title: Supreme- Rep 3-Layer 4

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

institute: UNIVERSITY OF FLORIDA

description: Library name: S-3-4

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program (Martin 2011) to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
Reads were aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference; v2.7.9a) and the Muscadinia rotundifolia ‘Noble’ genome (NCBI accession: PRJNA738474; Park et al., 2022) was used as the reference genome.
Mapped reads were processed with HTSeq (v0.11.2) (Anders et al., 2015), SAMtools, and in-house scripts developed by the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida to remove PCR duplicates and count uniquely mapped reads.
Differential expression analysis was conducted using the R package, DESeq2 (Love et al., 2014). Differentially expressed genes (DEGs) were identified with a log₂ fold change threshold of  ≥ 2 or ≤ –2 and adjusted p-values ≤ 0.05. KEGG enrichment analysis was performed using ShinyGO (Version 0.82, https://bioinformatics.sdstate.edu/go/). Transcription factor analysis was performed using the Plant Transcription Factor Database (PlantTFDB v5.0, https://planttfdb.gao-lab.org/). GO enrichment for candidate gene identification was performed using Panther’s Gene Ontology Resource (http://geneontology.org/). Predicted expression localization of candidates was performed using the University of Toronto’s eFP browser (https://bar.utoronto.ca/). All tools previously mentioned used the Vitis vinifera genome as a reference.
Assembly: Muscadinia rotundifolia ‘Noble’ genome (NCBI accession: PRJNA738474)
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

organism: Vitis rotundifolia

source_name: peel

extract_protocol:
Mature berries of ‘Alachua’, ‘Granny Val’, and ‘Supreme’ cultivars were harvested, and tissues were separated into four layers: epidermis/cuticle, hypodermis, mesocarp, and endocarp. Tissues were frozen in liquid nitrogen and stored at –80°C until further processing. Total RNA was isolated using the NucleoSpin RNA Plant and Fungi Kit (Macherey-Nagel, Hawthorne, NJ, USA), with a modified grinding step: 100–300 mg tissue was ground in 2 mL tubes with four 5-mm zirconia beads (Inframat Advanced Materials, Manchester, CT, USA) using a Mini-Beadbeater-96 (BioSpec Products, Bartlesville, OK, USA). RNA samples were treated with DNase using the PureLink™ DNase Kit (Invitrogen™, CA, USA) to remove residual DNA.
Total RNA  quality of sample was assessed using the Agilent TapeStation 4200 (Agilent Technologies, Inc). 250 ng of total RNA was used for library construction using NEB Ultra II Directional RNA-seq library preparation kit for Illumina according to manufacturer's protocol. First, 300 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide.

treatment_protocol: To assess relative skin thickness across muscadine cultivars, mature berries were harvested from 6 muscadine cultivars, 3 purple (‘Alachua’, ‘Paulk’, ‘Supreme’) and 3 green (‘Granny Val’, ‘Hall’, ‘Triumph’) from a research plot at the University of Florida Plant Science Research and Education Unit vineyard in Citra, Florida. Thirty berries per genotype were collected and transported to the postharvest laboratory in an icebox for dissection. Berry diameter was measured using ImageJ software.

value: peel

value: Seed


title: MDA-MB-231, 3D, sample 4

status: Public on Aug 03 2026

type: SRA

city: Grand Forks

first: Colin

last: Combs

state: North Dakota

address: 1301 N Columbia Rd

department: Biomedical Sciences

country: USA

institute: University of North Dakota

description: Library name: 231_3D_4

library_source: transcriptomic

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000, and 35 million 150 bp paired-end reads were obtained per sample. Preliminary quality control analysis of fastq files was performed with FastQC v0.11.9.
Adapters were trimmed using Trimmomatic v0.39
Reads were aligned to a human genome (hg38) with HISAT2 v2.2.1 software.
Successfully mapped clean reads were assigned to genomic features using featureCounts in Rsubread v2.18.0
Differentially expressed genes between sample groups were determined using DESeq2 v1.44.0 with a significance threshold of <0.05 Benjamini-Hochberg adjusted p-value.
Assembly: Reads were aligned to a human genome (hg38) with HISAT2 v2.2.1 software.
Supplementary files format and content: tab-delimited text files including fpkm normalized count values for each sample in the matrix.

molecule: total RNA

organism: Homo sapiens

growth_protocol: The triple negative breast cancer cell line MDA-MB-231 and human THP-1 cells were obtained from ATCC (Manassas, VA, USA). Cells were maintained in D-MEM/F-12 medium (Gibco, Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Thermo Fisher Scientific Inc., MA, USA). The cells were incubated at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were washed in PBS and lysed using RNAzol RT according to the RNAzol® RT Column Kit (Molecular Research Center, Cincinnati, OH) protocol. Briefly, the lysate was mixed with water and centrifuged at 12,000×g to remove DNA and proteins. Lysate was then diluted at a 1:1 ratio with isopropanol and added to a column before another 12,000×g centrifugation. RNA was then washed twice with 100% ethanol to remove impurities. RNA was then eluted using RNase-free deionized water and stored at -80°C. Concentrations were measured using a Qubit 4 Fluorometer, and purity was checked using a NanoDrop One spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Macrophage Differentiation and Polarization: THP-1 cells were stimulated with 100 nM phorbol-12-myristate 13-acetate (PMA) (Sigma-Aldrich, Saint Louis, MO, USA) in D-MEM/F-12 medium for 24 hours. Afterward, cells were activated for 24 hours into M1-like macrophages by treatment with 50ng/mL IFN-γ (R&D Systems Inc., Minneapolis, MN, USA) or into M2-like macrophages by treatment with 50ng/mL IL-4 (R&D Systems Inc., Minneapolis, MN, USA).  3D Co-cultured Spheroids: 10,000 MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate (Thermo Fisher Scientific Inc., MA, USA). After 24 h, 5,000 polarized M1-like or M2-like macrophages were seeded into each well for co-cultures. Monocultures and co-cultures were incubated for another 4 days at 37 °C in a humidified incubator with 5% CO2 before analysis or drug treatment.

tag: cell line

tag: cell type

value: triple negative breast cancer cell line

tag: treatment

value: MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate.


title: C82+4 follow-up

type: RNA

city: Heidelberg

first: Fabienne Dorothea

last: Lusky

address: Röntgenstr. 1

country: Germany

institute: Thoraxklinik at Heidelberg University Hospital

hyb_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website

data_processing: For statistical analysis we used R and the bioconductor package simpleaffy and affy, we transformed our data using RMA Algorithm

label: biotin

source_name: Whole blood

extract_protocol: We used the  PAXgene Blood RNA Kit according to the manufacturer’s instructions (PreAnalytiX, Hombrechtikon, CH)

treatment_protocol: Whole blood RNA was collected in PAXGene blood RNA tubes and incubated at room temperature for 2 hours to maximize cell lysis. Samples were stored frozen at  -80°C until processing

tag: sample type

value: follow-up

tag: group


title: mESC-Gata4, multi-LagTag, condition 5, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep1

city: Pasadena

first: Yodai

last: Takei

state: California

address: 1200 E California Blvd

institute: California Institute of Technology

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_5_rb_m6A_Ser2p_ms_Ser2p_rep1

library_source: genomic

data_processing:
The demultiplexing was performed with ‘bases2fastq’ tool (Element Biosciences). For the barcoded nb-Tn5 samples, the demultiplexing of the adapter barcodes was further performed with custom bash scripts making use of basic shell commands and the ‘seqtk’ package (seqtk-v1.5 https://github.com/lh3/seqtk).
Sequencing data was processed using the cutnrun pipeline v3.2.2 from nf-core (https://nf-co.re/cutandrun/3.2.2) with Nextflow v23.10.1.
Reads were aligned to the UCSC mm10 or hg38 genome using bowtie2 v.2.4.4, keeping only reads with a minimum alignment q score of 20. For the adapter barcoded samples, 42 bp from the 5’ end were removed with parameters --clip_r1 42 --clip_r2 42.
Aligned reads were masked using the CUT&RUN suspect list regions.
Bigwigs were generated from the alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14 mouse embryonic stem cells (E14Tg2a.4) were maintained on 0.1% gelatin coated plates under the serum/LIF condition in DMEM supplemented with 15% ES-grade fetal bovine serum (FBS), 1,000 units/mL leukemia inhibitory factor (LIF), 1× non-essential amino acids, 1 mM sodium pyruvate, 55 μM 2-mercaptoethanol, and 1× Penicillin-Streptomycin-Glutamine. mESC-Gata4 cells were maintained on 0.1% gelatin coated plates under the serum/LIF/2i condition by supplementing the serum/LIF medium with 1 μM PD0325901 and 3 μM CHIR99021. The human HCT116 cells (ATCC CCL‐247) were maintained in McCoy's 5A (modified) medium supplemented with 10% FBS and 1× Penicillin-Streptomycin. All cell lines were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 50 μL of 1% formaldehyde in 1× PBS at room temperature for 5 minutes on 96-well plates.
Cells were permeabilized with 0.5% Triton-X in 1× PBS. For LagTag, additional treatment with 5% RNaseA/T1 Mix as well as NaOH denaturation were performed. These treatments were omitted in CUT&Tag experiments unless noted. Samples were incubated with primary antibodies in blocking buffer (1× PBS, 1% BSA, and 0.05% Triton-X), then with nb-Tn5 transposomes (in-house) in wash 300 buffer (20 mM HEPES pH 7.4, 300 mM NaCl, and 0.05% Triton-X) supplemented with 0.1% BSA. Tagmentation was then performed in wash 300 buffer supplemented with 10 mM MgCl2 and 0.1% BSA. The DNA fragments were extracted using 20 μL SDS release buffer (10 mM TAPS buffer pH 8.5, 0.2% SDS, and 5% thermolabile proteinase K), then neutralized with 12 μL of 10% Triton-X for PCR input. Libraries were prepared by mixing 21 μL input, 2 μL each of i5 and i7 primers (10 μM stock), and 25 μL of NEBNext High-Fidelity 2X PCR Master Mix. PCR was performed as follows: 5 min at 58°C, 5 min at 72°C, and 45 sec at 98°C followed by 13-15 cycles of 15 sec at 98°C and 10 sec at 60°C, and a final extension at 72°C for 1 min. The amplified libraries were purified using 1.3× magnetic beads.

treatment_protocol: The mESC-Gata4 differentiation to endodermal cells was induced by 1 μg/mL Dox induction and LIF withdrawal for 24 hours. For LagTag, the adenine methyltransferase fusion proteins were stabilized with 1 μM Shield-1 for 16 hours in the engineered cells.

value: embryonic stem cell

tag: genotype

value: 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation

tag: antibody

value: m6A (Invitrogen MA5-35350), RNAPIISer2p (Cosmo Bio USA MCA-MABI0602-100-EX)


title: Supreme- Rep 2-Layer 4

description: Library name: S-2-4

tag: tissue


title: MDA-MB-231, 3D, sample 3

description: Library name: 231_3D_3


title: mESC-Gata4, multi-LagTag, condition 4, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep3

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_4_rb_m6A_Ser2p_ms_Ser2p_rep3

value: 1 μM Shield-1 for 16 hours for endpoint recording


title: Supreme- Rep 1-Layer 3

description: Library name: S-1-3

value: Endocarp


title: C74+4 follow-up

scan_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website


title: MDA-MB-231, 3D, sample 2

description: Library name: 231_3D_2


title: mESC-Gata4, multi-LagTag, condition 4, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_4_rb_m6A_Ser2p_ms_Ser2p_rep2


title: MDA-MB-231, 3D, sample 1

description: Library name: 231_3D_1


title: Granny Val -Rep 3 - Layer 4

description: Library name: G-3-4


title: C67+4 follow-up

label_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website


title: Granny Val - Rep 2 -Layer 3

description: Library name: G-2-3


title: MDA-MB-231, 2D, sample 4

description: Library name: 231_2D_4


title: mESC-Gata4, multi-LagTag, condition 3, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep3

