title: Col_wildtype rep2

description: Library name: Col_rep2


title: ATAC-seq AID-DIvA U2OS knockout-treated-0min-biol-rep2

status: Public on Jan 29 2026

type: SRA

city: Heidelberg

first: Ali

last: Bakr

address: Im Neuenheimer Feld 280

department: Cancer Epigenomics

country: Germany

institute: Deutsches Krebsforschungszentrum

description: Library name: knockout-treated-0min-rep2

library_source: genomic

data_processing:
Reads were processed using the nf-core/atacseq pipeline
Assembly: GRCh37/hg19
Supplementary files format and content: bigwig files

molecule: genomic DNA

organism: Homo sapiens

source_name: bone

extract_protocol:
50,000 viable cells were collected before and after 4-OHT treatment and lysed in cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0. 1% digitonin, 1% NP40, 0.1% Tween-20) and incubated on ice for 5 min to isolate the nuclei
nuclei were pelleted by centrifugation at 1,000 x g for 5 min at 4 °C. The nuclei pellets were resuspended in transposition buffer (Illumina) containing 0.1% digitonin, 0.1% Tween-20, and 2.5 μL of Tagment DNA Enzyme 1 (Illumina) was added onto samples. The samples were mixed in a thermomixer at 1000 rpm for 30 min at 37 °C. 5M guanidium thiocyanate were added to the samples to stop the tagmentation reaction. DNA was then purified by AMPure XP PCR Purification (Beckman Coulter, A63880). The libraries were amplified by real-time quantitative PCR adding of NEBNext® High Fidelity 2X PCR mix, 10 μM Custom Nextera PCR Forward Primer, 10 μM Custom Nextera PCR Barcode Primers, and SYBR Green (1X final concentration). The library amplification program was as follows: 5 min at 72 °C for gap repair, 30 s at 98 °C for initial melting, 10 s at 98°C, 30 s at 63°C, and 30 s at 72°C for amplification. Libraries were subsequently purified using 1.4X AMPure beads. DNA concentration was measured using the Qubit instrument, and Quality control was performed on a Tape station using the Agilent High Sensitivity DNA Kit

treatment_protocol: Wild-type and ID3-KO AID-DIvA cells were treated with 300 nM 4-hydroxytamoxifen (4-OHT) for 6 hours at 37 °C to induce AsiSI localization to the nucleus and generate DSBs

tag: tissue

value: bone

tag: cell line

value: AID-DIvA U2OS

tag: cell type

value: osteosarcoma

tag: genotype

tag: treatment


title: Vim-KO RAW264.7 cells, 1 µg/mL LPS, 12 h, rep1

city: Yokohama

first: Xian-Yang

last: Qin

address: 1-7-22 Suehiro, Tsurumi

department: RIKEN Center for Integrative Medical Sciences

country: Japan

institute: Institute of Physical and Chemical Research

description:
Library name: Sample20
Column name in TPM_WTvsKO_RNA_seq.csv: KO_LPS1

library_source: transcriptomic

data_processing:
Raw sequencing reads were processed using Salmon.
Assembly: UCSC mm10 (GRCm38)
Supplementary files format and content: csv files include TPM values for each Sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
RNA was extracted using a FastGene RNA Basic Kit (NIPPON Genetics).
RNA-seq libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: macrophage-like cell line

value: Vim-KO

value: LPS

tag: rna extraction_date


title: M22 wild-type, unstressed control (0 min), replicate 2

city: Fayetteville

first: Carson

middle: Len

last: Stacy

state: AR

address: 850 W. Dickson St. Rm 601

department: Biological Sciences

country: USA

institute: University of Arkansas

description:
Library name: M22_WT_CTRL_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_CTRL_rep2

data_processing:
Raw reads were trimmed and filtered using TrimGalore (version 0.6.7), a wrapper for cutadapt (version 3.4), with default settings to remove Illumina adapters. Reads with phred quality scores <20 or a post-trimming length <20 bp were discarded. Trimmed reads were mapped to the S288C genome (SacCer3 R64-1-1, Ensembl accession GCA_000146045.2) using STAR (version 2.7.10a) [62] implemented through the nf-core/rnaseq (v 3.10.1) pipeline [63]. Alignment used  a GTF containing only chromosomal protein-coding genes. Gene counts were generated using RSEM (version 1.3.1, [64]). A median of approximately 17 million reads (range: 12.4-69.5 million) were successfully mapped per sample, representing over 95% of trimmed reads successfully mapped.
Differential expression analysis was performed in edgeR (v. 4.4.2) with a negative binomial quasi likelihood (QL) generalized linear model [65,66], following TMM normalization. Genes with fewer than 10 counts across all samples were excluded from subsequent analysis. The QL model included sample type (e.g., M22 hog1∆ unstressed, M22 hog1∆ NaCl stressed, M22 hog1∆ ethanol stressed, etc.) and biological replicate as factors. Contrasts of interest included comparisons of wild-type vs hog1∆ mutants and the stress response (stress vs. unstressed) for each strain individually (e.g., the S288C wild-type NaCl response, the S288c hog1∆ NaCl response), as well as comparisons of strain stress responses (e.g., S288C wild-type NaCl response vs the S288c hog1∆ NaCl response). Genes were considered differentially expressed if they met a Benjamini-Hochberg false discovery rate (FDR) cutoff of < 0.01 and at least a ±1.5-fold change in expression. To identify Hog1-affected genes across all strains, all replicates were used. Counts for each sample were subsampled down to lowest read depth of any sample and samples were then subset to biological triplicate.
Assembly: SacCer3 R64-1-1
Supplementary files format and content: Tab separated values (tsv) file containing a matrix of raw fractional counts for all samples.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae strains were grown at 30°C with orbital shaking (270 rpm) in YPD (1% yeast extract, 2% peptone, 2% dextrose). ~5 unique colonies per replicate experiment were grown overnight to saturation in YPD. Cells were then sub-cultured for at least 8 generations (~16 hours) to mid-log phase (OD600 0.3 - 0.6 on a Unico spectrophotometer).

extract_protocol:
RNA was extracted using the ‘hot phenol’ method, with a detailed protocol available on protocols.io DOI 10.17504/protocols.io.inwcdfe. Phenol-extracted RNA was treated with DNaseI (Ambion), and then purified with a Quick-RNA MiniPrep Plus Kit (Zymo Research) including the optional on-column DNase step. RNA quantity was measured using a Qubit fluorometer (Fisher), and all samples were confirmed to have a RIN > 9 as assessed by an Agilent 2200 Tapestation.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche) and KAPA Single-Indexed Adapter Set A + B, according to manufacturer specifications with minor modifications. Starting samples consisted of 500 ng, which were then polyA-enriched, fragmented to an average size of 200-300 nucleotides, and then cDNA libraries were amplified for 9 PCR cycles. A detailed protocol is available on protocols.io DOI 10.17504/protocols.io.uueewte.

treatment_protocol: For each biological replicate, an unstressed control sample was collected, and then the culture was split and exposed to stress media with final concentrations: 0.4 M NaCl, 5% (v/v) ethanol, or 0.4 mM H2O2. Cells were incubated in the stress for either 30 min (ethanol and H2O2) or 45 min (NaCl), timepoints which encompass the peak response for each stressor. Unstressed and stressed samples were collected by centrifugation at 1,500 x g for 1 min, flash frozen in liquid nitrogen, and stored at -80°C until RNA extraction.

value: budding yeast cells

value: wild-type (HOG1/HOG1)

value: unstressed control (0 min)

tag: batch


title: Actin KO rep2

city: Be'er Sheva

first: Dan

last: Levy

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben-Gurion University

description: Library name: Sample 2

data_processing:
Raw sequences were quality trimmed and filtered using Trim Galore (version 0.4.5) (quality cutoff=25, length cutoff=25) and cutadapt (version 1.15)
Alignment of the reads to the human genome (Homo_sapiens.GRCh38) was done with RSEM (version 1.2.28 option ‘bowtie2’) and calculation of number of reads per gene per sample was also done with RSEM
Assembly: GRCH38
Supplementary files format and content: Count Matrix for all samples

growth_protocol: HCT116  were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), penicillin-streptomycin , 2 mg/ml L-glutamine and non-essential amino acids.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel)
mRNA library preparation (poly A enrichment)

value: Actin KO


title: M22 wild-type, 0.4 M NaCl (45 min), replicate 3

description:
Library name: M22_WT_NaCl_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_NaCl_rep3

value: 0.4 M NaCl (45 min)


title: IgG_Control cells

description: Library name: Sample 8

data_processing:
Trim Galore v0.4.5 (length= 25, q- 25)
FastQC v0.12.0 was used for reads quality control
BWA Mapper (v0.7.12,  t=20, B= 5) aligned paired-end reads to reference human genome assembly hg38 and to  spike-in control (Escherichia coli) reference genome assembly
SAMtools removed PCR duplicates and created coordinate-sorted BAM files
Bigwig files were created by bamCoverage
Assembly: Reads that refer to off-chromosome locations were removed with BedClip v377 and sorted by Bedtools v2.30.0
Supplementary files format and content: Bigwig files of each sample and corresponding IgG control were created with bedGraphToBigWig v2.8 by deepTools.
Supplementary files format and content: Peak calling results by Macs2 and SEACR  are presented as bed files
Library strategy: CUT&Run

extract_protocol:
Genomic DNA
EpiCypher CUT&RUN library kit Protocol

value: SETD3 CT Cells


title: Actin KO rep1

description: Library name: Sample 1


title: M22 wild-type, 0.4 M NaCl (45 min), replicate 2

description:
Library name: M22_WT_NaCl_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_NaCl_rep2


title: Actin KO rep3

description: Library name: Sample 3


title: Vim-KO RAW264.7 cells, PBS, 12 h, rep1

description:
Library name: Sample18
Column name in TPM_WTvsKO_RNA_seq.csv: KO_PBS1

value: PBS


title: M22 wild-type, unstressed control (0 min), replicate 1

description:
Library name: M22_WT_CTRL_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_CTRL_rep1


title: BRG1_SETD3_KO2 cells

description: Library name: Sample 7

value: SETD3 KO Cells


title: ATAC-seq AID-DIvA U2OS knockout-untreated-biol-rep3

description: Library name: knockout-untreated-rep3

value: untreated


title: ACTB-WT rep1

description: Library name: Sample 4

value: Actin WT over-expression


title: ATAC-seq AID-DIvA U2OS knockout-untreated-biol-rep2

description: Library name: knockout-untreated-rep2


title: M22 wild-type, unstressed control (0 min), replicate 3

description:
Library name: M22_WT_CTRL_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_CTRL_rep3


title: ATAC-seq AID-DIvA U2OS knockout-treated-0min-biol-rep1

description: Library name: knockout-treated-0min-rep1


title: ACTB-WT rep2

description: Library name: Sample 5


title: YPS606 hog1Δ, 5% (v/v) ethanol (30 min), replicate 4

description:
Library name: YPS606_hog1del_EtOH_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_EtOH_rep4

value: hog1 KO (hog1/hog1)

value: 5% (v/v) ethanol (30 min)


title: Vim-KO RAW264.7 cells, 1 µg/mL LPS, 12 h, rep2

description:
Library name: Sample21
Column name in TPM_WTvsKO_RNA_seq.csv: KO_LPS2


title: ATAC-seq AID-DIvA U2OS knockout-treated-0min-biol-rep3

description: Library name: knockout-treated-0min-rep3

value: bone

value: AID-DIvA U2OS


title: Vim-KO RAW264.7 cells, PBS, 12 h, rep2

description:
Library name: Sample19
Column name in TPM_WTvsKO_RNA_seq.csv: KO_PBS2

value: macrophage-like cell line


title: BRG1_SETD3_KO1 cells

description: Library name: Sample 6


title: WT RAW264.7 cells, 1 µg/mL LPS, 12 h, rep2

description:
Library name: Sample17
Column name in TPM_WTvsKO_RNA_seq.csv: WT_LPS2

