title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D6, Well Replicate 2

description:
Library name: W69D6-2
column name in both processed data files: Low_D6_2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D6, Well Replicate 1

status: Public on Feb 20 2026

type: SRA

city: Madison

first: Sean

middle: P.

last: Palecek

state: Wisconsin

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

country: USA

institute: University of Wisconsin-Madison

description:
Library name: W69D6-1
column name in both processed data files: Low_D6_1

library_source: transcriptomic

data_processing:
Raw FASTQ files were mapped to the human genome (hg38+decoy) using STAR v2.5.3a
Gene-level transcript abundances were calculated using featureCounts v2.0.3
Assembly: Assembly: hg38+decoy
Supplementary files format and content: csv files starting with featureCounts include gene-level counts for each sample and gene, csv files starting with TPM include transcipts per million values for each sample and gene

molecule: polyA RNA

organism: Homo sapiens

source_name: WTC11 hiPSC line

growth_protocol: hPSCs were differentiated using the GiWi protocol as described previously. On Day -2, hPSCs were detached and singularized with Accutase (Innovative Cell Technology AT104) for 5 min prior to quenching 1:1 v/v in DMEM/F12 (ThermoFisher 11330032). Subsequently, hPSCs were counted and resuspended at cell densities optimized for cardiomyocyte differentiation for each hPSC line. hPSCs were resuspended in mTeSR1 with 5 μM Y-27632 (Tocris 1254) and seeded onto Matrigel-coated 12-well plates in 2 mL of media. To facilitate even cell attachment on Day -2, plates were left at room temperature for 30 min prior to maintenance in a cell culture incubator. On Day -1, medium was replaced with mTeSR1. On Day 0, differentiation was induced with CHIR99021 (Selleckchem S1263) at a concentration between 6-12 μM, optimized for cardiomyocyte differentiation for each hPSC line. CHIR99021 was added to RPMI1640 medium (Life Technologies 11875119) with 2% v/v B27 minus insulin (B27-). After Day 0, protocol timing is dependent on hPSC line as previously established. For WTC11 hiPSCs, media was replaced with B27- and 5 μM IWP2 (Tocris 3533) on Day 2 and on Day 4 with B27-. On Days 6, 8, 10, and 13, media was replaced with RPMI1640 with 2% v/v B27 with insulin (B27+, Life Technologies 17504044) until collection on Day 16. In GiWi hPSCs (IMR90-4 hiPSCs and H9 hESCs), media was replaced on Days 1 and 5 with B27- and on Day 3 with 1:1 v/v B27-:conditioned medium with 5 μM IWP2. On Days 7, 10, and 13, media was replaced with B27+ until collection on Day 16.

extract_protocol:
For both the multi-omic collection experiment and the RNA sequencing only collection, RNA was harvested from Trizol-collected samples by tri-phasic extraction followed by purification and concentration with Zymo Direct-zol MiniPrep Plus columns (including on-column DNAase treatment). 500ng of total RNA per sample was used for the construction of sequencing libraries.
For the multi-omic collection experiment, mRNA libraries for RNA sequencing were constructed using the Illumina TruSeq Stranded mRNA kit and sequenced on an Illumina NovaSeq6000. For the RNA sequencing only collection experiment, total RNA libraries for RNA sequencing were constructed using the Takara SMARTer Stranded Total RNA Kit - HI Mammalian and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: After hPSC-CM differentiation was completed and flow cytometry was performed to quantify hPSC-CM differentiation purity (%cTnT+ cells), differentiations were classified as either high or low purity. Subsequently, temporally trizol-collected high and low purity hPSC-CM differentiation samples were further processed for RNA sequencing.

tag: cell line

value: WTC11 hiPSC line

tag: time

tag: treatment

value: low purity hPSC-CM differentiaiton

tag: batch

value: RNAseq from multi-omics experiment


title: Control_2

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
FASTQ files were extracted and sequencing adapters and low-quality reads were removed by Cutadapt (v.2.3)
Quality of the processed FASTQ files were checked by FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0)
EdgeR (v.3.26.1) was used to identify differentially expressed genes.
Assembly: Assembly: Esembl GRCm38.102
Supplementary files format and content: Supplementary files format and content: CSV, raw counts of sequencing reads on the gene level

molecule: total RNA

organism: Mus musculus

source_name: heart ventricle

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committees.

extract_protocol:
Total RNA from the embryonic heart ventricles was isolated using TRIzol (Invitrogen) from tissues using standard protocol. rRNA-depleted libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina) RNA-sequencing was processed by GENEWIZ using Illumina platform (paired-ended, 150bp read-length)
rRNA-depletion library

tag: tissue

value: heart ventricle

tag: developmental stage

tag: genotype


title: Control_3


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D4, Well Replicate 4

description:
Library name: W69D4-4
column name in both processed data files: Low_D4_4


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D2, Well Replicate 4

description:
Library name: W69D2-4
column name in both processed data files: Low_D2_4


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D4, Well Replicate 1

description:
Library name: W69D4-1
column name in both processed data files: Low_D4_1


title: AcKO_1


title: CUT&Tag PARIS-IgG sample

city: Baltimore

first: Ji-Yang

last: Song

state: MD

address: 733 North Broadway St.

institute: Johns Hopkins University School of Medicine

description:
Library name: PARIS_IgG_S3
CUT&Tag profiling of PARIS binding in hippocampal tissue

library_source: genomic

data_processing:
Reads were trimmed and aligned to the mouse genome (mm10) using Bowtie2 with default parameters recommended for CUT&Tag.
Aligned reads were filtered to remove low-quality reads, unmapped reads, secondary alignments, and PCR duplicates.
Signal tracks were generated using deepTools with RPKM normalization.
Peak calling was performed using SEACR in stringent mode with the IgG control sample as background.
Peak BED files and normalized bigWig tracks were generated for downstream visualization and analysis.
Assembly: mm10 (Mus musculus reference genome)
Supplementary files format and content: Normalized coverage tracks are provided as bigWig files representing genome-wide PARIS-FLAG and IgG control signal.
Supplementary files format and content: SEACR peak files are provided as BED files containing called peak regions and summit annotations.
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: hippocampus

growth_protocol: Not applicable.

extract_protocol:
CUT&Tag libraries were prepared from hippocampal tissue of CamK-PARIS mice. Tissue was dissociated, permeabilized, and incubated with an anti-FLAG antibody to capture PARIS-bound chromatin. An IgG antibody was used as a negative control. Concanavalin A–bound nuclei were incubated with secondary antibody and pA-Tn5 transposome, followed by tagmentation. DNA fragments were extracted and PCR-amplified to generate indexed libraries. Libraries were size-selected, quantified, and sequenced as paired-end runs on an Illumina platform.
Reads were trimmed and aligned to the mouse reference genome (mm10) using Bowtie2 with default CUT&Tag parameters. Aligned reads were filtered to remove low-quality and duplicate reads. Peaks were called with SEACR using the IgG sample as control. bigWig signal tracks were generated from filtered alignments using deepTools with RPKM normalization. Processed data include normalized bigWig coverage tracks and SEACR peak BED files.

treatment_protocol: No treatment was applied.

tag: strain

value: hippocampus

value: CamK-PARIS

tag: antibody

value: anti-IgG


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D2, Well Replicate 3

description:
Library name: W69D2-3
column name in both processed data files: Low_D2_3


title: Control_1


title: CUT&Tag PARIS-FLAG sample

description:
Library name: PARIS_FLAG_S2
CUT&Tag profiling of PARIS binding in hippocampal tissue

value: anti-FLAG


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D0, Well Replicate 2

description:
Library name: W69D0-2
column name in both processed data files: Low_D0_2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D2, Well Replicate 2

description:
Library name: W69D2-2
column name in both processed data files: Low_D2_2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D4, Well Replicate 3

description:
Library name: W69D4-3
column name in both processed data files: Low_D4_3


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D0, Well Replicate 4

description:
Library name: W69D0-4
column name in both processed data files: Low_D0_4


title: AcKO_2


title: UV-RIP-seq-293T HEK cells, rep1

city: Shenzhen

first: Hao

last: Chen

address: 1088 Xueyuan Avenue

country: China

institute: Southern University of Science and Technology (SUSTech)

description: Library name: UV-RIP-seq-1

data_processing:
The CRISPRi/Cas9 screening data analysis was performed by MAGeCK (v0.5.9.5) as previously described. MAGeCK RRA method was used to evaluate the abundance of sgRNAs and identify gene hits.  UV-RIP-seq: Raw sequencing reads were processed by adapter and quality trimming using Trim Galore. Clean reads were aligned to the reference genome with STAR, and only uniquely mapped reads were retained after removing PCR duplicates with Picard.
Assembly: GRCm39.genome.fa or  GRCh38.p14.genome.fa
Supplementary files format and content: UV-RIP-seq-1.xlsx
Supplementary files format and content: UV-RIP-seq-2.xlsx
Supplementary files format and content: control_die.gene_summary.txt
Supplementary files format and content: control_die.sgrna_summary.txt
Library strategy: iCLIP

source_name: 293T HEK cells

growth_protocol: B16 melanoma cells and 293T HEK cells were purchased from Wuhan Pricella Biotechnology. All cells were authenticated by STR profiling and testing for mycoplasma contamination was performed with a MycAway one-step mycoplasma detection kit (Yeasen). Unless otherwise noted, all cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, BI) and 1% penicillin-streptomycin (Thermo Fisher Scientific) and maintained in a 37°C humidified incubator with 5% CO2.

extract_protocol:
CRISPR/Cas9 library screening For generating stably expressed Cas9 in B16 melanoma cells, the vector containing the coding sequence of both Cas9 and fluorescence protein was introduced into cells via lentiviral transduction. The transduced cells were then screened according to fluorescence and sorted by flow cytometry. For individual gene knockdown in B16 cells, sgRNAs were stably transfected into B16 cells with Cas9 stably expression. Subsequently, cells were selected with 2 μg/mL of puromycin for 7 days for screens. Infected cells were cultured in galactose medium or glucose medium  for 48 hours. Dead ceclls cultured in  galactose-basic medium and living cells cultured in complete medium were harvested to extract genomic DNA (gDNA) and amplify sgRNA from 5 μg gDNA using 2 X PCR Master Mix.                                                                                UV-RIP-seq Cells were washed with ice-cold PBS containing protease inhibitors, UV-crosslinked at 400 mJ/cm², and collected by scraping. The pellet was lysed sequentially in low-salt lysis buffer (50 mM Hepes-KOH, pH 7.5, 10 mM NaCl, 1 mM EDTA, 10% glycerol, 0.2% NP-40, 1% Triton X-100) and high-salt lysis buffer (600 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% DOC). Lysates were incubated with EOLA1 antibody in IP buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% DOC). Beads were washed sequentially with low-salt wash buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1), high-salt wash buffer (500 mM NaCl, same components), and LiCl wash buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris, pH 8.1), followed by TE buffer. RNA–protein complexes were eluted in elution buffer (10 mM Tris, pH 8.0, 1 mM EDTA, 1% SDS), digested with Proteinase K, and extracted by phenol–chloroform, followed by ethanol precipitation.   Recovered RNA was treated with DNase I.
CRISPR/Cas9 library screening    Dead ceclls cultured in  galactose-basic medium and living cells cultured in complete medium were harvested to extract genomic DNA (gDNA) and amplify sgRNA from 5 μg gDNA using 2 X PCR Master Mix. The prepared libraries were then subjected to massive parallel high-throughput sequencing by Berry Genomics.                                                                                UV-RIP-seq      Purified RNA was treated with PNK, and the RNA library was prepared by VAHTSTM Small RNA Library Prep Kit for Illumina®.

value: 293T HEK cells


title: UV-RIP-seq-293T HEK cells, rep2

description: Library name: UV-RIP-seq-2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D0, Well Replicate 3

description:
Library name: W69D0-3
column name in both processed data files: Low_D0_3


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D0, Well Replicate 1

description:
Library name: W69D0-1
column name in both processed data files: Low_D0_1


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D2, Well Replicate 1

description:
Library name: W69D2-1
column name in both processed data files: Low_D2_1


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D4, Well Replicate 2

description:
Library name: W69D4-2
column name in both processed data files: Low_D4_2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D16, Well Replicate 3

description:
Library name: W52D16-3
column name in both processed data files: High_D16_3

value: high purity hPSC-CM differentiation


title: Group H (high temperature) second peak (P2), fish 5

type: RNA

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

hyb_protocol: Labels were hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Skin

label_protocol: RNA was amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Atlantic salmon post-smolt (n=720, ~50g, Aquagen, Norway) were transferred to the Aquaculture Research Station (Kårvika, Troms, Norway), where they were acclimated for 4 weeks in six flow-through tanks (900L, n=120 fish per tank) where water temperatures were ca. 8°C and dissolved O2 saturation levels were ≥80% prior to the start of the experiment.