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_3_rb_m6A_Ser2p_ms_Ser2p_rep3

value: 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation along with 1 μM Shield-1 for 16 hours for endpoint recording


title: C65+4 follow-up


title: mESC-Gata4, multi-LagTag, condition 3, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_3_rb_m6A_Ser2p_ms_Ser2p_rep2


title: Exercise patient 5 Visit 3 cfDNA 5mC

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Library name: E3-5 cfDNA 5mC

data_processing:
To analyze the MeDIP-seq data, high-quality reads from MeDIP-seq were aligned to the human reference genome (GRCH38/hg38) using bwa-mem2. Mapped reads were processed using MEDIPS R package58 to compute genome-wide methylation signals in every 300bp sliding window. The resulting count data were normalized using the trimmed mean of M-values (TMM) methods to account for differences in library size across samples. Peaks whose midpoint was located from 2000bp upstream to 500bp downstream of transcription start sites (TSS) were defined as promoter peaks. The promoter methylation level was quantified by averaging the Relative Methylation Score (RMS) across all windows covering promoter region. RMS is a normalized metric that adjusts for sequencing read coverage and CpG density, enabling cross-sample and locus-level comparisons. For differential methylation analysis, DMRs in both tissue and cfDNA were first identified separately within the exercise and control groups by comparing pre- and post-intervention using a generalized linear model (GLM)-based approach in MEDIPS package, which utilizes the edgeR framework to model over-dispersed count data via a negative binomial distribution73. FDR correction was performed using Benjamini–Hochberg (BH). However, no windows met the adjusted p-value threshold of 0.05 during DMR detection from tissue-derived DNA. Therefore, in this study, DMRs were defined as regions with a minimum coverage of 5 reads per window, an absolute log2 fold change (|log2FC|) ≥2, and an unadjusted p-value < 0.01for both cfDNA- and tissue-derived datasets. Exercise-induced DMRs (eDMRs) were identified based on two criteria: (1) DMRs that appeared exclusively in the exercise group but not in the control group, and (2) DMRs that were detected in both groups but exhibited opposite methylation changes between pre- and post-intervention. Therefore, the identified eDMRs not only capture the time-dependent methylation changes but also reflect exercise intervention.
Assembly: hg38
Supplementary files format and content: Each .rds file contains the corresponding MEDIP R object.

source_name: Serum

extract_protocol:
Genome-wide DNA methylation profiling was performed using MeDIP-seq on both colonic biopsy tissue DNA and cfDNA, following the published methods
genomic DNA was sheared to 200-600bp fragments, denatured to single strands, and immunoprecipitated with a monoclonal antibody against 5-methylcytosine. The enriched methylated DNA fragments were then subjected to high-throughput sequencing using Illumina HiSeq platform

value: Serum


title: MDA-MB-231, 2D, sample 2

description: Library name: 231_2D_2


title: C63+4 follow-up


title: mESC-Gata4, multi-LagTag, condition 3, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep1

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_3_rb_m6A_Ser2p_ms_Ser2p_rep1


title: Granny Val - Rep 1 - Layer 2

description: Library name: G-1-2

value: Exocarp


title: MDA-MB-231, 2D, sample 1

description: Library name: 231_2D_1


title: mESC-Gata4, multi-LagTag, condition 2, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep3

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_2_rb_m6A_Ser2p_ms_Ser2p_rep3

value: 1 μM Shield-1 for 16 hours for prior recording


title: C51+4 follow-up


title: Alachua - Rep 3 -Layer 3

description: Library name: A-3-3


title: CON012_re

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

country: Australia

institute: CMRI

description: Library name: CON012_re

data_processing:
FASTQ files were processed into gene and transcript counts
The cleaned sequence reads were aligned against the Homo sapiens genome (Build version hg38), and the STAR aligner (v2.5.3a) was used to map unique reads to the genomic sequences14.
RNA-Seq raw fastq files were quality checked by FastQC (version 0.11.9), and trimming of adapters and quality filtering were then performed by AdapterRemoval (version 2.3.2). Trimmed and quality filtered paired-end reads were aligned to the human GRCh38 reference genome by using STAR (version 2.7.9a) with default parameters. Gene expression was quantified by counting the number of reads aligned to each Ensembl gene model using featureCounts (version 2.0.1).
Assembly: Human hg38
Supplementary files format and content: tsv file for read count matrix from the same samples

extract_protocol: This workflow includes RNA extraction from PAXgene™ blood RNA tubes, depletion of ribosomal RNA via hybrid capture (Illumina Ribo-Zero), and Illumina TruSeq Stranded Total RNA Library Preparation (input 200-1000 ng of Total RNA). The stranded RNA samples are sequenced on the Illumina NovaSeq 6000 next generation sequencing platform (2 x 150 base pair) for a depth of 50 million paired end reads.

treatment_protocol: Children with cystic fibrosis versus healthy controls

value: Whole blood

tag: gender

value: F

tag: age

value: Control


title: C50+4 follow-up


title: mESC-Gata4, multi-LagTag, condition 2, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_2_rb_m6A_Ser2p_ms_Ser2p_rep2


title: Alachua - Rep 2 -Layer 2

description: Library name: A-2-2

value: peel


title: CON011

description: Library name: CON011


title: Exercise patient 4 Visit 3 Tissue 5mC

description: Library name: E3-4 Tissue 5mC

source_name: colonic tissues

value: colonic tissues


title: Exercise patient 5 Visit 3 cfDNA Input Control

description: Library name: E3-5 cfDNA IC


title: C47+4 follow-up


title: Alachua - Rep 1- Layer 1

description: Library name: A-1-1

value: Cuticle


title: CON010

description: Library name: CON010

value: M


title: mESC-Gata4, multi-LagTag, condition 1, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep3

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_1_rb_m6A_Ser2p_ms_Ser2p_rep3

value: 1 μM Shield-1 for 16 hours for prior recording, followed by 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation


title: C44+4 follow-up

value: follow-up


title: Supreme- Rep 2-Layer 1

description: Library name: 9-S-2-1


title: CON009

description: Library name: CON009


title: pfoa_EC5_24_rep2

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Library name: SF_311

data_processing:
The  quality assessment of all RNA-Seq datasets was conducted using FastQC v0.12.1
Trimming of reads, including removal of low-quality ends and adapters, was performed using cutadapt v4.4_dev with Python 3.8.10 with default parameters.
the trimmed and adapter-clipped raw reads underwent a second round of quality checks using FastQC v0.12.1
The RNA sequencing reads were aligned to the human reference genome assembly GRCh38 using the HISAT2 algorithm and its corresponding genome indexes.
Transcript abundance was determined using the featurecounts function from the Rsubread package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample. EnsemblID on the rows and samples on the columns.

molecule: polyA RNA

growth_protocol: THP-1 cells (ATCC TIB-202, USA) were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% FBS (Gibco, USA) (culture media). Cells were cultured in 75 cm2 flasks at a density < 1 × 106 cells/ml. Cells were differentiated in 12 well plates, with 500,000 cells/ well (127,000 cells/cm2), in the culture media supplemented with 50 nM of phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich, USA) for 48h

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen, Germany) according to vendor’s instructions. RNA quality was assessd by Bioanalyzer. Only high quality samples were sequenced.
Novogene NGS RNA Library Prep Set (PT042)

value: macrophage

value: WT

value: PFOA

tag: time

tag: replicate

tag: concentration

tag: concentration unit

value: nM


title: mESC-Gata4, multi-LagTag, condition 1, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_1_rb_m6A_Ser2p_ms_Ser2p_rep2

value: embryonic stem cell

value: m6A (Invitrogen MA5-35350), RNAPIISer2p (Cosmo Bio USA MCA-MABI0602-100-EX)


title: pfoa_EC5_24_rep3

description: Library name: SF_312


title: C42+4 follow-up


title: CON008

description: Library name: CON008


title: Supreme- Rep 1-Layer 4

description: Library name: 8-S-1-4

value: Seed


title: mESC-Gata4, multi-LagTag, condition 1, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep1

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_1_rb_m6A_Ser2p_ms_Ser2p_rep1


title: C37+4 follow-up


title: CON007

description: Library name: CON007


title: Supreme- Rep 1-Layer 1

description: Library name: 6-S-1-1


title: E14, multi-LagTag, condition 2, M.EcoGII-LMNB1 m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: E14_multi_LagTag_2_rb_m6A_LMNB1_ms_Ser2p_rep2

data_processing:
The demultiplexing was performed with ‘bases2fastq’ tool (Element Biosciences). For the barcoded nb-Tn5 samples, the demultiplexing of the adapter barcodes was further performed with custom bash scripts making use of basic shell commands and the ‘seqtk’ package (seqtk-v1.5 https://github.com/lh3/seqtk).
Sequencing data was processed using the cutnrun pipeline v3.2.2 from nf-core (https://nf-co.re/cutandrun/3.2.2) with Nextflow v23.10.1.
Reads were aligned to the UCSC mm10 or hg38 genome using bowtie2 v.2.4.4, keeping only reads with a minimum alignment q score of 20. For the adapter barcoded samples, 42 bp from the 5’ end were removed with parameters --clip_r1 42 --clip_r2 42.
Aligned reads were masked using the CUT&RUN suspect list regions.
Bigwigs were generated from the alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: DD-linker-M.EcoGII-LMNB1, single clone

value: 1 μM Shield-1 for 16 hours


title: CON006

description: Library name: CON006

value: Whole blood

value: F


title: C36+4 follow-up


title: E14, multi-LagTag, condition 2, M.EcoGII-LMNB1 m6A (rb), RNAPIISer2p (ms), rep1

description: Library name: E14_multi_LagTag_2_rb_m6A_LMNB1_ms_Ser2p_rep1


title: C34+4 follow-up


title: CON005

description: Library name: CON005

value: Control


title: Supreme- Rep 3-Layer 3

description: Library name: 3-S-3-3

value: peel

value: Endocarp


title: E14, multi-LagTag, condition 1, M.EcoGII-TAF3x3 m6A (rb), RNAPIISer2p (ms), rep2

description: Library name: E14_multi_LagTag_1_rb_m6A_TAF3_ms_Ser2p_rep2


title: Alachua - Rep 1- Layer 2

description: Library name: 34-A-1-2

value: Exocarp


title: C33+4 follow-up


title: Supreme- Rep 1-Layer 2

description: Library name: 5-S-1-2


title: Alachua - Rep 2- Layer 4

description: Library name: 32-A-2-4


title: CON004

description: Library name: CON004

value: M


title: mESC-Gata4, multi-LagTag, condition 2, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep1