value: WT


title: ATAC-seq AID-DIvA U2OS knockout-untreated-biol-rep1

description: Library name: knockout-untreated-rep1

value: osteosarcoma


title: M22 wild-type, unstressed control (0 min), replicate 4

description:
Library name: M22_WT_CTRL_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_CTRL_rep4

value: budding yeast cells


title: ATAC-seq AID-DIvA U2OS control-treated-0min-biol-rep3

description: Library name: control-treated-0min-rep3

value: wt


title: WT RAW264.7 cells, 1 µg/mL LPS, 12 h, rep1

description:
Library name: Sample16
Column name in TPM_WTvsKO_RNA_seq.csv: WT_LPS1

value: LPS


title: YPS606 hog1Δ, 5% (v/v) ethanol (30 min), replicate 3

description:
Library name: YPS606_hog1del_EtOH_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_EtOH_rep3


title: BRG1_Control cells

description: Library name: Sample 5


title: WT RAW264.7 cells, PBS, 12 h, rep1

description:
Library name: Sample14
Column name in TPM_WTvsKO_RNA_seq.csv: WT_PBS1


title: ATAC-seq AID-DIvA U2OS control-treated-0min-biol-rep2

description: Library name: control-treated-0min-rep2


title: HTR5_GFP_IP_rep2

city: Beijing

first: Xiaoyi

last: Li

address: west beichen

department: Chinese Academy of Sciences

country: China

institute: Institute of Genetics and Developmental Biology

description: Library name: HTR5_GFP_IP_rep2

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1. Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2.
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp.
Average ChIP-seq profiles were generated using deepTools utility plotProfile.
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Plants were grown under long day conditions (16h light/8h dark) at 22°C

extract_protocol:
Nuclei were extracted, and mononucleosomes were generated using micrococcal nuclease (NEB, M0247S) digestion.Immunoprecipitation was conducted with anti-GFP (Thermo Fisher Scientific, A11122).
The input DNA and immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

treatment_protocol: ChIP-seq was performed using 10-day-old seedlings, which were fixed with 1% formaldehyde.

value: Seedlings

tag: chip antibody

value: GFP (Thermo Fisher Scientific, A11122)


title: YPS606 hog1Δ, 5% (v/v) ethanol (30 min), replicate 2

description:
Library name: YPS606_hog1del_EtOH_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_EtOH_rep2


title: ATAC-seq AID-DIvA U2OS control-untreated-biol-rep3

description: Library name: control-untreated-rep3


title: Flag_Empty_IgG_Control cells

description: Library name: Sample 4

value: SETD3 CT Cells


title: YPS606 hog1Δ, 0.4 mM H2O2 (30 min), replicate 4

description:
Library name: YPS606_hog1del_H2O2_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_H2O2_rep4


title: WT RAW264.7 cells, PBS, 12 h, rep2

description:
Library name: Sample15
Column name in TPM_WTvsKO_RNA_seq.csv: WT_PBS2

value: PBS


title: ATAC-seq AID-DIvA U2OS control-untreated-biol-rep2

description: Library name: control-untreated-rep2


title: ATAC-seq AID-DIvA U2OS control-treated-0min-biol-rep1

description: Library name: control-treated-0min-rep1


title: Flag_Actin_Control cells

description: Library name: Sample 1


title: WT C57BL/6J (liver macrophage depletion), LPS i.p.

description:
Library name: Sample5
Column name in TPM_liver_RNA_seq.csv: Mφ-_LPS

source_name: Liver

value: Liver


title: TG2-KO C57BL/6J, PBS i.p.

description:
Library name: Sample6
Column name in TPM_liver_RNA_seq.csv: TG2-KO_PBS


title: ATAC-seq AID-DIvA U2OS control-untreated-biol-rep1

description: Library name: control-untreated-rep1

value: untreated


title: Hnf1a flox pancreatic cells 4

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

data_processing:
All primary analysis was carried out using CLC Genomics Server 21.0.4. Raw reads were first trimmed to remove potential read-through adapter sequences at the 3’end. Further, reads were trimmed based on quality scores and ambiguous nucleotides, e.g. due to stretches of Ns. A maximum of 2 ambiguous nucleotides were allowed in a read. The trimmed reads were mapped to Mouse ribosomal RNA (rRNA) repetitive unit and only reads that didn’t map to rRNA were used for gene quantification. The reads were then mapped to the Mouse genome GRCm38 v. 80 and annotated using the ENSEMBL GRCm38 v. 86 mRNA annotation.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 and incorporated in the EdgeR Bioconductor package Robinson et al., 2010.
For all unsupervised analysis, only genes were considered with at least 10 counts summed over all samples. A variance stabilizing transformation was performed on the raw count matrix using the function vst of the R package DESeq2 version 1.28.1. The 500 genes with the highest variance were used for the principal component analysis. The variance was calculated agnostically to the pre-defined groups (blind=TRUE). The 35 genes with the highest variance across samples were selected for hierarchical clustering.
Genome_build: GRCm38 v. 80
Supplementary_files_format_and_content: xlsx file include normalized TPM values for each sample

source_name: Pancreatic islet cells

extract_protocol:
Pancreas were digested with collagenase, islets extracted with histopaque gradient, and mRNA extracted using the Qiagen RNeasy Micro Kit (50)
QIAseq Stranded mRNA Select Kit with FastSelect rRNA depletion (QIAGEN) and further proccesed with standard illumina protocols

tag: strain

value: mixed background

tag: glyceamia

value: hyperglyceamia

value: hmz

tag: Sex

value: female


title: YPS606 hog1Δ, 0.4 mM H2O2 (30 min), replicate 3

description:
Library name: YPS606_hog1del_H2O2_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_H2O2_rep3

value: hog1 KO (hog1/hog1)


title: YPS606 hog1Δ, 5% (v/v) ethanol (30 min), replicate 1

description:
Library name: YPS606_hog1del_EtOH_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_EtOH_rep1

value: 5% (v/v) ethanol (30 min)


title: YPS606 hog1Δ, 0.4 mM H2O2 (30 min), replicate 1

description:
Library name: YPS606_hog1del_H2O2_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_H2O2_rep1


title: WT C57BL/6J (no liver macrophage depletion), LPS i.p.

description:
Library name: Sample4
Column name in TPM_liver_RNA_seq.csv: Mφ+_LPS

value: WT


title: Flag_Actin_SETD3_KO2 cells

description: Library name: Sample 3

value: SETD3 KO Cells


title: WT C57BL/6J, 30 mg/kg LPS plus 100mg/kg CTM i.p.

description:
Library name: Sample3
Column name in TPM_liver_RNA_seq.csv: LPS.plus.CTM

value: LPS plus CTM


title: Hnf1a flox pancreatic cells 3


title: YPS606 hog1Δ, 0.4 mM H2O2 (30 min), replicate 2

description:
Library name: YPS606_hog1del_H2O2_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_H2O2_rep2

value: budding yeast cells


title: Flag_Actin_SETD3_KO1 cells

description: Library name: Sample 2


title: Jurkat, TRAIL-treated, replicate 2, V5 ChIP

city: Berkeley

first: Britt

last: Glaunsinger

state: CA

address: 565 Li Ka Shing Center

department: Department of Plant and Microbial Biology

institute: University of California, Berkeley

description: Library name: V5_TRAIL_rep2_ChIP

data_processing:
Basecalls were performed using bcl2fastq v.2.17 for NovaSeq output
ChIP-seq reads were trimmed using Trimmomatic v.0.39 with default settings for paired-end reads.
The hg38 and yeast (GCA_000146045.2) genomes were manually indexed using the bowtie2-build command. ChIP-seq reads were then separately aligned to the two genomes with bowtie2 v.2.5.4 using the --maxins 1500 parameter to account for a read's maximum length.
Coverage profiles generated for all ChIP-seq datasets were produced using DeepTools v. 3.5.5. BigWig files were first generated with the bamCoverage command for each bam file from each sample mapped to the hg38 genome with the following parameters --binSize 10, --smoothLength 30, --extendReads, --centerReads, --normalizeUsing None, and --scaleFactor with their respective spike-in normalized scale factor.
Assembly: hg38, yeast (GCA_000146045.2)
Supplementary files format and content: bigWig

source_name: Jurkat

growth_protocol: Jurkat cells stably expressing doxycycline-inducible, siRNA-resistant 6xHis-TFIIB-V5 were maintained in RPMI 1640 media (Gibco) supplemented with 10% Tet-free fetal bovine serum, 1X GlutaMAX (Gibco), 1x Pen-Strep (Gibco), 1 mM sodium pyruvate (Gibco), and 10 ug/mL blasticidin HCl (Gibco) in a humidified chamber at 37℃ and 5% CO2. Cells were kept at densities between 0.5-2x10^6 cells/mL.

extract_protocol:
Cells were then cross-linked in 1% formaldehyde in DPBS (Gibco) for 5 minutes at room temperature, quenched in 0.125 M glycine, and washed three times with DPBS (Gibco). Cross-linked cells were harvested and lysed with 1 ml ChIP lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) by rotation for 10 min. Nuclei were collected by centrifugation at 1,700 × g for 5 min at 4°C, washed once with ChIP shearing buffer (50 mM Tris-Cl, pH 7.5, 10 mM EDTA, 0.1% SDS), and then resuspended in 1 ml of ChIP shearing buffer. Chromatin was then sheared for 8 min using a Covaris S220 focused ultrasonicator at 140 power, a 5% duty cycle, and 200 bursts/cycle. Chromatin was spun at 15,000 × g for 5 min at 4°C, and the pellet was discarded. 10 μg of chromatin was incubated with 5 μg rabbit monoclonal anti-RPB1 NTD (clone D8L4Y; Cell Signaling 14958), rabbit polyclonal anti-V5 (Abcam ab15828), or rabbit IgG (Abcam ab37415) overnight. 6xHis pulldown was attempted in parallel but yielded insufficient quality and was excluded from further analysis. 25 μl of mixed protein A and G Dynabeads (Thermo Fisher) were added, and the tubes were rotated for 2 hours at 4°C. Dynabeads were then washed with low-salt immune complex (20 mM Tris pH 8.0, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 0.1% SDS), high-salt immune complex (20 mM Tris pH 8.0, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 0.1% SDS), lithium chloride immune complex (10 mM Tris pH 8.0, 0.25 M LiCl, 1% NP-40, 1% deoxycholic acid, 1 mM EDTA), and Tris-EDTA for 5 min each at 4°C with rotation. DNA was eluted from the beads in elution buffer (150 mM NaCl, 50 μg/ml proteinase K) and incubated at 50°C for 2 h and then at 65°C overnight. DNA was purified using an Oligo Clean and Concentrator kit (Zymo), eluted in nuclease-free water, and then used to generate libraries for ChIP-seq.
Libraries for ChIP-seq were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) with NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors DNA Set 1). Equal amounts of sample eluted DNA and spike-in DNA (yeast spike-in DNA – Cell Signaling) were used within each experiment and amplified for 3-10 cycles based on NEB recommendations and sequenced on a NovaSeq X 10B (Illumina) with 150 paired-end reads.

treatment_protocol: After 24h of doxycyline-induction (2.5 ug/mL) of siRNA-resistant 6xHis-TFIIB-V5 in Jurkat cells, endogenous protein was knocked down by siRNA. siRNA treatments for ChIP-sequencing were performed on 10x10^6 Jurkat cells with 10 uM each of On-Target Plus human GTF2B siRNA SmartPool and Accell human GTF2B siRNA SmartPool for a total of 80x10^6 cells. siRNAs were nucleofected using the Neon Transfection System (Invitrogen) according to the manufacturer’s instructions at 1700V, 1x20ms pulse-length. Cells were plated in fresh media with doxycycline following siRNA treatment. After 24 h siRNA, 40x10^6 cells were dosed with either 250 ng/mL SUPERKILLER TRAIL (Enzo) or mock diluant for 4 h.