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Two replicate tanks per regime were subjected to constant 12°C, constant 17°C or fluctuation between 12 and 17°C. All six tanks were first acclimated to 12°C for one week. Temperature in the four tanks subjected to constant 17°C or fluctuating 12/17°C regime was increased by 1°C per day up to 17°C and then held for 5 days before another 5 days were used to decrease temperature to 12°C. Fish were then held at 12°C for further 5 five days and the cycle was repeated.

value: Skin

tag: temperature

value: high


title: Group H (high temperature) second peak (P2), fish 6


title: Group H (high temperature) second peak (P2), fish 4


title: Group H (high temperature) second peak (P2), fish 2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D16, Well Replicate 2

description:
Library name: W52D16-2
column name in both processed data files: High_D16_2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D13, Well Replicate 3

description:
Library name: W52D13-3
column name in both processed data files: High_D13_3


title: Group H (high temperature) second peak (P2), fish 1


title: Group H (high temperature) second peak (P2), fish 3


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D13, Well Replicate 2

description:
Library name: W52D13-2
column name in both processed data files: High_D13_2


title: Group F (fluctuating temperature) second peak (P2), fish 6

value: fluctuating


title: Group F (fluctuating temperature) second peak (P2), fish 5


title: Group F (fluctuating temperature) second peak (P2), fish 4


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D10, Well Replicate 2

description:
Library name: W52D10-2
column name in both processed data files: High_D10_2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D8, Well Replicate 4

description:
Library name: W52D8-4
column name in both processed data files: High_D8_4


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D6, Well Replicate 4

description:
Library name: W52D6-4
column name in both processed data files: High_D6_4


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D8, Well Replicate 2

description:
Library name: W52D8-2
column name in both processed data files: High_D8_2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D8, Well Replicate 1

description:
Library name: W52D8-1
column name in both processed data files: High_D8_1


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D16, Well Replicate 1

description:
Library name: W52D16-1
column name in both processed data files: High_D16_1


title: Group T12 (optimum temperature) second peak (P2), fish 6

value: optimum


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D6, Well Replicate 2

description:
Library name: W52D6-2
column name in both processed data files: High_D6_2


title: Group F (fluctuating temperature) second peak (P2), fish 1


title: Group F (fluctuating temperature) second peak (P2), fish 2


title: Group F (fluctuating temperature) second peak (P2), fish 3


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D6, Well Replicate 3

description:
Library name: W52D6-3
column name in both processed data files: High_D6_3


title: Group T12 (optimum temperature) second peak (P2), fish 5


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D4, Well Replicate 3

description:
Library name: W52D4-3
column name in both processed data files: High_D4_3


title: Group T12 (optimum temperature) second peak (P2), fish 4


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D6, Well Replicate 1

description:
Library name: W52D6-1
column name in both processed data files: High_D6_1


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D4, Well Replicate 1

description:
Library name: W52D4-1
column name in both processed data files: High_D4_1


title: Group H (high temperature) first peak (P1), fish 6


title: Group T12 (optimum temperature) second peak (P2), fish 3


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D4, Well Replicate 4

description:
Library name: W52D4-4
column name in both processed data files: High_D4_4


title: Group T12 (optimum temperature) second peak (P2), fish 2


title: Group H (high temperature) first peak (P1), fish 5


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D2, Well Replicate 3

description:
Library name: W52D2-3
column name in both processed data files: High_D2_3


title: Group T12 (optimum temperature) second peak (P2), fish 1


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D2, Well Replicate 2

description:
Library name: W52D2-2
column name in both processed data files: High_D2_2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D2, Well Replicate 4

description:
Library name: W52D2-4
column name in both processed data files: High_D2_4


title: Group H (high temperature) first peak (P1), fish 2


title: Group H (high temperature) first peak (P1), fish 4


title: Group H (high temperature) first peak (P1), fish 3


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D4, Well Replicate 2

description:
Library name: W52D4-2
column name in both processed data files: High_D4_2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D0, Well Replicate 4

description:
Library name: W52D0-4
column name in both processed data files: High_D0_4


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D2, Well Replicate 1

description:
Library name: W52D2-1
column name in both processed data files: High_D2_1


title: Group H (high temperature) first peak (P1), fish 1


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D0, Well Replicate 2

description:
Library name: W52D0-2
column name in both processed data files: High_D0_2


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D0, Well Replicate 3

description:
Library name: W52D0-3
column name in both processed data files: High_D0_3


title: Group F (fluctuating temperature) first peak (P1), fish 6


title: Group F (fluctuating temperature) first peak (P1), fish 5


title: Group F (fluctuating temperature) first peak (P1), fish 4


title: WTC11 hiPSC, Passage 52, high purity hPSM-CM differentiation, D0, Well Replicate 1

description:
Library name: W52D0-1
column name in both processed data files: High_D0_1


title: Listeria2

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description: Library name: Listeria1

data_processing:
Paired-end FASTQ files were quality-checked using FastQC (integrated in Trim Galore). Adapter trimming and additional quality filtering were performed with Trim Galore (v0.6.7 or newer) in paired-end mode using default parameters and Cutadapt as the underlying trimming tool. Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.4.5 or newer) with the parameters --end-to-end --very-sensitive --no-mixed --no-discordant --dovetail, which are particularly suitable for the short, paired-end fragments typical of CUT&Tag experiments. Alignments (SAM format) were converted to BAM using SAMtools (v1.15). BAM files were sorted with Sambamba (v0.8.2). Duplicates were marked and removed, and only properly paired, mapped, non-duplicate reads without auxiliary alignment tags ([XS] == null) were retained using Sambamba’s filtering module. Reads mapping to genomic blacklist regions (ENCODE hg38-blacklist.v2) were removed with SAMtools view using the -U (unmapped in bed) option. The resulting filtered, blacklist-removed BAM files were used for downstream analysis and visualization. For visualization on the UCSC Genome Browser or IGV, normalized BigWig tracks were generated as follows: genome coverage was calculated in bedGraph format using bedtools genomecov (-bg -pc), the bedGraph was sorted by chromosome and start position, and finally converted to BigWig using bedGraphToBigWig (UCSC tools) with the hg38 chromosome sizes file. Peak calling was performed using SEACR (v1.3) in stringent mode for each mark. Resulting peak sets were used for all subsequent differential accessibility and annotation analyses.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: organoid

growth_protocol: Human small intestinal and colonic epithelial organoids were established from endoscopic biopsies of the ascending colon obtained with informed consent from de-identified donors. Organoids were generated following a modified protocol based on 41 42. Briefly, biopsies were digested in 2 mg/ml collagenase IA, filtered through a 70 µm strainer, and pelleted (150g, 5 min). The epithelial fraction was resuspended in cold wash medium (DMEM/F12 50:50 with 10% FBS, 1× Pen/Strep) and embedded in 30 µl Matrigel. After polymerization (10 min, 37 °C, inverted), 450 µl of complete epithelial organoid medium was added, supplemented for the first 48 h with CHIR 99021 (2.5 µg ml⁻¹) to activate Wnt/β-catenin signaling. ROCK inhibitor (Y-27632) and TGFBR1 inhibitor were included to prevent anoikis and suppress serum-derived TGF-β activity. Cultures were passaged 1:1–1:2 depending on organoid density and morphology.

extract_protocol:
CUT&Tag libraries for Pol II were generated from human intestinal organoids exposed to vehicle or Listeria monocytogenes (3 biological replicates). Nuclei were isolated from Listeria-infected and control human intestinal organoids by gentle douncing in NE1 buffer. CUT&Tag was performed on 100,000 nuclei per sample following the established protocol. Nuclei were immobilised on concanavalin A-coated magnetic beads and incubated overnight at 4°C with anti-RPB1 (Pol II) antibody (CST 2629) in digitonin-containing antibody buffer. After washing, a mouse secondary antibody and pre-loaded pAG-Tn5 adapter complex (EpiCypher) were sequentially applied, followed by tagmentation at 37°C for 1 h. DNA was released by heat in SDS buffer, neutralized, and purified by spin columns.
Libraries were generated using NEBNext High-Fidelity PCR Master Mix and Nextera i5/i7 indexed primers, amplified for 11 cycles, size-selected with AMPure beads, quantified, assessed on a TapeStation, pooled equimolarly, and sequenced on the NovaSeq X Plus (PE150; ~20 million reads/sample)

treatment_protocol: With and without Listeria

value: organoid

tag: cell type

value: epithelial

value: Listeria


title: Listeria

description: Library name: Listeria2


title: Group F (fluctuating temperature) first peak (P1), fish 1


title: CUT&RUN IgG control in MXP5 IK1 rep1

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

description:
Library name: MXP5_IgG_IK_rep1
CUT&RUN IgG control in MXP5 after IK1 induction, rep1

data_processing:
CUT&RUNTools analysis pipeline was used for processing [Zhu, 2019]. Briefly, reads were trimmed and aligned to the hg38 genome. Narrow peaks were called from deduplicated reads with MACS2 (v2.2.9.1) and ssvQC(v 1.0.22) was used to assess signal enrichment over IgG controls.
Assembly: hg38
Supplementary files format and content: BED files containing genome-wide ChromHMM segmentations (15-state model) for MXP5 cells under control or IK1-induced conditions. Each row defines a genomic interval labeled with a chromatin state (E1–E15).
Library strategy: CUT&RUN

growth_protocol: Cells were cultured at 37°C in a humidified incubator with 5% CO₂ in MEMα GlutaMAX (Gibco) supplemented with 20% FBS.

extract_protocol:
The CUTANA CUT&RUN kit (EpiCypher #14-1048) was used according to manufacturer’s instructions, using 500,000 cells per reaction. Briefly, Concanavalin A beads were used to immobilize cells and .5 μg of individual antibodies against H3K4me3 (Epicypher #13-0041), H3K27me3 (Active Motif, #39159), H3K9me3(Active Motif, #39161) or H3K36me3 (Active Motif #61101) were incubated overnight at 4°C with light rocking using  1 μL control IgG (Epicypher #13-0042) antibodies. Antibody chromatin complexes were treated with pAG-MNase for 2 hours at 4°C and DNA fragments were purified.
DNA concentration was measured with a Qubit fluorometer and 5-10ng of purified DNA was input into sequencing library preparation with NEBNext UltraII kit (NEB # E7645). Library size was assessed with an Agilent Bioanalyzer and sequenced paired-end 150bp with Illumina.