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_2_rb_m6A_Ser2p_ms_Ser2p_rep1

value: 1 μM Shield-1 for 16 hours for prior recording


title: C30+4 follow-up

value: follow-up


title: E14, multi-LagTag, condition 1, M.EcoGII-TAF3x3 m6A (rb), RNAPIISer2p (ms), rep1

description: Library name: E14_multi_LagTag_1_rb_m6A_TAF3_ms_Ser2p_rep1


title: E14, multi-CUT&Tag, condition 3, RNAPIISer2p (rb), H3K27me3 (ms), rep2

description: Library name: E14_multi_CUTTag_3_rb_Ser2p_ms_H3K27me3_rep2

value: RNAPIISer2p (Cell Signaling 13499S), H3K27me3 (Active Motif 61018)


title: CON003_re

description: Library name: CON003_re


title: C23+4 follow-up


title: Alachua - Rep 1 -Layer 3

description: Library name: 30-A-1-3


title: CON002

description: Library name: CON002


title: CON001

description: Library name: CON001


title: E14, multi-CUT&Tag, condition 3, RNAPIISer2p (rb), H3K27me3 (ms), rep1

description: Library name: E14_multi_CUTTag_3_rb_Ser2p_ms_H3K27me3_rep1


title: Supreme- Rep 3-Layer 2

description: Library name: 2-S-3-2


title: C21+4 follow-up


title: E14, multi-CUT&Tag, condition 2, H3K4me3 (rb), RNAPIISer2p (ms), rep2

description: Library name: E14_multi_CUTTag_2_rb_H3K4me3_ms_Ser2p_rep2

value: H3K4me3 (Cell Signaling 9751T), RNAPIISer2p (Cosmo Bio USA MCA-MABI0602-100-EX)


title: Alachua - Rep 2 -Layer 1

description: Library name: 29-A-2-1

value: Cuticle


title: C20+4 follow-up


title: CF01703

description: Library name: CF01703

value: Post-treatment


title: CF01701_re

description: Library name: CF01701_re

value: Pre-treatment


title: Granny Val - Rep 1 - Layer 4

description: Library name: 27-G-1-4

value: Seed


title: E14, multi-CUT&Tag, condition 2, H3K4me3 (rb), RNAPIISer2p (ms), rep1

description: Library name: E14_multi_CUTTag_2_rb_H3K4me3_ms_Ser2p_rep1

value: embryonic stem cell


title: C17+4 follow-up


title: E14, multi-CUT&Tag, condition 1, H3K27me3 (rb), RNAPIISer2p (ms), rep2

description: Library name: E14_multi_CUTTag_1_rb_H3K27me3_ms_Ser2p_rep2

value: H3K27me3 (Cell Signaling 9733S), RNAPIISer2p (Cosmo Bio USA MCA-MABI0602-100-EX)


title: MDA-MB-231 Coculture with M2 Macrophages, sample 1

description: Library name: 231+M2_1

source_name: MDA-MB-231 and THP-1

value: MDA-MB-231 and THP-1

value: triple negative breast cancer cell line and M2-like macrophage polarized peripheral blood monocyte THP-1 cells

value: Following 24 hours of stimulation with 100 nM PMA in D-MEM/F, THP-1 cells were activated for 24 hours with 50 ng/mL IL-4 to induce an M2-macrophage state. 10,000 MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate along with 5,000 polarized M2-like macrophages cells and co-cultured for 4 days at 37 °C in a humidified incubator with 5% CO2.


title: mESC-Gata4, multi-LagTag, condition 6, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep3

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_6_rb_m6A_Ser2p_ms_Ser2p_rep3

value: m6A (Invitrogen MA5-35350), RNAPIISer2p (Cosmo Bio USA MCA-MABI0602-100-EX)


title: Alachua - Rep 1 -Layer 4

description: Library name: 26-A-1-4

value: peel


title: C16+4 follow-up


title: MDA-MB-231 Coculture with M1 Macrophages, sample 3

description: Library name: 231+M1_3

value: triple negative breast cancer cell line and M1-like macrophage polarized peripheral blood monocyte THP-1 cells

value: Following 24 hours of stimulation with 100 nM PMA in D-MEM/F, THP-1 cells were activated for 24 hours with 50 ng/mL ifn-γ to induce an M1-macrophage state. 10,000 MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate along with 5,000 polarized M1-like macrophages cells and co-cultured for 4 days at 37 °C in a humidified incubator with 5% CO2.


title: MDA-MB-231 Coculture with M1 Macrophages, sample 4

description: Library name: 231+M1_4


title: CF01603

description: Library name: CF01603

value: Whole blood

value: M


title: C95+4 follow-up

value: follow-up


title: C84+4 follow-up


title: E14, multi-CUT&Tag, condition 1, H3K27me3 (rb), RNAPIISer2p (ms), rep1

description: Library name: E14_multi_CUTTag_1_rb_H3K27me3_ms_Ser2p_rep1


title: mESC-Gata4, multi-LagTag, condition 6, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep1

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_6_rb_m6A_Ser2p_ms_Ser2p_rep1


title: CF01601_re

description: Library name: CF01601_re


title: Alachua - Rep 2 -Layer 3

description: Library name: 25-A-2-3

value: Endocarp


title: AUa4-13_S13

city: Boston

first: Anil

last: Upreti

state: MA

address: 20 Staniford St

department: Ophthalmology, Harvard Medical School

institute: Schepens Eye Research Institute, Mass Eye and Ear

description: Library name: NTC A

data_processing:
Raw read sequences were analyzed for quality using FastQC and MultiQC. Adapters and low-quality bases were trimmed using Cutadapt 3.4  and Trim Galore 0.6.5-1 with the parameters -q 20 --phred33 --length 20.
Human genome GRCh38 was indexed using Hisat2 (2.1.0-4), incorporating splice junctions from Gencode GTF gencode.v46.primary_assembly.annotation.gtf file. Stringtie 2.1.5  and gencode GTF annotation gencode. v46.primary_assembly.annotation.gtf was used to generate gene counts. DESeq2 1.34.0 was used to determine differential expression.
Assembly: GRCh38
Supplementary files format and content: ARPE19 normalized count matrix file from DESeq2
Supplementary files format and content: HMREC normalized count matrix file from DESeq2

source_name: HMREC

growth_protocol: ARPE19 cells were purchased from ATCC (CRL-2302). RPE media was prepared as previously described (38). N2 Medium Supplement 1/100 (vol/vol), glutamine 1/100 (vol/vol), non-essential amino acid solution 1/100 (vol/vol), hydrocortisone (20 µg/l), taurine (250 mg/l) and triiodo-thyronin (0.013 µg/l) in alpha MEM + 5% heat inactivated FBS (Hyclone, Logan, UT, USA) or without FBS. 100µg/ml Normocin was used as an antibiotic and antifungal agent. Cells were grown on transwells and cultured for 30 days. Human retinal microvascular endothelial cells (HRMECs) purchased at P3 from Cell Systems Corporation (Kirkland, WA, USA) were incubated at 37°C with 5% CO2. HRMECs were plated at P6 using endothelial growth media (EGM‐2) (Lonza, Basel, Switzerland) supplemented with 2% FBS (Atlanta Biologicals, GA, USA), 1% penicillin/streptomycin, and 1% L‐glutamine (Lonza). Cells were treated at P7 in endothelial basal media (EBM‐2) (Lonza) supplemented with 2% FBS, 1% penicillin/streptomycin, and 1% L‐glutamine.

extract_protocol:
consisting of 100,000 cells. Total RNA was extracted from using the RNeasy Plus Mini Kit (Qiagen; 74134), following the manufacturer’s instructions. RNA quality was assessed using an Tapestation and samples with an RNA Integrity Number (RIN) >8 were used for sequencing.
Libraries were constructed by Simches Research Center, Next Generation Sequencing Core, Massachusetts General Hospital (Boston, MA, USA) using a NEBNext Ultra II Directional RNA Library Prep Kit (Ipswich, MA, USA).

treatment_protocol: Transfections were performed using 25 nM ASO mismatch control (M2) or EFEMP1 ASO diluted in optiMEM reduced serum media (ThermoFisher Scientific; 31985070). Diluted constructs were packaged using Lipofectamine RNAiMAX Transfection reagent (ThermoFisher Scientific; 13778150) in optiMEM, and administered to the explants for 48 hours before the media was exchanged with normal growth medium

value: HMREC

value: Endothelial

value: WT

tag: batch


title: C15+4 follow-up


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pluripotent, rep3

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c6_rep3

value: RNAPIISer2p (Cell Signaling 13499S)


title: CF01403

description: Library name: CF01403

value: Post-treatment


title: Granny Val - Rep 3 - Layer 3

description: Library name: 23-G-3-3


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pluripotent, rep2

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c6_rep2

value: embryonic stem cell


title: Alachua - Rep 3 -Layer 1

description: Library name: 22-A-3-1

value: Cuticle


title: CF01401_re

description: Library name: CF01401_re

value: Pre-treatment


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, pluripotent, rep1

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c6_rep1


title: CF01303

description: Library name: CF01303


title: Granny Val - Rep 3 - Layer 2

description: Library name: 20-G-3-2

value: Exocarp


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, differentiation, rep3

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c5_rep3

value: 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation


title: Supreme - Rep 3 - Layer 1

description: Library name: 1-S-3-1

value: peel


title: C10+4 follow-up


title: CF01301_re

description: Library name: CF01301_re


title: Granny Val - Rep 2 - Layer 1

description: Library name: 19-G-2-1


title: CF01203

description: Library name: CF01203


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, differentiation, rep2

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c5_rep2


title: mESC-Gata4 (M.EcoGII-RNAPIISer2_mintbody), CUT&Tag, RNAPIISer2p, differentiation, rep1

description: Library name: mESC_Gata4_clone2_1_CUTTag_Ser2p_c5_rep1


title: C7+4 follow-up


title: C78+4 follow-up


title: C1+4 follow-up


title: Granny Val - Rep 3 - Layer 1

description: Library name: 17-G-3-1


title: CF01201_re

description: Library name: CF01201_re


title: C9+4 follow-up


title: C72+4 follow-up


title: mESC-Gata4, multi-LagTag, condition 4, M.EcoGII-RNAPIISer2p_mintbody m6A (rb), RNAPIISer2p (ms), rep1

description: Library name: mESC_Gata4_clone2_1_multi_LagTag_4_rb_m6A_Ser2p_ms_Ser2p_rep1

value: 1 μM Shield-1 for 16 hours for endpoint recording

value: m6A (Invitrogen MA5-35350), RNAPIISer2p (Cosmo Bio USA MCA-MABI0602-100-EX)


title: mESC-Gata4, CUT&Tag, RNAPIISer2p, pluripotent, rep3

description: Library name: mESC_Gata4_CUTTag_Ser2p_c6_rep3


title: Granny Val -Rep 2 - Layer 4

description: Library name: 16-G-2-4

value: Seed


title: CF01103

description: Library name: CF01103

value: Whole blood

value: M


title: 95BC

city: Pisa

first: Francesca

last: Scebba

address: Piazza martiri della libertà 33

country: Italy

institute: Scuola Superiore Sant'Anna

description: Library name: 30804-087

data_processing:
Analysis was performed using CLC Genomics Server 21.0.4 with the QIAseq miRNA Quantification workflow and standard parameters. Reads were mapped to miRBase v22 after trimming of common sequences, UMIs, and adapters, followed by filtering of reads shorter than 15 nt or longer than 55 nt. Reads were then deduplicated based on their UMIs by grouping reads with the same start position, strand, and identical UMI. Singleton UMI groups were merged into non-singleton groups when their UMI differed by a single nucleotide (SNP), with assignment to the largest matching group.
All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped the human genome GRCh38 with ENSEMBL GRCh38 version 97 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings.
Assembly: miRBase version 22
Supplementary files format and content: excel file with total miRNa count for each miRNA and each sample

source_name: saliva

extract_protocol:
RNA was isolated from 200 μl using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturer’s instructions
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 5 μl total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Agilent DNA 1000 Chip)