value: Jurkat

value: T cell

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V13

value: TRAIL treatment


title: Hnf1a flox pancreatic cells 2

value: male


title: Jurkat, TRAIL-treated, replicate 2, RPB1 ChIP

description: Library name: Rpb1_TRAIL_rep2_ChIP

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V14

value: Rpb1NTD (Cell Signaling #14958)


title: YPS606 hog1Δ, 0.4 M NaCl (45 min), replicate 4

description:
Library name: YPS606_hog1del_NaCl_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_NaCl_rep4

value: 0.4 M NaCl (45 min)


title: TG2-KO C57BL/6J, 30 mg/kg LPS i.p.

description:
Library name: Sample7
Column name in TPM_liver_RNA_seq.csv: TG2-KO_LPS

value: Liver

value: LPS


title: WT C57BL/6J, 30 mg/kg LPS i.p.

description:
Library name: Sample2
Column name in TPM_liver_RNA_seq.csv: LPS


title: YPS606 hog1Δ, 0.4 M NaCl (45 min), replicate 3

description:
Library name: YPS606_hog1del_NaCl_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_NaCl_rep3


title: Jurkat, mock-treated, biol rep 2, RPB1 ChIP

description: Library name: Rpb1_mock_rep2_ChIP

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V12


title: Jurkat, mock-treated, biol rep 2, V5 ChIP

description: Library name: V5_mock_rep2_ChIP

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V11


title: WT pancreatic cells 7

value: mixed background

value: normal

value: wt

value: female


title: YPS606 hog1Δ, 0.4 M NaCl (45 min), replicate 2

description:
Library name: YPS606_hog1del_NaCl_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_NaCl_rep2

value: budding yeast cells

value: hog1 KO (hog1/hog1)


title: 5A4 NP1 BasA complement induced replicate 3

city: Bryan

first: Jon

middle: T

last: Skare

state: TX

address: 8447 John Sharp Pkwy

institute: Texas A&M University Health Science Center

description: Library name: C06

data_processing:
CLC Genomics Workbench v25.0.1
Trimmed reads were mapped to B. burgdorferi B31 reference genome (NCBI ID: GCF_000008685.2) allowing only 1 hit per read.
Minimum length fraction: 0.9 and Minimum similarity fraction: 0.9
Read count extraction and normalization were determined in CLC Genomics Workbench
Assembly: GCF_000008685.2
Supplementary files format and content: .xlsx file includes raw counts for each Sample

organism: Borreliella burgdorferi B31

source_name: bacterial

growth_protocol: B. burgdorferi were grown in BSK-II media to 5-8 x 107 cells/mL  in either uninduced (32ºC, pH 7.6, 1% CO2) or induced (37ºC, pH 6.8, 5% CO2) growth conditions

extract_protocol:
Total RNA was extracted using hot phenol chloroform extraction and was Dnase (Roche) treated following manufacturer's instructions. 2 ug of RNA was sent to SeqCenter (Pittsburgh) for library preparation and sequencing.
Libraries were prepared using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit.

value: bacterial

value: BasA complement

value: induced


title: WT C57BL/6J, PBS i.p.

description:
Library name: Sample1
Column name in TPM_liver_RNA_seq.csv: PBS

value: WT

value: PBS


title: 5A4 NP1 BasA mutant induced replicate 3

description: Library name: C05

value: BasA mutant


title: Jurkat, TRAIL-treated, replicate 1, RPB1 ChIP

description: Library name: Rpb1_TRAIL_rep1_ChIP

value: Jurkat

value: T cell

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V10

value: TRAIL treatment

value: Rpb1NTD (Cell Signaling #14958)


title: Jurkat, TRAIL-treated, replicate 1, V5 ChIP

description: Library name: V5_TRAIL_rep1_ChIP

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V9


title: Hnf1a flox pancreatic cells 1

value: mixed background

value: hyperglyceamia

value: hmz


title: YPS606 hog1Δ, unstressed control (0 min), replicate 4

description:
Library name: YPS606_hog1del_CTRL_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_CTRL_rep4

value: budding yeast cells

value: unstressed control (0 min)


title: Jurkat, mock-treated, biol rep 1, RPB1 ChIP

description: Library name: Rpb1_mock_rep1_ChIP

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V8


title: WT pancreatic cells 6

value: normal

value: wt

value: female


title: YPS606 hog1Δ, 0.4 M NaCl (45 min), replicate 1

description:
Library name: YPS606_hog1del_NaCl_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_NaCl_rep1

value: hog1 KO (hog1/hog1)

value: 0.4 M NaCl (45 min)


title: 5A4 NP1 induced replicate 3

description: Library name: C04

value: bacterial

value: Parent

value: induced


title: 5A4 NP1 BasA complement uninduced replicate 3

description: Library name: C03

value: BasA complement

value: uninduced


title: Jurkat, mock-treated, biol rep 1, V5 ChIP

description: Library name: V5_mock_rep1_ChIP

value: Jurkat

value: T cell

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V7


title: WT pancreatic cells 3

value: mixed background

value: male


title: YPS606 hog1Δ, unstressed control (0 min), replicate 1

description:
Library name: YPS606_hog1del_CTRL_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_CTRL_rep1

value: budding yeast cells

value: unstressed control (0 min)


title: YPS606 hog1Δ, unstressed control (0 min), replicate 3

description:
Library name: YPS606_hog1del_CTRL_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_CTRL_rep3


title: YPS606 hog1Δ, unstressed control (0 min), replicate 2

description:
Library name: YPS606_hog1del_CTRL_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_hog1del_CTRL_rep2


title: WT pancreatic cells 2

value: normal


title: WT pancreatic cells 4

value: wt


title: Jurkat, TRAIL-treated, input

description: Library name: TRAIL_input

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V6

value: TRAIL treatment


title: WT pancreatic cells 5

value: female


title: 5A4 NP1 BasA complement induced replicate 2

description: Library name: B06

value: bacterial


title: YPS606 wild-type, 5% (v/v) ethanol (30 min), replicate 4

description:
Library name: YPS606_WT_EtOH_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_EtOH_rep4

value: wild-type (HOG1/HOG1)

value: 5% (v/v) ethanol (30 min)


title: S_Ahypo_R3

city: Irapuato

first: Alfredo

middle: Heriberto

last: Herrera

state: Guanajuato

address: Libr.  Norte Carr. Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

description:
Library name: SAMPLE 18
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:S_Ahypo_R3

data_processing:
EdgeR package
The overrepresented sequences (OVERrepseq1.fasta) and the quality of the raw reads were determined using the FASTQC program (Andrews 2010). Low-quality reads (QC<20) and overrepresented sequences were trimmed with TRIMMOMATIC
Transcriptome assemblies of A. hybridus and A. hypochondriacus were obtained using TRINITY v2.1.1 with –normalize_reads and --trimmomatic default parameters. Transcripts redundancy from trinity “genes” was filtered with CD-HIT at 90% of identities on the sequences
High-quality reads of each library were mapped using (BOWTIE v2.3.0 very sensitive parameters to the transcriptome of A. hybridus or A. hypochondriacus, respectively. An in-house script was used to count unique reads from the SAM files. A table count reads matrix was constructed in an R environment and used to obtain the differentially expressed genes (DEG) Pairwise analysis of stressed (drought or salinity) plant samples vs control plant samples.
Assembly: Transcrptome assembly in this project for both species
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Amaranthus hypochondriacus

source_name: Leaves

growth_protocol: Amaranthus hypochondriacus cv. Nutrisol and Amaranthus hybridus lines were obtained from the National Institute of Forestry, Agricultural and Livestock Research (INIFAP), Texcoco, Mexico. Seeds were placed on a sterile wet substrate (BM2 Germination Mix, Berger, CA) at 4 °C for 12 h. Subsequently, they were transferred to a growth chamber at 25 °C and cycles of 12 h light/dark cycles. After 11 days in the growth chamber, the seedlings were transferred to a greenhouse in plastic pots 10 cm in diameter and 20 cm high; 12-15 plants per species were placed for each of the three experimental groups: control, drought, and salinity

extract_protocol:
Total RNA samples were extracted from three biological replicates of leaves stressed (salinity or drought) and non-stressed (watered) plants using the TRIZol protocol specified by the manufacturer (Invitrogen, GIBCO-BLR)
TruSeq libraries of all samples were sequenced by the Illumina NextSeq 500 1x75 HIGH at the LANGEBIO facilities

treatment_protocol: Control plants were watered every third day during the 19 days after entering the greenhouse (until they were one month old), and treatments were started. For saline stress, 100 ml of 0.15 M NaCl was applied daily for 7 days, 100 ml of 0.3 M NaCl for the next four days, and 100 ml of 0.5 M NaCl during the last three days. The plants subjected to water stress were kept without irrigation during the 14 days of the treatment. Three biological replicates of mature non-senescent leaves were collected (leaves 5, 6, and 7 from the plant´s apex).

value: Leaves

value: Wild Type

value: Drought


title: WT pancreatic cells 1


title: Jurkat, mock-treated, input

description: Library name: Mock_input

value: Jurkat

value: T cell

value: Endogenous TFIIB siRNA, expressing si-RNA resistant 6xHis-TFIIB-V5


title: 5A4 NP1 induced replicate 2

description: Library name: B04

value: Parent

value: induced


title: 5A4 NP1 BasA mutant uninduced replicate 3

description: Library name: C02

value: BasA mutant

value: uninduced


title: YPS606 wild-type, 5% (v/v) ethanol (30 min), replicate 2

description:
Library name: YPS606_WT_EtOH_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_EtOH_rep2

value: budding yeast cells


title: S_Ahypo_R1

description:
Library name: SAMPLE 16
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:S_Ahypo_R1


title: YPS606 wild-type, 5% (v/v) ethanol (30 min), replicate 3

description:
Library name: YPS606_WT_EtOH_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_EtOH_rep3


title: S_Ahypo_R2

description:
Library name: SAMPLE 17
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:S_Ahypo_R2


title: SA_Ahypo_R3

description:
Library name: SAMPLE 12
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:SA_Ahypo_R3

value: Salinity


title: 5A4 NP1 BasA mutant induced replicate 2

description: Library name: B05


title: hiPSC-derived teratoma 4w

city: Tokyo

first: Yusuke

last: Soma

address: Haneda-kuko 1-1-4, Ota-ku

institute: Fujita Health University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.38 tool.
The reads were mapped using STAR 2.7.5c (GitHub, San Francisco, CA, USA).
The reads assigned to the hg38 reference were classified as human reads, and all samples were separated into human and mouse reads.
The aligned reads were subjected to downstream analyses using StrandNGS 3.4 software (Agilent Technologies, Inc.).
The read counts allocated for each gene and transcript (Ensembl Database 2016.12.01) were quantified using a Transcripts Per Million (TPM) method.
Assembly: hg38 and mm10
Supplementary files format and content: An excel file includes raw counts and TPM values for all samples.

source_name: hiPSC-derived teratoma

growth_protocol: hiPSCs were maintained in the modified StemFit medium AS103C.

extract_protocol:
Total RNA was extracted using miRNeasy Micro Kit (QIAGEN, Hilden, Germany).
Total RNA obtained from each sample was subjected to a sequencing library construction using SMART-Seq Stranded Kit (Takara Clontech, Shiga, Japan) according to the manufacturer’s protocols.

treatment_protocol: On day 0, hiPSCs were incubated with RPMI-1640 supplemented with 2% B27 supplement without insulin, 6 μM CHIR99021, and 1 ng/mL bone morphogenic protein 4 for 1 day. On day 3, the cells were incubated with RPMI-1640 supplemented with B27 supplement without insulin and 5 μM IWR-1. On day 6, the cells were incubated with RPMI-1640 supplemented with B27 supplement without insulin.  On day 7, the cells were incubated in MEM-α  supplemented with 5% FBS and 2 mM sodium pyruvate. On day 10, the cells were resuspended in MEM-α supplemented with 5% FBS, 2 mM sodium pyruvate, and 6 μM Orlistat. The cells were plated in dishes coated with collagen type I. On day 13, the culture medium was replaced with glucose- and glutamine-free media supplemented with 4 mM lactate, the modified StemFit medium AS501. On days 14–16, the medium was replaced daily with the AS501 medium. On day 17, the cells were dispensed into microtubes for cryopreservation using CryoStor CS10.

