title: E. coli K12 MG1655, rpoS deletion strain, RNA-seq, mid-exponential phase, 37°C, replicate 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

data_processing:
Sequenced reads of E. coli K-12 MG1655 samples were mapped onto NC_000913.3 reference genome sequence using bowtie v2.0.0 with parameters -X 1000 -n 2 -3 3 -S.
Transcript Per Million (TPM) were calculated using featureCounts in R. Differentially expressed genes were identifiec using DEseq2 in R.
Binding intensity of sigma factors was calculated by Signal to Noise ratio (S/N)
Assembly: NC_000913.3
Supplementary files format and content: Tab-delimited text files (.tsv) include TPM values and DEGs for samples.

organism: Escherichia coli K-12

growth_protocol: E. coli K-12 MG1655 cells and it derivates were grown to mid-exponential phase (OD600 ≈ 0.6)  aerobically at 37°C in 100ml of M9 minimal media supplemented with 0.2% glucose. E. coli K-12 MG1655 were grown to mid-exponential phase at 37°C  with constant agitation.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a Qubit 4.0 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared using KAPA RNA Hyper Prep kit for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: rpoS deletion


title: T47D treated with PIK75 for 2 hr ChIP PolII

status: Public on Jun 20 2026

type: SRA

city: Taipei

first: Yi-Ru

last: Tseng

address: No. 201, Sec. 2, Sh ipai Rd.

country: Taiwan

institute: Taipei Veterans General Hospita

description:
Library name: T47D_2h_PolII
T47D treated with PIK75 for 2 hr ChIP PolⅡ

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using CLC Genomics Workbench 25.0.1 (Trim Reads 3.0) with quality trimming (quality limit = 0.01), ambiguous base trimming (maximum ambiguities = 2), and automatic adapter trimming using the TruSeq Trim Adapter List.
Reads were mapped to Homo sapiens (GRCh38.p14) with Map Reads to Reference 2.0, duplicate reads were removed using Remove Duplicate Mapped Reads 0.3, and peak calling was performed using Transcription Chip-Seq 2.0 and Histone Chip-Seq 0.14 with the parameters described above.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF-7 and T-47D were treated with DMEM/F12 and RPMI 1640 medium,   supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Cell were fixed with 1% paraformaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Pico sonication device
ChIP-seq

treatment_protocol: shRNA knockdown of CDK7, overexpress CDK6 in breast cancer cells or treat CDK7 inhibitor

tag: cell line

tag: cell type

value: breast

tag: treatment

tag: chip antibody

value: Pol II (Santa Cruz Biotechnology, sc-899)


title: After competition biol rep 3

first: Po-Yin

last: Chen

address: 128 Section 2, Academia Road, Nankang

institute: Academia Sinica

description: Library name: Sample 6

data_processing:
Raw paired-end sequencing reads provided in FASTQ format were processed using a custom C++ analysis pipeline utilizing the SeqAn sequence analysis library.
To isolate the targeted mutation region, the script scanned each read for the upstream plasmid flanking sequence pattern “ATCTGTATATCTAGA”.
Upon detection, the immediate downstream 450 bp sequence region was extracted. Because the raw reads were sequenced in the reverse-complement orientation relative to the hcp1 coding sequence, the extracted fragments were converted to their true 5' to 3' reverse-complement sequences to restore the original gene coding frame. The corrected DNA segments were subsequently translated in silico into primary protein sequences using the standard genetic code.
To minimize the impact of sequencing artifacts, unique DNA and protein variants were compiled into frequency tables, and only high-confidence variants with an absolute read abundance threshold of ≥ 5 counts were preserved for downstream analysis. High-confidence variant sequences were globally aligned against wild-type hcp1 nucleotide and amino acid reference templates. Mutation detection was conducted to systematically log substitutions, insertions, deletions (indels), or premature stop codons.
Supplementary files format and content: csv files include read counts for each variant

organism: Pseudomonas aeruginosa PAO1

growth_protocol: P. aeruginosa PAO1 ∆hcp1 cells carrying hcp1 mutant library were cultured in LB with 15 μg/mL gentamicin, 25 μg/mL irgasan at 37°C.

extract_protocol:
Bacterial cells were harvested and the plasmids were extracted using Maxi Plasmid DNA Kit (Geneaid).
10 ng of the extracted plasmid DNA was used as the template for a first-round PCR amplification (18 cycles) of the hcp1 gene region using target-specific primers with adapter overhangs (listed in Supplementary Table X). Amplicons of the expected size (~561 bp) were gel-purified using a QIAquick Gel Extraction Kit. To generate sequencing libraries, 10 ng of the purified first-round PCR products was subjected to a second-round PCR (8 cycles) using KAPA HiFi HotStart ReadyMix to incorporate Illumina i5 and i7 index sequences (Illumina DNA/RNA UD Indexes Set D, Tagmentation). The indexed amplicons were subsequently purified using SPRI beads (Beckman Coulter), quantified, and validated for the expected library fragment size. The individual libraries were then normalized to 2 nM, pooled, and quantified using the KAPA Library Quantification Kit for Illumina Sequencing Platforms. The final pooled libraries were further validated using an Agilent 5200 Fragment Analyzer.

tag: strain

tag: genotype

value: hcp1 deleted

value: after interbacterial competition against Enterobacter cloacae


title: Control 3

city: Bengbu

first: Jing

last: Wu

address: Donghai road 2600

country: China

institute: Bengbu Medical University

description:
Library name: Sampe 6
HEK‑293T cells were treated with 300 µL of YFD culture supernatant for 24 hours.

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarityraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: total RNA

growth_protocol: The C. albicans strain (SC5314) was grown in yeast peptone dextrose (YPD) broth containing antibiotics (gentamicin and chloramphenicol) at 30 °C for 24 h. The yeast form supernatant (YFCS) was collected by centrifugation, filtered through a 0.22 μm membrane, and stored at −80 °C for subsequent experiments. HEK-293T cells were cultured in DMEM (Servicebio, G4524-500 mL) with 10% fetal bovine serum (Servicebio, G8002-500 mL) and 1% penicillin and 1% streptomycin (Servicebio, G4003-100 mL, 100x). Cells were cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA of cells or tissues were isolated with RNA extraction reagent (Servicebio, Cat#: G3013). cDNA was synthesized from 1 μg of total RNA with SweScript RT II First Strand cDNA Synthesis Kit (Servicebio, Cat#: G3333.). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitollowing manufacturer's protocols.

treatment_protocol: HEK‑293T cells were seeded in 12‑well plates. YFCS and its control YFD medium (300 μL each) for 24 hours.

value: Human Embryonic Kidney 293 cells expressing SV40 large T antigen

value: WT

value: Uninoculated YPD supernatant


title: T47D treated with DMSO ChIP PolII

description:
Library name: T47D_DMSO_PolII
T47D treated with DMSO ChIP PolⅡ

value: DMSO


title: After competition biol rep 2

description: Library name: Sample 5


title: Control 2

description:
Library name: Sampe 5
HEK‑293T cells were treated with 300 µL of YFD culture supernatant for 24 hours.


title: RNA-Seq control_1

city: Beijing

first: Yushu

last: Zou

address: 38 Xueyuan Rd

institute: Peking University

data_processing:
Chip-seq raw reads were mapped to the human genome hg19 using bowtie(1.1.2) with defult parameters. Chip peaks were called using danpos(2.2.2) with de significance cut off p-value <= 1e-10. BigWig files were generated using WigToBigWig tools.
RNA-seq raw reads were mapped to the human genome hg19 using Tophat(v.2.1.1) with default parameters. SAM/BAM file formats were transformed by samtools (0.1.19-44428cd). Expression value (number of raw reads) for each gene was determined by the software HTSeq version v.0.11.3 under the parameters --stranded=no and --mode= intersection-nonempty.  Normalized (the TMM method) expression values were determined by edgeR version 3.40.2 ran with an R version 4.2.2.
Assembly: hg19
Supplementary files format and content: For Chip-seq data, BigWig files were generated.
Supplementary files format and content: For RNA-Seq data, BigWig files and tab-delimited text files contian raw count values for each gene of each sample.

source_name: umbilical vein

extract_protocol:
ChIP-Seq: DNA and protein were cross-linked by 1% formaldehyde. Chromatin was isolated and sonicated into 100-300 bp fragments. Then the DNA-protein complex was precipitated with control IgG or antibodies against LMO2 overnight at 4°C followed by protein A/G conjugated magnetic beads for 1 hr. Cross-links were reversed to extract DNA. RNA-Seq: HUVECs cells (3.3×106) transfected with LMO2 or negative control siRNA for 72 hr were harvested. RNA was extracted using the FastPure cell/tissue total RNA isolation kit V2 (Vazyme, cat. RC112-01).
ChIP-Seq: 10 ng enriched DNA and input DNA were sent to Novogene for library preparation using the KAPA HTP library preparation kit and sequenced in Illumina NovaSeq 6000 to obtain 20 million read pairs per sample. RNA-Seq: RNA samples were submitted to Annoroad Gene Technology Corporation (Beijing) for library construction and sequencing. Briefly, following the RNA quality check, ribosomal RNA was removed using Epicentre Ribo-ZeroTM Gold  Kits. Then sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s manual.