value: saliva

value: female

value: breast cancer


title: mESC-Gata4, CUT&Tag, RNAPIISer2p, pluripotent, rep2

description: Library name: mESC_Gata4_CUTTag_Ser2p_c6_rep2


title: Alachua - Rep 3- Layer 4

description: Library name: 15-A-3-4


title: mESC-Gata4, CUT&Tag, RNAPIISer2p, pluripotent, rep1

description: Library name: mESC_Gata4_CUTTag_Ser2p_c6_rep1


title: mESC-Gata4, CUT&Tag, RNAPIISer2p, differentiation, rep3

description: Library name: mESC_Gata4_CUTTag_Ser2p_c5_rep3


title: Alachua - Rep 3- Layer 2

description: Library name: 14-A-3-2


title: Granny Val -Rep 1 - Layer 1

description: Library name: 12-G-1-1


title: CF01001_re

description: Library name: CF01001_re


title: CF01003

description: Library name: CF01003


title: C400 baseline

value: baseline

value: CHTIO


title: Supreme - Rep 2 - Layer 3

description: Library name: 11-S-2-3

value: Endocarp


title: mESC-Gata4, CUT&Tag, RNAPIISer2p, differentiation, rep2

description: Library name: mESC_Gata4_CUTTag_Ser2p_c5_rep2

value: embryonic stem cell

value: RNAPIISer2p (Cell Signaling 13499S)


title: C323 baseline


title: C331 baseline


title: CF00903

description: Library name: CF00903

value: F

value: Post-treatment


title: C322 baseline


title: C320 baseline


title: mESC-Gata4, CUT&Tag, RNAPIISer2p, differentiation, rep1

description: Library name: mESC_Gata4_CUTTag_Ser2p_c5_rep1

value: 1 μg/mL Dox induction and LIF withdrawal for 24 hours for endodermal differentiation


title: Supreme- Rep 2-Layer 2

description: Library name: 10-S-2-2

value: peel

value: Exocarp


title: CF00901

description: Library name: CF00901

value: Pre-treatment


title: C312 baseline


title: E14, LagTag, M.EcoGII-mCherry, rep3

description: Library name: E14_LagTag_mCherry_rep3

value: 1 μM Shield-1 for 16 hours

value: m6A (Invitrogen MA5-35350)


title: HT-1080 cells w/ siHNRNPH1 pooled replicates

city: Bethesda

first: Natasha

middle: J

last: Caplen

state: Maryland

address: 37 Convent Dr, Bldg 37, Rm 6128

department: National Cancer Institute

institute: National Institutes of Health

description:
Library name: HT-1080 siHNRNPH1
Full length transcripts by IsoSeq

data_processing:
Short-read RNA-seq data was processed using the CCR Collaborative Bioinformatics Resource (CCBR) RNAseq pipeline, RENEE (https://ccbr.github.io/RENEE/latest/#table-of-contents).
PacBio long read RNA-seq data was processed using the official Iso-Seq software, installed as a bioconda package.
Assembly: GRCh38.p13 Release 41, Ensembl version 107
Supplementary files format and content: RSEM.transcript.variants.expected_count.all_samples.txt is a tab-delimited counts file containing transcript variant counts for each sample (short-read data)
Supplementary files format and content: gff files include full length transcript data from long-read RNA-seq. Can be viewed in IGV.

growth_protocol: HEK-293T cells were grown in DMEM and HT-1080 cells were grown in EMEM. Media was supplemented with 10% FBS and Plasmocin prophylactic at 37°C, 5% CO2.

extract_protocol:
We isolated RNA from three biological replicates 48-hours post-transfection using the Maxwell 16 LEV simplyRNA purification kit (Promega, Madison, WI).
Library preparation information for both short-read and long-read sequenicng runs can be found here: https://crtp.ccr.cancer.gov/sf/protocols-resources/

treatment_protocol: To deplete HNRNPH1, we plated 250,000 cells per well of a six-well plate and transfected cells with 20 nM siRNA complexed with 4.5 µL/well Lipofectamine RNAi-Max (Invitrogen, Thermo Fisher Scientific).


title: CF00803_re

description: Library name: CF00803_re

value: Whole blood

value: M


title: E14, LagTag, M.EcoGII-mCherry, rep2

description: Library name: E14_LagTag_mCherry_rep2


title: HT-1080 cells w/ siNegative pooled replicates

description:
Library name: HT-1080 siNegative
Full length transcripts by IsoSeq

value: siNegative


title: SPTD15

city: Kunming

first: Ye

last: Li

address: Kunming University of Science and Technology

country: China

description:
Library name: SPTD15
Sepsis with thyroid dysfunction, patient 5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count and fpkm value for each Sample

source_name: Peripheral blood

extract_protocol:
RNA was extracted from Peripheral blood using TRIzol reagent. Briefly, Peripheral blood were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: Peripheral blood

value: Sepsis with thyroid dysfunction


title: SPTD14

institute: Kunming University of Science and Technology

description:
Library name: SPTD14
Sepsis with thyroid dysfunction, patient 4


title: CF00703

description: Library name: CF00703


title: E14, LagTag, M.EcoGII-mCherry, single DD, rep2

description: Library name: E14_LagTag_induce_DD_mCherry_rep2

value: DD-linker-M.EcoGII-mCherry, polyclonal


title: C289 baseline

value: baseline

value: CHTIO


title: E14, LagTag, M.EcoGII-mCherry, single DD, rep1

description: Library name: E14_LagTag_induce_DD_mCherry_rep1

value: embryonic stem cell


title: C288 baseline


title: C280 baseline


title: CF00603

description: Library name: CF00603

value: F


title: C262 baseline


title: C290 baseline


title: C261 baseline


title: E14, LagTag, M.EcoGII-mCherry, dual DD, rep2

description: Library name: E14_LagTag_induce_DD_mCherry_DD_rep2


title: SPTD12

description:
Library name: SPTD12
Sepsis with thyroid dysfunction, patient 2


title: CF00601_re

description: Library name: CF00601_re


title: E14, LagTag, M.EcoGII-mCherry, dual DD, rep1

description: Library name: E14_LagTag_induce_DD_mCherry_DD_rep1


title: C251 baseline


title: SPTD11

description:
Library name: SPTD11
Sepsis with thyroid dysfunction, patient 1


title: CF00503

description: Library name: CF00503

value: Post-treatment


title: SP8

description:
Library name: SP8
Sepsis without thyroid dysfunction, patient 3

value: Sepsis without thyroid dysfunction


title: CF00501

description: Library name: CF00501


title: SP7

description:
Library name: SP7
Sepsis without thyroid dysfunction, patient 2


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, single DD, rep2

description: Library name: E14_LagTag_induce_DD_Ser2p_rep2


title: C239 baseline


title: CF00403

description: Library name: CF00403


title: C235 baseline


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, dual DD, rep2

description: Library name: E14_LagTag_induce_DD_Ser2p_DD_rep2


title: C238 baseline


title: SP6

description:
Library name: SP6
Sepsis without thyroid dysfunction, patient 1


title: CF00401

description: Library name: CF00401


title: C221 baseline


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, dual DD, rep1

description: Library name: E14_LagTag_induce_DD_Ser2p_DD_rep1


title: C220 baseline


title: CF00303

description: Library name: CF00303


title: EG10

description:
Library name: EG10
Sepsis with thyroid dysfunction, patient 8


title: EG9

description:
Library name: EG9
Sepsis with thyroid dysfunction, patient 7


title: CF00301_re

description: Library name: CF00301_re


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, 50 mM NaOH, 5 min, rep1

description: Library name: E14_LagTag_denat_Ser2p_lowx5min_rep1


title: EG8

description:
Library name: EG8
Sepsis with thyroid dysfunction, patient 6


title: CF00203

description: Library name: CF00203


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, 50 mM NaOH, 30 min, rep2

description: Library name: E14_LagTag_denat_Ser2p_lowx30min_rep2


title: C218 baseline


title: EG7

description:
Library name: EG7
Sepsis with thyroid dysfunction, patient 5


title: C217 baseline


title: CF00201

description: Library name: CF00201


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, 50 mM NaOH, 30 min, rep1

description: Library name: E14_LagTag_denat_Ser2p_lowx30min_rep1


title: C210 baseline


title: EG6

description:
Library name: EG6
Sepsis with thyroid dysfunction, patient 4


title: CF00103

description: Library name: CF00103


title: C206 baseline


title: EG5

description:
Library name: EG5
Sepsis with thyroid dysfunction, patient 3


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, 500 mM NaOH, 30 min, rep2

description: Library name: E14_LagTag_denat_Ser2p_highx30min_rep2


title: EG3

description:
Library name: EG3
Sepsis with thyroid dysfunction, patient 2


title: CF00101

description: Library name: CF00101


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, 500 mM NaOH, 30 min, rep1

description: Library name: E14_LagTag_denat_Ser2p_highx30min_rep1


title: Jurkat cells, pEF-TaxMac-Mra18C9, rep5

city: Lyon

first: Thomas

last: Duchateau

state: Rhône

address: 46 allée d'Italie

country: France

institute: ENS de Lyon

data_processing:
Data were initially processed by Novogene
As verification, we performed quality check using fastQC (v.0.11.8)
Reads were trimmed to eliminate adaptors, low quality reads, short reads using fastp (v.0.23.2) using the following parameters : qualified_quality_phred = 30, cut_right, cut_window_size = 5, cut_mean_quality = 30, length_required = 80
Reads where pseudo-mapped using SALMON v.1.10.1 (seqBias, GCBias) on human transcriptome GRCh38 with additional sequences corresponding to plasmid vector and Tax variants transcripts
Counts and normalized counts were further processed and analysed using DESeq2 package (v.1.42.1) in Rstudio (R v.4.3 and later)
Assembly: GRCh38
Supplementary files format and content: SALMON folder compressed .tar containing quant.sf file, TPM and number of reads for each sample.

source_name: Jurkat

growth_protocol: Jurkat cells were maintained in RPMI medium supplemented with 10% fœtal bovine serum (FBS) and penicillin/streptomycine in humid atmosphere, 5% CO2, 37°C

extract_protocol:
RNA were extracted using NucleoSpin RNA (Macherey-Nagel) and eluted with Rnase-free water (60 µL). Quality of RNA was assessed by Naodrop (concentration, 260/280 and 260/230 ratio > 2) prior sending to Novogene.
The library construction was performed by Novogene prior to sequencing.

treatment_protocol: Jurkat (4 millions / replicates) were co-microporated with pEF-Tax-myc plasmids (10 µg / 1 million cells) and pMACS-LNGFR (10 µg / 1 million cells) using Neon Transfection kit (ThermoFisher) and cultivated during 20h in RPMI + FBS 10%, in humid atmosphere, 5% CO2, 37°C. LNGFR+ cells (i.e. Tax+ cells) were sorted using POSSELD program on AutoMACS Pro Separator and aliquots of total, negative and positive fractions were used to confirm Tax expression and enrichment in Tax+ cells by flow cytometry.