value: hiPSC-derived teratoma

value: 253G4 hiPSC

value: hiPSC-teratoma cells


title: hiPSC-derived teratoma 12w


title: 5A4 NP1 BasA complement uninduced replicate 2

description: Library name: B03

value: bacterial

value: BasA complement


title: YPS606 wild-type, 0.4 mM H2O2 (30 min), replicate 4

description:
Library name: YPS606_WT_H2O2_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_H2O2_rep4

value: wild-type (HOG1/HOG1)


title: hiPSC-CM tissue 12w No3

source_name: hiPSC-CM tissue

value: hiPSC-CM tissue

value: hiPSC-cardiomyocytes


title: SA_Ahypo_R1

description:
Library name: SAMPLE 10
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:SA_Ahypo_R1

value: Leaves

value: Wild Type


title: 5A4 NP1 BasA mutant uninduced replicate 2

description: Library name: B02


title: 5A4 NP1 uninduced replicate 2

description: Library name: B01


title: SA_Ahypo_R2

description:
Library name: SAMPLE 11
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:SA_Ahypo_R2


title: YPS606 wild-type, 0.4 mM H2O2 (30 min), replicate 3

description:
Library name: YPS606_WT_H2O2_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_H2O2_rep3


title: hiPSC-CM tissue 4w No1


title: 5A4 NP1 uninduced replicate 3

description: Library name: C01


title: hiPSC-derived teratoma 2w


title: Ahypo_R3

description:
Library name: SAMPLE 6
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:Ahypo_R3

value: Control


title: YPS606 wild-type, 0.4 mM H2O2 (30 min), replicate 1

description:
Library name: YPS606_WT_H2O2_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_H2O2_rep1


title: hiPSC-CM tissue 12w No2


title: 5A4 NP1 BasA complement induced replicate 1

description: Library name: A06


title: 5A4 NP1 BasA mutant induced replicate 1

description: Library name: A05


title: Ahypo_R2

description:
Library name: SAMPLE 5
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:Ahypo_R2


title: hiPSC-CM tissue 2w


title: hiPSC-CM tissue 4w No2


title: Ahypo_R1

description:
Library name: SAMPLE 4
Raw_Counts_AhypoEs.txt
Column names in Raw_Counts .txt file:Ahypo_R1


title: YPS606 wild-type, 5% (v/v) ethanol (30 min), replicate 1

description:
Library name: YPS606_WT_EtOH_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_EtOH_rep1

value: 5% (v/v) ethanol (30 min)


title: YPS606 wild-type, 0.4 M NaCl (45 min), replicate 4

description:
Library name: YPS606_WT_NaCl_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_NaCl_rep4

value: 0.4 M NaCl (45 min)


title: YPS606 wild-type, 0.4 M NaCl (45 min), replicate 3

description:
Library name: YPS606_WT_NaCl_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_NaCl_rep3


title: hiPSC-CM tissue 12w No1


title: YPS606 wild-type, 0.4 M NaCl (45 min), replicate 2

description:
Library name: YPS606_WT_NaCl_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_NaCl_rep2


title: 5A4 NP1 BasA mutant uninduced replicate 1

description: Library name: A02

value: BasA mutant


title: YPS606 wild-type, 0.4 mM H2O2 (30 min), replicate 2

description:
Library name: YPS606_WT_H2O2_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_H2O2_rep2


title: YPS606 wild-type, 0.4 M NaCl (45 min), replicate 1

description:
Library name: YPS606_WT_NaCl_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_NaCl_rep1


title: 5A4 NP1 induced replicate 1

description: Library name: A04

value: Parent

value: induced


title: 5A4 NP1 BasA complement uninduced replicate 1

description: Library name: A03

value: uninduced


title: scRNA_Seq_KD_2_28dpi

first: Jaime

last: Diaz-Larrosa

state: Baden Württemberg

address: INF 580

department: Epigenetics

institute: DKFZ

description:
Library name: scRNA_Seq_sample5
10X genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed with the CellRanger v4.0.0 software including intronic counts and using Seurat v4.3.0 and SeuratObject v4.1.3
Seurat objects were initialized with a minimum of 3 cells and 100 features per cell as well as default parameters for the rest of the functions. Cells with more than 5 % of mitochondrial counts as well as over 2000 or less than 20 unique feature counts were filtered out.
Data were then normalized with a scale factor of 10,000 and highly variable features were identified with the vst method, selecting the top 2,000 features for downstream analysis. Data scaling was performed with 50 principal components, leading to the selection of 9 or 11 dimensions for downstream Resolutions ≤ 0.1 were used throughout the analysis.
The most differentially expressed genes between the detected clusters were identified using the FindAllMarkers function considering genes present in a minimum fraction of 25% of the cells. These genes were then used for cluster identification and the top 5 genes of each identified cluster were considered as the respective gene signature.
Assembly: pvir_genome_ncbi_v1.0
Supplementary files format and content: Tab separated values files and matrix files

organism: Procambarus virginalis

source_name: Hemolymph

extract_protocol:
Hemolymph was extracted 28 days post injection and after a short centrifugation step to remove other components, individual cells were ressupended in PBS
10,000 cells per sample were processed with the Chromium Single Cell Reagent Kit (10X genomics, v3.1 chemistry) according to manufacturer’s protocol

treatment_protocol: dsRNA for control (GFP) or Dnmt1 were injected into the hemolymph stream of crayfish animals

value: Hemolymph

value: Hemocytes

value: Dnmt1 Knockdown

value: dsDnmt1 injection


title: 5A4 NP1 uninduced replicate 1

description: Library name: A01

value: bacterial


title: YPS606 wild-type, unstressed control (0 min), replicate 4

description:
Library name: YPS606_WT_CTRL_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_CTRL_rep4

value: budding yeast cells

value: wild-type (HOG1/HOG1)

value: unstressed control (0 min)


title: Mouse_Heart_HFD_PPARa_ChIP-seq

city: Newark

first: Jiyeon

last: Park

state: NJ

address: 185 South Orange Ave.

department: Department of Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

description: Library name: HFD_PPARa

data_processing:
Raw reads were aligned to the mm10 reference genome using Bowtie2 after adapter and quality trimming.
MACS3 was used to call peaks from aligned BAM files. Peak annotations were conducted using the ChIPseeker package in R. BAM files were converted to bedGraph and bigWig using bedtools and UCSC tools.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) files were generated for visualization on the UCSC Genome Browser.

source_name: heart

growth_protocol: Mice were fed a high-fat diet (60 kcal%) or a control normal diet for 1 month.

extract_protocol:
Heart tissues were cross-linked and chromatin was fragmented. Immunoprecipitation was performed using anti-PPARa, anti-RelA, and anti-p50 antibodies.
ChIP and library preparation were performed by Active Motif using the FactorPath™ service. Libraries were constructed from immunoprecipitated DNA following standard protocols and sequenced on the Illumina HiSeq 2500 platform.

treatment_protocol: High-fat diet consumption to induce diastolic dysfunction and elevate plasma free fatty acids.

value: heart

value: wild-type

value: High-fat diet

value: anti-PPARa


title: Mouse_Heart_HFD_p50_ChIP-seq

description: Library name: HFD_p50


title: YPS606 wild-type, unstressed control (0 min), replicate 3

description:
Library name: YPS606_WT_CTRL_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_CTRL_rep3


title: scRNA_Seq_Control_3_28dpi

description:
Library name: scRNA_Seq_sample3
10X genomics

value: Control

value: dsGFP injection


title: Mouse_Heart_ND_PPARa_ChIP-seq

description: Library name: ND_PPARa

value: Normal Diet


title: scRNA_Seq_Control_2_28dpi

description:
Library name: scRNA_Seq_sample2
10X genomics


title: Mouse_Heart_ND_p50_ChIP-seq

description: Library name: ND_p50


title: Control_2_RNAseq

description:
Library name: RNA_Seq_sample2
Column name: Control_2

data_processing:
Raw data were processed using Hisat2 (v2.2.1) and counts produced using feature counts
Genes with low counts (< 10 across all samples) were filtered out and differential expression analysis was done using DESeq
Assembly: pvir_genome_ncbi_v1.0
Supplementary files format and content: TPM values. Tab separated.

extract_protocol:
28 days post injection animals were bled.  Hemocyte RNA was purified using the RiboPure kit (Invitrogen, #AM1924) and processed using the RNA clean-up and concentrator kit (Zymo Research, #R1013)
TruSeq stranded


title: YPS606 wild-type, unstressed control (0 min), replicate 1

description:
Library name: YPS606_WT_CTRL_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_CTRL_rep1


title: YPS606 wild-type, unstressed control (0 min), replicate 2

description:
Library name: YPS606_WT_CTRL_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: YPS606_WT_CTRL_rep2


title: scRNA_Seq_KD_3_28dpi

description:
Library name: scRNA_Seq_sample6
10X genomics


title: scRNA_Seq_Control_1_28dpi

description:
Library name: scRNA_Seq_sample1
10X genomics


title: Dehalococcoides mccartyi, 1,2,4-TCB, rep3

status: Public on Jan 28 2026

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

description: Library name: EA_1_2_4_TCB_rep3

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v1.15 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of processed reads to Dehalococcoides mccartyi CBDB1 reference genome using segemehl (Hoffmann et al., 2009) v0.3.4 with READemption (Förstner et al., 2014) v2.0.3 (parameters: align -l 12 -a 95)
Coverage calculation via READemption coverage
Calculation of raw read counts via READemption (parameters: gene_quanti -o 10 --features "CDS,riboswitch,RNase_P_RNA,rRNA,tmRNA,tRNA,sRNA")
Differential expression analysis via DESeq2 (Love et al., 2014) v1.24.0 with fold-change shrinkage applied by setting the parameter betaPrior to TRUE
Normalization of raw coverage files by DESeq2 size factors
Assembly: GCF_000009025.1
Supplementary files format and content: Character (TAB) separated value file containing raw read counts (Raw_count_table.csv)
Supplementary files format and content: Coverage files in wiggle format (*.wig) normalized by DESeq2 size factors

organism: Dehalococcoides mccartyi CBDB1

source_name: Dehalococcoides mccartyi cells

growth_protocol: CBDB1 cells were cultivated anaerobically at 30 °C in 200 ml serum bottles in 150 ml of Ti(III)-citrate-reduced (1.5 mM), carbonate-buffered synthetic medium. The medium was inoculated to a cell amount of 1 x 10^7 cells ml^-1. Hydrogen served as electron donor and acetate (5 mM) as carbon source (Adrian et al. 2000). The cultures were overlaid with the electron acceptor 1,2,3-TCB or 1,2,4-TCB dissolved in hexadecane (400 mM) to a nominal concentration of 10 mM. The cultures were harvested in the transition phase.

extract_protocol:
For RNA extraction the Total RNA Mini Kit (A&A BIOTECHNOLOGY) was used. The RNA was eluted with 100 µl distilled, diethylpyrocarbonate treated H20, treated with DNase I (NEB) to remove remaining DNA and stored at -80°C. For RNA precipitation 2.5 M ammonium acetate and 3.5 vol. of 99 % ethanol were added to 100 µl RNA suspension. The mix was stored at -80 °C for at least 30 min. The RNA was pelleted by centrifugation at 21.400 x g for 20 min at 4°C. Then the pellet was washed with ice cold ethanol (70 %) and dried. The dried pellet was stored at -80°C until shipping.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). cDNA libraries suitable for sequencing were prepared from 400 ng of total RNA after DNase I treatment (Thermo Fisher). RNAs were fragmented using Mg2+ ions 2 min 45 sec (NEBNext Magnesium RNA fragmentation module) and were treated with T4 PNK for phosphorylation/dephosphorylation and RppH for decapping followed by NEBNext® Multiplex Small RNA Library Prep (New England Biolabs). 15 PCR cycles were performed with 15 sec elongation time. Libraries were quantified by QubitTM dsDNA HS Assay Kit 3.0 Fluorometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies) before pooling.