treatment_protocol: MXP5 stably expressing wild-type IK1 or control were induced with 1 μg/mL doxycycline for 24 hours.

value: IgG


title: Group T12 (optimum temperature) first peak (P1), fish 4


title: Group F (fluctuating temperature) first peak (P1), fish 2


title: Group T12 (optimum temperature) first peak (P1), fish 5


title: Ctrl2

description: Library name: Ctrl1

value: Control


title: Group T12 (optimum temperature) first peak (P1), fish 6


title: Group T12 (optimum temperature) first peak (P1), fish 1


title: Group F (fluctuating temperature) first peak (P1), fish 3


title: CUT&RUN IgG control in MXP5 IK1 rep2

description:
Library name: MXP5_IgG_IK_rep2
CUT&RUN IgG control in MXP5 after IK1 induction, rep2


title: Group T12 (optimum temperature) first peak (P1), fish 3


title: Ctrl

description: Library name: Ctrl2


title: Group T12 (optimum temperature) first peak (P1), fish 2


title: CUT&RUN of H3K9me3 in MXP5 IK1 rep1

description:
Library name: MXP5_H3K9me3_IK_rep1
CUT&RUN for H3K9me3 in MXP5 after IK1 induction, rep1


title: Listeria1

description: Library name: Listeria


title: CUT&RUN IgG control in MXP5 control rep1

description:
Library name: MXP5_IgG_GFP_rep1
CUT&RUN IgG control in MXP5 with empty vector (GFP), rep1

value: control


title: Group H (high temperature) before trial, fish 4


title: Ctrl1

description: Library name: Ctrl


title: Group H (high temperature) before trial, fish 3


title: CUT&RUN of H3K4me3 in MXP5 IK1 rep1

description:
Library name: MXP5_H3K4me3_IK_rep1
CUT&RUN for H3K4me3 in MXP5 after IK1 induction, rep1


title: Group F (fluctuating temperature) before trial, fish 4


title: CUT&RUN of H3K9me3 in MXP5 control rep1

description:
Library name: MXP5_H3K9me3_GFP_rep1
CUT&RUN for H3K9me3 in MXP5 with empty vector (GFP), rep1


title: CUT&RUN of H3K9me3 in MXP5 control rep2

description:
Library name: MXP5_H3K9me3_GFP_rep2
CUT&RUN for H3K9me3 in MXP5 with empty vector (GFP), rep2


title: Group H (high temperature) before trial, fish 1


title: CUT&RUN of H3K27me3 in MXP5 IK1 rep2

description:
Library name: MXP5_H3K27me3_IK_rep2
CUT&RUN for H3K27me3 in MXP5 after IK1 induction, rep2


title: Group F (fluctuating temperature) before trial, fish 2


title: CUT&RUN of H3K4me3 in MXP5 IK1 rep2

description:
Library name: MXP5_H3K4me3_IK_rep2
CUT&RUN for H3K4me3 in MXP5 after IK1 induction, rep2


title: CUT&RUN of H3K4me3 in MXP5 control rep1

description:
Library name: MXP5_H3K4me3_GFP_rep1
CUT&RUN for H3K4me3 in MXP5 with empty vector (GFP), rep1


title: CUT&RUN of H3K27me3 in MXP5 control rep2

description:
Library name: MXP5_H3K27me3_GFP_rep2
CUT&RUN for H3K27me3 in MXP5 with empty vector (GFP), rep2


title: Group H (high temperature) before trial, fish 2


title: Group F (fluctuating temperature) before trial, fish 1


title: Group T12 (optimum temperature) before trial, fish 3


title: CUT&RUN of H3K27me3 in MXP5 control rep1

description:
Library name: MXP5_H3K27me3_GFP_rep1
CUT&RUN for H3K27me3 in MXP5 with empty vector (GFP), rep1


title: Group T12 (optimum temperature) before trial, fish 2


title: 20190816_VR0816

city: Guangzhou

first: Ruifeng

last: Liu

state: Guangdong province

address: Jinsui Road, 7#

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description:
Library name: Sample 22
10x Genomics
AIC_scRNA_h5ad.tar.gz

library_source: transcriptomic single cell

data_processing:
We used Cell Ranger 3.0.2 and Macaca fascicularis genome version 5.0 to build the 10X reference (cellranger mkgtf), and create the counts matrices of each dataset from the samples.
The counts matrices were fed into the SCANPY pipeline (SCANPY version 1.9.1)), and combined all the counts matrices from 22 samples for data quality control.
We employed Scrublet (version 0.2.1) 110 and the marker gene expression patterns to determine the doublets in the UMAP visualization and excluded the doublets from the next step analysis.
The cell clusters were determined based on the UMAP visualization and leiden algorithm embedded in the SCANPY analysis routine.
Assembly: MFA_5.0
Supplementary files format and content: tar files generated by Cell Ranger (version 5.0.1)
Supplementary files format and content: mtx and tsv files generated by Cell Ranger (version 5.0.1)

organism: Macaca fascicularis

source_name: Brain

extract_protocol:
The 300-μm-thick tissue slices from the brain were collected and the white matter was removed.The AIC gray matter of the tissue was cut into small pieces so that it could be easily dissociated.In some cases, the slices were microdissected under a dissection microscope, and the superior layers and the deep layers were isolated as different samples to locate the neuron clusters in the cortical layers. The tissue pieces were transferred to dissociation solution for incubation about one hour with sustained carbonation, followed by gentle trituration using fire-polished glass Pasteur pipettes.The dissociation solution contains 30 U/mL papain (Worthington, LS003127), 0.05% trypsin-EDTA (Gibco, 25300054) and 2.5 mg/mL DNase I (Sigma, D5025) in ACSF warmed at 34 ℃for 10 min before use. Cell suspensions were filtered through a 40-μm cell strainer (BD Falcon, 352350) to eliminate cell clumps. Using the Dead Cell Removal Kit (MACS, 130090101), the dead cells and debris were removed from the suspension. The cells were washed twice and resuspended in PBS with 0.01% BSA (Sigma, B2064), and the cell concentration was estimated using a cell counter (Bio-Rad, TC20).
Libraries were prepared following the manufacturer's protocol for the 10x Genomics Single Cell 3' v2 assay. In brief, single-cell suspensions were combined with master mix, partitioning oil, and gel beads on a microfluidic chip to form gel bead-in-emulsions (GEMs). Within each GEM, poly-A RNA from lysed cells was reverse transcribed. The resulting cDNA molecules were tagged with an Illumina-compatible R1 primer sequence, a unique molecular identifier (UMI), and a cell-specific 10x Barcode. After breaking the emulsions, all barcoded cDNA was pooled, purified with Silane DynaBeads, and amplified by PCR. cDNA fragments of the appropriate size were then selected using SPRIselect beads. During final library construction, Illumina adapter sequences (P5 and P7), the R2 primer sequence, and a sample index were incorporated to generate sequencing-ready constructs.

value: Brain

value: neurons,Neuroglia

value: WT


title: Group F (fluctuating temperature) before trial, fish 3


title: CUT&RUN of H3K27me3 in MXP5 IK1 rep1

description:
Library name: MXP5_H3K27me3_IK_rep1
CUT&RUN for H3K27me3 in MXP5 after IK1 induction, rep1


title: CUT&RUN of H3K4me3 in MXP5 control rep2

description:
Library name: MXP5_H3K4me3_GFP_rep2
CUT&RUN for H3K4me3 in MXP5 with empty vector (GFP), rep2


title: Group T12 (optimum temperature) before trial, fish 4


title: 20190808_VR_50808

description:
Library name: Sample 21
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: HiChIP of H3K27ac in MXP5 IK1 rep2

description:
Library name: MXP5_HiChIP_IK1_rep2
HiChIP for H3K27ac in MXP5 after IK1 induction, rep2

data_processing:
HiChIP analysis was performed using the HiC-Pro pipeline to generate valid interaction pairs from Bowtie2-aligned reads (hg38). Only uniquely mapped, non-duplicate reads from valid ligation products were retained. Downstream interaction analysis was performed using FitHiChIP (v11.0) with peak-to-all interactions (IntType=3) at 10 kb resolution. Loops were called within a distance range of 20 kb to 4 Mb, and significant interactions were identified at FDR < 0.01 using coverage bias regression (BiasType=1) and merging of nearby interactions (MergeInt=1). MXP5 H3K27ac peaks were used as anchors. FitHiChIP was run in both replicate and pooled modes across conditions.
Assembly: hg38
Supplementary files format and content: BEDPE for high-confidence chromatin interactions identified using FitHiChIP (bin size = 10 kb; interaction distance: 20 kb–4 Mb), filtered at FDR < 0.01. Each row contains a pair of interacting genomic regions, interaction score, and FitHiChIP formatting for IGV compatibility.
Library strategy: HiChIP

extract_protocol:
HiChIP was performed using the HiC+ kit (Arima A101020), according to the manufacturer’s protocols, with slight modifications. Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, quenched with 125mM glycine. HiC was performed using the Arima protocol with 15 μg of chromatin per sample. Chromatin was then sheared to average size of 500 bp using Covaris S220 sonicator, followed by incubation with 4 μl of H3K27Ac antibody (Active Motif, 39135) overnight and chromatin immunoprecipitation with protein A/G magnetic beads (Pierce 88803), followed by washes according to the Arima protocol.
Capture of biotinylated fragments and library building was performed using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat # 21024) according to manufacturer’s instructions.


title: HiChIP of H3K27ac in MXP5 IK1 rep1

description:
Library name: MXP5_HiChIP_IK1_rep1
HiChIP for H3K27ac in MXP5 after IK1 induction, rep1


title: 20190808_VR230808

description:
Library name: Sample 20
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: HiChIP of H3K27ac in MXP5 control rep1

description:
Library name: MXP5_HiChIP_CTRL_rep1
HiChIP for H3K27ac in MXP5 control, rep1


title: HiChIP of H3K27ac in MXP5 control rep2

description:
Library name: MXP5_HiChIP_CTRL_rep2
HiChIP for H3K27ac in MXP5 control, rep2


title: ATAC-seq of PDX2 IK1 rep2

description:
Library name: PDX2_ATAC_IK_rep2
ATAC-seq for PDX2 IK1, rep2

data_processing:
Data were aligned to the hg38 reference genome using BWA-MEM.
Processed ATAC-seq peak files were generated using MACS2 (v2.2.9). PCR duplicates were removed, reads mapping to ENCODE blacklist regions were excluded, and peaks were called using default MACS2 narrowPeak parameters.
Assembly: hg38
Supplementary files format and content: Processed data consist of peak calls in BED/narrowPeak format generated by MACS2. Each file lists genomic coordinates of ATAC-seq peaks with peak score, significance, and summit position.