value: Jurkat

value: immortalized human T lymphocyte

value: WT + TaxMac-Mra18C9


title: CF00801_re

description: Library name: CF00801_re

value: Pre-treatment


title: C204 baseline


title: E14, LagTag, M.EcoGII-TAF3x3, rep2

description: Library name: E14_LagTag_TAF3x3_rep2

value: 1 μM Shield-1 for 16 hours

value: m6A (Invitrogen MA5-35350)


title: E14, LagTag, M.EcoGII-mCherry, rep1

description: Library name: E14_LagTag_mCherry_rep1


title: EG2

description:
Library name: EG2
Sepsis with thyroid dysfunction, patient 1


title: C202 baseline


title: C283 baseline


title: C198 baseline


title: CF00701_re

description: Library name: CF00701_re

value: Whole blood


title: Jurkat cells, pEF-TaxMac-Mra18C9, rep4


title: C185 baseline


title: ctrl4

description:
Library name: ctrl4
Sepsis without thyroid dysfunction, patient 4


title: SPTD13

description:
Library name: SPTD13
Sepsis with thyroid dysfunction, patient 3


title: ctrl5

description:
Library name: ctrl5
Sepsis without thyroid dysfunction, patient 5


title: E14, LagTag, M.EcoGII-TAF3x3, rep1

description: Library name: E14_LagTag_TAF3x3_rep1


title: Jurkat cells, pEF-TaxMac-Mra18C9, rep3


title: Jurkat cells, pEF-TaxMac-Mra18C9, rep2


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, rep3

description: Library name: E14_LagTag_Ser2p_rep3


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, rep2

description: Library name: E14_LagTag_Ser2p_rep2


title: ctrl3

description:
Library name: ctrl3
Sepsis without thyroid dysfunction, patient 3


title: Jurkat cells, pEF-TaxMac-Mra18C9, rep1


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, rep1

description: Library name: E14_LagTag_Ser2p_rep1


title: ctrl2

description:
Library name: ctrl2
Sepsis without thyroid dysfunction, patient 2


title: C180 baseline


title: Jurkat cells, pEF-Tax1c-AusCSK-myc, rep5

value: WT + Tax1c-AusCSK


title: C169 baseline


title: C176 baseline


title: C162 baseline


title: ctrl1

description:
Library name: ctrl1
Sepsis without thyroid dysfunction, patient 1

value: Peripheral blood


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, single DD, rep1

description: Library name: E14_LagTag_induce_DD_Ser2p_rep1


title: Jurkat cells, pEF-Tax1c-AusCSK-myc, rep4


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (Sigma), rep2

description: Library name: E14_LagTag_Ser2p_m6A_Sigma_rep2

value: m6A (Sigma-Aldrich SAB5600251)


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (Sigma), rep1

description: Library name: E14_LagTag_Ser2p_m6A_Sigma_rep1


title: OE_GAS6_3

city: Shanghai

first: Yaodi

last: Shao

address: 2699 West Gaoke Road

institute: Shanghai First Maternity and Infant Hospital

description: Library name: OE_GAS6_3

data_processing:
Raw fastq sequencing files stored in the Rawdata folder underwent quality inspection using FastQC software. Trim Galore was utilized to remove sequencing adapters and low-quality reads. RPM-normalized BigWig coverage signal files were converted from aligned BAM files and saved in the Bigwig folder for genome browser visualization.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Raw data: gzipped paired-end FASTQ files deposited in the Rawdata directory, containing raw sequencing reads for biological replicates of empty vector control and GAS6-overexpressing cell groups. Processed data: normalized BigWig files stored in the Bigwig directory, displaying genome-wide read density signals of each sample.

extract_protocol:
Total RNA was extracted from empty vector control and GAS6-overexpressing OVCAR-8 human ovarian cancer cell lines using TRIzol reagent (Invitrogen) in accordance with the manufacturer’s protocols. RNA integrity was evaluated via Agilent 2100 Bioanalyzer (all samples had RIN ≥7.0), while RNA concentration was quantified with a Qubit fluorometer. DNase I digestion was conducted to eliminate genomic DNA contamination prior to RNA library construction.
Qualified total RNA was subjected to mRNA enrichment with oligo (dT) magnetic beads. Purified mRNA was fragmented into short segments by fragmentation buffer. Random hexamer primers were applied to synthesize first-strand cDNA, and second-strand cDNA was subsequently generated. After terminal end repair, A-tailing and sequencing adapter ligation, fragments of appropriate length were purified and amplified by PCR to generate the final cDNA library. Paired-end RNA-seq was carried out on the Illumina sequencing platform.

value: human ovarian cancer cells


title: C161 baseline

value: baseline


title: OE_GAS6_2

description: Library name: OE_GAS6_2


title: Jurkat cells, pEF-Tax1c-AusCSK-myc, rep2


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (Millipore), rep1

description: Library name: E14_LagTag_Ser2p_m6A_Millipore_rep1

value: m6A (Millipore ABE572-I)


title: C159 baseline


title: OE_GAS6_1

description: Library name: OE_GAS6_1


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (Invitrogen), rep2

description: Library name: E14_LagTag_Ser2p_m6A_Invitrogen_rep2

value: embryonic stem cell


title: C150 baseline


title: C149 baseline


title: Jurkat cells, pEF-Tax1c-EM5-myc, rep5

value: WT + Tax1c-EM5


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (Invitrogen), rep1

description: Library name: E14_LagTag_Ser2p_m6A_Invitrogen_rep1


title: MOCK_2

description: Library name: MOCK_2


title: Jurkat cells, pEF-Tax1c-EM5-myc, rep4


title: C139 baseline


title: C138 baseline


title: Jurkat cells, pEF-Tax1c-EM5-myc, rep3


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (CellSignaling), rep2

description: Library name: E14_LagTag_Ser2p_m6A_CellSignaling_rep2

value: m6A (Cell Signaling 56593T)


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (CellSignaling), rep1

description: Library name: E14_LagTag_Ser2p_m6A_CellSignaling_rep1


title: Jurkat cells, pEF-Tax1c-EM5-myc, rep2


title: Conventional T cells, donor 8341, condition TC, ATAC-seq

city: San Francisco

first: Qizhi

last: Tang

state: CA

address: 513 Parnassus Ave HSW 1102

department: Diabetes Center

institute: University of California, San Francisco

description:
Library name: 1433-27-8341-TC
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

data_processing:
adapter trimming: Cutadapt 3.5; Nextera/Tn5 mosaic-end adapter (CTGTCTCTTATACACATCT) trimmed from both reads (-a / -A); 3' quality trim at Q20 (-q 20); reads shorter than 20 bp discarded (-m 20).
alignment: Bowtie2 2.4.5 to hg38, paired-end,--very-sensitive --no-discordant --no-mixed -X 2000; coordinate-sorted with SAMtools.
filtering: SAMtools 1.13; retained properly-paired primary alignments with MAPQ >= 30 (view -f 2 -q 30 -F 2828 = exclude unmapped, mate-unmapped,secondary, QC-fail, supplementary); mitochondrial reads (chrM/MT) then removed. Non-canonical contigs are retained at this stage and removed later, during consensus construction.
duplicate removal: Picard MarkDuplicates 2.27.4, REMOVE_DUPLICATES=true.
peak calling: MACS2 2.2.9.1, per sample: callpeak -f BAMPE -g hs --keep-dup all --nomodel -q 0.05. The per-sample narrowPeak files are the deposited per-sample processed data and may include peaks on non-canonical contigs.
consensus peaks: per-sample MACS2 summits pooled, restricted to canonical chromosomes (chr1-22, X, Y), extended +/-250 bp with bedtools 2.30.0 to fixed 501-bp intervals (intervals clipped at chromosome ends discarded),ENCODE hg38 blacklist regions (ENCFF356LFX, hg38-blacklist.v2) removed, and overlaps resolved greedily by descending MACS2 -log10(q) score (iterative overlap peak merging; Corces et al. 2018) -> 104,749 non-overlapping consensus peaks.
quantification: featureCounts (Subread) 2.0.3, -p --countReadPairs -F SAF over the consensus peaks; fragment (read-pair)sample. counts per peak per sample.
Assembly: hg38
Supplementary files format and content:
<sample>_peaks.narrowPeak.gz : MACS2 per-sample peak calls (ENCODE narrowPeak, BED6+4), one file per sample.
fixedwidth_consensus_peaks.bed.gz : consensus peak set, 104,749 fixed-width 501-bp peaks; columns chr, start, end, peak_id, score.
fixedwidth_consensus_peak_counts.txt.gz : featureCounts raw fragment-count matrix, 104,749 consensus peaks x 22 samples (line 1 = featureCounts provenance comment; line 2 = header: Geneid, Chr, Start, End, Strand, Length, then one column per sample).

source_name: Tconv

growth_protocol: Primary human Tregs (CD4+ CD25+ CD127-/low) were isolated from 4 donors (1104, 4980, 7570, 8341) and stimulated with 25 ul/ml anti-CD3/CD2/CD28 ImmunoCult on days 0, 9, and 18. Cells were harvested on day 25.

extract_protocol:
50,000 cells per sample were isolated into PBS + 2% BSA, and extracted in 100 μl detergent (100 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice for 5 min to release nuclei.
Pelleted nuclei were incubated for 30 min with Tagment DNA Enzyme (Tn5) transposase. The reaction was stopped and DNA purified using the MinElute Reaction Cleanup kit. Eluted DNA was amplified with the NEBNext High-Fidelity 2x PCR Master Mix using Nextera index primers. The indexed libraries were purified using the MinElute PCR Reaction Cleanup before sequencing on an Illumina NovaSeq X with PE reads

treatment_protocol: Cells were treated with 300 IU/ml IL-2 only (cond. C) or IL2 + either 25 ng/ml IL-6 (cond. 6), 20 ng/ml IL-1B (cond. 1B), 20 ng/ml IL-23 (cond. 23), or IL-6 + IL-1B + IL-23 (cond. A). Primary human Tconv treated with IL-2 grown under the same conditions are included as a reference control (cond. TC)

value: Tconv

value: conventional T cell (Tconv)

value: wild-type

value: donor 8341, condition TC


title: C133 baseline


title: E14, LagTag, M.EcoGII-LMNB1, rep3

description: Library name: E14_LagTag_LMNB1_rep3

value: DD-linker-M.EcoGII-LMNB1, single clone


title: Conventional T cells, donor 7570, condition TC, ATAC-seq

description:
Library name: 1433-26-7570-TC
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 7570, condition TC


title: C129 baseline


title: Jurkat cells, pEF-Tax1c-EM5-myc, rep1

value: Jurkat

value: immortalized human T lymphocyte


title: E14, LagTag, M.EcoGII-LMNB1, rep2

description: Library name: E14_LagTag_LMNB1_rep2

value: 1 μM Shield-1 for 16 hours

value: m6A (Invitrogen MA5-35350)


title: Conventional T cells, donor 4980, condition TC, ATAC-seq

description:
Library name: 1433-25-4980-TC
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 4980, condition TC


title: Jurkat cells, pEF-Tax1b-SF26-myc, rep5

value: WT + Tax1b-SF30


title: C116 baseline

value: baseline


title: Conventional T cells, donor 1104, condition TC, ATAC-seq

description:
Library name: 1433-24-1104-TC
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 1104, condition TC


title: Jurkat cells, pEF-Tax1b-SF26-myc, rep4

value: WT + Tax1b-SF29


title: C113 baseline


title: E14, LagTag, EspM-TAF3x3, rep3

description: Library name: E14_LagTag_EspM_TAF3x3_rep3

value: embryonic stem cell


title: C112 baseline


title: Jurkat cells, pEF-Tax1b-SF26-myc, rep3

value: WT + Tax1b-SF28


title: E14, LagTag, EspM-TAF3x3, rep2

description: Library name: E14_LagTag_EspM_TAF3x3_rep2


title: Regulatory T cells, donor 8341, condition A, ATAC-seq

description:
Library name: 1433-23-8341-A
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

source_name: Treg

value: Treg

value: regulatory T cell (Treg)