treatment_protocol: The cell suspension (100 ml) was first pelleted at 3661 x g for 45 min and 4°C, then the cells were resuspended in 2 ml of the supernatant and transferred to 2 ml Eppendorf tubes to be pelleted at 9520 x g and 4 °C for 30 min. The CBDB1 cell pellets in 100 µl remaining supernatant were stored at -80°C until further processing.

value: Dehalococcoides mccartyi cells

tag: electron acceptor

tag: replicate


title: KD_2_RNAseq

description:
Library name: RNA_Seq_sample4
Column name: KD_2


title: Mouse_Heart_HFD_RelA_ChIP-seq

description: Library name: HFD_RelA

value: anti-RelA


title: scRNA_Seq_KD_1_28dpi

description:
Library name: scRNA_Seq_sample4
10X genomics

value: Hemolymph


title: Dehalococcoides mccartyi, 1,2,3-TCB, rep1

description: Library name: EA_1_2_3_TCB_rep1


title: Gracie OMX treated - 2

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Library name: Gracie-Treated-2

data_processing:
Illumina sequence reads were mapped to CanFam3.1 genome for Garcie canine cell line and mm39 genome for DLM8 mouse cell lines using STAR aligner with default settings
FeatureCount tool from subread package was used to extract raw gene count data
Assembly: CanFam3.1 for canine and GRCm39 for mouse cell line data mapping
Supplementary files format and content: Excel file include gene level raw count values for treated and control cell lines for both canine and mouse: Canine_Mouse_CellLines_Raw_CountData.xlsx

organism: Canis lupus familiaris

source_name: Gracie

growth_protocol: All cells were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, MEM Vitamin solution, 2 mM L-glutamine, 1 mM sodium pyruvate, non-essential amino acids, and antibiotic/antimycotic solution, in a 37°C humidified atmosphere of 5% CO2 and serially passaged by trypsinization.

extract_protocol:
Cells were washed with PBS, then lysed in plate using the RNeasy  RLT buffer with 2-mercaptoethanol.  The lysate was then applied to QIAshredder before completing the RNeasy protocol with DNase digestion as per manufacturer’s recommendations.
The mRNA-seq libraries were generated from 200 ng of total RNA using the Universal Plus™ mRNA-Seq with NuQuant® kit following the manufacturer’s instructions. Briefly, RNA underwent poly(A) selection, fragmentation, cDNA synthesis, end repair, adapter ligation with Unique Dual Indexes (UDIs), and PCR amplification, yielding Illumina-ready libraries

treatment_protocol: Cells were plated overnight in 6-well plate at 50% confluency.  The following day, media was replaced with media containing 50 nM OMXor DMSO control.

value: Gracie

value: osteosarcoma

value: WT

value: 50 nM OMX, 6 hours


title: Control_1_RNAseq

description:
Library name: RNA_Seq_sample1
Column name: Control_1

value: Hemocytes


title: Dehalococcoides mccartyi, 1,2,4-TCB, rep1

description: Library name: EA_1_2_4_TCB_rep1


title: Dehalococcoides mccartyi, 1,2,3-TCB, rep2

description: Library name: EA_1_2_3_TCB_rep2


title: Gracie OMX treated - 1

description: Library name: Gracie-Treated-1


title: Gracie OMX treated - 3

description: Library name: Gracie-Treated-3


title: Mouse_Heart_ND_RelA_ChIP-seq

description: Library name: ND_RelA


title: Gracie untreated - 2

description: Library name: Gracie-Control-2

value: Untreated


title: D6

type: RNA

city: Jinan

first: Yunhong

last: Zhang

state: Shandong

address: No. 4655, Daxue Road, Changqing District, Jinan, Shandong

institute: Shandong University of Traditional Chinese Medicine

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression (4*180K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: PBMC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Venous blood samples were obtained after overnight fasting at study inclusion. Samples were processed within 4 h of collection. PBMCs were isolated by Ficoll density-gradient centrifugation.

value: whole blood

value: female

tag: age


title: Gracie untreated - 1

description: Library name: Gracie-Control-1


title: D1

value: male


title: Dehalococcoides mccartyi, 1,2,3-TCB, rep3

description: Library name: EA_1_2_3_TCB_rep3


title: Dehalococcoides mccartyi, 1,2,4-TCB, rep2

description: Library name: EA_1_2_4_TCB_rep2


title: C3


title: D4


title: C6


title: D3


title: D5


title: MDA-MB-231- MSCV-control-CLM296-replicate 3

city: Halifax

first: Paola

last: Marcato

state: NS

address: 5850 College street

country: Canada

institute: Dalhousie University

description:
Library name: n3_MSCV_CLM296
colunm name in featurecounts.csv:n3_MSCV_CLM296

data_processing:
Fastqc-for quality check
cutadapt for Trimming adapters
STAR - for alignment
featurecounts for rpkm counts
Assembly: hg38
Supplementary files format and content: comma separated file contains counts for all samples
Supplementary files format and content: tab limited file for RPKM of individual samples

source_name: Breast

extract_protocol:
RNA was extracted using Invitrogen Purelink Total RNA extraction kit
Stranded poly(A) mRNA library preparation (NEBNext)

value: Breast

value: Triple negative breast cancer cells

value: Overexpression control


title: MDA-MB-231- MSCV-control-No treatment-replicate 3

description:
Library name: n3_MSCV
colunm name in featurecounts.csv:n3_MSCV

value: No Treatment


title: MDA-MB-231- ALDH1A3 overexpression-CLM296-replicate 3

description:
Library name: n3_OE_CLM296
colunm name in featurecounts.csv:n3_OE_CLM296

value: ALDH1A3 Overexpression


title: MDA-MB-231- ALDH1A3 overexpression-CLM296-replicate 2

description:
Library name: n2_OE_CLM296
colunm name in featurecounts.csv:n2_OE_CLM296


title: D2


title: MDA-MB-231- MSCV-control-CLM296-replicate 1

description:
Library name: n1_MSCV_CLM296
colunm name in featurecounts.csv:n1_MSCV_CLM296


title: MDA-MB-231- MSCV-control-CLM296-replicate 2

description:
Library name: n2_MSCV_CLM296
colunm name in featurecounts.csv:n2_MSCV_CLM296


title: C2


title: MDA-MB-231- MSCV-control-No treatment-replicate 1

description:
Library name: n1_MSCV
colunm name in featurecounts.csv:n1_MSCV


title: MDA-MB-231- MSCV-control-No treatment-replicate 2

description:
Library name: n2_MSCV
colunm name in featurecounts.csv:n2_MSCV


title: C1


title: MDA-MB-231- ALDH1A3 overexpression-No treatment-replicate 2

description:
Library name: n2_OE
colunm name in featurecounts.csv:n2_OE


title: MDA-MB-231- ALDH1A3 overexpression-No treatment-replicate 1

description:
Library name: n1_OE
colunm name in featurecounts.csv:n1_OE


title: PEO1, pLKO.1, Fulvestrant, 48h, 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 8_PEO1-pLKO1-10-uM-Fulvestrant-48h-2_8_S8

data_processing:
QC was performed with MultiQC and reads were trimmed to remove the adapters from reads using cutadapt. RNA-seq data was aligned using bowtie2 algorithm via RSEM V1.3.3 software to estimate read counts using gene information from Ensemble transcriptome version GRCh37.
Assembly: Human Hg19
Supplementary files format and content: Text formatted RSEM gene expression raw counts

growth_protocol: RPMI-1640, 10% FBS, 1% pen/strep, 2 μg/mL puromycin.

extract_protocol:
Total RNA was extracted from cells using QIAshredder columns (QIAGEN) and RNeasy Mini kit (QIAGEN), followed by DNase digestion.
Libraries for RNA sequencing were prepared using the Stranded mRNAseq Library Preparation kit (Illumina, San Diego, CA) as per manufacturer’s instructions starting with an input of 500 ng of RNA and 9 cycles of final PCR amplification.  Library size was assessed using the 4200 Tapestation and the High-sensitivity DNA 5000 assay (Agilent, Santa Clara, CA).

treatment_protocol: Cell were treated with or without 10 μM Fulvestrant combined with 100 pM E2 for 48 hours.

value: Ovarian cancer cell

value: Fulvestrant


title: MDA-MB-231- ALDH1A3 overexpression-CLM296-replicate 1

description:
Library name: n1_OE_CLM296
colunm name in featurecounts.csv:n1_OE_CLM296


title: MDA-MB-231- ALDH1A3 overexpression-No treatment-replicate 3

description:
Library name: n3_OE
colunm name in featurecounts.csv:n3_OE


title: Gracie untreated - 3

description: Library name: Gracie-Control-3


title: C4


title: PEO1, pLKO.1, Fulvestrant, 0h, 3

description: Library name: 3_PEO1-pLKO1-0h-3_3_S3

value: unt


title: PEO1, pLKO.1, Fulvestrant, 48h, 3

description: Library name: 9_PEO1-pLKO1-10-uM-Fulvestrant-48h-3_9_S9


title: PEO1, pLKO.1, Fulvestrant, 48h, 1

description: Library name: 7_PEO1-pLKO1-10-uM-Fulvestrant-48h-1_7_S7


title: PEO1, pLKO.1, Fulvestrant, 0h, 2

description: Library name: 2_PEO1-pLKO1-0h-2_2_S2


title: PEO1, pLKO.1, Fulvestrant, 0h, 1

description: Library name: 1_PEO1-pLKO1-0h-1_1_S1


title: PEO1, shp53, Fulvestrant, 0h, 2

description: Library name: 11_PEO1-shp53-0h-2_11_S11


title: PEO1, shp53, Fulvestrant, 48h, 1

description: Library name: 16_PEO1-shp53-10-uM-Fulvestrant-48h-1_16_S16


title: PEO1, shp53, Fulvestrant, 0h, 3

description: Library name: 12_PEO1-shp53-0h-3_12_S12


title: PEO1, shp53, Fulvestrant, 48h, 3

description: Library name: 18_PEO1-shp53-10-uM-Fulvestrant-48h-3_18_S18


title: Group Squashed

first: Dennis

last: Discher

state: Pennsylvania

address: 129 Towne Bldg

institute: University of Pennsylvania

description:
Library name: Squashed
10X Genomics

data_processing:
All analysis was performed using R 4.3.2 & RStudio 2.23.12.1+402
Assembly: GRCh38
Supplementary files format and content: .fastq

source_name: Lung

extract_protocol:
A549 (CCL-185) were confined or not using Polydimethylsiloxane (PDMS, RTV615-010) micropillars
the Chromium Single Cell Gene Expression kit (v3.1, single index, Catalog no. PN-1000128; PN-1000127; PN-1000213) from 10X Genomics per the manufacturer's instructions.

value: Lung

value: Epithelial

value: adenocarcinoma

value: Squashed


title: PRMS_R1_43_baseline

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

description:
Library name: PRMS_R1_43_baseline
colnames in paired_1L_geneCounts.txt : PRMS_R1_43_baseline

data_processing:
Mayo Analysis Pipeline for RNA-seq (MAP-RSeq, version 3.1.4) was used to process raw RNA-Seq fastq data, including read alignment, quality control, and gene expression quantification.
Assembly: GRCh38 (hg38)
Supplementary files format and content: paired_1L_geneCounts.txt
Supplementary files format and content: paired_1L_FPKM.txt

source_name: tumor

growth_protocol: Protocol-defined 1L therapy was letrozole 2.5 mg/day on days 1-28 with palbociclib 125 mg on days 1-21 of a 28-day cycle. Palbociclib dose reductions were made in accordance with FDA guidelines. For premenopausal patients, an LHRH agonist (goserelin 3.6 mg or leuprolide 3.75-7.5 mg) was required on day 1 of each treatment cycle.

extract_protocol: RNA libraries were prepared according to the manufacturer's instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). Tempus xR assays were used for whole-exome capture sequencing.