tag: tissue

value: umbilical vein

value: HUVEC

value: Human endothelial cell

value: Negative control siRNA


title: ChIP-Seq input

value: IgG antibody


title: E. coli K12 MG1655, wild-type, RNA-seq, mid-exponential phase, 37°C, replicate 2

country: South Korea

value: Wild-type


title: Ctrl, rep 4

city: Toronto

first: Giacomo

last: Furlan

state: ONTARIO

address: 25 Orde St

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
Library name: Sample 4
Ctrl_D

data_processing:
Read quality was assessed using FastQC. Paired-end reads were trimmed using Trim Galore, and only high-quality reads passing these steps were retained for downstream analysis.
Reads were aligned to the Mus musculus reference genome (mm10) using Bowtie2 (v2.4.1). Unaligned reads, mitochondrial reads, and PCR duplicates were removed at this stage.
Peak calling was performed with MACS3 (v3.0.3), using --nomodel and --nolambda parameters. Peaks overlapping with mouse ENCODE blacklist regions were excluded.
Differential accessibility analysis was performed in R using the DiffBind package (v3.16.0). Regions were considered significantly differentially accessible with a false discovery rate (FDR) < 0.05 and an absolute log₂ fold change > 1.
Genomic regions were annotated to nearby genes using GREAT (McLean et al., 2010), with the following settings: proximal = ±5 kb from transcription start site (TSS); distal = up to 1000 kb.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing normalized counts for all peaks in all samples

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in standard serum/LIF medium consisting of DMEM GlutaMAX supplemented with sodium pyruvate, 15% fetal bovine serum, 0.1 mM non-essential amino acids, 50 U mL-1 penicillin–streptomycin, 0.1 mM 2-mercaptoethanol, and 1,000 U mL-1 ESGRO LIF.

extract_protocol:
50,000 live cells were collected and resuspended in cold resuspension buffer (RSB: 10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂) supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Following lysis, nuclei were washed in RSB containing 0.1% NP-40 and subjected to tagmentation using the transposition mixture: 25 μL of 2× TD buffer, 2.5 μL of Tn5 transposase (100 nM final concentration), 16.5 μL of 1× PBS, 0.5 μL of 1% digitonin, 0.5 μL of 10% Tween-20, and 5 μL of nuclease-free water. After transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 Kit.
Library amplification was carried out as per protocol (Corces et al., 2017). Amplified libraries were purified using AMPure XP beads with a double-sided size selection to remove both primer dimers and large fragments (>1000 bp). Final libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit, pooled at equimolar concentrations, and sequenced on a NovaSeq X platform with a 10B flow cell, generating 150 bp paired-end reads.

treatment_protocol: To induce in vitro pausing, 200nM of the mTOR inhibitor INK128 was added to the culture medium for 24 hours.

value: embryonic stem cells

value: control condition


title: T47D knowdown CDK7 repeat 2

description: Library name: T47D-shCDK7-2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to H.  sapiens, GRCh38 using CLC Genomics Workbench (v 25.0.3) (parameters- default)
Read count extraction  were performed using CLC Genomics Workbench (v 25.0.3)
Normalization were performed using CLC Genomics Workbench (v 25.0.3)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: MCF-7 and T-47D were treated with DMEM/F12 and RPMI 1640 medium, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen™) and 1–bromo–3–chloropropane (BCP) (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries
RNA-seq

value: knowdown with CDK7


description:
Library name: MCF7_24h_Ser5
MCF7 treated with PIK75 for 24 hr ChIP CTD-Ser5

value: breast

value: CTD Ser-5 (Merck Millipore, 04-1572)


title: After competition biol rep 1

description: Library name: Sample 4

value: hcp1 deleted


title: E. coli K12 MG1655, rpoS deletion strain, RNA-seq, mid-exponential phase, 37°C, replicate 1

value: rpoS deletion


title: E. coli K12 MG1655, wild-type, RNA-seq, mid-exponential phase, 37°C, replicate 1


title: Control 1

description:
Library name: Sampe 4
HEK‑293T cells were treated with 300 µL of YFD culture supernatant for 24 hours.

value: Human Embryonic Kidney 293 cells expressing SV40 large T antigen


title: T47D knowdown CDK7 repeat 1

description: Library name: T47D-shCDK7-1


title: Before competition biol rep 3

description: Library name: Sample 3

value: before interbacterial competition against Enterobacter cloacae


title: YFCS treatment 3

description:
Library name: Sampe 3
HEK‑293T cells were treated with 300 µL of yeast‑form Candida albicans culture supernatant for 25 hours.

value: WT

value: Culture supernatant of yeast-form Candida albicans


title: E. coli K12 MG1655, RpoS, ChIP-exo, mid-exponentialphase, 37°C, replicate 2

data_processing:
Sequenced reads of E. coli K-12 MG1655 samples were mapped onto NC_000913.3 reference genome sequence using bowtie v1.0.0 in ChEAP with default options.
RpoS binding sites were identified using DEOCSU(DEep-learning Optimized ChIP-exo peak calling SUite).
Binding intensity of sigma factors was calculated by Signal to Noise ratio (S/N)
Assembly: NC_000913.3
Supplementary files format and content: Binding sites and their intensities of ChIP-mini datasets were included.

growth_protocol: E. coli K-12 MG1655 cells were grown to mid-exponential phase (OD600 ≈ 0.6)  aerobically at 37°C in 100ml of M9 minimal media supplemented with 0.2% glucose. E. coli K-12 MG1655 were grown to mid-exponential phase at 37°C  with constant agitation.

extract_protocol:
Chromatin Immunoprecipitation (ChIP)
KAPA HiFi HotStart ReadyMix

value: Anti-RpoS


title: T47D knowdown vecter repeat 2

description: Library name: T47D-pLKO-2

value: vecter


title: Before competition biol rep 2

description: Library name: Sample 2


title: N2 adult day 2, DMSO, rep 3, trial 2

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

country: USA

institute: University of Oregon

description:
Library name: N2_2_DMSO_r3_tr2
N2_additional_controls.featureCounts.txt

data_processing:
Subread v2.0.2 was used to build a custom C. elegans reference genome package with default parameters.
Sequenced reads contained in single-end FASTQ files were mapped to the WBcel235 reference genome using Subread with parameter -t 0.
Uniquely mapped reads were assigned to genes using the Subread featureCounts package with parameters -t exon -g gene_id.
Assembly: WBcel235 (build 108)
Supplementary files format and content: Tab-delimited tables of raw gene counts for every gene and sample, for (1) two-group comparisons in wild type at each age, (2) additional wild type control series, and (3) skn-1 and daf-16 mutants at two ages.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans N2, PX991 (daf-16(fx107)), and EU1 (skn-1(zu67)) strains were maintained at 20°C and 80% RH on 60 mm nematode growth medium (NGM) plates seeded with E. coli OP50-1.

extract_protocol:
Worms were picked into 0.2 mL tubes containing 45 µL lysis buffer, 4 µL RNA-secure, 5 µL proteinase K and flash frozen with liquid nitrogen.
Libraries were prepared using the KAPA mRNA HyperPrep kit (KK8580 from Kapa Biosystems) as per manufacture protocol except that the total volume was adjusted to 1/4 per reaction.

treatment_protocol: Sulforaphane (Santa Cruz Biotech, sc-207495D) was mixed with DMSO (dimethyl sulfoxide) to create a stock solution. Stock solutions (DMSO for the controls) were then diluted with water to create working solutions and distributed onto 35 mm NGM plates containing 51 µM FUdR and previously seeded with OP50-1. Plates were treated with compound solutions such that the final volume was assumed equal to the volume of agar and the final concentration of DMSO was 0.25%. Worms were synchronized and added to treatment plates beginning on day 1 of adulthood. Biological replicates were aged and collected in tandem, with the exception of EU1, where biological replicates 4, 5, and 6 were temporally independent. Approximately 50 worms total were collected per age, intervention, and replicate.

value: whole worm

tag: age

value: adult day 2

value: DMSO control


title: YFCS treatment 2

description:
Library name: Sampe 2
HEK‑293T cells were treated with 300 µL of yeast‑form Candida albicans culture supernatant for 24 hours.


title: E. coli K12 MG1655, RpoS, ChIP-exo, mid-exponentialphase, 37°C, replicate 1

value: Wild-type


title: Before competition biol rep 1

description: Library name: Sample 1


title: T47D knowdown vecter repeat 1

description: Library name: T47D-pLKO-1


title: N2 adult day 2, DMSO, rep 2, trial 3

description:
Library name: N2_2_DMSO_r2_tr3
N2_additional_controls.featureCounts.txt


title: YFCS treatment 1

description:
Library name: Sampe 1
HEK‑293T cells were treated with 300 µL of yeast‑form Candida albicans culture supernatant for 24 hours.