value: donor 8341, condition A


title: Regulatory T cells, donor 8341, condition 23, ATAC-seq

description:
Library name: 1433-22-8341-23
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: wild-type

value: donor 8341, condition 23


title: Jurkat cells, pEF-Tax1b-SF26-myc, rep2

value: WT + Tax1b-SF27


title: C109 baseline


title: E14, LagTag, EspM-TAF3x3, rep1

description: Library name: E14_LagTag_EspM_TAF3x3_rep1


title: C107 baseline


title: E14, LagTag, M.EcoGII-CBX7x2, rep2

description: Library name: E14_LagTag_CBX7x2_rep2


title: C102 baseline


title: Regulatory T cells, donor 8341, condition C, ATAC-seq

description:
Library name: 1433-18-8341-C
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 8341, condition C


title: Jurkat cells, pEF-Tax1aB-ATK-myc, rep5

value: Jurkat

value: immortalized human T lymphocyte

value: WT + Tax1aB-ATK


title: E14, LagTag, M.EcoGII-CBX7x2, rep1

description: Library name: E14_LagTag_CBX7x2_rep1

value: 1 μM Shield-1 for 16 hours

value: m6A (Invitrogen MA5-35350)


title: Regulatory T cells, donor 7570, condition A, ATAC-seq

description:
Library name: 1433-17-7570-A
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 7570, condition A


title: Jurkat cells, pEF-Tax1aB-ATK-myc, rep4


title: C95 baseline

value: baseline


title: E14, CUT&Tag, RNAPIISer2p, 50 mM NaOH, 5 min, rep2

description: Library name: E14_CUTTag_denat_Ser2p_rep2

value: RNAPIISer2p (Cell Signaling 13499S)


title: C89 baseline


title: Regulatory T cells, donor 7570, condition 6, ATAC-seq

description:
Library name: 1433-16-7570-6
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 7570, condition 6


title: Jurkat cells, pEF-Tax1aB-ATK-myc, rep3


title: E14, CUT&Tag, RNAPIISer2p, 50 mM NaOH, 5 min, rep1

description: Library name: E14_CUTTag_denat_Ser2p_rep1

value: embryonic stem cell


title: Regulatory T cells, donor 7570, condition 1B, ATAC-seq

description:
Library name: 1433-15-7570-1B
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: Treg

value: donor 7570, condition 1B


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, m6A (Millipore), rep2

description: Library name: E14_LagTag_Ser2p_m6A_Millipore_rep2

value: m6A (Millipore ABE572-I)


title: Jurkat cells, pEF-Tax1aB-ATK-myc, rep2


title: Jurkat cells, pEF-Tax1c-AusCSK-myc, rep3

value: WT + Tax1c-AusCSK


title: C84 baseline


title: E14, CUT&Tag, RNAPIISer2p, rep2

description: Library name: E14_CUTTag_Ser2p_rep2


title: Regulatory T cells, donor 7570, condition C, ATAC-seq

description:
Library name: 1433-13-7570-C
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: regulatory T cell (Treg)

value: wild-type

value: donor 7570, condition C


title: Jurkat cells, pEF-Tax1aB-ATK-myc, rep1

value: Jurkat


title: C82 baseline


title: Jurkat cells, pEF-Tax1c-AusCSK-myc, rep1

value: immortalized human T lymphocyte


title: MOCK_3

description: Library name: MOCK_3

value: human ovarian cancer cells


title: E14, CUT&Tag, RNAPIISer2p, rep1

description: Library name: E14_CUTTag_Ser2p_rep1


title: Regulatory T cells, donor 4980, condition A, ATAC-seq

description:
Library name: 1433-12-4980-A
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 4980, condition A


title: Jurkat cells, pEF-myc, rep5

value: WT


title: E14, CUT&Tag, LaminB1, rep2

description: Library name: E14_CUTTag_LaminB1_rep2

value: LaminB1 (Abcam ab16048)


title: C78 baseline

value: baseline


title: Regulatory T cells, donor 4980, condition 23, ATAC-seq

description:
Library name: 1433-11-4980-23
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 4980, condition 23


title: MOCK_1

description: Library name: MOCK_1


title: Jurkat cells, pEF-myc, rep4


title: CF01101_re

description: Library name: CF01101_re

value: Whole blood

value: M

value: Pre-treatment


title: E14, CUT&Tag, LaminB1, rep1

description: Library name: E14_CUTTag_LaminB1_rep1

value: embryonic stem cell


title: C74 baseline


title: Regulatory T cells, donor 4980, condition 6, ATAC-seq

description:
Library name: 1433-10-4980-6
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: Treg

value: donor 4980, condition 6


title: C72 baseline


title: Jurkat cells, pEF-myc, rep3


title: E14, CUT&Tag, H3K4me3, rep2

description: Library name: E14_CUTTag_H3K4me3_rep2

value: H3K4me3 (Cell Signaling 9751T)


title: Regulatory T cells, donor 4980, condition 1B, ATAC-seq

description:
Library name: 1433-09-4980-1B
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: regulatory T cell (Treg)

value: wild-type

value: donor 4980, condition 1B


title: Jurkat cells, pEF-myc, rep2

value: Jurkat

value: immortalized human T lymphocyte


title: C67 baseline


title: E14, CUT&Tag, H3K4me3, rep1

description: Library name: E14_CUTTag_H3K4me3_rep1


title: E14, LagTag, M.EcoGII-LMNB1, rep1

description: Library name: E14_LagTag_LMNB1_rep1

value: DD-linker-M.EcoGII-LMNB1, single clone

value: 1 μM Shield-1 for 16 hours

value: m6A (Invitrogen MA5-35350)


title: Jurkat cells, pEF-myc, rep1

value: WT


title: Regulatory T cells, donor 4980, condition C, ATAC-seq

description:
Library name: 1433-07-4980-C
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 4980, condition C


title: E14, CUT&Tag, H3K27me3, rep2

description: Library name: E14_CUTTag_H3K27me3_rep2

value: H3K27me3 (Cell Signaling 9733S)


title: Regulatory T cells, donor 1104, condition A, ATAC-seq

description:
Library name: 1433-06-1104-A
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 1104, condition A


title: IMIM-PC-2, TSA-treated

city: Elche

first: Miguel

last: Saceda

state: Valencian Community

address: Unidad de Investigación del Hospital geneCami de la Almazara 11, edificio Anexo II

department: Unidad de Investigación

country: Spain

institute: Fundacion para el Fomento de la Investigacion Sanitaria y Biomédica de la Comunidad Valenciana

hyb_protocol: Once synthesized and purified, 15 µg of cRNA from each preparation were fragmented to prepare the hybridization mixtures. The hybridization procedures were performed by PROGENIKA SA. Quality controls for the hybridizations included the detection of spike-in controls and the assessment of 3'/5' signal ratios for housekeeping genes.

scan_protocol: After hybridization, arrays were washed, stained, and scanned following the standard Affymetrix protocols. The scanned images were processed using the Affymetrix GCOS 1.2 software to generate the corresponding CEL files for subsequent analysis.

data_processing: Prior to array comparison, data from each array were scaled to minimize discrepancies due to variables such as sample preparation, hybridization, and other technical factors. Using the Affymetrix GCOS 1.2 software, all arrays were scaled by setting the target mean intensity to an arbitrary value of 100. GCOS calculates the average intensity of the entire array by averaging the signal values of all probe sets, excluding the highest and lowest 2% of values. This mean intensity is then multiplied by a scaling factor to adjust it to the user-defined target value (in this case, 100). Scaling factors for arrays within the same experiment are expected to be similar and, as far as possible, close to 1. In this study, the scaling factors applied to each sample fell within the acceptable limits established by Affymetrix.

source_name: Pancreatic adenocarcinoma, TSA-treated (1 uM, 6 h)

label_protocol: Starting from 2 µg of each sample, cDNA was synthesized using the One-Cycle cDNA Synthesis Kit (Affymetrix) following the manufacturer’s Expression Analysis Technical Manual. Subsequently, cRNA was generated from the cDNA using the Affymetrix IVT Labeling Kit according to the provided protocol. The resulting cRNA was purified with the Affymetrix GeneChip Sample Cleanup Module and recovered in a final volume of 22 µL of RNase-free water. The quantity and quality of the biotinylated cRNA were assessed by spectrophotometric measurement using a NanoDrop device and by electrophoresis on an agarose gel.

growth_protocol: Pancreatic cells were cultured at 37°C in a humidified atmosphere containing 5% CO₂ in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Leukemia cell lines were maintained in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol: RNA was isolated using the NZY Total RNA Isolation Kit following manufacturer's instructions.

treatment_protocol: L1210 and L1210R cells were plated at a density of 3×10⁵ cells/mL and treated with 1 µM TSA in the presence or absence of 100 µM AEBSF for 6 hours. Pancreatic cell lines were treated with 1 µM TSA for 6 hours after reaching 80% confluence.

value: TSA-induced cell death sensitive


title: C65 baseline

value: baseline


title: E14, CUT&Tag, H3K27me3, rep1

description: Library name: E14_CUTTag_H3K27me3_rep1

value: embryonic stem cell


title: Regulatory T cells, donor 1104, condition 23, ATAC-seq

description:
Library name: 1433-05-1104-23
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: Treg

value: donor 1104, condition 23


title: C63 baseline


title: IMIM-PC-2, control

source_name: Pancreatic adenocarcinoma, untreated control


title: C61 baseline


title: Atorvastatin plus hexachlorobenzene, biological replicate 2

city: Mannheim

first: Lucia

last: Coli

address: Theodor-Kutzer-Ufer 1-3

institute: Universitätsklinikum Mannheim

description:
Library name: AT_HCB_8C_rep2
Male Wistar rat liver; atorvastatin plus HCB-treated; biological replicate 2; original Azenta sample ID: 8C; count-matrix column: dataaligned8C-Aligned.sortedByCoord.out.bam.

data_processing:
Raw paired-end sequencing reads were cleaned using fastp version 0.23.4.
Cleaned reads were aligned using STAR version 2.7.10b to the Rattus norvegicus reference genome mRatBN7.2 with Ensembl release 111 annotation.
Gene-level raw counts were generated using featureCounts with exon features (-t exon), gene IDs as meta-features (-g geneid), paired-end mode (-p), chimeric fragment exclusion (-C), and the annotation file mRatBN7.2Rattusnorvegicus.mRatBN7.2.111.gtf. Gene name, gene source, and gene biotype were included as extra attributes.
Genes were prefiltered before differential expression analysis. Genes were retained when they had raw counts of at least 5 in at least 3 samples. Differential expression analysis was performed in R version 4.3.2 using DESeq2 version 1.42.1 with a design based on treatment group only.
Differential expression results were exported with log2 fold-change shrinkage using the ashr algorithm. Differentially expressed genes were selected using adjusted p value < 0.05 and absolute log2 fold change > 2. Principal component analysis and sample correlation analysis were performed using variance-stabilizing transformed data.
Assembly: mRatBN7.2 (Rattus norvegicus), Ensembl release 111
Supplementary files format and content: all-counts-annotated.txt is a tab-delimited annotated gene-level raw count matrix. Rows correspond to Rattus norvegicus Ensembl gene identifiers. Columns include genomic coordinates, gene name, gene source, gene biotype, and unnormalized integer read counts for eight bulk RNA-seq libraries.
Supplementary files format and content: all-counts-annotated-summary.txt is a tab-delimited featureCounts assignment summary containing assigned and unassigned read categories for each library.
Supplementary files format and content: readme-all-counts-annotated.txt describes file structure, sample-to-column mapping, and processing

organism: Rattus norvegicus

source_name: liver

growth_protocol: Male Wistar rats were used from the vivarium of the Faculty of Pharmacy and Biochemistry of the University of Buenos Aires. At the beginning of the treatment, they had a weight of 160 g, were housed with free access to standard chow (Purina 3; Cabañas S.C.A., Argentina) and water. They were kept under a 12-hour light-dark cycle, at a temperature of 19 ± 2 °C and a humidity of 45-75%.

