 3

description:
Library name: 105min_As_rep3
colname in Time_Course_Counts_File.csv: 105min_rep3


title: Arsenite stressed (45min), polyA+ RNA, replicate 2

description:
Library name: 45min_As_rep2
colname in Time_Course_Counts_File.csv: 45min_rep2


title: Arsenite stressed (105min), polyA+ RNA, replicate 2

description:
Library name: 105min_As_rep2
colname in Time_Course_Counts_File.csv: 105min_rep2


title: Arsenite stressed (30min), polyA+ RNA, replicate 3

description:
Library name: 30min_As_rep3
colname in Time_Course_Counts_File.csv: 30min_rep3


title: Unstressed (0min), polyA+ RNA, replicate 2

description:
Library name: 0min_unstressed_rep2
colname in Time_Course_Counts_File.csv: 0min_rep2

value: Untreated


title: Arsenite stressed (15min), polyA+ RNA, replicate 2

description:
Library name: 15min_As_rep2
colname in Time_Course_Counts_File.csv: 15min_rep2


title: Arsenite stressed (15min), polyA+ RNA, replicate 3

description:
Library name: 15min_As_rep3
colname in Time_Course_Counts_File.csv: 15min_rep3


title: Arsenite stress, cytoplasmic RNA, replicate 3

description:
Library name: As_Cyto_rep3
colname in Nuc_Cyto_Total_Counts_File.csv: As_Cyto_Rpe3

molecule: cytoplasmic RNA


title: Unstressed (0min), polyA+ RNA, replicate 1

description:
Library name: 0min_unstressed_rep1
colname in Time_Course_Counts_File.csv: 0min_rep1


title: Arsenite stressed (30min), polyA+ RNA, replicate 2

description:
Library name: 30min_As_rep2
colname in Time_Course_Counts_File.csv: 30min_rep2


title: Patient 1 Tumor tissues


title: Unstressed (0min), polyA+ RNA, replicate 3

description:
Library name: 0min_unstressed_rep3
colname in Time_Course_Counts_File.csv: 0min_rep3


title: Patient 3 Tumor tissues


title: Arsenite stress, cytoplasmic RNA, replicate 2

description:
Library name: As_Cyto_rep2
colname in Nuc_Cyto_Total_Counts_File.csv: As_Cyto_Rep2


title: Arsenite stressed, nuclear RNA, replicate 3

description:
Library name: As_Nuc_rep3
colname in Nuc_Cyto_Total_Counts_File.csv: As_Nuc_Rep3

molecule: nuclear RNA


title: Arsenite stressed (45min), polyA+ RNA, replicate 3

description:
Library name: 45min_As_rep3
colname in Time_Course_Counts_File.csv: 45min_rep3


title: Arsenite stressed, nuclear RNA, replicate 2

description:
Library name: As_Nuc_rep2
colname in Nuc_Cyto_Total_Counts_File.csv: As_Nuc_Rep2


title: Arsenite stress, cytoplasmic RNA, replicate 1

description:
Library name: As_Cyto_rep1
colname in Nuc_Cyto_Total_Counts_File.csv: As_Cyto_Rep1


title: Arsenite stressed, nuclear RNA, replicate 1

description:
Library name: As_Nuc_rep1
colname in Nuc_Cyto_Total_Counts_File.csv: As_Nuc_Rep1


title: Arsenite stressed (30min), polyA+ RNA, replicate 1

description:
Library name: 30min_As_rep1
colname in Time_Course_Counts_File.csv: 30min_rep1


title: Arsenite stressed, total RNA, replicate 3

description:
Library name: As_Total_rep3
colname in Nuc_Cyto_Total_Counts_File.csv: As_Total_Rep3


title: Unstressed, cytoplasmic RNA, replicate 2

description:
Library name: Un_Cyto_rep2
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Cyto_Rep2


title: Arsenite stressed, total RNA, replicate 1

description:
Library name: As_Total_rep1
colname in Nuc_Cyto_Total_Counts_File.csv: As_Total_Rep1


title: Patient 1 Adjacent non-tumorous tissues

description: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) .


title: Unstressed, total RNA, replicate 3

description:
Library name: Un_Total_rep3
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Total_Rep3


title: Unstressed, nuclear RNA, replicate 2

description:
Library name: Un_Nuc_rep2
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Nuc_Rep2


title: Unstressed, cytoplasmic RNA, replicate 1

description:
Library name: Un_Cyto_rep1
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Cyto_Rep1


title: Unstressed, cytoplasmic RNA, replicate 3

description:
Library name: Un_Cyto_rep3
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Cyto_Rep3


title: Unstressed, total RNA, replicate 2

description:
Library name: Un_Total_rep2
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Total_Rep2


title: Unstressed, nuclear RNA, replicate 1

description:
Library name: Un_Nuc_rep1
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Nuc_Rep1


title: Arsenite stressed, total RNA, replicate 2

description:
Library name: As_Total_rep2
colname in Nuc_Cyto_Total_Counts_File.csv: As_Total_Rep2