title: Ctrl, rep 1

description:
Library name: Sample 1
Ctrl_A

value: embryonic stem cells


title: CCT3-2

status: Public on Jun 19 2026

city: Nanjing

first: lingxiu

last: Tong

state: Jiangsu

address: Nanjing Medical University 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu Province, P.R. China

institute: Nanjing Medical University

description: Library name: sample3

data_processing:
Illumina bcl2fastq v2.20 software was used for base calling and sample demultiplexing
Assembly: mm10
Supplementary files format and content: BAM files containing aligned reads for all PABPC1 IP, CCT3 IP and Input samples (2 biological replicates each)

extract_protocol:
Cell pellets were resuspended in eCLIP lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with 1 mM PMSF, protease inhibitor cocktail and RNase inhibitor (Superase-in). Lysates were sonicated on ice and treated with RNase I to fragment RNA. Immunoprecipitation was performed using anti-PABPC1 antibody and anti-CCT3 antibody conjugated to protein G magnetic beads overnight at 4°C
eCLIP libraries were constructed following the standard enhanced crosslinking immunoprecipitation protocol. Briefly, RNA fragments bound to beads were dephosphorylated, ligated to 3' RNA adapters, reverse transcribed with barcoded primers, and PCR amplified. Input control libraries were prepared in parallel from the same cell lysates without immunoprecipitation

value: mouse spermatocyte cells


title: Gsk3b (IEC-/-) RNA-Seq, rep2

city: Suzhou

first: Xiaoqin

last: Yang

address: NO. 199 Renai Road

institute: Soochow University

description: Library name: Gsk3b (IEC-/-) RNA-Seq 2

data_processing:
Sequencing reads were mapped to the mouse reference genome (mm10) with TopHat software. Then, read counts were calculated using GFOLD software. Differentially expressed genes were identified with the limma-edgeR workflow.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include reads count for each Sample

molecule: polyA RNA

source_name: colon cancer tissues

extract_protocol:
RNA samples are extracted using TRIzol reagent, typically following the manufacturer’s instructions.
Sequencing libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA), adhering to the manufacturer's instructions. Index codes were added to assign sequences to individual samples. The indexed samples were then clustered on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina), following the provided guidelines. Finally, these RNA-Seq libraries were then clustered and sequenced on an illumina Novaseq 6000 platform (Illumina, San Diego, California, United States) using the PE150 strategy.

value: colon cancer tissues


title: Gsk3b (IEC+/+) RNA-Seq, rep2

description: Library name: Gsk3b (IEC+/+) RNA-Seq 2


title: Gsk3b (IEC-/-) RNA-Seq, rep1

description: Library name: Gsk3b (IEC-/-) RNA-Seq 1


title: Gsk3b (IEC+/+) RNA-Seq, rep1

description: Library name: Gsk3b (IEC+/+) RNA-Seq 1


title: Gsk3b (IEC+/+) scRNA-Seq 1

description:
Library name: Gsk3b (IEC+/+) scRNA-Seq 1
10x Genomics v3

library_source: transcriptomic single cell

data_processing:
Sequencing was carried out on the Illumina NovaSeq 6000 PE150 platform by OE Biotech Co., Ltd. (Shanghai, China).
FASTQ files were processed and aligned to the mm10 mouse reference genome using Cell Ranger software from 10x Genomics, with unique molecular identifier (UMI) counts compiled for each barcode. The UMI count matrix was subsequently analyzed using the Seurat R package. To remove low quality cells and potential multiplets, a set of filtering criteria was applied: (1) cells with fewer than 200 genes, (2) UMI counts below 1000, (3) log10GenesPerUMI less than 0.7, (4) mitochondrial RNA UMI proportion greater than 10%, and (5) hemoglobin RNA UMI proportion greater than 5%. To further identify potential doublets, the DoubletFinder package was utilized. Library size normalization was performed using the NormalizeData function to obtain normalized gene expression data. The "LogNormalize" method was used, which normalizes gene expression measurements for each cell by total expression, scales by a factor of 10,000, and applies a log transformation.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrix files

source_name: colon cancer

extract_protocol:
The scRNA seq analysis involved colon tumors from AOM/DSS-induced Gsk3β IEC+/+ and Gsk3β IEC-/- mice. Tumors were digested into single cell suspensions.
The scRNA seq libraries were created using the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits, following the manufacturer’s guidelines.

value: colon cancer


title: B220+CD3ε+CD45+, X cells, Rep.1

city: Wakayama

first: Yutaka

last: Nakamura

state: Wakayama

address: Shichi-bancho 25-1

department: Pharmaceutical Science

country: Japan

institute: Wakayama-Medical University

description:
Library name: Sample 4
Column name in RawCount_Matrix_ann.txt: X_cell4

data_processing:
The quallity of sequence reads was assessed with FastQC (Ver. 0.11.7)
Adaptor sequences and low quality (<20) bases were trimed by Trimmomatic software (Ver. 0.38) (parameters - illuminaclip: path/to/adapter.fa:2:30:20 leading:20, trailing:20, slidingwindow:4:15, minlen:36)
The trimed reads were aligned to the reference genome (mm10) using RNA-seq aligner HISAT2 (Ver. 2.1.0) and converted with Samtools (Ver. 1.9)
The read count extraction were performed by featureCounts (Ver.1.6.3)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Small intestine

extract_protocol:
RNA was harvested by PureLink RNA Mini Kit (Thermo Fisher Scientific) with PureLink Dnase.
RNA libraries for RNA-Seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit.

value: Small intestine

tag: sample group

value: B220+CD3ε+CD45+, X cells


title: B220+CD3ε+CD45+, X cells, Rep.3

description:
Library name: Sample 6
Column name in RawCount_Matrix_ann.txt: X_cell8


title: Gsk3b (IEC-/-) scRNA-Seq 1

description:
Library name: Gsk3b (IEC-/-) scRNA-Seq 1
10x Genomics v3


title: B220+CD3ε+CD45+, X cells, Rep.2

description:
Library name: Sample 5
Column name in RawCount_Matrix_ann.txt: X_cell6


title: B220-CD3ε+CD45+, T cells, Rep.3

description:
Library name: Sample 3
Column name in RawCount_Matrix_ann.txt: T_cell7

value: B220-CD3ε+CD45+, T cells


title: No Depletion pool

city: Cambridge

first: John

last: Xu

address: biomedical campus

country: United Kingdom

institute: Cambridge

description: Library name: UPX_002

data_processing:
The cleaned reads were aligned to the mouse/ rat reference genome using the star aligner (v2.7.10a) within a Singularity container, against Rattus_norvegicus.Rnor_6.0.102.gtf  and Mus_musculus.GRCm39.104. star was run with default parameters and the --quantMode TranscriptomeSAM option enabled, which produces transcriptome-aligned reads for downstream quantification. Gene- and transcript-level expression was quantified using rsem (v1.3.3). rsem was executed in paired-end mode with the star transcriptome-aligned reads as input, generating both raw read counts and normalized expression values (transcripts per million, TPM). Quality control reports from all steps (fastqc, trimmomatic (RRID:SCR_011848), star, and rsem) were aggregated using MultiQC to provide a comprehensive overview of data quality. Finally, downstream analyses—including differential expression testing, pathway enrichment analysis, unsupervised clustering, and data visualization—were performed using the OmicsPlayground platform (v2.8.19) with an FDR = 0.05. Gene expression values were normalized to counts per million and log-transformed for comparison across samples. Heatmaps were generated using Heatmapper (). MCL clustering (inflation parameter = 1.5) and DBSCAN clustering (epsilon = 15) were generated using string V.12.0 (www.string-db.org) (RRID:SCR_005223).
Transcript abundance quantification and normalization were performed across all experimental groups and presented in Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Assembly: Rattus_norvegicus.Rnor_6.0.102.gtf
Supplementary files format and content: raw_counts

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: Rat microglia nuclei

growth_protocol: Primary rat microglia were maintained in microglial culture media under standard humidified conditions at 37 °C with 5% CO₂, with in defined microglia culture medium consisting of DMEM/F12 supplemented with N2, 1 mM sodium pyruvate, 50 µg ml⁻¹ insulin, 3 mg ml⁻¹ N-acetylcysteine, 1.5 µg ml⁻¹ cholesterol, macrophage colony-stimulating factor (mCSF; 20 ng ml⁻¹ for rat, 100 ng ml⁻¹ for human) and transforming growth factor-β (TGFβ; 2 ng ml⁻¹ for rat, 5 ng ml⁻¹ for human), with optional penicillin–streptomycin. Feeding experiments were performed the day after seeding.