extract_protocol:
Fresh-frozen liver tissue samples were submitted to Azenta Life Sciences (formerly GENEWIZ) for RNA quality control and RNA-seq. Total RNA quality and quantity were assessed using NanoDrop 2000 spectrophotometry, Qubit RNA quantification, and Agilent TapeStation RNA ScreenTape analysis. Fresh-frozen liver tissue was used as input material for RNA extraction and subsequent library preparation.
RNA-seq libraries were prepared and sequenced by Azenta Life Sciences. Libraries were sequenced using an Illumina HiSeq platform with a 2 x 150-bp paired-end configuration.

treatment_protocol: Twenty male Wistar rats were randomly assigned to four experimental groups (n = 5 per group): (i) Control (vehicle only), (ii) Atorvastatin (AT, 5 mg/kg b.w./day, administered in drinking water), (iii) Hexachlorobenzene (HCB, 100 mg/kg b.w., administered by oral gavage three times per week for 30 days), and (iv) AT + HCB.  Animals were sacrificed on day 37 by intraperitoneal injection of ketamine/xylazine.  AT was administered in the drinking water at a dose of 5 mg per 20 mL, with each rat receiving 20 mL of water per day. HCB was dissolved in water containing 0.5% Tween-20 (0.5 ml/100 ml) at a concentration of 40 mg/ml; HCB doses were selected based on previously published studies from this group. For transcriptomic analysis, liver samples from two animals per group (n = 2) were selected for RNA sequencing.

value: liver

value: atorvastatin (AT), 5 mg/kg body weight/day, administered in drinking water for 30 days; hexachlorobenzene (HCB), 100 mg/kg body weight, oral gavage, three times per week for 30 days


title: RWP-1, TSA-treated


title: C51 baseline


title: Regulatory T cells, donor 1104, condition 6, ATAC-seq

description:
Library name: 1433-04-1104-6
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: regulatory T cell (Treg)

value: wild-type

value: donor 1104, condition 6


title: Atorvastatin plus hexachlorobenzene, biological replicate 1

description:
Library name: AT_HCB_7C_rep1
Male Wistar rat liver; atorvastatin plus HCB-treated; biological replicate 1; original Azenta sample ID: 7C; count-matrix column: dataaligned7C-Aligned.sortedByCoord.out.bam.


title: RWP-1, control


title: Regulatory T cells, donor 1104, condition 1B, ATAC-seq

description:
Library name: 1433-03-1104-1B
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 1104, condition 1B


title: C50 baseline


title: Regulatory T cells, donor 1104, condition C, ATAC-seq

description:
Library name: 1433-01-1104-C
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 1104, condition C


title: PANC-1, TSA-treated


title: Atorvastatin, biological replicate 2

description:
Library name: AT_6C_rep2
Male Wistar rat liver; atorvastatin-treated; biological replicate 2; original Azenta sample ID: 6C; count-matrix column: dataaligned6C-Aligned.sortedByCoord.out.bam.

value: atorvastatin, 5 mg/kg body weight/day, drinking water, 30 days


title: Regulatory T cells, donor 8341, condition 1B, ATAC-seq

description:
Library name: 1433-20-8341-1B
100,000 cells input; bulk ATAC-seq via Tn5 tagmentation

value: donor 8341, condition 1B


title: Atorvastatin, biological replicate 1

description:
Library name: AT_5C_rep1
Male Wistar rat liver; atorvastatin-treated; biological replicate 1; original Azenta sample ID: 5C; count-matrix column: dataaligned5C-Aligned.sortedByCoord.out.bam.


title: Jurkat cells, pEF-Tax1b-SF26-myc, rep1

value: Jurkat

value: immortalized human T lymphocyte

value: WT + Tax1b-SF26


title: HEK-293T cells w/ siHNRNPH1 pooled replicates

description:
Library name: HEK-293T siHNRNPH1
Full length transcripts by IsoSeq


title: PANC-1, control

value: TSA-induced cell death sensitive


title: IMIM-PC-1, TSA-treated


title: C47 baseline

value: baseline


title: Control, biological replicate 2

description:
Library name: Control_4C_rep2
Male Wistar rat liver; vehicle control; biological replicate 2; original Azenta sample ID: 4C; count-matrix column: dataaligned4C-Aligned.sortedByCoord.out.bam.

value: vehicle control


title: C44 baseline


title: HEK-293T cells w/ siNegative pooled replicates

description:
Library name: HEK-293T siNegative
Full length transcripts by IsoSeq

value: siNegative


title: Hexachlorobenzene, biological replicate 2

description:
Library name: HCB_3C_rep2
Male Wistar rat liver; HCB-treated; biological replicate 2; original Azenta sample ID: 3C; count-matrix column: dataaligned3C-Aligned.sortedByCoord.out.bam.

value: hexachlorobenzene, 100 mg/kg body weight, oral gavage, three times/week, 30 days


title: C42 baseline


title: S18_THY1_RIS

city: Barcelona

first: Lucía

last: Prohens Coll

state: Barcelona

address: Casanova 143, Facultat de Medicina, Dept de Fonamens Clínics, Unitat de Farmacologia, Planta 1, ala Nord

department: Basic Clinical Practice

institute: Universitat de Barcelona

description: Library name: Sample 18

data_processing:
Raw sequencing reads were generated in FASTQ format.
Read quality was assessed using FastQC.
Adapter sequences and low-quality bases were removed from raw reads.
Filtered reads were aligned to the mouse reference genome.
Gene-level read counts were obtained from aligned reads.
Downstream normalization and differential expression analyses were performed in R.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files containing raw gene-level read counts for each individual sample. Each file corresponds to one RNA-seq sample and includes unnormalized count values.
Supplementary files format and content: A supplemental comma-separated values (CSV) file containing the combined raw count matrix (genes × samples), generated by merging individual sample count files, with gene symbols as row identifiers and unnormalized count values.

source_name: Frontal Cortex

growth_protocol: Adult male mice were housed under standard laboratory conditions with controlled temperature and humidity, on a 12 h light/dark cycle, with food and water available ad libitum.

extract_protocol:
Frontal cortices were dissected, pooled (five animals per sample), and dissociated into a single-cell suspension. Microglia, astrocytes and neurons were sequentially isolated using an antibody-based immunopanning protocol involving depletion of endothelial cells, capture of CD45+ microglia, depletion of oligodendrocytes and oligodendrocyte precursor cells, and subsequent isolation of Thy1+ neurons and HepaCAM+ astrocytes. Total RNA was extracted directly from each immunopanned cell fraction using the Total RNA Extraction Miniprep kit (Viogene), following the manufacturer’s instructions.
RNA-seq libraries were prepared from 20 ng of total RNA using the QIAseq FastSelect RNA Library Kit (QIAGEN), including rRNA depletion and cDNA synthesis with random hexamer and oligo-dT primers. Libraries were purified, amplified and quantified, and sequenced as paired-end reads on an Illumina NextSeq 2000 System.

treatment_protocol: Mice were treated once daily from postnatal day 60 to 74 with vehicle, clozapine (10 mg/kg), or risperidone (1 mg/kg) administered intraperitoneally. Animals were sacrificed at postnatal day 75.

value: Frontal Cortex

value: neuron fractions

value: risperidone


title: IMIM-PC-1, control


title: C37 baseline


title: Hexachlorobenzene, biological replicate 1

description:
Library name: HCB_2C_rep1
Male Wistar rat liver; HCB-treated; biological replicate 1; original Azenta sample ID: 2C; count-matrix column: dataaligned2C-Aligned.sortedByCoord.out.bam.

value: liver


title: S17_THY1_RIS

description: Library name: Sample 17


title: WT (Col-0) vs ces mutant lines, Mock vs Hpa

city: Freising

first: Brigitte

last: Poppenberger

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: TUM School of Life Sciences

institute: Technical University of Munich

description:
Library name: Fang_Veronica_RNAseq
Mock treated and Hpa-infected Col-0, ces-D, 35S:CES_YFP, ces-tM, ces-qM

library_source: transcriptomic single cell

data_processing:
Data were processed using zUMIs pipeline
Analysis was performed using DESeq2, PANTHER (2024 release), and custom Python scripts utilizing Matplotlib, Plotly, NumPy, SciPy, and Pandas. DEGs were identified using FDR=0.05
Assembly: TAIR10
Supplementary files format and content: readcounts file generated using zUMIs pipeline
Supplementary files format and content: sample names and their corresponding barcodes

organism: Arabidopsis thaliana

source_name: 21 dag soil-grown aerial tissue

growth_protocol: Seeds were germinated on ½ MS medium (Duchefa Biochemie, Haarlem, The Netherlands), transferred to soil 7-8 days after germination and grown under long-day conditions (16 h light/8 h dark, 80 µmol m⁻² s⁻¹, 50% humidity) in a controlled environment growth cabinet (Bright Boy, CLF Plant Climatics, Wertingen, Germany) maintained at 21°C +/- 2 for the required amounts of time.

extract_protocol:
RNA was extracted from 3-week-old mock-treated or Hpa-infected Arabidopsis plants using the E.Z.N.A. Plant RNA Kit (Omega Bio-Tek, Norcross, GA, USA) with the difficult sample protocol in the manufacturer’s instructions. RNA RIN quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were prepared using a modified SCRB-seq protocol with barcoded oligo-dT primers (IDT, Coralville, IA, USA) and reverse transcription using KAPA HiFi HotStart polymerase (Roche/KAPA Biosystems, Wilmington, MA, USA). Tagmentation and library PCR were performed with Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA, USA). Libraries were size-selected on 2% E-Gel EX Agarose Gels (Thermo Fisher Scientific). Sequencing was done on an Illumina HiSeq1500 (Illumina)

treatment_protocol: Hpa isolate Noco2 was propagated on wild-type A. thaliana Col-0 plants, leaves were harvested, placed in tubes with double-distilled water and vortexed. The suspension was then filtering through Miracloth (Millipore-Sigma, Burlington, MA, USA), and the spore concentration was adjusted to 5 × 10⁴ conidiospores/ ml using a hemacytometer (Paul Marienfeld GmbH, Lauda-Königshofen, Germany). Two-week-old plants were inoculated by spraying with the spore suspension or water as a control using a standard atomizer. Following inoculation, plants were placed in sealed trays and incubated at 18°C under 16 h light/8 h dark photoperiod and a relative humidity of 90–100%.

value: 21 dag soil-grown aerial tissue

value: Mock treated and Hpa-infected


title: Control, biological replicate 1

description:
Library name: Control_1C_rep1
Male Wistar rat liver; vehicle control; biological replicate 1; original Azenta sample ID: 1C; count-matrix column: dataaligned1C-Aligned.sortedByCoord.out.bam.