title: BEA24P061_GL_35_T4_Chem_RNA

city: Stockholm

first: Gintare

last: Lasaviciute

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University

description: Library name: P32606_1035

data_processing:
Raw Counts (Aligner: STAR, Ref.genome: Ensembl Homo_sapiens.GRCh38.dna.primary_assembly.fa, Gene quantification method: featureCounts, Gene ref: Ensembl Homo_sapiens.GRCh38.112)
Data was normalized using DeSeq2
R version 4.3.3 was used to perform some data analysis. "dplyr", "biomaRt", "clusterProfiler", "org.Hs.eg.db" and "ggplot2" packages were used for the data analysis.
Assembly: Ensembl Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: RNA-Seq raw count matrix as a txt file

source_name: Large intestine, colon

growth_protocol: A total of 0.12x106 Caco-2 cells were seeded into 24-well plates containing polyethylene membrane (Stem Cell Technologies). Cells were differentiated for 14 days, changing medium every 3-4 days. DMEM medium was supplemented with 1,15 mg/ml RA (Sigma Aldrich), 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were incubated at 37°C with 5% CO2 throughout the experiments.

extract_protocol:
RNA was isolated using the mirVana miRNA Isolation kit (Ambion by Life Technologies), following the protocol for total RNA extraction.
Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 200 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina Novaseq Plus 10B flowcell 300 cycles kit sequencing run, generating 150 base paired end reads with dual index 10+10 base pairs. Basecalling and demultiplexing was performed using bcl2fastq (v2.20.0) software with default settings generating Fastq files for further downstream mapping and analysis.

treatment_protocol: Differentiated Caco-2 cells were exposed to 50 µg/ml of 5 FU on the apical and basolateral sides for 24 h or were left unexposed as a control. Following 24 h, cells were washed twice with PBS and then bacterial components were added for 72 h.

value: Large intestine, colon

value: Enterocyte

value: 24h chemo, then 72h with/without postbiotics


title: BEA24P061_GL_31_T4_5_FU_RNA

description: Library name: P32606_1031


title: BEA24P061_GL_32_T4_5_FU_plus_LR_RNA

description: Library name: P32606_1032


title: BEA24P061_GL_33_T4_5_FU_plus_EPS_RNA

description: Library name: P32606_1033


title: BEA24P061_GL_34_T4_5_FU_plus_MV_RNA

description: Library name: P32606_1034


title: Unstressed, total RNA, replicate 1

description:
Library name: Un_Total_rep1
colname in Nuc_Cyto_Total_Counts_File.csv: Un_Total_Rep1


title: BEA24P061_GL_27_T3_5_FU_plus_LR_RNA

description: Library name: P32606_1027


title: BEA24P061_GL_29_T3_5_FU_plus_MV_RNA

description: Library name: P32606_1029


title: BEA24P061_GL_28_T3_5_FU_plus_EPS_RNA

description: Library name: P32606_1028


title: BEA24P061_GL_26_T3_5_FU_RNA

description: Library name: P32606_1026


title: BEA24P061_GL_22_T2_5_FU_plus_LR_RNA

description: Library name: P32606_1022


title: granulosa cells, hCG, 12h, PGR_ChIP, Rep3

city: Lexington

first: Hayce

last: Jeon

state: KENTUCKY

address: 800 Rose Street

department: Dept. of OB/GYN

institute: University of Kentucky

description: Library name: Sample4_12h_H_PGR

data_processing:
FASTQ files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina). Adaptors have been trimmed from the 3' end of the reads, resulting in 760,113,797 filtered reads. Trimmed reads were aligned to the human genome version of GRCh38 from NCBI using BWA (0.7.17-r1188).
Peak calling was performed with MACS2 (2.2.7.1) using default settings and input DNA as a control to identify regions of enriched binding. For the hCG-treated group, peaks from three replicates were merged using MACS2 Consensus to obtain a consensus set of peaks.
Assembly: GRCh38
Supplementary files format and content: BigWig, NarrowPeak (except for Input)

source_name: Ovary

growth_protocol: Cells were obatined from IVF patients at the time of oocyte retrieval and subjected to a Percoll gradient to isolate granulosa cells. Isolated granulosa cells were then cultured in Opti-MEM supplemented with 1x antibiotics/antimycotics and 10% fetal bovine serum for 6 days to regain the responsiveness to hCG.

extract_protocol:
Chromatin was extracted from cells fixed with 1.1% formaldehyde and fragmented using sonication.
Libraries from purified DNA from ChIP and input samples were prepared with the UltraLow System V2 DNA-Seq Library Preparation Kit (Tecan; Durham, NC, USA). The libraries were pooled and quantitated by qPCR and sequenced on one 10B lane for 101 cycles from one end of the fragments on a NovaSeq X Plus with V1.0 sequenced kits (Illumina).

treatment_protocol: After the acclimation period, the cells were undergone serum startvation for 1 h and then treated with or without hCG 12 h.

value: Ovary

value: primary human granulosa/lutein cells

value: hCG

value: PGR (Cell Signaling, #8757)


title: BEA24P061_GL_25_T2_Chem_RNA

description: Library name: P32606_1025


title: granulosa cells, hCG, 12h, Input, Rep2

description: Library name: Sample3_12h_H_Input


title: granulosa cells, hCG, 12h, PGR_ChIP, Rep1

description: Library name: Sample2_12h_H_PGR


title: BEA24P061_GL_21_T2_5_FU_RNA

description: Library name: P32606_1021