extract_protocol:
Nuclear RNA was isolated from primary rat microglial subcellular fractions following feeding conditions using Trizol and phenol-chloroform extraction. mRNA was subsequently purified using the PureLink RNA Mini Kit (Thermo Fisher Scientific, 12183018) with on-column DNase treatment. RNA samples underwent post-DNase digestion to minimize genomic DNA contamination prior to library preparation. RNA integrity and concentration were assessed using the RNA ScreenTape system (reagent: Agilent, #5067-5577, RNA ScreenTape: Agilent, 5067-5576, TapeStation: 4200 TapeStation System, Agilent) and NanoDrop spectrophotometry. Only high-quality RNA (RNA integrity number (RIN) > 7) was used for downstream applications.
RNA libraries were prepared from purified nuclear RNA using ERCC RNA Spike-In Mix controls using QIAseq® UPXome Low Input Kit (334705) and sequenced on the Illumina NovaSeq platform (SP flow cell configuration) using paired-end 150 bp sequencing read configuration.  UPX-002 ACCAGACTTG-CGATGAGCAC No Depletion pool UPX-003 ACTGGCGAAC-GATAAGTCGA Pool 1 1-12 UPX-004 GCGTTAGGCA-TCACGCCTTG Pool 2 13-24 UPX-005 TTATCGGCCT-AGGAACACAA Pool 3 25-35

treatment_protocol: Primary rat microglia were exposed to purified myelin debris, Pellet 1 fractions (brain tissue devoid of myelin), or control media conditions prior to nuclear RNA isolation. Experimental groups included: (1) myelin-fed rat microglia nuclei RNA (MN), (2) control rat microglia nuclei RNA (CN), (3) myelin-fed rat microglia cytoplasm RNA (MC), (4) control rat microglia cytoplasm RNA (CC), (5) input myelin RNA (MO/ MO+; ribosomal depletion and no depletion runs), and (6) Pellet 1-fed rat microglia nuclei RNA (PN), (7) Pellet 1-fed rat microglia cytoplasm RNA (PC) and (8) Pellet 1 RNA (P1).

value: Rat microglia nuclei

value: Myelin-fed

tag: batch


title: B220-CD3ε+CD45+, T cells, Rep.1

description:
Library name: Sample 1
Column name in RawCount_Matrix_ann.txt: T_cell1

value: WT


title: B220-CD3ε+CD45+, T cells, Rep.2

description:
Library name: Sample 2
Column name in RawCount_Matrix_ann.txt: T_cell3


title: J774A.1 cells/HOCl 100µM-3

first: Chaorui

last: Guo

state: Jiang Su

address: Longmian Avenue No.639

institute: China Pharmaceutical University

description: Library name: SampleD3

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software to obtain mapped reads. FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: txt file includes FPKM values for each sample

growth_protocol: Murine macrophage-like J774A.1 cells (purchased from Cell Resource Center, Peking Union Medical College) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, KeyGEN) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37°C in a 5% CO2 incubator.

extract_protocol:
RNA samples were colleted using TRIzol® (Magen).
RNA libraries were prepared using ABclonal mRNA-seq Lib Prep Kit (ABclonal, China). Sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument.

treatment_protocol: cells were treated with cell media or HOCl (0, 20, 100 μM) in HBSS for 1 h and re-incubated in full cell media for 24 h before collected

value: macrophage


title: J774A.1 cells/HOCl 100µM-2

description: Library name: SampleD2


title: J774A.1 cells/HOCl 20µM-3

description: Library name: SampleC3


title: J774A.1 cells/HOCl 100µM-1

description: Library name: SampleD1


title: J774A.1 cells/HBSS-2

description: Library name: SampleB2


title: J774A.1 cells/HOCl 20µM-2

description: Library name: SampleC2


title: J774A.1 cells/HOCl 20µM-1

description: Library name: SampleC1


title: J774A.1 cells/HBSS-3

description: Library name: SampleB3


title: J774A.1 cells/HBSS-1

description: Library name: SampleB1


title: J774A.1 cells/cell media-3

description: Library name: SampleA3


title: J774A.1 cells/cell media-2

description: Library name: SampleA2


title: J774A.1 cells/cell media-1

description: Library name: SampleA1


title: CD4 T cells 5 VDJ

city: Milwaukee

first: Yi-Guang

state: WI

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

description:
Library name: 5_VDJ
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islets

extract_protocol:
Islet infiltrating cells were isolated from four Cre+-Tnfrsf9+/+ and four Cre+-Tnfrsf9fl/fl 7-10-week-old females The pancreas was inflated using a 30-gauge needle by injecting 3-5 mL of HBSS containing 0.5 U/mL collagenase P solution (Roche Diagnostics) and 10 μg/mL DNase (Sigma) into the bile duct. The inflated pancreas was digested at 37°C for 15 min. Next, the digested pancreas was washed three times with 10 mL of HBSS containing 2% FBS. Each individual pancreas was then suspended in 5 mL complete RPMI 1640. Islets were visualized under a dissecting microscope and hand-picked. Pelleted islets were suspended in 200 μL of enzyme free cell dissociation buffer (Life Technologies). Cells were then washed with 500 μL of HBSS, resuspended in FACS buffer. Cells were incubated with 5 µg/mL Fc block (anti-mouse CD16/CD32 clone 2.4G2, BioXCell). Each cell pool was then stained with anti-CD45.1, anti-CD4, and a unique hashtag antibody for 30 minutes at 4ºC, washed, and passed through a 30 µm filter. All stained cells were combined and simultaneously sorted into CD45.1+CD4+ and CD45.1+CD4- samples on a FACSAria III (BD Biosciences).
Sequencing libraries were prepared using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10X Genomics).

value: pancreatic islets

value: CD4 T cells

value: wildtype + knockout


title: CD4 T cells 5 HT

description:
Library name: 5_HT
10x Genomics


title: CD4 T cells 5 GEX

description:
Library name: 5_GEX
10x Genomics


title: non-CD4 T cells 3 VDJ

description:
Library name: 3_VDJ
10x Genomics

value: Immune cells


title: CD4 T cells 4 VDJ

description:
Library name: 4_VDJ
10x Genomics


title: CD4 T cells 4 GEX

description:
Library name: 4_GEX
10x Genomics


title: CD4 T cells 4 HT

description:
Library name: 4_HT
10x Genomics


title: N2 adult day 2, DMSO, rep 1, trial 2

description:
Library name: N2_2_DMSO_r1_tr2
N2_additional_controls.featureCounts.txt

value: whole worm

value: adult day 2

value: DMSO control


title: non-CD4 T cells 3 HT

description:
Library name: 3_HT
10x Genomics


title: Paraburkholderia busanensis P39 grown alone, biological replicate 1

city: Busan

first: Young-Su

last: Seo

address: Geumjeong-Gu

department: Microbiology

institute: Pusan National University

description:
Library name: P39_1
P39 grown alone; biological replicate 1

data_processing:
Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1468790 and the sample-specific SRR accessions listed in this metadata file.
Reads were aligned to the Paraburkholderia busanensis P39 reference genome represented by GenBank accessions CP058248 and CP058249.
Gene-level raw count data contained 6,805 genes across six samples.
Genes with a zero count in at least one of the six samples were excluded before statistical testing, leaving 5,256 genes for downstream analysis.
Read count data were normalized using Relative Log Expression normalization in DESeq2. Regularized log transformation and log2(count+1) values were used for visualization and quality assessment.
Differential expression between P39_CS and P39 was tested using DESeq2 nbinomWaldTest. Significant genes were identified using |fold change| >= 2 and raw p-value < 0.05.
Hierarchical clustering was performed using Euclidean distance and complete linkage.
Assembly: Paraburkholderia busanensis P39 genome, GenBank accessions CP058248 and CP058249.
Supplementary files format and content: P39_RNAseq_raw_counts_matrix.txt is a tab-delimited matrix containing gene identifiers, annotation columns, and raw read counts for all six samples. Sample columns are named P39_1, P39_2, P39_3, P39_CS_1, P39_CS_2, and P39_CS_3.
Supplementary files format and content: P39_RNAseq_FPKM_matrix.txt is a tab-delimited matrix containing gene identifiers, annotation columns, and FPKM values for all six samples.
Supplementary files format and content: P39_RNAseq_RLE_normalized_counts_matrix.txt is a tab-delimited matrix containing gene identifiers, gene symbols, and RLE-normalized count values for all six samples.
Supplementary files format and content: Gene features are traceable by locus/gene identifiers and chromosome coordinates in the processed matrices, with reference genome accessions CP058248 and CP058249.

organism: Paraburkholderia busanensis

source_name: bacterial cells

growth_protocol: Paraburkholderia busanensis P39 was cultured under laboratory conditions for RNA-seq analysis. Samples consisted of P39 grown alone and P39 exposed to Colletotrichum scovillei KC05 fungal biomass, with three biological replicates per condition.

extract_protocol:
Total RNA was isolated from each bacterial sample and quality-checked before library preparation for transcriptome sequencing by Macrogen.
Paired-end RNA-seq libraries were constructed and sequenced by Macrogen on an Illumina HiSeq 4000 platform.

treatment_protocol: For the P39_CS condition, Paraburkholderia busanensis P39 was exposed to fungal biomass of Colletotrichum scovillei KC05 before RNA extraction. The P39 control condition was grown without fungal biomass exposure.