extract_protocol:
ATAC-seq was performed using the opti-ATAC protocol with 50,000 cells per condition, each with two independent biological replicates. Cells were washed with cold PBS and lysed on ice for 5 minutes in 50 μL of lysis buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl₂, 0.1% Triton X-100, protease inhibitors). Nuclei were pelleted at 2500 rpm for 5 minutes and resuspended in 20 μL of transposition mix (10 μL TD buffer, 0.8 μL Tn5 transposase (Illumina, 9.2 μL water). Transposition was performed at 37°C for 30 minutes.
Tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen), and libraries amplified using NEBNext High-Fidelity PCR Master Mix with barcoded Nextera primers. Libraries were double size-selected with AMPure XP beads (Beckman Coulter) to retain fragments between 150–1000 bp, quality-checked on an Agilent Bioanalyzer, and sequenced as paired-end 150 bp reads on an Illumina NovaSeq platform.

treatment_protocol: MXP5 and PDX2 stably expressing wild-type IK1 or control were induced with 1 μg/mL doxycycline for 24 hours.


title: ATAC-seq of PDX2 control rep1

description:
Library name: PDX2_ATAC_GFP_rep1
ATAC-seq for PDX2 CON, rep1


title: ATAC-seq of PDX2 IK1 rep1

description:
Library name: PDX2_ATAC_IK_rep1
ATAC-seq for PDX2 IK1, rep1


title: ATAC-seq of PDX2 control rep2

description:
Library name: PDX2_ATAC_GFP_rep2
ATAC-seq for PDX2 CON, rep2


title: 20190806_VR10806

description:
Library name: Sample 16
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20190806_VL110806

description:
Library name: Sample 14
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20190806_VL120806

description:
Library name: Sample 15
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: ATAC-seq of MXP5 IK1 rep1

description:
Library name: MXP5_ATAC_IK_rep1
ATAC-seq for MXP5 IK1, rep1


title: 20190619_VL10619

description:
Library name: Sample 12
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20190806_VR20806

description:
Library name: Sample 17
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20190808_VL_50808

description:
Library name: Sample 19
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: Group T12 (optimum temperature) before trial, fish 1


title: ATAC-seq of MXP5 control rep2

description:
Library name: MXP5_ATAC_GFP_rep2
ATAC-seq for MXP5 CON, rep2


title: 20190808_VL230808

description:
Library name: Sample 18
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20190404_VENR3

description:
Library name: Sample 11
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: ATAC-seq of MXP5 control rep1

description:
Library name: MXP5_ATAC_GFP_rep1
ATAC-seq for MXP5 CON, rep1


title: RNA-seq of SHMT2 of sh3

city: Lanzhou

first: Dongao

last: Fan

address: No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, P.R.China

institute: Lanzhou University

description: Library name: sh3

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Supplementary files format and content: CSV file including Reads count for each sample

source_name: cell line

extract_protocol:
Total RNA was isolated from PANC-1 cells using TRIzol reagent according to the manufacturer's protocol.
RNA-seq library was constructed by using NEBNext Ultra II RNA Library Prep Kit for illumina.

value: cell line

value: pancreatic cancer cell


title: 20190404_VENR2-1

description:
Library name: Sample 9
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: ATAC-seq of MXP5 IK1 rep2

description:
Library name: MXP5_ATAC_IK_rep2
ATAC-seq for MXP5 IK1, rep2


title: 20190619_VR10619

description:
Library name: Sample 13
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20190404_VENR2-2

description:
Library name: Sample 10
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: RNA-seq of SHMT2 of sh2

description: Library name: sh2


title: 20190404_VENL4

description:
Library name: Sample 8
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: RNA-seq of SHMT2 of sh1

description: Library name: sh1


title: 20190318_VEN-R24

description:
Library name: Sample 7
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20190318_VEN-L13

description:
Library name: Sample 6
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20181108VEN_R_5

description:
Library name: Sample 5
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: RNA-seq of SHMT2 of nc3

description: Library name: nc3


title: RNA-seq of SHMT2 of nc1

description: Library name: nc1


title: 20181108VEN_R_4

description:
Library name: Sample 4
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: Human, Islets, shCHD3-4, Replicate 3 (RRID:SAMN49540983)

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

description: Library name: shCHD3-4_3

data_processing:
The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the GRCh38_ens109 reference genome. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses were compared across donor-matched samples following DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: GRCh38_ens109
Supplementary files format and content: Relative fold changes were compared across each individual shRNA treatment group and included in table

source_name: pancreatic islets

extract_protocol:
approximately 100 pseudoislets per condition were collected and RNA was isolated according to the manufacturer’s protocol (Zymo Research).
cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). A dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. The average size of the library insert was approximately 300-400 bp

value: pancreatic islets


title: 20181108VEN_R_3

description:
Library name: Sample 3
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: 20181108VEN_R_1

description:
Library name: Sample 1
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: Human, Islets, shCHD3-4, Replicate 2 (RRID: SAMN48439620)

description: Library name: shCHD3-4_2


title: Human, Islets, shCHD3-4, Replicate 1 (RRID: SAMN47834917)

description: Library name: shCHD3-4_1


title: 20181108VEN_R_2

description:
Library name: Sample 2
10x Genomics
AIC_scRNA_h5ad.tar.gz


title: Human, Islets, shCHD4, Replicate 3 (RRID:SAMN49540983)

description: Library name: shCHD4_3


title: Human, Islets, shCHD4, Replicate 2 (RRID: SAMN48439620)

description: Library name: shCHD4_2


title: RNA-seq of SHMT2 of nc2

description: Library name: nc2


title: CRISPR Screen, B16-F10 melanoma cells, Die, rep3

description: Library name: die-3

data_processing:
The CRISPRi/Cas9 screening data analysis was performed by MAGeCK (v0.5.9.5) as previously described. MAGeCK RRA method was used to evaluate the abundance of sgRNAs and identify gene hits.  UV-RIP-seq: Raw sequencing reads were processed by adapter and quality trimming using Trim Galore. Clean reads were aligned to the reference genome with STAR, and only uniquely mapped reads were retained after removing PCR duplicates with Picard.
Assembly: GRCm39.genome.fa or  GRCh38.p14.genome.fa
Supplementary files format and content: UV-RIP-seq-1.xlsx
Supplementary files format and content: UV-RIP-seq-2.xlsx
Supplementary files format and content: control_die.gene_summary.txt
Supplementary files format and content: control_die.sgrna_summary.txt
Library strategy: CRISPR Screen

source_name: B16-F10 melanoma cells

value: B16-F10 melanoma cells

value: Cells were cultured in galactose-containing medium


title: Human, Islets, shCHD4, Replicate 1 (RRID: SAMN47834917)

description: Library name: shCHD4_1


title: CRISPR Screen, B16-F10 melanoma cells, Die, rep1

description: Library name: die-1


title: Human, Islets, shCHD3, Replicate 3 (RRID:SAMN49540983)

description: Library name: shCHD3_3


title: CRISPR Screen, B16-F10 melanoma cells, Die, rep2

description: Library name: die-2


title: CRISPR Screen, B16-F10 melanoma cells, control, rep1

description: Library name: con-1

value: Cells were cultured in glucose-containing medium


title: CRISPR Screen, B16-F10 melanoma cells, control, rep2

description: Library name: con-2


title: Human, Islets, shCHD3, Replicate 2 (RRID: SAMN48439620)

description: Library name: shCHD3_2


title: Breast cancer serum sample 444

city: Santander

first: Inés

last: Gómez-Acebo

state: CANTABRIA

address: Avda. Cardenal Herrera Oria S/N

country: Spain

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

data_processing: Cq values were determined using the second derivative method in Roche LightCycler software. Quality control included melting curve analysis, exclusion of reactions with more than one melting temperature, deviation from reference melting temperatures, and low amplification efficiency. Endogenous miRNAs let-7d-5p and let-7i-5p were used as internal reference controls. Expression data were normalized and subsequently log2-transformed for statistical analysis. Batch information is provided in the sample annotations.

label: SYBR Green

source_name: Serum

label_protocol: Not applicable. Quantification was performed using SYBR Green chemistry.

growth_protocol: Not applicable. Human serum samples collected from participants in the MCC-Spain study.

extract_protocol: Total RNA was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN). Serum samples were thawed on ice and centrifuged at 3,000×g for 5 minutes at 4 °C. Buffer RPL containing carrier RNA and spike-in template mix was added, followed by Buffer RPP. RNA was eluted in 50 µL according to the manufacturer’s protocol.

treatment_protocol: Blood samples were collected prior to any oncological treatment (surgery, chemotherapy, or radiotherapy).

value: Serum

value: case

value: Basal-like

tag: age


title: Seq_GEX_1

city: Rochester

first: Ruoqiao

last: Wang

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester Medical Center

description:
Library name: Seq_GEX_1
10x Genomics

data_processing:
Demultiplexing FASTQ files, feature barcode analysis, and alignment to the GRCh38 reference genome were processed using Cell Ranger (v7.1.0), followed by downstream analysis in Seurat (5.3.0) under R version 4.3.3. Cells that express <200 genes, >7500 genes, and >25% mitochondrial genes were filtered out for initial quality control. Gene counts were followed by normalization using SCTransform while regressing out mito- chondrial percentage. Antibody-derived tag (ADT) counts were normalized using CLR and demultiplexed with a positive quantile threshold of 0.99. Anchor-based reciprocal PCA (RPCA) integration method was used for batch correction.
Assembly: GRCh38
Supplementary files format and content: Single-cell RNA-seq data were analyzed using Seurat (v5.3.0) in R (v4.3.3), and saved in rds format. Cells with <200 genes, >7,500 genes, or >25% mitochondrial expression were removed during quality control. RNA counts were normalized using SCTransform with mitochondrial percentage regressed out. ADT counts were normalized using CLR and demultiplexed using a 0.99 positive quantile threshold. Datasets were integrated using anchor-based RPCA integration for batch correction.
Library strategy: CITE-seq

source_name: PBMCs

extract_protocol:
Cell sorting and monocyte isolation Monocytes were isolated from cryopreserved PBMCs or from whole blood. For whole blood, 6 mL of 1:1 RPMI-diluted blood was thawed at 37◦C and transferred into 44 mL of 2 mM EDTA + 2% FBS in 1X DPBS, followed by centrifugation at 500 ×g for 5 minutes. The supernatant was removed, cells were washed with 800 μL staining buffer (0.5% BSA in 1X DPBS), and centrifuged again at 500 ×g for 5 minutes. After discarding the supernatant, cells were resuspended in 1 mL 1X DPBS. Then, cell suspensions were stained with titrated antibodies against CD14, CD16, CD56 (NK cells), CD20, CD19 (B cells), and CD3 (T cells), scaled to the number of cells per million. Samples were barcoded with 2 μL TotalSeq-B anti-human hashtag antibodies (BioLegend), and Zombie Red viability dye was added at 1:1000. Samples were incubated for 25 minutes at room temperature in the dark, diluted in 1 mL staining buffer, and centrifuged at 500 ×g for 5 minutes. After removing the supernatant, cells were resuspended in 300 μL of staining buffer and passed through a 40 μm strainer to obtain a single-cell suspension.  Monocytes were sorted on a BD FACSAria II flow cytometer using the following gating strategy: SSC-A/FSC-A profile → FSC-H/FSC-W (Singlets) → SSC-H/SSC-W (Singlets) → Zombie Red- (Live cells) → Lineage- (Exclusion of B, T, and NK cells)→ CD14+ and/or CD16+ (Monocytes). Flow-sorted cells were evaluated for viability and concentration using a Bio-Rad TC20 automated cell counter with Trypan Blue staining and then pooled based on cell counts. The pooled cell suspension was loaded into the Chromium Controller (10X Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs) following the manufacturer’s protocol.
Prior to flow sorting, cells were labeled with TotalSeq-B anti-human hashtag antibodies, anti-CD298 and anti-beta2-microglobulin, (BioLegend) for cell. Flow sorted cells were evaluated for viability and concentration on a BioRad TC20 automated cell counter with trypan and pooled based on cell counts. The pooled cell suspension was loaded into the Chromium Controller (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs), per manufacturer’s protocol. Single-cell RNA-Seq libraries were prepared using Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics). Briefly, GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. Following cDNA synthesis, GEMs were broken and the pooled cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher). The purified cDNA product was then amplified by limited PCR to generate a 3’ cDNA library. Enzymatic fragmentation and size selection is used to optimize the cDNA amplicon size and indexed Illumina sequencing libraries were constructed via end-repair, A-tailing, adaptor ligation, and PCR.  Hashtag library amplification was performed following SPRI bead purification of amplified hashtag and cell surface protein amplicons from above using the 10X Genomics Feature Barcoding library prep kit. Amplified libraries were purified using AMPure XP (Beckman Coulter, Indianapolis, IN) beads and quantified by Qubit dsDNA assay (ThermoFisher, Waltham, MA) and Bioanalyzer HSDNA (Agilent, Santa Clara, CA) analysis.  Hashtag libraries were pooled with 10x Genomics 3’ gene expression libraries for sequencing on Illumina’s NovaSeq 6000.