title: S16_THY1_CLZ

description: Library name: Sample 16

value: clozapine


title: Damaraland mole-rat, liver, DMR1

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: Fdam_Liver_Rep3

data_processing:
Sequencing adaptors and low-quality reads were removed using Cutadapt with the following parameters: a minimum read length of 25 bp after trimming (-m 25), a minimum sequence quality score of 30 (-q 30), and the removal of any reads containing more than one N base (--max-n 1).
Trimmed reads from each species were pseudo-aligned and quantified to their respective reference transcriptome using Salmon v.013.1, with a decoy-aware index. The pseudo-mapping process included corrections for GC content bias (--gcBias) and sequence-specific biases (--seqBias). Quantification was performed at the transcript level.
For each species, we summarised transcript-level abundance estimates generated by Salmon to the gene level using the tximport v1.24 R package, with counts corrected for effective transcript length via the lengthScaledTPM method. To enable cross-species comparisons, we retained only one-to-one orthologous genes. We then merged gene-level count matrices across species and imported them into DESeq2. We normalised the combined dataset across all samples using the median-of-ratios method implemented in DESeq2, which adjusts for library size by computing sample-specific size factors as the median of ratios of observed counts to a pseudo-reference (the geometric mean across samples for each gene). To account for technical variation introduced by different data sources, we included a batch term in the DESeq2 model (~species + data source). Finally, we applied the variance-stabilising transformation (VST) to the normalised counts, which were then used for downstream analyses.
Assembly: The reference genome and transcriptomes for naked mole-rat (HetGla1.0), Damara mole-rat (DMRv1.0), guinea pig (Cavpor3.0) and mouse (GRCm38) were downloaded from Ensembl v102
Supplementary files format and content: Vst-normalised counts across 13,929 one-to-one orthologous for each sample in the study

organism: Fukomys damarensis

extract_protocol:
Total RNA was extracted from 10-50 mg of tissue samples, previously flash-frozen in dry ice and kept at -80C. Briefly, frozen tissue samples were homogenised in lysis buffer (RNAEasy, Qiagen) using homogenisation beads (Precellys hard tissue homogenising tubes CK28) in a FastPrep-24 tissue homogeniser (MP Biosciences) with three 20 s pulses at a speed of 4.5 m/s. Homogenised tissue lysates were used directly for RNA extraction using a commercial RNA extraction kit (RNEasy, Qiagen).
500 ng of total RNA from each sample were used for preparation of total RNA-sequencing libraries with NEBNext UltraTM II RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, total RNA was depleted of ribosomal RNA (rRNA) with rRNA Depletion Kit v2 (New England Biolabs) and RNA sample purification beads. rRNA-depleted RNA was used for preparation of cDNA and RNA-sequencing libraries following manufacturer specifications, with 12-15 minutes of RNA fragmentation at 94C and 10 cycles of PCR amplification. RNA-sequencing libraries were quantified by quantitative PCR with Kapa Illumina library quantification kit (Roche diagnostics) in a Roche LC480 instrument. RNA-seq libraries were then pooled in equimolar concentrations and sequenced in an Illumina NovaSeq instrument by commercial supplier Novogene UK.

tag: Sex

value: male

tag: age (months)

tag: individual


title: cas5Δ/Δcrz1Δ/Δ, 0.2 M calcium, rep 3

first: JIHONG

last: liu

state: Shanghai

address: No. 320 Yueyang Road, Shanghai

institute: siii

description: Library name: sample 22

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

organism: Candida albicans

source_name: C. albicans

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

tag: sample group

value: cas5Δ/Δcrz1Δ/Δ, 0.2 M calcium

tag: cell type

value: C. albicans

value: 0.2 M calcium


title: S15_THY1_CLZ

description: Library name: Sample 15

tag: treatment


title: C34 baseline

city: Heidelberg

first: Fabienne Dorothea

last: Lusky

address: Röntgenstr. 1

institute: Thoraxklinik at Heidelberg University Hospital

data_processing: For statistical analysis we used R and the bioconductor package simpleaffy and affy, we transformed our data using RMA Algorithm

extract_protocol: We used the  PAXgene Blood RNA Kit according to the manufacturer’s instructions (PreAnalytiX, Hombrechtikon, CH)

tag: sample type

tag: group


title: Damaraland mole-rat, liver, DMR4

description: Library name: Fdam_Liver_Rep5


title: S14_THY1_VEH

description: Library name: Sample 14

tag: genotype

value: vehicle


title: cas5Δ/Δcrz1Δ/Δ, 0.2 M calcium, rep 2

description: Library name: sample 21


title: C36 baseline


title: C33 baseline


title: cas5Δ/Δcrz1Δ/Δ, 0.2 M calcium, rep 1

description: Library name: sample 20


title: C30 baseline


title: cas5Δ/Δcrz1Δ/Δ, YPD, rep 3

description: Library name: sample 19

value: cas5Δ/Δcrz1Δ/Δ, YPD


title: S13_THY1_VEH

description: Library name: Sample 13

tag: tissue


title: Damaraland mole-rat, liver, DMR6

description: Library name: Fdam_Liver_Rep4

value: female


title: Damaraland mole-rat, liver, DMR3

description: Library name: Fdam_Liver_Rep2


title: E14, LagTag, M.EcoGII-RNAPIISer2p_mintbody, 50 mM NaOH, 5 min, rep2

city: Pasadena

first: Yodai

last: Takei

address: 1200 E California Blvd

institute: California Institute of Technology

description: Library name: E14_LagTag_denat_Ser2p_lowx5min_rep2

data_processing:
The demultiplexing was performed with ‘bases2fastq’ tool (Element Biosciences). For the barcoded nb-Tn5 samples, the demultiplexing of the adapter barcodes was further performed with custom bash scripts making use of basic shell commands and the ‘seqtk’ package (seqtk-v1.5 https://github.com/lh3/seqtk).
Sequencing data was processed using the cutnrun pipeline v3.2.2 from nf-core (https://nf-co.re/cutandrun/3.2.2) with Nextflow v23.10.1.
Reads were aligned to the UCSC mm10 or hg38 genome using bowtie2 v.2.4.4, keeping only reads with a minimum alignment q score of 20. For the adapter barcoded samples, 42 bp from the 5’ end were removed with parameters --clip_r1 42 --clip_r2 42.
Aligned reads were masked using the CUT&RUN suspect list regions.
Bigwigs were generated from the alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 50 μL of 1% formaldehyde in 1× PBS at room temperature for 5 minutes on 96-well plates.
Cells were permeabilized with 0.5% Triton-X in 1× PBS. For LagTag, additional treatment with 5% RNaseA/T1 Mix as well as NaOH denaturation were performed. These treatments were omitted in CUT&Tag experiments unless noted. Samples were incubated with primary antibodies in blocking buffer (1× PBS, 1% BSA, and 0.05% Triton-X), then with nb-Tn5 transposomes (in-house) in wash 300 buffer (20 mM HEPES pH 7.4, 300 mM NaCl, and 0.05% Triton-X) supplemented with 0.1% BSA. Tagmentation was then performed in wash 300 buffer supplemented with 10 mM MgCl2 and 0.1% BSA. The DNA fragments were extracted using 20 μL SDS release buffer (10 mM TAPS buffer pH 8.5, 0.2% SDS, and 5% thermolabile proteinase K), then neutralized with 12 μL of 10% Triton-X for PCR input. Libraries were prepared by mixing 21 μL input, 2 μL each of i5 and i7 primers (10 μM stock), and 25 μL of NEBNext High-Fidelity 2X PCR Master Mix. PCR was performed as follows: 5 min at 58°C, 5 min at 72°C, and 45 sec at 98°C followed by 13-15 cycles of 15 sec at 98°C and 10 sec at 60°C, and a final extension at 72°C for 1 min. The amplified libraries were purified using 1.3× magnetic beads.

tag: cell line

value: embryonic stem cell

value: 1 μM Shield-1 for 16 hours

tag: antibody

value: m6A (Invitrogen MA5-35350)


title: cas5Δ/Δcrz1Δ/Δ, YPD, rep 2

description: Library name: sample 18


title: C23 baseline

value: baseline


title: S12_HEPA_RIS

description: Library name: Sample 12

value: Frontal Cortex

value: astrocyte fractions


title: C21 baseline


title: cas5Δ/Δcrz1Δ/Δ, YPD, rep 1

description: Library name: sample 17


title: Damaraland mole-rat, heart, DMR11

description: Library name: Fdam_Heart_Rep4

source_name: heart

value: heart


title: Damaraland mole-rat, heart, DMR2

description: Library name: Fdam_Heart_Rep5


title: S9_HEPA_CLZ

description: Library name: Sample 9


title: C20 baseline

source_name: Whole blood


title: C16 baseline


title: Damaraland mole-rat, heart, DMR4

description: Library name: Fdam_Heart_Rep3


title: E16.5_F_WT

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Hybridized to Agilent-015087 arrays according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5 um

data_processing: Let x-norm = x - y + mean(y), where x = log10(Cy3), y =log10(Cy5). x-batch = x - median(new data) + median(old data) for every gene. The batched normalized value x-batch is used for the final processed VALUE using EX-Atlas program.

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions

extract_protocol: The samples were dissolved in the well with TRIzol reagent 1/2 mL. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqueous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer. ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.

treatment_protocol: Placentas (d.p.c 16.5 or 18.5) were harvested from wild-type (WT) and PLAC1 Knock-out (Plac1 null) mice

tag: strain

value: WT

value: Female

tag: age

value: Placenta

source_name: Universal probe


title: C15 baseline


title: Damaraland mole-rat, heart, DMR3

description: Library name: Fdam_Heart_Rep2

value: male


title: Damaraland mole-rat, heart, DMR1

description: Library name: Fdam_Heart_Rep1


title: C10 baseline


title: S6_CD45_RIS

description: Library name: Sample 6

value: microglia fractions

value: risperidone


title: C9 baseline


title: E18.5_M_Plac1 KO_1

data_processing: Let x-norm = x - y + mean(y), where x = log10(Cy3), y =log10(Cy5). x-batch = x - median(new data) + median(old data) for every gene. The batched normalized value x-batch is used for the final processed VALUE

source_name: Placenta_E18.5_M_Plac1 null

growth_protocol: Placenta from male mice at d.p.c 16.5 and 18.5 were harvested from wild-type (WT) and PLAC1 Knock-out (Plac1 null)

value: C57/Bl6_Plac1 null

value: Male

value: Universal probe


title: E18.5_M_WT_2


title: S5_CD45_RIS

description: Library name: Sample 5


title: CEN.PK2-1C, YPD, rep3

city: Pathumthani

first: Peerapat

last: Khamwachirapithak

address: Phahonyothin Road, Khlong Luang

country: Thailand

institute: Thammasat University

description: Library name: CENPK_3

data_processing:
FastQC
Reads were align to Saccer3 genome using the Hisat2
Sorting and indexing using Samtools
Duplication was removed by Picard tools
Raw read counts were normalized by DEseq2
Assembly: Saccer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Saccharomyces cerevisiae

source_name: Cell pellet

growth_protocol: Cells were cultured in YPD medium at 30°C and 250 rpm for 18 hours

extract_protocol:
RNA was extracted by RNeasy Mini Kit (Qiagen, Germany).
DNBSEQ stranded mRNA library

value: Cell pellet

value: Yeast cell

value: YPD


title: E18.5_M_WT_1


title: C1 baseline


title: CEN.PK2-1C, YPD, rep2

description: Library name: CENPK_2


title: BxPC-3, TSA-treated

value: TSA-induced cell death sensitive


title: E16.5_M_Plac1 KO_2

source_name: Placenta_E16.5_M_Plac1 null


title: CEN.PK2-1C, YPD, rep1

description: Library name: CENPK_1


title: S3_CD45_CLZ

description: Library name: Sample 3

value: clozapine


title: Beta-carotene-producing yeast, YPD, rep3

description: Library name: Beta_3

value: betacarotene

value: CrtI/E/YB


title: E16.5_M_Plac1 KO_1