value: bacterial cells

value: wild type


title: non-CD4 T cells 3 GEX

description:
Library name: 3_GEX
10x Genomics


title: non-CD4 T cells 2 VDJ

description:
Library name: 2_VDJ
10x Genomics


title: non-CD4 T cells 2 HT

description:
Library name: 2_HT
10x Genomics


title: non-CD4 T cells 2 GEX

description:
Library name: 2_GEX
10x Genomics


title: non-CD4 T cells 1 VDJ

description:
Library name: 1_VDJ
10x Genomics


title: non-CD4 T cells 1 HT

description:
Library name: 1_HT
10x Genomics


title: non-CD4 T cells 1 GEX

description:
Library name: 1_GEX
10x Genomics


title: con_input_3

city: Oklahoma City

first: Rahul

last: Rajala

state: Oklahoma

address: 825 NE 13th Street

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

description: Library name: Sample 12

data_processing:
Fastq generation was performed using Illumina’s CASAVA-1.8.2 software
Alignment of raw sequences using HISAT2 and independently by SALMON
Differential gene expression performed by DESEQ2 and edgeR
Assembly: HISAT2 (Mus_musculus.GRCm39.dna.primary_assembly) /SALMON (Mus_musculus.GRCm39.107.transcripts.fa.salmon)
Supplementary files format and content: Collated HISAT2 data given as ABCA_Datasheet.csv
Supplementary files format and content: Collated SALMON data given as ABCA_Datasheet_TPM.csv

source_name: Retina

extract_protocol:
RNA (before/after TRAP) was isolated using the Trizol/Pure Link RNA Kit (Ambion). SMARTer Ultra Low Input kit (Clontech) was used for RNA conversion (5 ng for tissue lysate, 10 ng for EC-TRAP samples).
cDNA samples were sheared using the Covaris E220 Focused Ultra-sonicator which was followed by Quant-iT PicoGreen quantification (Thermo Fisher Scientific, catalog number P11496). A total of 5 ng cDNA per sample was used for library preparation based on the KAPA Hyper Prep method (KAPA Biosystems, catalog number KK8504). Following NEXTflex adapter ligation (BIOO Scientific, catalog number 514104), libraries were size-selected based on a double bead purification prior to amplification.

treatment_protocol: Tissues were flash-frozen in liquid nitrogen following a cycloheximide perfusion and mechanically dissociated

value: Retina

value: polyA RNA


title: con_input_2

description: Library name: Sample 11


title: con_input_1

description: Library name: Sample 10


title: abc_input_3

description: Library name: Sample 9


title: abc_input_2

description: Library name: Sample 8


title: abc_input_1

description: Library name: Sample 7


title: con_bead_1

description: Library name: Sample 4

source_name: Rod PR

value: Rod PR


title: con_bead_2

description: Library name: Sample 5


title: abc_bead_3

description: Library name: Sample 3


title: abc_bead_2

description: Library name: Sample 2


title: con_bead_3

description: Library name: Sample 6


title: abc_bead_1

description: Library name: Sample 1


title: KO3_IP

city: Hangzhou

first: Long

last: Bai

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

data_processing:
library strategy: MeRIP-seq
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/). Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome mus musculus (Version: v101). Peak calling and diff peak analysis were performed by R package exomePeak (https://www.bioconductor.org/packages/3.3/bioc/html/exomePeak.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). HOMER (http://homer.ucsd.edu/homer/motif) was used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM.
Assembly: GRCm38
Supplementary files format and content: WT_IPVSWT_input_peak.xlsx
Supplementary files format and content: KO_IPVSKO_input_peak.xlsx

source_name: testis

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA).
Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: testis

value: KO


title: KO3_input


title: KO2_input


title: KO2_IP


title: KO1_input


title: Low, BMI 20, Age 89

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

description: Library name: L5

data_processing:
cellranger 8.0.1 mkfastq
cellranger 8.0.1 count using refdata-cellranger-GRCh38-3.0.0
Assembly: hg38
Supplementary files format and content: Zipped output from cellranger count including matrix.tsv.gz, barcodes.tsv.gz and features.tsv.gz files

source_name: endometrial adenocarcinoma

growth_protocol: Biobanked Flash Frozen Tissues

extract_protocol:
The Chromium Nuclei Isolation Kit (10x Genomics, PN-1000493) was used to isolate single nuclei. Tissue samples were thawed and dissociation tubes (PN-2000564) pre-chilled on dry ice. Samples were dissociated on wet ice using lysis buffer and pestle agitation until samples reached homogenization. Dissociated tissues were centrifuged in nuclei isolation columns (PN-2000562) for initial removal of cell debris. To remove remaining cell debris, pelleted nuclei were washed by resuspending nuclei pellet once in Debris Removal Buffer and three times in Wash and Resuspension Buffer respectively, with centrifugation between washes. Nuclei were resuspended in Wash and Resuspension buffer on ice for further analysis. RNA-seq was performed by the Wayne State University Genome Sciences Core.
After sequencing, the snRNA-seq library was demultiplexed using CellRanger mkfastq. Then, the CellRanger count was used to align the reference genome and tabulate counts by gene region.

treatment_protocol: Patients had either normal body mass indexI or obese body mass index

value: endometrial adenocarcinoma

tag: bmi


title: KO1_IP


title: WT3_IP

value: WT


title: WT3_input


title: WT2_IP


title: WT1_IP


title: WT1_input


title: A5ko18d_1

data_processing:
A cDNA library constructed by technology from the pooled RNA from testes samples of mice was sequenced run with Illumina Novaseq TM 6000 sequence platform. Using the Illumina paired-end RNA-seq,approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the < research species > reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCm38
Supplementary files format and content: fpkm, count

extract_protocol:
For RNA-seq, total RNA were extracted from both P12 and P18 WT and Alkbh5-/- male mice using TRIzol regent, and high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5μg) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) and fragmented into short fragments by Magnesium RNA Fragmentation Module (NEB, e6150). The cleaved RNA fragments were reverse-transcribed and used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, m0209), dUTP Solution (Thermo Fisher, R0133) and RNase H (NEB, m0297). Next, an A-base was added to the blunt ends of each strand to prepare them for ligation to the indexed adapters. After performing the size selection with AMPureXP beads, the ligated products were amplified with PCR and sequenced using the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China).

tag: developmental stage


title: WT2_input


title: A5ko18d_2


title: A5ko12d_2


title: A5ko12d_1


title: Muc13 KO mouse cornea_1

description:
Library name: Sample 1
The corneal tissue of Muc13 KO mouse.

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarityraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Cornea

growth_protocol: Male SPF Muc13-/- and WT mice (6 weeks old) were maintained on a 12-h light/dark cycle. Corneas were collected post-mortem and subjected to transcriptomic profiling via RNA-seq.

extract_protocol:
Total RNA of cells or tissues were isolated with RNA extraction reagent (Servicebio, Cat#: G3013). cDNA was synthesized from 1 μg of total RNA with SweScript RT II First Strand cDNA Synthesis Kit (Servicebio, Cat#: G3333.). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitollowing manufacturer's protocols.

value: Cornea

value: Muc13 knock out


title: A5wt18d_2


title: A5wt12d_2


title: A5wt18d_1


title: A5wt12d_1


title: heart, IP, experimental, biol rep 4

city: Chicago

first: Paul

middle: H.

last: Goldspink

state: IL

address: 909 S. Wolcott Ave

institute: University of Illinois Chicago

data_processing:
The reads were mapped to the mouse transcriptome UCSC/mm10 using STAR aligner (v. 2.5.2b) and processed with Samtools (v. 1.4.1). The bam files were processed using FeatureCounts (Subread package, v.1.5.2) to obtain raw counts. DESeq2 (v. 1.18.1) was used to identify differentially expressed genes and GraphPad Prism 10.2.2.
Assembly: UCSC/mm10
Supplementary files format and content: Raw count files (.txt) were generated using FeatureCounts (v1.5.2) ; Normalized count files (.xlsx) were generated by DESeq2 (version 1.18.1) The second tab of the (.xlsx) file labeled "filtered data" is where we removed any row data that didn't have at least 3 biol rep/ group and > 9.

source_name: heart

growth_protocol: Mice were housed and feed standard chow and water ad libitum compling with the US Public Health Service Policy on Humane Care and Use of Laboratory Animals.

extract_protocol:
Immunoprecipitated RNA was purified from the Dynabeads with an RNeasy plus mini kit (Qiagen cat #74134) following the protocol with minor modifications. Washed beads were eluted twice for 5 min ea at room temperature with 300 µl of RLT with β-mercaptoethanol added as directed by the manufacturer. The RNA from Pre-IP whole homogenate samples were (RNeasy plus mini kit) diluted (at least 10-fold) to a final volume of 600 µl at room temperature with RLT buffer with β-mercaptoethanol added as directed by the manufacturer. One additional 500 µl wash with RPE buffer was added to the protocol along with a 10 min room temperature incubation when 40 µl of the supplied RNase-free water was added to the center of the spin column to elute the RNA and reapplied once. The purified RNA was quantified and quality-checked via NanoDrop, Qubit, and an Agilent 4200 tapestation (All RINe values > 8.5).
A total of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: One group received saline (Sal); the other received 6 mg/kg 7 E. coli O111:B4 bacterial lipopolysaccharide (LPS) from Sigma-Aldrich (Cat # L2630) all injected intraperitoneally. If any animal died during either LPS or saline administration or did not survive the 12 h incubation, they were excluded from the study; however, no animals had to be excluded.

value: heart

value: endothelial cell enriched

value: Rpl22HA/+/ Cdh5CreERT2

value: lipopolysaccride


title: heart, IP, control, biol rep 3

value: saline


title: heart, IP, experimental, biol rep 3


title: heart, IP, experimental, biol rep 2


title: heart, IP, control, biol rep 4


title: heart, IP, control, biol rep 2


title: heart, IP, control, biol rep 1


title: heart, IP, experimental, biol rep 1


title: heart, Pre-IP, experimental, biol rep 4

value: whole heart lysate


title: UK1_15h_2

status: Public on Jun 22 2026

city: Boston

first: Carol

middle: A

last: Kumamoto

state: MA

address: 150 Harrison Ave.