value: PBMCs

value: monocytes


title: Breast cancer serum sample 443


title: Molm13,AML cells,IgG,DMSO,rep1

city: Miami

first: Ramin

last: Shiekhattar

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: University of Miami - Sylvester Comprehensive Cancer Center

description:
Library name: Molm13,AML cells,IgG,DMSO,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.

data_processing:
FASTQ files were analyzed using the NF-core cutandrun pipeline via Pluto.bio. After quality filtering and trimming with TrimGalore, reads were aligned to the GRCh38 human genome using Bowtie2. Duplicate reads were removed with Picard. Peaks were called using MACS2 by comparing target samples to IgG controls.
Assembly: hg38
Supplementary files format and content: peaks and genome tracks.
Library strategy: CUT&Run

source_name: Blood

growth_protocol: Human AML cell line Molm-13 was cultured in RPMI1640 with 10% FBS and 2% penicillin/streptomycin; cells were maintained Mycoplasma-free and regularly tested for contamination.

extract_protocol:
CUT&RUN was performed using the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, Cat. #14-1048) following the manufacturer’s protocol. Permeabilized MOLM-13 cells were bound to Concanavalin A beads, incubated with specific antibodies, and digested with pAG-MNase. DNA fragments were extracted using cleanup columns.
DNA fragments were purified using cleanup columns, and libraries were prepared with the CUTANA™ DNA Library Prep Kit (EpiCypher, SKU: 14-1001). Libraries were sequenced on an Illumina NovaSeq 6000, generating a minimum of 5 million paired-end 150 bp reads per sample.

treatment_protocol: AML cells were plated at 2 × 10⁵ cells/mL and treated with DMSO or test compounds for 24 hours before collection for downstream genome-wide assays.

value: Blood

value: AML cells

tag: chip antibody

value: anti-IgG (EpiCypher, SKU:13-0042K)

value: DMSO


title: Human, Islets, shControl, Replicate 3 (RRID:SAMN49540983)

description: Library name: shControl_3


title: Human, Islets, shControl, Replicate 2 (RRID: SAMN48439620)

description: Library name: shControl_2


title: Molm13,AML cells,H3K4me3,DMSO,rep2

description:
Library name: Molm13,AML cells,H3K4me3,DMSO,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.

value: anti-H3K4me3 (EpiCypher, SKU:13-0060)


title: Molm13,AML cells,IgG,DMSO,rep2

description:
Library name: Molm13,AML cells,IgG,DMSO,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.


title: Breast cancer serum sample 439

value: Control


title: Breast cancer serum sample 441

value: Luminal A


title: Human, Islets, shControl, Replicate 1 (RRID: SAMN47834917)

description: Library name: shControl_1


title: Breast cancer serum sample 442


title: Human, Islets, shCHD3, Replicate 1 (RRID: SAMN47834917)

description: Library name: shCHD3_1


title: Molm13,AML cells,H3K4me3,CORIN,rep1

description:
Library name: Molm13,AML cells,H3K4me3,CORIN,rep1
Cells treated with Corin (0.1 μM) for 24 hours.

value: CORIN


title: Molm13,AML cells,H3K4me3,DMSO,rep1

description:
Library name: Molm13,AML cells,H3K4me3,DMSO,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.


title: Molm13,AML cells,H3K4me3,CORIN,rep2

description:
Library name: Molm13,AML cells,H3K4me3,CORIN,rep2
Cells treated with Corin (0.1 μM) for 24 hours.


title: Breast cancer serum sample 440


title: Molm13,AML cells,LSD1-XL,DMSO,rep1

description:
Library name: Molm13,AML cells,LSD1-XL,DMSO,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.

value: anti-LSD1 (Abcam, ab17721)


title: Breast cancer serum sample 435


description:
Library name: Molm13,AML cells,H3K4me3,ATRA/CORIN,rep1
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.

value: ATRA/CORIN


description:
Library name: Molm13,AML cells,H3K4me3,ATRA/CORIN,rep2
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: Molm13,AML cells,H3K4me2,DMSO,rep2

description:
Library name: Molm13,AML cells,H3K4me2,DMSO,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.

value: anti-H3K4me2 (EpiCypher, SKU:13-0027)


title: Breast cancer serum sample 436


title: Breast cancer serum sample 437


title: SW620_INVITRO_CDK8CDK19_CL2_CCT251545_C

city: Sutton

first: Konstantinos

last: Mitsopoulos

state: London

address: 15 Cotswold Road

department: Cancer Therapeutics Unit

country: United Kingdom

institute: The Institute of Cancer Research

description: Replicate 2 of 3

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
# 1.Initialisation
library(limma)
# 2. Read in tab-delimited targets file
sw620_in_vitro_targets <- readTargets(sw620_in_vitro_sample_annotation.txt)
# 3. Use LIMMA's read.maimages function to load data into an RGList object
sw620_in_vitro_RG <- read.maimages(sw620_in_vitro_targets, source=agilent)
# 4. Subtract the background (optional, but recommended)
sw620_in_vitro_RG.b <- backgroundCorrect(sw620_in_vitro_RG, method=normexp, offset=50)
# 5. Normalize within and between the arrays - remove controls
sw620_in_vitro_MA.p <- normalizeWithinArrays(sw620_in_vitro_RG.b, method=loess)
sw620_in_vitro_MA.pAq <- normalizeBetweenArrays(sw620_in_vitro_MA.p, method=Aquantile)
sw620_in_vitro_MA2.pAq <- sw620_in_vitro_MA.pAq[sw620_in_vitro_MA.pAq$genes$ControlType==0,]
# 6. Use the avereps function to average replicate spots
sw620_in_vitro_MA2.ave <- avereps(sw620_in_vitro_MA2.pAq, ID=sw620_in_vitro_MA2.pAq$genes$ProbeName)
# 7. Whole spot contrasts (to use for deriving average expression):
write.table(sw620_in_vitro_MA2.ave$A, file = sw620_in_vitro_MA2_ave_A_expression_matrix.txt, sep=\t)
# 8. Within spot contrasts (to use for log2FC calculations)
write.table(sw620_in_vitro_MA2.ave$M, file = sw620_in_vitro_MA2_ave_M_expression_matrix.txt, sep=\t)

label_protocol: Cy5 (red): human reference standard (Stratagene), Cy3 (green): experimental samples

extract_protocol: standard protocol

tag: condition

value: in vitro

tag: cell line background

value: colorectal cell line

tag: clone

value: CDK8 and CDK19 KO, clone2

tag: compound

source_name: human reference standard

value: reference


title: Breast cancer serum sample 438

value: Serum


title: Molm13,AML cells,H3K4me2,DMSO,rep1

description:
Library name: Molm13,AML cells,H3K4me2,DMSO,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.

tag: cell line


title: Molm13,AML cells,H3K4me2,CORIN,rep2

description:
Library name: Molm13,AML cells,H3K4me2,CORIN,rep2
Cells treated with Corin (0.1 μM) for 24 hours.


title: Breast cancer serum sample 433

value: case


title: Breast cancer serum sample 431


title: Molm13,AML cells,H3K4me2,CORIN,rep1

description:
Library name: Molm13,AML cells,H3K4me2,CORIN,rep1
Cells treated with Corin (0.1 μM) for 24 hours.

value: Blood


title: Breast cancer serum sample 430


title: Molm13,AML cells,H3K27ac,DMSO,rep2

description:
Library name: Molm13,AML cells,H3K27ac,DMSO,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.

value: AML cells

value: anti-H3K27ac (EpiCypher, SKU:13-0059)


title: Breast cancer serum sample 434

value: Basal-like


title: Breast cancer serum sample 428


title: Breast cancer serum sample 432


title: Molm13,AML cells,H3K27ac,CORIN,rep1

description:
Library name: Molm13,AML cells,H3K27ac,CORIN,rep1
Cells treated with Corin (0.1 μM) for 24 hours.


title: Breast cancer serum sample 429


title: Breast cancer serum sample 425


title: Molm13,AML cells,H3K27ac,CORIN,rep2

description:
Library name: Molm13,AML cells,H3K27ac,CORIN,rep2
Cells treated with Corin (0.1 μM) for 24 hours.


title: Breast cancer serum sample 426


description:
Library name: Molm13,AML cells,H3K27ac,ATRA/CORIN,rep1
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: Breast cancer serum sample 424


title: Breast cancer serum sample 427


description:
Library name: Molm13,AML cells,H3K27ac,ATRA/CORIN,rep2
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: U937,Control,rep2

description:
Library name: U937,Control,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.

data_processing:
Raw FASTQ files were quality-filtered and trimmed using Trimmomatic to remove adapter sequences and low-quality bases. Trimmed reads were aligned to the human reference genome (hg38) using STAR aligner with default settings. Gene-level expression quantification was performed using RSEM against the human Ensembl reference transcriptome (release 97). Gene expression levels were normalized to Transcripts Per Million (TPM). DeepTools2 (bamCoverage function) was used to generate CPM-normalized bigwigs.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts per gene for all samples, Individual files per sample including normalized counts per gene by RSEM (.results), differentiall expression outputs by DEseq2 for the comparisons treatment vs control with 2 replicates each (*_deseq2_output.txt), and bigwig files include CPM-normalized stranded signal tracks per sample (*forward.bw and *reverse.bw).

source_name: blood

growth_protocol: Human AML cell lines (U-937, SKNO-1) were cultured in RPMI1640 with 10% FBS and 2% penicillin/streptomycin; SKNO-1 was additionally supplemented with 10 ng/mL GM-CSF. All cell lines were maintained Mycoplasma-free and regularly tested for contamination.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat. No. 74104) with on-column DNase digestion (Qiagen, Cat. No. 79254).
Libraries were prepared from 1 μg of DNase-treated RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, Cat. #20020596), following the manufacturer’s protocol. ERCC RNA Spike-In Mix (Invitrogen) was added according to instructions. Sequencing was performed on the Illumina NovaSeq 6000 platform, generating a minimum of 50 million 100 bp paired-end reads per sample.

value: blood

value: AML cell line

value: DMSO


title: U937,Control,rep1

description:
Library name: U937,Control,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.