treatment_protocol: RNA was isolated from the frozen tissue biopsies using Qiagen miRNeasy mini kit. The quality of the RNA was assessed by using the Agilent Bioanalyzer 2100.

value: tumor

value: baseline


title: KD_1_RNAseq

city: Heidelberg

description:
Library name: RNA_Seq_sample3
Column name: KD_1

value: Hemolymph

value: Hemocytes

value: Dnmt1 Knockdown

value: dsDnmt1 injection


title: AF SI DC2

city: Suwon

first: Jaeu

last: Yi

state: Gyeonggi-do

address: 206, World cup-ro

department: Department of Biological Science

country: South Korea

institute: Ajou University

description: Library name: AF2

data_processing:
Illumina Casava1.8 software used for basecalling.
Assembly: RNA-seq reads were aligned to mouse reference transcriptome build mm10 (M10, GRCm38.p4) from GENCODE (http://www.gencodegenes.org/mouse_releases/10.html)
Supplementary files format and content: Fragments Per Kilobase Million (FPKM) were calculated by RSEM with default parameters.
Supplementary files format and content: Differentially expressed genes were identified by edgeR-3.16.5 [49] given absolute fold change > 2 and FDR < 10-3

source_name: small intestinal lamina propria

extract_protocol:
DCs were purified with flow cytometory sorting and RNA was harvested with trizol. Illumina TruSeq RNA sample prep kit was used with 1ug of total RNA for the construction of sequencing libararies.
RNA libraries were prepared for sequencing using standard Illumina protocol

value: small intestinal lamina propria

value: dendritic cells

value: SILP DC


title: PRMS_R1_43_progression

description:
Library name: PRMS_R1_43_progression
colnames in paired_1L_geneCounts.txt : PRMS_R1_43_progression

value: progression


title: PRMS_R1_30_progression

description:
Library name: PRMS_R1_30_progression
colnames in paired_1L_geneCounts.txt : PRMS_R1_30_progression


title: PRMS_R1_31_baseline

description:
Library name: PRMS_R1_31_baseline
colnames in paired_1L_geneCounts.txt : PRMS_R1_31_baseline


title: PEO1, shp53, Fulvestrant, 0h, 1

description: Library name: 10_PEO1-shp53-0h-1_10_S10

value: Ovarian cancer cell


title: PRMS_R1_28_baseline

description:
Library name: PRMS_R1_28_baseline
colnames in paired_1L_geneCounts.txt : PRMS_R1_28_baseline


title: PANC1_LND_3_24h

city: Duarte

first: James

last: Figarola

address: 1500 E. Duarte Road

department: Diabetes-Metabo Res Inst-BRI

institute: City of Hope

description:
Library name: PANC1_LND_3_24h
read_counts_PANC1.txt

data_processing:
Illumina PartekFlow v12.9.1
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files. Sequence reads were trim from both 5' or 3' ends by filtering quality score less than 29; mapped  to GRCh38/hg38 using STAR v2.7.8a with validation of quality through pre-alignment and post-alignment quality assurance (QA)/quality control (QC) using Partek Flow
Aligned reads were further subjected to quantification using the Partek E/M algorithm using hg38 - Ensembl Transcripts release 114,  perform noise deduction by filtering counts less than 10; using only protein-coding gene to further normalization and differential gene expression using DESeq2 to compare controls vs treatment.
Assembly: GRCh38/hg38
Supplementary files format and content: Bulk RNAseq raw counts

growth_protocol: PDAC cells were grown in DMEM low glucose containing 10 % Fetal Bovine Serum (FBS ) in humidified atmosphere with 5 % CO2 at 370C overnight .

extract_protocol:
RNA extraction with the RNeasy Mini kit ( Qiagen ). 250 ng of total RNA per sample was used to prepare the libraries. RNA quality control (QC) was performed using the Agilent TapeStation RNA Tape, confirming RIN > 7.
Sequencing libraries were prepared using KAPA mRNA Hyper Prep kit ( Roche, cat. 08098123702)  according to the manufacturer's protocol. Final libraries were validated using the Agilent Bioanalyzer DNA High Sensitivity kit  and quantified with Qubit

treatment_protocol: PDAC cells  were treated with  vehicle control , SR4 5 uM  , Lonidamine 300 uM  and their combination for 24 h.

value: pancreatic cancer cell line

value: Lonidamine treated

value: 24 h  Lonidamine treatment


title: PANC1_C_3_24h

description:
Library name: PANC1_C_3_24h
read_counts_PANC1.txt

value: Control

value: 24 h control (vehicle ) treatment


title: PRMS_R1_28_progression

description:
Library name: PRMS_R1_28_progression
colnames in paired_1L_geneCounts.txt : PRMS_R1_28_progression


title: BXPC3_SR4_LND_3_24h

description:
Library name: BXPC3_SR4_LND_3_24h
read_counts_BXPC3.txt

value: SR4 and Lonidamine treated

value: 24 h  SR4 and Lonidamine  treatment


title: PRMS_F1_16_baseline

description:
Library name: PRMS_F1_16_baseline
colnames in paired_1L_geneCounts.txt : PRMS_F1_16_baseline

value: tumor

value: baseline


title: PANC1_SR4_3_24h

description:
Library name: PANC1_SR4_3_24h
read_counts_PANC1.txt

value: SR4 treated

value: 24 h  SR4 treatment


title: PANC1_SR4_LND_3_24h

description:
Library name: PANC1_SR4_LND_3_24h
read_counts_PANC1.txt


title: PRMS_R1_30_baseline

description:
Library name: PRMS_R1_30_baseline
colnames in paired_1L_geneCounts.txt : PRMS_R1_30_baseline


title: BXPC3_SR4_4_24h

description:
Library name: BXPC3_SR4_4_24h
read_counts_BXPC3.txt


title: BXPC3_LND_3_24h

description:
Library name: BXPC3_LND_3_24h
read_counts_BXPC3.txt


title: BXPC3_C_3_24h

description:
Library name: BXPC3_C_3_24h
read_counts_BXPC3.txt


title: PRMS_R1_31_progression

description:
Library name: PRMS_R1_31_progression
colnames in paired_1L_geneCounts.txt : PRMS_R1_31_progression


title: PRMS_F1_16_progression

description:
Library name: PRMS_F1_16_progression
colnames in paired_1L_geneCounts.txt : PRMS_F1_16_progression


title: PEO1, shp53, Fulvestrant, 48h, 2

description: Library name: 17_PEO1-shp53-10-uM-Fulvestrant-48h-2_17_S17

value: Fulvestrant


title: Group Control

description:
Library name: Control
10X Genomics

value: Lung

value: Epithelial

value: adenocarcinoma


title: PANC1_SR4_LND_2_24h

description:
Library name: PANC1_SR4_LND_2_24h
read_counts_PANC1.txt


title: PANC1_LND_2_24h

description:
Library name: PANC1_LND_2_24h
read_counts_PANC1.txt


title: BXPC3_SR4_2_24h

description:
Library name: BXPC3_SR4_2_24h
read_counts_BXPC3.txt


title: BXPC3_SR4_LND_2_24h

description:
Library name: BXPC3_SR4_LND_2_24h
read_counts_BXPC3.txt


title: BXPC3_C_2_24h

description:
Library name: BXPC3_C_2_24h
read_counts_BXPC3.txt


title: BXPC3_LND_2_24h

description:
Library name: BXPC3_LND_2_24h
read_counts_BXPC3.txt


title: DLM8 OMX treated - 3

description: Library name: DLM8-Treated-3

value: osteosarcoma

value: WT

value: 50 nM OMX, 6 hours


title: PANC1_SR4_1_24h

description:
Library name: PANC1_SR4_1_24h
read_counts_PANC1.txt

value: pancreatic cancer cell line


title: PANC1_SR4_2_24h

description:
Library name: PANC1_SR4_2_24h
read_counts_PANC1.txt


title: PANC1_C_2_24h

description:
Library name: PANC1_C_2_24h
read_counts_PANC1.txt


title: C5

value: whole blood

value: female


title: BXPC3_C_1_24h

description:
Library name: BXPC3_C_1_24h
read_counts_BXPC3.txt

value: Control

value: 24 h control (vehicle ) treatment


title: DLM8 OMX treated - 2

description: Library name: DLM8-Treated-2


title: BXPC3_SR4_1_24h

description:
Library name: BXPC3_SR4_1_24h
read_counts_BXPC3.txt


title: DLM8 untreated - 3

description: Library name: DLM8-Control-3

value: Untreated


title: PANC1_LND_1_24h

description:
Library name: PANC1_LND_1_24h
read_counts_PANC1.txt

value: Lonidamine treated

value: 24 h  Lonidamine treatment


title: BXPC3_SR4_LND_1_24h

description:
Library name: BXPC3_SR4_LND_1_24h
read_counts_BXPC3.txt

value: SR4 and Lonidamine treated

value: 24 h  SR4 and Lonidamine  treatment


title: PANC1_C_1_24h

description:
Library name: PANC1_C_1_24h
read_counts_PANC1.txt


title: Peripheral blood sorted CD2 KO CART19

first: Marco

last: Ruella

address: 3400 Civic Center Blvd

description:
Library name: Sample 3
10X Genomics/Azenta

data_processing:
The de-multiplexing, barcoding, mapping,  gene coutning, and aggregation was performed using CellRanger (10X; v5.0.1 or higher)
Assembly: GRCh38
Supplementary files format and content: filtered matrix h5 files for input into Seurat

source_name: peripheral blood (NSG)

extract_protocol:
Library was prepared according to manufacturers instructions for the 10X Genomics 5' v2 Chemistry GEX (+ Feature Barcoding for model 1). User Guide, CG000331 Revision E was used for library preparation steps. DNA quality was assessed prior to NGS via BioAnalyzer High Sensitivity DNA.
scRNA-seq GEX (gene expression)

treatment_protocol: FACS purified CART19 cells were washed 2x in PBS + 0.04% PBS, and then resuspended in the same solution prior to loading onto 10X Genomics chips.

value: peripheral blood (NSG)

value: primary T cell

value: CD2 sgRNA+Cas9


title: Individual Mouse Hashtag - CD2 KO CART19

description:
Library name: Sample 4
10X Genomics/Azenta


title: PANC1_SR4_LND_1_24h

description:
Library name: PANC1_SR4_LND_1_24h
read_counts_PANC1.txt


title: DLM8 OMX treated - 1

description: Library name: DLM8-Treated-1


title: PRMS_R2_66

description:
Library name: PRMS_R2_66
colnames in GeneCounts.txt:PRMS_R2_66

data_processing:
Mayo Analysis Pipeline for RNA-seq (MAP-RSeq, version 3.1.1) was used to process raw RNA-Seq fastq data, including read alignment, quality control, and gene expression quantification.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes CQN normalized gene expression for each sample

extract_protocol:
RNA was isolated from the frozen tissue biopsies using Qiagen miRNeasy mini kit. The quality of the RNA was assessed by using the Agilent Bioanalyzer 2100.
RNA libraries were prepared according to the manufacturer's instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). Tempus xR assays were used for whole-exome capture sequencing.

treatment_protocol: Protocol-defined 1L therapy was letrozole 2.5 mg/day on days 1-28 with palbociclib 125 mg on days 1-21 of a 28-day cycle. Palbociclib dose reductions were made in accordance with FDA guidelines. For premenopausal patients, an LHRH agonist (goserelin 3.6 mg or leuprolide 3.75-7.5 mg) was required on day 1 of each treatment cycle.