department: Department of Molecular Biology and Microbiology

institute: Tufts University

description:
Library name: Sample 4
10x Genomics

data_processing:
Initial data analysis including demultiplexing, barcode processing and aligning reads to the human genome was performed using Cell Ranger.
Assembly: human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Clostridioides difficile
Homo sapiens

source_name: Colonoid line CJ50

growth_protocol: Preparation of colonoid monolayers on transwells. Colonoid line CJ50 was derived from colonic biopsies obtained from a 67 year old Chinese female undergoing routine outpatient colonoscopy for colorectal cancer screening at Tufts Medical Center (IRB #11652, principal investigator: Jatin Roper). The cells were propagated in Matrigel (Corning 356231) as described previously [29]. Medium compo-sition was as described [22] except that L-WRN conditioned medium (L-WRN cells ATCC CRL- 3276 [30]) was used at 65% instead of L-WNT3A, R-Spondin and Noggin conditioned media, Primocin (InvivoGen ant-pm-1) was used instead of pen-strep and 5 uM Y27632 (Rho kinase inhibitor, Sigma Y0503) was added for the first 48 hrs of culturing. For preparation of monolayers on transwells, colonoid spheres were recovered from Matrigel, washed with PBS and digested with TrypLE Express (Gibco 12605-010) for 2.5 min at 37oC. After digestion, cells were diluted with 1 volume advanced DMEM (Invi-trogen 12634-028), 1% Glutamax (Gibco 35050-061), 20% FBS (Fisher 26140079) and filtered through a 40 um cell strainer. Cells were diluted with 0.4% Trypan blue, counted with a Corning CytoSmart counter and diluted to 2.5 x 106 cells/ml with warmed 65% LWRN medium containing Y27632. Matrigel was diluted with CMGF- to 33 or 66 ug protein/mL, 125 ul was applied to each 6.5mm diameter, 0.4 um pore, polycarbonate filter transwell (Costar 3413) and incubated at 37oC for 2 hours. Liquid was removed from the transwell, the basolateral compartment was filled with 0.5 ml 65% medium and 50 ul of medium was added to the apical compartment. Cells (2.5 x 105 cells per 6.5 mm diameter transwell) were added and the seeded transwells were incubated in a tissue culture incubator with 5% CO2 at 37oC. The next day, transwells were given fresh 65% L-WRN medium containing 5 uM Y27632 (Sigma Y0503), replacing the basolateral medium and adding 0.2 ml to the apical compartment. The next day, the medium was changed to 65% without Y27632 (0.4 ml apically and 0.5 ml basolaterally) and was changed again after 2 days when the mono-layer was typically confluent. Confluent monolayers were differentiated by washing with CMGF-, followed by feeding with Differentiation Medium (DM) [22, 31] containing Primocin. Medium was changed the next day with DM containing Primocin. Monolayers were fed 2 days later (day 3) (DM without Primocin) and in the late afternoon of day 4 or in the morning of day 5 (DM without Primocin). Monolayers were inoculated with pre-germinated spores on day 5. For measurement of trans-epithelial electrical resistance (TEER), a Millicell ERS-2 volt/ohm meter was used following manufacturer’s protocol.

extract_protocol:
Monolayers were cultured on 12 mm diameter 0.4 um polycarbonate filters (Millicell PIHP01250) and differentiated as described above. Spores were treated with glycine and sodium cholate, as above, collected by centrifugation (Eppendorf 5415, 13200 rpm, 5 min) resuspended in PBS and 1 x 105 spores in 10 ul or PBS was added to the apical medium. Transwells were incubated as described above. After 4, 15, 20 or 25 hours of incubation, monolayers were washed with 100 ul PBS, EDTA 0.5 mM, pH 8 and incubated with TrypLE Express, 600 ul in the basolateral and 400 ul in the apical compartments at 37oC for 12 min. One hundred ul 50% FBS was added to the apical compartment and the cells were suspended by pipeting up and down several times. Cells were passed through a 40 um cell strainer and recovered in tubes precoated with 0.1% BSA. The transwells were then washed with 400 ul CMGF-, which was passed through the strainer and combined with the previous filtrate. Cells were collected by centrifugation at 300g x 5 min. Most of the supernatant was gently removed. Cells were resuspended in 1 ml of 0.04% BSA, 5 uM Y27632 and collected as above. Using a wide bore tip, the pellet was resuspended in the remaining supernatant by pipetting up and down. Cells were counted with a Corning Cytosmart counter and adjusted to 1 x 106 cells/ml.
The remaining steps were performed following manufacturer’s protocol. Briefly, the cell suspension was loaded along with reagents, barcoded Single Cell 3’ v3.1 Gel Beads and Partitioning Oil onto the Chromium Next GEM Chip G. Cells were partitioned into GEMS using the Chromium Controller. Gel beads were then dissolved, releasing primers, and the cells were lysed. Reverse transcription was performed to generate cDNA tagged with cell specific barcodes and Illumina TruSeq Read 1 sequencing primer. GEMS were broken and first strand cDNA was purified and PCR amplified. After enzymatic fragmentation followed by size selection, the cDNA was PCR amplified, incorporating a sample index and primers P5, P7, and TruSeq Read 2 for Illumina sequencing. Library quality was assessed using an Agilent Bioanalyzer. Paired end sequencing was performed by the Tufts University Genomics Core Facility.

treatment_protocol: Co-culturing C. difficile with colonoid monolayers. Pre-germinated spores (approximately 5 x 107 per ml) were prepared as above and 10ul of the preparation was added gently to the apical medium of the transwell. Control samples were inoculated with 10ul of buffer. The plates were wrapped with Parafilm and incubated in a standard tissue culture incubator (37oC, 5% CO2, room air). At various times, transwells were taken into the anaerobic chamber (2 transwells at a time) to estimate the number of bacteria per transwell. The first 170 ul of apical medium was carefully removed. This medium was not turbid and was discarded. The second approximately 170 ul of medium was collected into the pipet tip and used to wash the monolayer twice, then collected into a pre-weighed tube. For inoculated transwells, this sample was typically turbid. 10 ul of this sample was immediately diluted with 1 ml of pre-reduced PBS to measure CFU. The remainder of the sample was removed from the chamber and weighed to determine the volume recovered from each transwell after correction for the 10 ul removed for CFU. Transwell monolayers were removed from the chamber and fixed with 4% para-formaldehyde for 15 min at room temp, followed by washing 3 times with PBS at room temperature. Transwells were stored at 4oC in PBS. For some experiments, transwells were inoculated with vegetative C. difficile cells. Strains were grown in pre-reduced TY broth and harvested during log phase. A sample of each culture was diluted 1/50 into pre-reduced PBS. DM medium was pre-reduced and 0.4 ml was transferred to a gasketed screw cap tube for each inoculation. 10 ul of bacteria diluted in PBS was added to each tube (or PBS only for mock inoculation). The caps were screwed on tightly and tubes removed from the chamber. The transwells were inoculated by removing their apical medium and replacing it with the bacteria-containing medium. Transwells were inoculated with approximately 5 x 104 CFU.

value: Colonoid line CJ50

tag: infection

value: infected


title: heart, Pre-IP, experimental, biol rep 3


title: heart, Pre-IP, experimental, biol rep 2


title: heart, Pre-IP, control, biol rep 4


title: heart, Pre-IP, control, biol rep 2


title: heart, Pre-IP, experimental, biol rep 1


title: heart, Pre-IP, control, biol rep 3


title: Pkm2_wt_input_3

data_processing:
Fastq generation was performed using Illumina’s CASAVA-1.8.2 software
Alignment of raw sequences using HISAT2 and independently by SALMON
Differential gene expression performed by DESEQ2 and edgeR
Assembly: HISAT2 (Mus_musculus.GRCm39.dna.primary_assembly) /SALMON (Mus_musculus.GRCm39.107.transcripts.fa.salmon)
Supplementary files format and content: Collated HISAT2 data given as (FinalCountsSheet.csv)

extract_protocol:
RNA (before/after TRAP) was isolated using the Trizol/Pure Link RNA Kit (Ambion).
Libraries were prepared by MedGenome TM, (Foster CA)

value: Retina


title: heart, Pre-IP, control, biol rep 1


title: Pkm2_wt_input_2


title: L02 cells，Control，FFAs750μM，rep2

city: Chongqing

first: Xiaohe

last: Luo

state: Chongqing

address: No. 165, Xincheng Road, Wanzhou District, Chongqing

department: Central lab

institute: Chongqing University Three Gorges Hospital

description:
Library name: Sample 2
Column name in ExpressionProfile.txt: Control_2

data_processing:
RNA-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample,  please see the ExpressionProfile.txt for details.

growth_protocol: L02 hepatocytes were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Retains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina Truseq RNA Sample Prep Kit (Cat#FC-111-1001) was used with 1ug of total RNA for the construction.
RNA libraries were prepared for sequencing using stantard Illumina protocols.