title: Breast cancer serum sample 423

value: Luminal A


title: Breast cancer serum sample 421


title: Breast cancer serum sample 419


title: Breast cancer serum sample 420

value: Luminal B


title: U937,ATRA,rep1

description:
Library name: U937,ATRA,rep1
Cells treated with ATRA (0.1 μM) for 24 hours.

value: ATRA


title: U937,Corin,rep1

description:
Library name: U937,Corin,rep1
Cells treated with Corin (0.1 μM) for 24 hours.

value: CORIN


title: U937,ATRA,rep2

description:
Library name: U937,ATRA,rep2
Cells treated with ATRA (0.1 μM) for 24 hours.


title: U937,ATRA,Corin,rep2

description:
Library name: U937,ATRA,Corin,rep2
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.

value: ATRA/CORIN


title: Breast cancer serum sample 417


title: U937,ATRA,Corin,rep1

description:
Library name: U937,ATRA,Corin,rep1
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: U937,Corin,rep2

description:
Library name: U937,Corin,rep2
Cells treated with Corin (0.1 μM) for 24 hours.


title: SKNO1,Control,rep2

description:
Library name: SKNO1,Control,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.


title: Breast cancer serum sample 416


title: Breast cancer serum sample 422


title: Breast cancer serum sample 418


title: Breast cancer serum sample 414

value: Control


title: AHet_P21_2

data_processing:
FASTQ files were extracted and sequencing adapters and low-quality reads were removed by Cutadapt (v.2.3)
Quality of the processed FASTQ files were checked by FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0)
EdgeR (v.3.26.1) was used to identify differentially expressed genes.
Assembly: Assembly: Esembl GRCm38.102
Supplementary files format and content: Supplementary files format and content: CSV, raw counts of sequencing reads on the gene level

source_name: Heart ventricle

value: Heart ventricle

tag: Sex

value: Male


title: Breast cancer serum sample 413

value: Serum


title: Breast cancer serum sample 415

value: case


title: Breast cancer serum sample 412


title: SKNO1,Corin,rep2

description:
Library name: SKNO1,Corin,rep2
Cells treated with Corin (0.1 μM) for 24 hours.

tag: treatment


title: SKNO1,ATRA,rep2

description:
Library name: SKNO1,ATRA,rep2
Cells treated with ATRA (0.1 μM) for 24 hours.


title: SKNO1,Corin,rep1

description:
Library name: SKNO1,Corin,rep1
Cells treated with Corin (0.1 μM) for 24 hours.


title: SKNO1,Control,rep1

description:
Library name: SKNO1,Control,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.


title: Breast cancer serum sample 411


title: SKNO1,ATRA/Corin,rep1

description:
Library name: SKNO1,ATRA/Corin,rep1
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: Breast cancer serum sample 409


title: SKNO1,ATRA,rep1

description:
Library name: SKNO1,ATRA,rep1
Cells treated with ATRA (0.1 μM) for 24 hours.


title: SKNO1,ATRA/Corin,rep2

description:
Library name: SKNO1,ATRA/Corin,rep2
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: Breast cancer serum sample 410


title: Breast cancer serum sample 406


title: Breast cancer serum sample 408


title: Breast cancer serum sample 404


title: Breast cancer serum sample 407


title: U937,CORIN,rep2

description:
Library name: U937,CORIN,rep2
Cells treated with Corin (0.1 μM) for 24 hours.

data_processing:
ATAC-seq data were processed using the ENCODE ATAC-seq pipeline (v1) with default parameters. Paired-end raw FASTQ reads trimmed using cutadapt. Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2. Resulting BAM files were filtered to exclude mitochondrial reads and PCR duplicates using SAMtools and Picard MarkDuplicates. Paired-end reads were processed to retain only properly paired, uniquely mapped reads with mapping quality ≥30. Reads were shifted +4 bp (forward strand) and −5 bp (reverse strand) to account for Tn5 insertion bias. Peaks were called using MACS2 with a p-value threshold of 0.01. Replicate concordance and IDR analysis were performed analogously to ChIP-seq data. Signal tracks were generated for individual and pooled replicates.
Assembly: hg38
Supplementary files format and content: bigwigs and peaks.

growth_protocol: Human AML cell line U-937 were cultured in RPMI1640 with 10% FBS and 2% penicillin/streptomycin; SKNO-1 was additionally supplemented with 10 ng/mL GM-CSF. All cell lines were maintained Mycoplasma-free and regularly tested for contamination.

extract_protocol:
After processing samples using the ATAC-seq protocol, the recovered DNA was used for PCR amplification
Following tagmentation and adapter ligation, DNA was PCR-amplified and purified. Library quality was assessed using TapeStation for fragment size. Libraries were sequenced as paired-end reads on an Illumina platform NovaSeq 6000.


title: U937,ATRA,rep1


title: U937,ATRA,rep2


title: U937,Ctrl,rep2

description:
Library name: U937,Ctrl,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.


title: U937,Ctrl,rep1

description:
Library name: U937,Ctrl,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.


title: Breast cancer serum sample 400


title: U937,ATRA/CORIN,rep2

description:
Library name: U937,ATRA/CORIN,rep2
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: Breast cancer serum sample 403


title: U937,CORIN,rep1

description:
Library name: U937,CORIN,rep1
Cells treated with Corin (0.1 μM) for 24 hours.


title: Breast cancer serum sample 402


title: U937,ATRA/CORIN,rep1

description:
Library name: U937,ATRA/CORIN,rep1
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: Breast cancer serum sample 399


title: Breast cancer serum sample 405


title: Breast cancer serum sample 401


title: U-937,AML cells,ctrl,H3K4me2,rep2

description:
Library name: U-937,AML cells,ctrl,H3K4me2,rep2
Cells treated with DMSO (0.1 μM) for 24 hours.

data_processing:
ChIP-seq data were processed with the standardized ChIP-seq ENCODE Pipeline (v2) (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
Raw FASTQ files were processed with Trimmomatic for adapter trimming.
Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2
Duplicate reads were removed using Picard,, and alignments were filtered to retain uniquely mapping reads with a mapping quality of ≥30.
DeepTools2 was used to generate CPM normalized bigwigs. Optimal peaks per condition were identified using MACS2 with IDR analysis. The peaks significantly enriched compared to their corresponding Input control for a given treatment (optimal peaks with fold change > 3 and a q-value < 0.01) were used for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigwigs and IDR optimal peaks (except for input samples).

growth_protocol: Human AML cell line U-937 was cultured in RPMI1640 with 10% FBS and 2% penicillin/streptomycin. Cell line was maintained Mycoplasma-free and regularly tested for contamination.

extract_protocol:
After processing samples using the ChIP protocol, the recovered DNA was reverse crosslinked overnight at 65°C, treated with RNase A and Proteinase K, purified by phenol-chloroform extraction, and quantified with Qubit. DNA was used for library prep with the NEBNext Ultra DNA Library Prep Kit (NEB, #E7370).
DNA was purified using phenol-chloroform extraction and eluted in 50 µL nuclease-free water. DNA concentrations were measured using a Qubit 3 fluorometer with dsDNA High Sensitivity reagents (Thermo Fisher Scientific, Cat. #Q32851). ChIP DNA was used for library preparation with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs Cat. #E7370) according to the manufacturer’s instructions. Fragment size distribution was analyzed using a Tapestation 2200 with D1000 ScreenTape (Agilent Technologies, Cat. #5067–5582). Libraries were quantified with Qubit and sequenced (paired-end, 75 bp) on the Illumina NovaSeq 6000 platform.

value: Abcam Cat. #ab32356


title: Breast cancer serum sample 398


title: U-937,AML cells,ctrl,H3K4me2,rep1

description:
Library name: U-937,AML cells,ctrl,H3K4me2,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.

value: AML cells


title: Breast cancer serum sample 397


title: U-937,AML cells,ctrl,INPUT,rep1

description:
Library name: U-937,AML cells,ctrl,INPUT,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.


title: AHet_P21_3

extract_protocol:
Total RNA from the embryonic heart ventricles was isolated using TRIzol (Invitrogen) from tissues using standard protocol. rRNA-depleted libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina) RNA-sequencing was processed by GENEWIZ using Illumina platform (paired-ended, 150bp read-length)
rRNA-depletion library


title: Breast cancer serum sample 395


title: Breast cancer serum sample 396


title: U-937,AML cells,CORIN,H3K4me2,rep1

description:
Library name: U-937,AML cells,CORIN,H3K4me2,rep1
Cells treated with Corin (0.1 μM) for 24 hours.


title: U-937,AML cells,ATRA,INPUT,rep1

description:
Library name: U-937,AML cells,ATRA,INPUT,rep1
Cells treated with ATRA (0.1 μM) for 24 hours.


title: U-937,AML cells,CORIN,H3K4me2,rep2

description:
Library name: U-937,AML cells,CORIN,H3K4me2,rep2
Cells treated with Corin (0.1 μM) for 24 hours.


title: Breast cancer serum sample 394


title: Breast cancer serum sample 393


title: Breast cancer serum sample 392


title: U-937,AML cells,CORIN,INPUT,rep1

description:
Library name: U-937,AML cells,CORIN,INPUT,rep1
Cells treated with Corin(0.1 μM) for 24 hours.


title: Molm13,AML cells,H3K27ac,DMSO,rep1

description:
Library name: Molm13,AML cells,H3K27ac,DMSO,rep1
Cells treated with DMSO (0.1 μM) for 24 hours.

value: Blood

value: anti-H3K27ac (EpiCypher, SKU:13-0059)


title: U-937,AML cells,ATRA,H3K4me2,rep1

description:
Library name: U-937,AML cells,ATRA,H3K4me2,rep1
Cells treated with ATRA (0.1 μM) for 24 hours.

value: blood


title: U-937,AML cells,ATRA/CORIN,INPUT,rep1

description:
Library name: U-937,AML cells,ATRA/CORIN,INPUT,rep1
Cells treated with ATRA/CORIN (each 0.1 μM) for 24 hours.


title: U-937,AML cells,ATRA/CORIN,H3K4me2,rep2

description:
Library name: U-937,AML cells,ATRA/CORIN,H3K4me2,rep2
Cells treated with ATRA/CORIN (each 0.1 μM) for 24 hours.


title: Breast cancer serum sample 390


title: U-937,AML cells,ATRA/CORIN,H3K4me2,rep1

description:
Library name: U-937,AML cells,ATRA/CORIN,H3K4me2,rep1
Cells treated with ATRA/CORIN (each, 0.1 μM) for 24 hours.


title: Breast cancer serum sample 389


title: Breast cancer serum sample 388


title: FIL7

city: Shanghai

first: Hongrui

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

description:
Library name: 14
Column name in processed file: FIL7

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Then  clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome Hg38 using HISAT2
FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs)
Assembly: Hg38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes FPKM for each sample

source_name: adipose tissue

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

value: adipose tissue

value: Primary cells

value: adipocyte

value: Nornal


title: U-937,AML cells,ATRA,H3K4me2,rep2

description:
Library name: U-937,AML cells,ATRA,H3K4me2,rep2
Cells treated with ATRA (0.1 μM) for 24 hours.