value: tumor

value: palbociclib, letrozole


title: PRMS_R1_58

description:
Library name: PRMS_R1_58
colnames in GeneCounts.txt:PRMS_R1_58


title: BXPC3_LND_1_24h

description:
Library name: BXPC3_LND_1_24h
read_counts_BXPC3.txt


title: Mnk3, CRISPRi, scramble, With stimulation, replicate 1, merged

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
Library name: Mnk3i_Scramble_YesDox_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Scramble_YesDox_rep1_merged

data_processing:
Raw paired-end FASTQ files were processed using kallisto (Bray et al., 2016) to quantify transcript abundances against the GRCm39 (mm10) mouse reference transcriptome (GENCODE release M32). An index of the reference transcripts was first built with kallisto index. Transcript-level quantification was then performed for each sample using kallisto quant with 100 bootstrap replicates to estimate technical uncertainty.
Transcript-level abundance estimates were subsequently summarized to the gene level in R using the tximport package (v1.30.0) together with a transcript-to-gene mapping file. Sample metadata, including experimental condition, CRISPR status, and replicate information, were compiled into a metadata table. Gene-level count matrices generated by tximport were then used as input for normalization and differential expression analysis with DESeq2 (v1.38.0).
Assembly: GRCm39
Supplementary files format and content: Raw read count (processed by Kallisto) and used for differential analysis with DESeq
Supplementary files format and content: DESeq design: ~1 + Type + CRISPR + Stim + Stim:CRISPR

source_name: derived from fetal thymocytes

growth_protocol: MNK3 cell lines (NIH Swiss mice; Allan 2015) were cultured in DMEM with glucose/pyruvate/L glutamine supplemented with 10% fetal bovine serum, 1X Penicillin-Streptomycin, 10 ng/ml mouse recombinant IL-2 and IL-7 (R&D Systems), and 50 µM 2-mercaptoethanol. Media for CRISPRi MNK3 (MNK3i) cells contained 10 µg/ml blasticidin S, and media for CRISPRa MNK3 (MNK3a) cells contained 10 µg/ml blasticidin S and 1250 µg/ml hygromycin B. MNK3i/a cells with sgRNA additionally received 2 µg/ml of puromycin.

extract_protocol:
RNA was harvested by spin column (Qiagen RNeasy kit) for RT-qPCR and RNAseq, in triplicate.
Standard polyA selected bulk mRNA seq libraries were generated for Illumina 100bp paired-end sequencing (Illumina platform, University of Cincinnati Genomics, Epigenomics, and Sequencing Core, Cincinnati, OH, USA). RNAseq samples were performed in triplicate.

treatment_protocol: CRISPRi/a Cell Line Generation: MNK3i cells were generated as described in Saini et al (2025 bioRxiv) from parental MNK3. In brief, MNK3 cells were transduced with lentivirus containing pLenti CMV rtTA3 Blast (Addgene #26429), selected by blasticidin S, and then infected with TRE3G-dCas9-KRAB-P2A-mCherry lentivirus. Following incubation with doxycycline, mCherry positive cells were subcloned and Western blot confirmed robust expression of doxycycline-inducible dCas9-KRAB. MNK3a cells were lentivirally engineered from MNK3 to constitutively express the dCas9-VP64 fusion gene (Addgene #61425) and the MS2-p65-HSF1 transactivator complex (Addgene #89308), selected by blasticidin S and hygromycin B, and subcloned. All cells were tested for mycoplasma. Sequences for guides targeting the Cln3 region were based on sgRNA libraries from Horlbeck et al 2016 for MNK3i and Joung et al 2017 for MNK3a (See below). sgRNA non-targeting guides (Scramble) were generated too. sgRNA sequences and their reverse complement were synthesized by Sigma, annealed, and cloned into lenti sgRNA(MS2)_puro optimized backbone (Addgene #73797) for MNK3a or sgOpti (Addgene #85681) for MNK3i using Esp3I digestion as previously described (Moyer and Holland, 2015). sgRNA plasmid integration was confirmed by Sanger Sequencing (Ohio State Comprehensive Cancer Center Genomics Core, Columbus, OH, USA). Lentiviral plasmids pMD2.G (Addgene #12259) and psPAX2 (Addgene #12260) were transfected along with the sgRNA plasmid into HEK293T cells (Mirus TransIT-293T transfection reagent). Lentivirus media was harvested and filtered 48-72hr post-transfection. Puromycin selection began 36hr after lentiviral guide transduction into MNK3i/a cells (polybrene). Bulk transduced populations were used for experiments and maintained in selection antibiotics. RT-qPCR confirmed repression (MNK3i lines after 48hr doxycycline incubation) or overexpression (MNK3a) of target genes relative to Actb and respective scramble control (Trizol RNA isolation; Verso cDNA synthesis).  Cln3 CRISPRi/a Experiments: MNK3i Cln3 (Cln3_63) and Scr (Scr) were incubated with 2 µg/ml doxycycline for 48hr and then stimulated with 10 ng/ml IL-1B and IL-23 (R&D Systems). MNK3a Cln3 (Cln3_56) and Scr (ScrB) were stimulated with 1.5 ng/ml IL-1B and IL-23. Cells were harvested 21hr after cytokine stimulation and stained for intracellular IL-17F and IL-22 (eBioscience IL-22 clone 1H8PWSR and IL-17F clone eBio18F10; BD Life Sciences Cytofix/Cytoperm kit). Expression of IL-17F and IL-22 were assessed on FACSymphony (BD Life Sciences) and compared against respective scramble control.  MNK3i sgRNA: Scramble_Ci_1 GCACTACCAGAGCTAACTCA Scramble_Ci_2 TGAGTTAGCTCTGGTAGTGC Cln3_Ci3363_1 GCACGTGATGGAAGGCTCAC Cln3_Ci3363_2 GTGAGCCTTCCATCACGTGC  MNK3a sgRNA: ScrB_Ca_NT13_1 GCGGTTACCGCGAAAACCAT ScrB_Ca_NT13_2 ATGGTTTTCGCGGTAACCGC Cln3_Ca57756_1 GGAACTCACAGTAAGCTGTG Cln3_Ca57756_2 CACAGCTTACTGTGAGTTCC  RTqPCR Primers (Oltz lab or based on sequences from Origene): Il17f qPCR mF GAAGAAGCAGCCATTGGAGA Il17f qPCR mR TACCTCCCTCAGAATGGCAA Il22 qPCR mF CCGAGGAGTCAGTGCTAAGG Il22 qPCR mR CATGTAGGGCTGGAACCTGT ActB qPCR mF GGCTGTATTCCCCTCCATCG ActB qPCR mR CCAGTTGGTAACAATGCCATGT Cln3_qPCR_mF GGATAGTCGGAGTGTCCTTTGG Cln3_qPCR_mR CTCCTGCTTGAGGATGTCATGG

value: derived from fetal thymocytes

value: Mouse Innate Lymphoid Cell Line

value: Scramble CRISPRi

value: stimulated


title: PRMS_R2_57

description:
Library name: PRMS_R2_57
colnames in GeneCounts.txt:PRMS_R2_57


title: DLM8 untreated - 1

description: Library name: DLM8-Control-1

value: osteosarcoma

value: WT


title: DLM8 untreated - 2

description: Library name: DLM8-Control-2


title: Individual Mouse Hashtag - CD2 WT CART19

description:
Library name: Sample 2
10X Genomics/Azenta

value: mock-electroporation (Cas9 only)


title: Mnk3, CRISPRi, scramble, With stimulation, replicate 2, merged

description:
Library name: Mnk3i_Scramble_YesDox_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Scramble_YesDox_rep2_merged


title: Mnk3, CRISPRi, CLN3, With stimulation, replicate 3, merged

description:
Library name: Mnk3i_Cln3-63_YesDox_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Cln3-63_YesDox_rep3_merged

value: CLN3 CRISPRi


title: PRMS_R2_42

description:
Library name: PRMS_R2_42
colnames in GeneCounts.txt:PRMS_R2_42


title: Mnk3, CRISPRi, scramble, With stimulation, replicate 3, merged

description:
Library name: Mnk3i_Scramble_YesDox_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Scramble_YesDox_rep3_merged


title: PRMS_R1_54

description:
Library name: PRMS_R1_54
colnames in GeneCounts.txt:PRMS_R1_54


title: PRMS_R1_65

description:
Library name: PRMS_R1_65
colnames in GeneCounts.txt:PRMS_R1_65


title: PRMS_R2_63

description:
Library name: PRMS_R2_63
colnames in GeneCounts.txt:PRMS_R2_63


title: Mnk3, CRISPRi, CLN3, With stimulation, replicate 1, merged

description:
Library name: Mnk3i_Cln3-63_YesDox_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Cln3-63_YesDox_rep1_merged


title: Mnk3, CRISPRi, scramble, No stimulation, replicate 3, merged

description:
Library name: Mnk3i_Scramble_NoDox_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Scramble_NoDox_rep3_merged

value: not stimulated


title: Mnk3, CRISPRi, scramble, No stimulation, replicate 1, merged

description:
Library name: Mnk3i_Scramble_NoDox_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Scramble_NoDox_rep1_merged


title: Mnk3, CRISPRi, scramble, No stimulation, replicate 2, merged

description:
Library name: Mnk3i_Scramble_NoDox_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Scramble_NoDox_rep2_merged


title: PRMS_R1_51

description:
Library name: PRMS_R1_51
colnames in GeneCounts.txt:PRMS_R1_51


title: Peripheral blood sorted CD2 WT CART19

description:
Library name: Sample 1
10X Genomics/Azenta


title: PRMS_R1_31

description:
Library name: PRMS_R1_31
colnames in GeneCounts.txt:PRMS_R1_31


title: PRMS_F2_56

description:
Library name: PRMS_F2_56
colnames in GeneCounts.txt:PRMS_F2_56


title: Mnk3, CRISPRa, scramble, With stimulation, replicate 3, merged

description:
Library name: Mnk3a_Scramble_Yes_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Scramble_Yes_rep3_merged

value: Scramble CRISPRa


title: PRMS_R2_53

description:
Library name: PRMS_R2_53
colnames in GeneCounts.txt:PRMS_R2_53


title: Mnk3, CRISPRa, scramble, With stimulation, replicate 1, merged

description:
Library name: Mnk3a_Scramble_Yes_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Scramble_Yes_rep1_merged


title: PRMS_R1_38

description:
Library name: PRMS_R1_38
colnames in GeneCounts.txt:PRMS_R1_38


title: Mnk3, CRISPRi, CLN3, No stimulation, replicate 1, merged

description:
Library name: Mnk3i_Cln3-63_NoDox_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Cln3-63_NoDox_rep1_merged


title: PRMS_R1_50

description:
Library name: PRMS_R1_50
colnames in GeneCounts.txt:PRMS_R1_50


title: Mnk3, CRISPRi, CLN3, No stimulation, replicate 2, merged

description:
Library name: Mnk3i_Cln3-63_NoDox_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Cln3-63_NoDox_rep2_merged


title: Mnk3, CRISPRa, scramble, No stimulation, replicate 3, merged

description:
Library name: Mnk3a_Scramble_No_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Scramble_No_rep3_merged


title: PRMS_R1_25

description:
Library name: PRMS_R1_25
colnames in GeneCounts.txt:PRMS_R1_25


title: Mnk3, CRISPRi, CLN3, With stimulation, replicate 2, merged

description:
Library name: Mnk3i_Cln3-63_YesDox_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Cln3-63_YesDox_rep2_merged


title: PRMS_R1_43

description:
Library name: PRMS_R1_43
colnames in GeneCounts.txt:PRMS_R1_43


title: PRMS_R1_09

description:
Library name: PRMS_R1_09
colnames in GeneCounts.txt:PRMS_R1_09


title: PRMS_R1_30

description:
Library name: PRMS_R1_30
colnames in GeneCounts.txt:PRMS_R1_30


title: Mnk3, CRISPRi, CLN3, No stimulation, replicate 3, merged

description:
Library name: Mnk3i_Cln3-63_NoDox_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3i_Cln3-63_NoDox_rep3_merged


title: PRMS_R1_11

description:
Library name: PRMS_R1_11
colnames in GeneCounts.txt:PRMS_R1_11


title: Mnk3, CRISPRa, scramble, No stimulation, replicate 2, merged

description:
Library name: Mnk3a_Scramble_No_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Scramble_No_rep2_merged


title: Mnk3, CRISPRa, scramble, With stimulation, replicate 2, merged

description:
Library name: Mnk3a_Scramble_Yes_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Scramble_Yes_rep2_merged


title: Mnk3, CRISPRa, scramble, No stimulation, replicate 1, merged

description:
Library name: Mnk3a_Scramble_No_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Scramble_No_rep1_merged


title: PRMS_R1_06

description:
Library name: PRMS_R1_06
colnames in GeneCounts.txt:PRMS_R1_06


title: PRMS_R2_37

description:
Library name: PRMS_R2_37
colnames in GeneCounts.txt:PRMS_R2_37


title: Mnk3, CRISPRa, CLN3, No stimulation, replicate 1, merged

description:
Library name: Mnk3a_Cln3-56_No_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Cln3-56_No_rep1_merged

value: CLN3 CRISPRa


title: PRMS_R1_10

description:
Library name: PRMS_R1_10
colnames in GeneCounts.txt:PRMS_R1_10


title: e14.5 lung AJ BMS 4

city: College Station

first: Masako

last: Suzuki

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

description: Library name: YS16

data_processing:
After checking the quality of the sequencing files using FastQC and trimming low-quality reads and adapter sequences using Cutadapt, the obtained sequences were aligned to the mouse GRCm39 reference genome with the gencode vM36 gene annotation using STAR aligner.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

extract_protocol:
Total RNA was isolated with RNeasy mini kit (QIAGEN).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Pregnant mice were orally administered the inverse pan retinoic acid receptor (RAR) agonist, BMS493 (BMS) (3.75 µg/g/day) (B6688, Sigma-Aldrich) or corn oil from E9.5 to E14.5. Dams were sacrificed for embryonic lung analyses at E14.5.