treatment_protocol: Cells were fed with DMEM supplemented with 10% FBS and 750uM FFAs for 24 hours.

value: human embryonic hepatocytes


title: Pkm2_wt_input_1


title: Pkm2_ko_input_2


title: Pkm2_ko_input_1


title: Pkm2_ko_input_3


title: Pkm2_wt_bead_3

value: Rod PR


title: Pkm2_wt_bead_2


title: Pkm2_wt_bead_1


title: Pkm2_ko_bead_3


title: Pkm2_ko_bead_2


title: AJ12_S1pr1KO

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
Raw data from illumina was transformed to Sequenced Reads by CASAVA base recognition (Base Calling)
Raw data was filtered by Novogene Corporation Inc. according to the following steps; 1) reads containing adaptors were removed, and 2)reads containing bases that could not be determined were also removed.
STAR software was used to align reads to reference genome
FPKM was used to estimate gene expression levels. This method considers both sequencing depth and gene length on counting of fragments. (Mortazavi et al. 2008, https://doi.org/10.1038/nmeth.1226)
The readcount from Gene Expression Analysis was used to determine the differential expression analysis
Assembly: Mus Musculus(GRCm39/mm39)
Supplementary files format and content: txt file includes raw counts for each sample
Supplementary files format and content: txt file includes fpkm values for each sample

source_name: Lung

extract_protocol:
Total RNA was extracted from the lungs using QIAzol Lysis Reagent (Qiagen, Cat No./ID: 79306) and processed as per the manufacturer’s instructions.
RNA libraries were prepared using standard Illumina protocols from Novogene Corporation Inc.(Sacramento, CA 95826)

treatment_protocol: After the mice were sacrificed, the lung tissue samples were collected and immediately placed in RNAlater stabilization solution (ThermoFisher Scientific, cat# AM7021) and placed at 4 degrees Celsius for 24 hours before storing at -80 degrees Celsius.

value: Lung

value: MMTV-Cre;S1pr1fl/fl; MMTV-PyMT

tag: time

value: 4.5 months

value: Lung metastasis


title: AJ11_S1pr1KO


title: Pkm2_ko_bead_1


title: AJ10_S1pr1KO


title: AJ9_S1pr1KO


title: AJ7_C3_KO


title: AJ8_C3_KO


title: AJ6_C3_KO


title: AJ5_C3_KO


title: AJ3_WT

value: MMTV-PyMT

value: WT


title: AJ4_WT


title: AJ2_WT


title: AJ1_WT


title: Trophoblast stem cells, WT input, biol rep 2 [WT Sample 2 input]

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Drive NW

institute: University of Calgary

description: WT Sample 2 input

data_processing:
Sequence reads were mapped to GrCM38/mm10 using  STAR aligner (sorted by coordinate) and bowtie2 aligner with samtools (MAPQ >1) for the RNA-seq and meDIP-seq fastq files, respectively.
Read count extraction and normalization were performed on the RNA-seq BAM files using htseq count (order=pos, mode=intersection-nonempty, stranded=reverse)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts per gene

source_name: Trophoblast stem cells

growth_protocol: Trophoblast stem cells were maintained in 20% FBS in RPMI1640, supplemented with antibiotics/antimycotics, sodium pyruvate, BME, bFGF, and heparin in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was harvested using Trizol reagent and DNA was harvested using standard SDS lysis buffer
RNA libraries for RNA-seq were prepared using Ultra II Directional RNA Library Prep kit. meDIP libraries were prepared using NEB ultra II DNA Library Prep kit.

tag: mouse line

value: Trophoblast stem cells

value: stem


title: Trophoblast stem cells, WT input, biol rep 1 [WT Sample 1 input]

description: WT Sample 1 input


title: Trophoblast stem cells, Peg3 KO input, biol rep 1 [Peg3 KO Sample 1 input]

description: Peg3 KO Sample 1 input

value: Peg3 KO


title: Trophoblast stem cells, WT meDIP-seq, biol rep 6 [WT Sample 6 meDIP]

description: WT Sample 6 meDIP


title: Trophoblast stem cells, WT meDIP-seq, biol rep 2 [WT Sample 2 meDIP]

description: WT Sample 2 meDIP


title: Trophoblast stem cells, WT meDIP-seq, biol rep 5 [WT Sample 5 meDIP]

description: WT Sample 5 meDIP


title: Trophoblast stem cells, WT meDIP-seq, biol rep 3 [WT Sample 3 meDIP]

description: WT Sample 3 meDIP


title: Trophoblast stem cells, WT meDIP-seq, biol rep 1 [WT Sample 1 meDIP]

description: WT Sample 1 meDIP


title: Trophoblast stem cells, Peg3 KO meDIP-seq, biol rep 4 [Peg3 KO Sample 4 meDIP]

description: Peg3 KO Sample 4 meDIP


title: Trophoblast stem cells, WT meDIP-seq, biol rep 4 [WT Sample 4 meDIP]

description: WT Sample 4 meDIP


title: Trophoblast stem cells, Peg3 KO meDIP-seq, biol rep 2 [Peg3 KO Sample 2 meDIP]

description: Peg3 KO Sample 2 meDIP


title: Trophoblast stem cells, Peg3 KO meDIP-seq, biol rep 1 [Peg3 KO Sample 1 meDIP]

description: Peg3 KO Sample 1 meDIP


title: Trophoblast stem cells, Peg3 KO meDIP-seq, biol rep 3 [Peg3 KO Sample 3 meDIP]

description: Peg3 KO Sample 3 meDIP


title: Trophoblast stem cells, Day4, WT RNA-seq, biol rep 3 [D4-WT9]

description: Day 4 Peg3 WT sample 3

value: Day 4


title: Trophoblast stem cells, Day4, WT RNA-seq, biol rep 4 [D4-WT17]

description: Day 4 Peg3 WT sample 4


title: Trophoblast stem cells, Day4, Peg3 KO RNA-seq, biol rep 3 [Day4-KO44]

description: Day 4 Peg3 KO sample 3


title: Trophoblast stem cells, Day4, Peg3 KO RNA-seq, biol rep 2 [D4-KO34]

description: Day 4 Peg3 KO sample 2


title: RKO cells, HL6_2, Day1

city: Shanghai

first: Jun

last: Liang

address: Meilong Road

institute: East China University of Science and Technology

description: Library name: RKO_HL6_2

data_processing:
Raw FASTQ files were demultiplexed and converted to FASTQ format by the sequencing platform's standard pipeline. Reads were quality-checked using FastQC (v0.11.9). Adaptor sequences and low-quality reads were trimmed using Trimmomatic (v0.39) with parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Clean reads were aligned to the human reference genome GRCh38.p13 using STAR (v2.7.10a) with default parameters (--sjdbGTFfile gencode.v44.annotation.gtf). Sort and index were performed with Samtools (v1.16). Reads aligning to genes were counted using featureCounts (v2.0.3, Subread package) with parameters -g gene_id -t exon -s 0against the GENCODE annotation (release 44, 2023). Counts were normalized to TPM using custom scripts. Differential expression analysis was performed using DESeq2 (v1.40.0) with a threshold of FDR < 0.05 and |log2FC| > 1.
Assembly: GRCh38
Supplementary files format and content: Gene-level abundance estimates (TPM) generated by Salmon, aggregated from transcript-level quantifications using tximport (R/Bioconductor).

organism: Homo

source_name: Human colorectal cancer cells

growth_protocol: RKO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted using TRIzol reagent (Invitrogen) or equivalent RNA extraction kit, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer . Poly(A)+ mRNA was enriched from ~1 µg total RNA using oligo(dT) magnetic beads. Enriched mRNA was fragmented in fragmentation buffer at 94°C for 5–8 min. First-strand cDNA was synthesized using random hexamer primers and SuperScript II/III reverse transcriptase, followed by second-strand cDNA synthesis with DNA Polymerase I and RNase H. Double-stranded cDNA was end-repaired, 3′-adenylated, and Illumina sequencing adapters were ligated. Ligated products were purified and amplified by PCR to generate the final cDNA library. Library quality and insert size were evaluated on an Agilent 2100 Bioanalyzer (typical fragment size ~200–300 bp), and library concentration was quantified by Qubit or qPCR. Libraries were sequenced on an Illumina [HiSeq 2500 / NovaSeq 6000] platform to generate [paired-end / single-end] reads (2 × 150 bp / 150 bp).

value: Human colorectal cancer cells

value: RKO

value: cell line

value: HL7 treatment

value: Day 1


title: RKO cells, HL6_3, Day1

description: Library name: RKO_HL6_3

value: HL8 treatment


title: Patient S3, ovarian Sertoli Leydig tumor

city: Castellón de la Plana

first: Guillermo

last: Peris

state: CAstellón

address: Av. Vicent Sos Baynat, s/n

department: Llenguatges i Sistemes Informàtics

country: Spain

institute: Universitat Jaume I

description: Library name: S3T

data_processing:
BBDuk from the BBMap toolkit for sequencing adapter removal and read trimming.
RNA paired-end reads were aligned to GRCh38.p14 human genome assembly with STAR v2.7.11b
Gene and transposable elements reads were quantified with TElocal  software from part of TEToolkit suite.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file with TElocal counts for genes and transposable elements for each sample.