value: ATRA


title: Breast cancer serum sample 387


title: FIL6

description:
Library name: 13
Column name in processed file: FIL6


title: FIL5

description:
Library name: 12
Column name in processed file: FIL5


title: Breast cancer serum sample 386


title: Breast cancer serum sample 391


title: FIL2

description:
Library name: 9
Column name in processed file: FIL2


title: Breast cancer serum sample 382


title: FIL4

description:
Library name: 11
Column name in processed file: FIL4


title: FIL3

description:
Library name: 10
Column name in processed file: FIL3


title: Breast cancer serum sample 384


title: FIL1

description:
Library name: 8
Column name in processed file: FIL1


title: CON-7

description:
Library name: 7
Column name in processed file: CON-7

value: PIK3CA mutation


title: Breast cancer serum sample 381


title: Breast cancer serum sample 383


title: CON-6

description:
Library name: 6
Column name in processed file: CON-6


title: CON-4

description:
Library name: 4
Column name in processed file: CON-4


title: Breast cancer serum sample 378


title: Breast cancer serum sample 380


title: CON-3

description:
Library name: 3
Column name in processed file: CON-3


title: Breast cancer serum sample 377


title: Breast cancer serum sample 379


title: CON-2

description:
Library name: 2
Column name in processed file: CON-2


title: Breast cancer serum sample 376


title: Breast cancer serum sample 385


title: Breast cancer serum sample 374


title: CON-1

description:
Library name: 1
Column name in processed file: CON-1


title: WT_rep1

city: Redwood City

first: Jin

address: 2800 Bridge Parkway

institute: Altos Labs

description: 10X Genomics

data_processing:
Base calls were simultaneously demultiplexed based on i5 and i7 barcodes and converted to fastq format using BCL Covert v4.0.3 from Illumina.
Teratoma sequencing reads were mapped to a joint human and mouse reference genome (GRCh38 and GRCm38 2024-A available from 10X Genomics) using cellranger v8.0.1 with default settings.
Assembly: GRCh38, v108
Supplementary files format and content: Cellranger output

extract_protocol:
The teratoma samples were dissociated to single nuclei suspension using the SingulatorTM 200 system from S2 Genomics.
Single nuclei preparation was performed in accordance with 10x Genomics Single Cell 3’ Gene Expression v3.1 Dual Index protocol (10x Genomics #1000120, 1000268, 1000215), with a target of 10,000 nuclei per reaction.

value: H1 ESC

value: Human Embryonic Stem Cells


title: CON-5

description:
Library name: 5
Column name in processed file: CON-5


title: Breast cancer serum sample 373

value: Control


title: DATG_rep1

description: 10X Genomics

data_processing:
Base calls were simultaneously demultiplexed based on i5 and i7 barcodes and converted to fastq format using BCL Covert v4.0.3 from Illumina.
Gastruloid sequencing reads were mapped to the GRCh38 reference genome and annotated with GENCODE v42/Ensembl 108 genes using cellranger v8.0.1
Assembly: GRCh38, v108
Supplementary files format and content: Cellranger output

source_name: H1 ESC

extract_protocol:
The gastruloids were disassociated with ACCUTASE (STEMCELL Technologies #7920) at 37°C for 20 min
Single cell preparation was performed in accordance with 10x Genomics Single Cell 3’ Gene Expression v3.1 Dual Index protocol (10x Genomics #1000120, 1000268, 1000215), with a target of 10,000 cells per reaction


title: KO_rep1

description: 10X Genomics


title: Breast cancer serum sample 371


title: DATG_rep2

description: 10X Genomics


title: Breast cancer serum sample 372


title: Breast cancer serum sample 375


title: DATG_D5_SMADi_a

description:
Sample_149
smadi_peakCounts.txt

data_processing:
ATAC-seq FASTQ files were trimmed and aligned to the human reference genome (GRCh38, v108) using the nf-core/atacseq pipeline (v2.1.2)
The filtered BAM alignment files were shifted to account for Tn5 insertion biases using the alignmentSieve command in the deepTools2 suite
The MACS2 peak caller was used to call peaks for each sample
Assembly: GRCh38, v108
Supplementary files format and content: text file includes peak quantification for each sample.

growth_protocol: H1-hESCs WA01 (WiCell) and iPSC (derived from BJ fibroblasts cells from ATCC CRL-2522 using the Thermo CytoTune-iPS Sendai Reprogramming #A16517) confirmed via STR Profiling were cultured on Corning™ Matrigel™ hESC-Qualified Matrix (Fisher Scientific #08-774-552) or Geltrex™ LDEV-Free (Thermo Scientific #A1413202) coated cell culture dishes using mTeSR™ Plus media (STEMCELL Technologies #5825) with daily media changes.

extract_protocol:
The WT, KO, and ΔATG hESCs and trilineage differentiated cell pellets were sent to Actif Motif for extraction. cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).
Libraries were prepared in accordance with Actif Motif's internal protocol with tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017).

treatment_protocol:
Neural progenitor cells (NPCs): The differentiation of stem cells into NPCs was performed by using the STEMdiff™ SMADi Neural Induction Kit (STEMCELL Technologies #8581), following the manufacturer's protocol. Briefly, dissociated single cells were seeded on Geltrex™ coated 6-well plates at a density of 2 x 106 cells per well with 10 µM Y-27632 ROCK inhibitor on day 0. Cells were maintained in 2 mL of STEMdiff™ Neural Induction Medium + SMADi per well with daily media changes.
Definitive Endoderm: The differentiation of stem cells into definitive endoderm was performed by using the STEMdiff™ Definitive Endoderm Kit (STEMCELL Technologies #5110), following the manufacturer's protocol. Briefly, cells were first dissociated into single cells and then seeded on Matrigel™ coated 6-well plates at a density of 2 x 106 cells per well with 10 µM Y-27632 ROCK inhibitor on day 0. On day 1, the media was changed to 2 mL of medium 1 (diluted STEMdiff™ Definitive Endoderm Supplement MR and STEMdiff™ Definitive Endoderm Supplement CJ 1 in 100 in STEMdiff™ Endoderm Basal Medium). From day 2 to day 5, the media was changed daily to 2 mL medium 2 (diluted STEMdiff™ Definitive Endoderm Supplement CJ 1 in 100 in STEMdiff™ Endoderm Basal Medium).
Mesoderm: The differentiation of stem cells into mesoderm was performed by using the STEMdiff™ Mesoderm Induction Medium (STEMCELL Technologies #05221), following the manufacturer's protocol. The cells were first dissociated into single cells and then seeded on Matrigel™ coated 15 cm2 plates at a density of 7.5 x 106 cells in 20 mL mTesR medium with 10 µM Y-27632 ROCK inhibitor on day 0. On day 1, the media was changed to 45 mL STEMdiff™ Mesoderm Induction Medium. From day 2 to day 5, the media was changed daily.
H1-hESCs were differentiated into mesoderm germ layers using bone morphogenetic protein 4 (BMP4, Sigma-Aldrich #H4916). The hESCs were seeded at 0.5 x 106 cells per well in a Matrigel™ coated 6-well plate with mTeSR media on day 0 and changed to mTeSR + 50 ng/mL BMP4 on day 1 to day 5.
The spontaneous differentiation experiments were conducted according to  reference (18): hESCs were seeded at a density of 0.5 x 106 cells per well in a Matrigel™ coated 6-well plate with mTesR medium and changed to spontaneous differentiation medium (DMEM/F12, 15% knockout serum replacement, MEM non-essential amino acid solution, and 0.1 mM β-mercaptoethanol) on day 1 to day 5.


title: WT_rep2

description: 10X Genomics


title: Breast cancer serum sample 370


title: Breast cancer serum sample 367


title: WT_rep1

description: 10X Genomics


title: Breast cancer serum sample 366


title: Breast cancer serum sample 368


title: KO_D5_SMADi_a

description:
Sample_147
smadi_peakCounts.txt


title: Breast cancer serum sample 369


title: WT_D5_SMADi_b

description:
Sample_146
smadi_peakCounts.txt


title: Breast cancer serum sample 364


title: KO_D5_SMADi_b

description:
Sample_148
smadi_peakCounts.txt


title: Breast cancer serum sample 365


title: WT_D5_SMADi_a

description:
Sample_145
smadi_peakCounts.txt


title: Breast cancer serum sample 362


title: KO_D4_SMADi_b

description:
Sample_142
smadi_peakCounts.txt


title: DATG_D4_SMADi_b

description:
Sample_144
smadi_peakCounts.txt


title: Breast cancer serum sample 363


title: Breast cancer serum sample 361


title: Breast cancer serum sample 360

value: Basal-like


title: WT_D4_SMADi_a

description:
Sample_139
smadi_peakCounts.txt


title: KO_D1_SMADi_b

description:
Sample_124
smadi_peakCounts.txt


title: Breast cancer serum sample 357

value: Serum


title: Breast cancer serum sample 359

value: case


title: Breast cancer serum sample 355


title: WT_D1_SMADi_b

description:
Sample_122
smadi_peakCounts.txt


title: Breast cancer serum sample 358


title: DATG_D4_SMADi_a

description:
Sample_143
smadi_peakCounts.txt


title: Breast cancer serum sample 356


title: DATG_D5_BMP4_b

description:
Sample_66
meso_peakCounts.txt


title: WT_D4_SMADi_b

description:
Sample_140
smadi_peakCounts.txt


title: Breast cancer serum sample 354


title: Breast cancer serum sample 352


title: DATG_D5_BMP4_a

description:
Sample_65
meso_peakCounts.txt


title: Breast cancer serum sample 353


title: Breast cancer serum sample 351


title: DATG_D1_SMADi_a

description:
Sample_125
smadi_peakCounts.txt


title: KO_D1_SMADi_a

description:
Sample_123
smadi_peakCounts.txt


title: KO_D5_BMP4_b

description:
Sample_64
meso_peakCounts.txt


title: Breast cancer serum sample 349


title: Breast cancer serum sample 350


title: WT_D1_SMADi_a

description:
Sample_121
smadi_peakCounts.txt


title: Breast cancer serum sample 348


title: KO_D5_BMP4_a

description:
Sample_63
meso_peakCounts.txt


title: WT_D5_BMP4_a

description:
Sample_61
meso_peakCounts.txt


title: WT_D5_BMP4_b

description:
Sample_62
meso_peakCounts.txt


title: Breast cancer serum sample 347

value: Luminal A


title: KO_D4_BMP4_b

description:
Sample_52
meso_peakCounts.txt


title: Breast cancer serum sample 346


title: KO_D4_BMP4_a

description:
Sample_51
meso_peakCounts.txt


title: DATG_D4_BMP4_a

description:
Sample_53
meso_peakCounts.txt


title: Breast cancer serum sample 345


title: DATG_D4_BMP4_b

description:
Sample_54
meso_peakCounts.txt


title: Breast cancer serum sample 343

value: Luminal B


title: Breast cancer serum sample 344


title: DATG_D3_BMP4_a

description:
Sample_41
meso_peakCounts.txt


title: WT_D4_BMP4_b

description:
Sample_50
meso_peakCounts.txt


title: DATG_D3_BMP4_b

description:
Sample_42
meso_peakCounts.txt


title: KO_D3_BMP4_b

description:
Sample_40
meso_peakCounts.txt


title: Breast cancer serum sample 337


title: Breast cancer serum sample 336


title: Breast cancer serum sample 342


title: Breast cancer serum sample 341


title: Breast cancer serum sample 340


title: KO_D3_BMP4_a

description:
Sample_39
meso_peakCounts.txt


title: WT_D4_BMP4_a

description:
Sample_49
meso_peakCounts.txt


title: Breast cancer serum sample 338


title: WT_D3_BMP4_b

description:
Sample_38
meso_peakCounts.txt


title: Breast cancer serum sample 332


title: Breast cancer serum sample 333


title: DATG_D2_BMP4_a

description:
Sample_29
meso_peakCounts.txt


title: WT_D3_BMP4_a

description:
Sample_37
meso_peakCounts.txt


title: Breast cancer serum sample 335


title: Breast cancer serum sample 330


title: KO_D2_BMP4_b

description:
Sample_28
meso_peakCounts.txt


title: DATG_D1_BMP4_b

description:
Sample_18
meso_peakCounts.txt


title: Breast cancer serum sample 339


title: DATG_D2_BMP4_b

description:
Sample_30
meso_peakCounts.txt


title: WT_D2_BMP4_b

description:
Sample_26
meso_peakCounts.txt


title: IL-4 4

city: Edinburgh

first: Stephen

last: Jenkins

address: 47, Little France Crescent

department: Centre For Inflammation Research

institute: University of Edinburgh

description: Total RNA lysate was analyzed

data_processing: Data were imported into nSolver 4.0 software (Nanostring Technologies) and advanced anaysis performed with the nCounter Advanced Analysis package (version 2.0.115). Data were annotated by treatment group for  analysis (Olive Oil, Ccl4, IL-4). Grouped data were then analysed using the advanced analysis nSolver package according to the manufacturers instructions.   Analysis of samples from  olive oil and CCl4 + PBS treated animals were analysed separately from the analysis of CCl4 + IL-4 and CCl4 + PBS treatments.