value: Lung

value: A/J


title: Mnk3, CRISPRa, CLN3, With stimulation, replicate 2, merged

description:
Library name: Mnk3a_Cln3-56_Yes_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Cln3-56_Yes_rep2_merged


title: PRMS_R2_26

description:
Library name: PRMS_R2_26
colnames in GeneCounts.txt:PRMS_R2_26


title: Mnk3, CRISPRa, CLN3, With stimulation, replicate 3, merged

description:
Library name: Mnk3a_Cln3-56_Yes_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Cln3-56_Yes_rep3_merged


title: e14.5 lung B6 BMS 4

description: Library name: YS12


title: PRMS_R1_44

description:
Library name: PRMS_R1_44
colnames in GeneCounts.txt:PRMS_R1_44


title: PRMS_A1_46

description:
Library name: PRMS_A1_46
colnames in GeneCounts.txt:PRMS_A1_46


title: PRMS_R1_28

description:
Library name: PRMS_R1_28
colnames in GeneCounts.txt:PRMS_R1_28


title: PRMS_R2_60

description:
Library name: PRMS_R2_60
colnames in GeneCounts.txt:PRMS_R2_60


title: Mnk3, CRISPRa, CLN3, No stimulation, replicate 3, merged

description:
Library name: Mnk3a_Cln3-56_No_rep3_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Cln3-56_No_rep3_merged


title: Mnk3, CRISPRa, CLN3, No stimulation, replicate 2, merged

description:
Library name: Mnk3a_Cln3-56_No_rep2_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Cln3-56_No_rep2_merged


title: PRMS_R1_35

description:
Library name: PRMS_R1_35
colnames in GeneCounts.txt:PRMS_R1_35


title: e14.5 lung B6 control 3

description: Library name: YS9

value: Control


title: PRMS_A1_18

description:
Library name: PRMS_A1_18
colnames in GeneCounts.txt:PRMS_A1_18


title: e14.5 lung AJ BMS 2

description: Library name: YS8


title: e14.5 lung AJ control 4

description: Library name: YS14


title: Mnk3, CRISPRa, CLN3, With stimulation, replicate 1, merged

description:
Library name: Mnk3a_Cln3-56_Yes_rep1_merged
Column name in CRISPRia_CLN3_raw_counts.txt: Mnk3a_Cln3-56_Yes_rep1_merged


title: e14.5 lung AJ BMS 1

description: Library name: YS7


title: PRMS_R1_36

description:
Library name: PRMS_R1_36
colnames in GeneCounts.txt:PRMS_R1_36


title: PRMS_A1_17

description:
Library name: PRMS_A1_17
colnames in GeneCounts.txt:PRMS_A1_17


title: e14.5 lung  AJ BMS 3

description: Library name: YS15


title: e14.5 lung AJ control 3

description: Library name: YS13


title: PRMS_R2_02

description:
Library name: PRMS_R2_02
colnames in GeneCounts.txt:PRMS_R2_02


title: PRMS_R2_23

description:
Library name: PRMS_R2_23
colnames in GeneCounts.txt:PRMS_R2_23


title: e14.5 lung B6 BMS 3

description: Library name: YS11


title: PRMS_F1_15

description:
Library name: PRMS_F1_15
colnames in GeneCounts.txt:PRMS_F1_15


title: PRMS_R1_19

description:
Library name: PRMS_R1_19
colnames in GeneCounts.txt:PRMS_R1_19


title: PRMS_R1_01

description:
Library name: PRMS_R1_01
colnames in GeneCounts.txt:PRMS_R1_01


title: e14.5 lung B6 control 4

description: Library name: YS10


title: e14.5 lung B6 BMS 1

description: Library name: YS3


title: e14.5 lung AJ control 1

description: Library name: YS5


title: PRMS_R1_14

description:
Library name: PRMS_R1_14
colnames in GeneCounts.txt:PRMS_R1_14


title: hPDLSCs, LTA-treated, rep3

city: Changsha

first: yue

last: guo

address: 139 Renmin Middle Road

institute: the Second Xiangya Hospital

description: Library name: LTA3

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 platform (150 bp paired-end).
Raw reads were processed with Fastp to remove low-quality reads.
Clean reads were aligned to the human genome (hg38) using HISAT2.
Gene expression was quantified as FPKM values.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene across all samples

source_name: hPDLSCs

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA purity was measured using NanoDrop 2000 (Thermo Scientific), and integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit (Vazyme, China) following the manufacturer's instructions.

value: hPDLSCs

value: human periodontal ligament stem cells

value: Enterococcus LTA


title: hPDLSCs, LTA-treated, rep2

description: Library name: LTA2


title: hypoxia

city: Shanghai

first: Peilin

address: 600 Yishan Road

institute: Shanghai Sixth People's Hospital, Shanghai Jiao Tong University

description:
Library name: Sample 1
SeekGene

data_processing:
scRNA-seq data analysis and visualization were performed by SeekSoul® Online (https://seeksoul.online/index.html#/login)
Assembly: Mouse mm10
Supplementary files format and content: R serialized object (.rds) file

source_name: femoral bone

extract_protocol:
For the preparation of single cell suspension from femoral metaphysis, mice femur were dissected and cleared free of soft tissue. The epiphysis was removed gently by forceps and only the 3-mm-long metaphyseal regions from the growth plate were crushed with a mortar and pestle in DMEM medium. The crushed tissue and released cells were digested in 2mg/ml type I collagenase for 30min, filtered through 70μm cell strainer, washed once with ice-cold PBS and resuspended in DMEM medium.
Single-cell RNA-Seq libraries were prepared using SeekOne® DD Single Cell 3’ library preparation kit (SeekGene Catalog No.K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42℃for 90 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme N411-01), analyzed by Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic Qsep400). The libraries were then sequenced on illumina NovaSeq X Plus with PE150 read length.

value: femoral bone

value: female

value: chronic intermittent hypoxia


title: PRMS_F1_20

description:
Library name: PRMS_F1_20
colnames in GeneCounts.txt:PRMS_F1_20

value: tumor

value: palbociclib, letrozole


title: hPDLSCs, Control, rep3

description: Library name: C3

value: WT

value: control (no LTA)


title: e14.5 lung AJ control 2

description: Library name: YS6


title: PRMS_F1_16

description:
Library name: PRMS_F1_16
colnames in GeneCounts.txt:PRMS_F1_16


title: PRMS_R1_22

description:
Library name: PRMS_R1_22
colnames in GeneCounts.txt:PRMS_R1_22


title: e14.5 lung B6 BMS 2

description: Library name: YS4


title: hPDLSCs, Control, rep1

description: Library name: C1


title: e14.5 lung B6 control 2

description: Library name: YS2


title: Healthy MPCs in CKD serum biological replicate 3

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

description: Library name: H_O

data_processing:
Raw FASTQ  files underwent pre-alignment quality control and alignment at novagene using the GRCh38/HG38 reference genome. Differential gene expression analysis was performed in R (v4.4.2) using the DeSeq2 package was calculated comparing CKD and control samples. Raw p-values were adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) step-up method. FDR-adjusted p values less than 0.05 and log2 fold change values <0.5 or >0.5 were used as significance cutoffs.
Assembly: hg38
Supplementary files format and content: tab-delimited excel files include raw counts for each sample

source_name: Skeletal muscle

growth_protocol: MPCs were purified from muscle biopsies from Control participants or patients with CKD following overnight incubation in sterile 1% glucose at 4°C. Biopsy samples collected at Albert Einstein College of Medicine were shipped overnight on wet ice to the University of Kentucky; samples collected from both institutions were incubated ~24hr in sterile 1% glucose at 4°C prior to isolation per our prior methods. Briefly, muscles were minced in F10 containing 10% fetal bovine serum, dispase II (2.4 U/ml; Roche Applied Science, Indianapolis, IN, USA) and collagenase D (1 mg/ml; Sigma-Aldrich, St. Louis, MO, USA). The muscle slurry was incubated with agitation for 60 minutes at 37°C. Enzymes were subsequently refreshed and the muscle slurry was incubated with agitation for an additional 30 minutes. The muscle slurry was then filtered through a 40 μm filter and then spun at 500 g for 5 min to pellet cells. Cells were then plated on 10cm cell culture plates (Corning Primaria) and MPCs were isolated through multiple rounds of pre-plating until purity was reached  (Control: 92%, CKD: 89%, P = .55). MPCs were maintained in growth medium composed of Ham’s F10 (cat#11550043), 20% fetal bovine serum, 1% pen-streptavidin, and 5ng/ml basic fibroblast growth factor (bFGF). MPCs for RNA sequencing experiments were cultured in 10% control or CKD human serum. Media was refreshed every other day.

extract_protocol:
MPCs used for RNA sequencing were cultured for 4 days in 10% serum obtained from control participants or from patients with late stage CKD. Total RNA was extracted from primary MPCs by pipetting Trizol TRI Reagent (#R2050-1-200, Zymo Research) onto wells and manual scraping. RNA was isolated using the Direct-zol RNA Miniprep kit (#R2051, Zymo Research) per manufacturer’s instructions. RNA concentration and quality (average RIN: 9.7) was assessed with an RNA Nano chip kit on a bioanalyzer by the University of Kentucky Genomics Core Laboratory.
Six hundred nanograms of total RNA was sent to Novogene for library construction and sequencing on an NovaSeq PE150 system using a paired-end 150 bp dual-indexing protocol.

value: Skeletal muscle

value: Primary myogenic progenitor cells


title: Healthy MPCs in CKD serum biological replicate 2

description: Library name: H_CMB


title: C5_Replication_145

type: genomic

city: Potsdam

first: Amandeep

last: Singh

state: Brandenburg

address: Arthur-Scheunert-Allee 114-116

department: EOD

institute: German Institute of Human Nutrition

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing: ChAMP package in R environment

label: other

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

value: F

value: Blood cells


title: Healthy MPCs in control serum biological replicate 3

description: Library name: ESRD_O


title: e14.5 lung B6 control 1

description: Library name: YS1

value: Lung


title: normoxia

description:
Library name: Sample 2
SeekGene

value: normoxia


title: CKD MPCs in control serum biological replicate 3

description: Library name: CKD_C


title: hPDLSCs, LTA-treated, rep1

description: Library name: LTA1


title: C5_Replication_143


title: Healthy MPCs in control serum biological replicate 1

description: Library name: ESRD_A


title: hPDLSCs, Control, rep2

description: Library name: C2


title: CKD MPCs in control serum biological replicate 2

description: Library name: CKD_B