extract_protocol: For each of the indicated donor populations 5000 cells  were sorted into 2µl of RLT (QIAGEN). Immediately after, cells were centrifuged at 17,000g for 15 seconds. Centrifugation was repeated following vortxing of the pellet.  Cells where stored at -80degrees C until  analysis of the lysate using the nCounter Mouse Myeloid V2 panel on the nCounter platform.

treatment_protocol: C57BL/6JCrl mice were injected intraperitoneally with CCl4, which causes liver injury, or olive oil vehicle control. 24hrs later the CCl4-treated group were then given an intravenous injection of IL-4complex or PBS control and then 24hrs later the Ly6Chi blood monocytes were sorted for Nanostring analysis.

tag: injured/non-injured

value: CCl4 (injured)


title: Breast cancer serum sample 334

tag: tissue


title: WT_D2_BMP4_a

description:
Sample_25
meso_peakCounts.txt


title: Breast cancer serum sample 331


title: KO_D2_BMP4_a

description:
Sample_27
meso_peakCounts.txt


title: Breast cancer serum sample 328


title: DATG_D1_BMP4_a

description:
Sample_17
meso_peakCounts.txt


title: Breast cancer serum sample 327


title: Breast cancer serum sample 324


title: IL-4 2

description: Total RNA lysate was analyzed


title: IL-4 3

description: Total RNA lysate was analyzed


title: Breast cancer serum sample 326


title: IL-4 1

description: Total RNA lysate was analyzed


title: KO_D1_BMP4_b

description:
Sample_16
meso_peakCounts.txt


title: Breast cancer serum sample 325


title: CCl4 4

description: Total RNA lysate was analyzed

value: PBS


title: Breast cancer serum sample 329


title: Breast cancer serum sample 321


title: Breast cancer serum sample 320


title: WT_D1_BMP4_b

description:
Sample_14
meso_peakCounts.txt


title: CCl4 3

description: Total RNA lysate was analyzed


title: WT_D1_BMP4_a

description:
Sample_13
meso_peakCounts.txt


title: Breast cancer serum sample 323


title: Breast cancer serum sample 322


title: Breast cancer serum sample 318


title: Breast cancer serum sample 319


title: Breast cancer serum sample 317


title: Breast cancer serum sample 316


title: CCl4 2

description: Total RNA lysate was analyzed


title: Breast cancer serum sample 314


title: DATG_D0_b

description:
Sample_6
hesc_peakCounts.txt


title: Breast cancer serum sample 313


title: Breast cancer serum sample 315


title: KO_D1_BMP4_a

description:
Sample_15
meso_peakCounts.txt


title: CCl4 1

description: Total RNA lysate was analyzed


title: KO_D0_b

description:
Sample_4
hesc_peakCounts.txt


title: Breast cancer serum sample 312


title: Breast cancer serum sample 311


title: DATG_D0_a

description:
Sample_5
hesc_peakCounts.txt


title: Breast cancer serum sample 310


title: KO_D0_a

description:
Sample_3
hesc_peakCounts.txt


title: Olive Oil 3

description: Total RNA lysate was analyzed

value: Olive oil (non-injured)


title: Breast cancer serum sample 309


title: WT_D0_a

description:
Sample_1
hesc_peakCounts.txt


title: Olive Oil 1

description: Total RNA lysate was analyzed


title: Breast cancer serum sample 308


title: WT_D0_b

description:
Sample_2
hesc_peakCounts.txt


title: Breast cancer serum sample 307


title: Olive Oil 4

description: Total RNA lysate was analyzed


title: Breast cancer serum sample 305


title: Breast cancer serum sample 304


title: Olive Oil 2

description: Total RNA lysate was analyzed


title: Breast cancer serum sample 306


title: late_OE_lncPRESS1DATG_b

description:
Sample_120
rna_seq_gene_counts_length_scaled.tsv

data_processing:
RNA-seq FASTQ files were trimmed, aligned to the human reference genome (GRCh38, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0).
Assembly: GRCh38, v108
Supplementary files format and content: text file includes length scaled quantification for each sample.

extract_protocol:
The WT, KO, and ΔATG hESCs and trilineage differentiated cells were collected and RNA was extracted in accordance with Qiagen RNeasy Mini (Qiagen #74106) protocol with 650 uL lysis buffer.
Libraries were prepared in accordance with Illumina Stranded mRNA Prep, Ligation (Illumina #20040534) protocol using 100 ng RNA input.


title: Breast cancer serum sample 300


title: Breast cancer serum sample 303


title: Breast cancer serum sample 302


title: Epi CS 3

city: Chicago

first: Carl

last: Atkinson

state: Illinois

address: 300 e superior st

department: Surgery

institute: Northwestern University

description: Total mRNA was analyzed using NS_HS_TRANSPLANT_V1.0+PLS_UF_ATKINSON_T_C10824

data_processing: nCounter nSolver 4.0. instructions can be found here: https://university.nanostring.com/nsolver-40-analysis-software-user-manual/894752 and Advanced Analysis 2.0. instruction per manufacturer: https://university.nanostring.com/advanced-analysis-20-user-manual/894772

label: nCounter Hybridization Probe

source_name: alveolar epithelial cell (HAEC)

label_protocol: LL randomized the experiment and BG harvested RNA and analyzed via nCounter and nSolver.

growth_protocol: Emulate Alveolar Lung Chip Organoid System growth and maitenance protocol.

extract_protocol: Rneasy minikit from each channel of each chip.

treatment_protocol: For testing the effect of static cold storage, chips underwent a short hyperoxia cold storage envionrment perfused with perfadex plus solution (CS was 6 hr and IRI was 24hr).

value: primary cell


title: Epi CS 2


title: late_OE_lncPRESS1_a

description:
Sample_117
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 299


title: late_OE_lncPRESS1DATG_a

description:
Sample_119
rna_seq_gene_counts_length_scaled.tsv


title: late_OE_lncPRESS1_b

description:
Sample_118
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 298


title: Breast cancer serum sample 301


title: Breast cancer serum sample 297


title: Breast cancer serum sample 295


title: late_OE-lncSIRP_b

description:
Sample_116
rna_seq_gene_counts_length_scaled.tsv


title: Epi CS 1


title: late_OE-lncSIRP_a

description:
Sample_115
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 296


title: late_OE-vector_b

description:
Sample_114
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 293


title: Epi Normal 1


title: Breast cancer serum sample 291


title: Breast cancer serum sample 292


title: Breast cancer serum sample 294


title: Epi Normal 2


title: Epi Normal 3


title: late_OE-vector_a

description:
Sample_113
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 290


title: middle_OE_lncPRESS1DATG_b

description:
Sample_112
rna_seq_gene_counts_length_scaled.tsv


title: Endo CS 3

value: lung microvascular endothelial cell line


title: Endo CS 2


title: Breast cancer serum sample 288


title: Endo CS 1


title: middle_OE_lncPRESS1DATG_a

description:
Sample_111
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 285


title: Breast cancer serum sample 287


title: Breast cancer serum sample 289


title: Breast cancer serum sample 284


title: Breast cancer serum sample 286


title: middle_OE_lncPRESS1_b

description:
Sample_110
rna_seq_gene_counts_length_scaled.tsv


title: middle_OE_lncPRESS1_a

description:
Sample_109
rna_seq_gene_counts_length_scaled.tsv


title: Endo Normal 2


title: Breast cancer serum sample 281


title: Breast cancer serum sample 283


title: Breast cancer serum sample 282


title: HT-M3

city: haikou

first: yue

last: chen

address: No. 58 Renmin Avenue, Meilan District

institute: Hainan University

description:
Library name: sample18
18_FPKM

data_processing:
Total RNA was extracted from tissue samples. The concentration and purity of the extracted RNA were measured using Nanodrop 2000, while RNA integrity was assessed by agarose gel electrophoresis. The RQN value was determined using the Agilent 5300 system. For library construction, the RNA sample must meet the following criteria: a total amount of ≥1 μg, a concentration of ≥30 ng/μL, an RQN > 6.5, and an OD260/280 ratio between 1.8 and 2.2.
The 3' end of eukaryotic mRNA has a poly(A) tail. Magnetic beads with oligo(dT) sequences can hybridize with the poly(A) tail through A-T base pairing, allowing the isolation of mRNA from total RNA for transcriptome analysis.
Second-generation high-throughput sequencing platforms are designed for sequencing short DNA fragments. The enriched mRNA consists of full-length RNA sequences with an average length of several kilobases. Therefore, random fragmentation is required. By adding fragmentation buffer and optimizing the conditions, mRNA can be randomly fragmented into small fragments of approximately 300 bp.
Under the action of reverse transcriptase and using random primers, first-strand cDNA is synthesized from the mRNA template. Subsequently, the second strand is synthesized, forming a stable double-stranded structure.
The double-stranded cDNA has sticky ends. End Repair Mix is added to convert them into blunt ends. Subsequently, an A-base is added to the 3' end to facilitate the ligation of adapter sequences in the next step.The adapter-ligated products are purified and size-selected. The selected fragments are then subjected to PCR amplification, followed by purification to obtain the final library.
Assembly: GCF_014851395.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.（processed data.xlsx）

organism: Micropterus salmoides

source_name: gonad

extract_protocol:
RNA was harvested using Trizol reagent. 0.4 ug of total RNA was used for the construction of sequencing libraries；
RNA libraries were prepared for sequencing using standard Illumina protocols；

value: gonad


title: middle_OE-lncSIRP_b

description:
Sample_108
rna_seq_gene_counts_length_scaled.tsv


title: Endo Normal 3


title: Breast cancer serum sample 280


title: Endo Normal 1


title: middle_OE-lncSIRP_a

description:
Sample_107
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 278


title: HT-M2

description:
Library name: sample17
17_FPKM


title: Breast cancer serum sample 279


title: Breast cancer serum sample 277


title: middle_OE-vector_b

description:
Sample_106
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 276


title: HT-M1

description:
Library name: sample16
16_FPKM


title: middle_OE-vector_a

description:
Sample_105
rna_seq_gene_counts_length_scaled.tsv


title: Breast cancer serum sample 273


title: Breast cancer serum sample 274