source_name: Ovary

extract_protocol:
FFPE (formalin-fixed paraffin-embedded) tumour and normal tissue were obtained from NovoPath, Newcastle Upon Tyne hospitals NHS foundation. RNA extraction of FFPE curls (10x10um) each tumour and normal tissue was performed by Genewiz, Azenta.
QC, library preparation and RNA-sequencing of each tumour and normal tissue was performed using standard RNA-seq paired end (2x150bp) sequencing service by Genewiz, Azenta.

value: Ovary

tag: individual

value: Patient S3

tag: disease state

value: Sertoli Leydig tumor


title: Trophoblast stem cells, Day2, WT RNA-seq, biol rep 1 [D2-WT6]

description: Day 2 Peg3 WT sample 1

value: Day 2


title: Trophoblast stem cells, Day2, WT RNA-seq, biol rep 2 [D2-WT7]

description: Day 2 Peg3 WT sample 2


title: RKO cells, HL6_1, Day1

description: Library name: RKO_HL6_1

tag: cell line

value: HL6 treatment


title: RKO cells, DMSO_3, Day1

description: Library name: RKO_DMSO_3

tag: cell type

value: DMSO treatment


title: Trophoblast stem cells, Day2, Peg3 KO RNA-seq, biol rep 3 [Day2-KO44]

description: Day 2 Peg3 KO sample 3

tag: treatment


title: RKO cells, DMSO_1, Day1

description: Library name: RKO_DMSO_1

value: WT


title: Trophoblast stem cells, Day2, Peg3 KO RNA-seq, biol rep 1 [D2-KO19]

description: Day 2 Peg3 KO sample 1

value: Trophoblast stem cells


title: RKO cells, shDHODH_3, Day0

description: Library name: RKO_shDHODH_3

value: DHODH knockdown

value: Day 0


title: Paused, rep 4

city: Toronto

first: Giacomo

last: Furlan

address: 25 Orde St

institute: Lunenfeld-Tanenbaum Research Institute

description:
Library name: Sample 8
Ink_D

data_processing:
Read quality was assessed using FastQC. Paired-end reads were trimmed using Trim Galore, and only high-quality reads passing these steps were retained for downstream analysis.
Reads were aligned to the Mus musculus reference genome (mm10) using Bowtie2 (v2.4.1). Unaligned reads, mitochondrial reads, and PCR duplicates were removed at this stage.
Peak calling was performed with MACS3 (v3.0.3), using --nomodel and --nolambda parameters. Peaks overlapping with mouse ENCODE blacklist regions were excluded.
Differential accessibility analysis was performed in R using the DiffBind package (v3.16.0). Regions were considered significantly differentially accessible with a false discovery rate (FDR) < 0.05 and an absolute log₂ fold change > 1.
Genomic regions were annotated to nearby genes using GREAT (McLean et al., 2010), with the following settings: proximal = ±5 kb from transcription start site (TSS); distal = up to 1000 kb.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing normalized counts for all peaks in all samples

extract_protocol:
50,000 live cells were collected and resuspended in cold resuspension buffer (RSB: 10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂) supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Following lysis, nuclei were washed in RSB containing 0.1% NP-40 and subjected to tagmentation using the transposition mixture: 25 μL of 2× TD buffer, 2.5 μL of Tn5 transposase (100 nM final concentration), 16.5 μL of 1× PBS, 0.5 μL of 1% digitonin, 0.5 μL of 10% Tween-20, and 5 μL of nuclease-free water. After transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 Kit.
Library amplification was carried out as per protocol (Corces et al., 2017). Amplified libraries were purified using AMPure XP beads with a double-sided size selection to remove both primer dimers and large fragments (>1000 bp). Final libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit, pooled at equimolar concentrations, and sequenced on a NovaSeq X platform with a 10B flow cell, generating 150 bp paired-end reads.

value: embryonic stem cells

value: pausing conditions (200 nM INK128)


title: Trophoblast stem cells, Day0, WT RNA-seq, biol rep 3 [D0-WT9]

description: Day 0 Peg3 WT sample 3

value: stem (Day 0)


title: Trophoblast stem cells, Day0, WT RNA-seq, biol rep 2 [D0-WT7]

description: Day 0 Peg3 WT sample 2


title: Trophoblast stem cells, Day0, WT RNA-seq, biol rep 4 [D0-WT17]

description: Day 0 Peg3 WT sample 4


title: RKO cells, shNT_3, Day0

description: Library name: RKO_shNT_3

value: Human colorectal cancer cells

value: RKO

value: cell line


title: Trophoblast stem cells, Day0, WT RNA-seq, biol rep 1 [D0-WT6]

description: Day 0 Peg3 WT sample 1


title: RKO cells, shNT_2, Day0

description: Library name: RKO_shNT_2


title: Trophoblast stem cells, Day0, Peg3 KO RNA-seq, biol rep 3 [Day0-KO44]

description: Day 0 Peg3 KO sample 3

value: Peg3 KO


title: Paused, rep 3

description:
Library name: Sample 7
Ink_C


title: RKO cells, shNT_1, Day0

description: Library name: RKO_shNT_1


title: Trophoblast stem cells, Day0, Peg3 KO RNA-seq, biol rep 2 [D0-KO34]

description: Day 0 Peg3 KO sample 2


title: WTF

city: Ribeirão Preto

first: Matheus

middle: Mertz

last: Ribeiro

state: São Paulo

address: Av. Prof. Dr. Zeferino Vaz - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900

department: Faculty of Pharmaceutical Sciences of Ribeirão Preto

country: Brazil

institute: University of São Paulo

description: Library name: Sample6

data_processing:
Trimmed reads were then mapped to P. aeruginosa PA14 reference genome using Bowtie2 v.2.4.2 with default parameters for end-to-end alignment. Read summarization was performed using featureCounts. DESeq2 was employed to analyze differentially expressed genes.
Assembly: GCA_000002655.1 (A. fumigatus Af293) - GCF_000006765.1 (P. aeruginosa PAO1)
Supplementary files format and content: RNAseq_A_fumigatus.csv
Supplementary files format and content: RNAseq_P_Aeruginosa.csv

organism: Aspergillus fumigatus

source_name: biofilm

extract_protocol:
Total RNAs of cultures of early dual biofilm interactions of 24 and 48 h were extracted by the TRIzol method, treated with RQ1 RNase-free DNase I (Promega), and purified using the RNAeasy kit (Qiagen) according to the manufacturer’s instructions. The total RNA was quantified using a NanoDrop, and its integrity was analyzed using an Agilent 2100 Bioanalyzer. All RNA had a minimum RNA integrity number value of 8.0. For RNA sequencing, the cDNA libraries were constructed using the TruSeq Total RNA with Ribo Zero (Illumina, San Diego, CA, USA).
mRNA library  preparation (poly A enrichment)

value: biofilm

value: AF WT

value: Monoculture


title: SLNPAF

description: Library name: Sample5

value: AF slnA (mutant) + PA WT

value: Coculture


title: HepG2 ARID1B-KO IgG CUT&RUN, Sorafenib, rep2

city: Chapel Hill

first: Jacqueline

last: Brinkman

address: 120 Mason Farm Rd

department: Genetics

institute: Unversity of North Carolina-Chapel Holl

description: Library name: HepG2_ARID1B-KO_Sorafenib_IgG_rep2

data_processing:
Bowtie2 alignment to GRCh38. MACS2 peak calling (-f BAMPE). MSPC consensus peaks. csaw normalization. DESeq2 differential occupancy. deepTools bigWig generation.
Assembly: GRCh38 / hg38
Supplementary files format and content: RPKM-normalized bigWig (*_rpkm.bw), csaw-scaled bigWig (*_scaled.bw), MACS2 narrowPeak (*_peaks.narrowPeak; absent for IgG controls). Note: scaled bigWig absent for HepG2_ARID1B-KO_Sorafenib_IgG_rep1 and rep2.
Library strategy: CUT&Run

growth_protocol: HepG2 (CVCL_0027) and HLF (CVCL_2947) maintained at 37°C, 5% CO2 in DMEM/10% FBS/1% P-S.

extract_protocol:
CUT&RUN adapted from EpiCypher protocol. 200,000-500,000 cells, Concanavalin A beads, overnight primary antibody at 4°C (H3K4me3 CST #3076423; H3K27ac CST #2561016; ARID1B CST #65747 clone E1U7D; FOXA1; FOXA2; IgG CST #550038), guinea pig anti-rabbit secondary (Novus NBP1-72763 1:100), pAG-MNase 700 ng/ml 1 h 4°C, CaCl2 digestion on ice 30 min, stop buffer quench, Zymo D4014 cleanup.
KAPA HyperPrep Kit (Roche #07962363001). 14 PCR cycles. Paired-end 50 bp or 150 bp reads on Illumina NextSeq 1000 (HepG2) or NovaSeq X Plus 10B (HLF).

treatment_protocol: Sorafenib: 5 µM (Selleckchem S1040) 48 h. Vehicle: equivalent DMSO. ARID1B-KO by CRISPR/Cas9.

value: sorafenib 5 µM, 48 h

tag: antibody

value: IgG

tag: biological replicate


title: HepG2 ARID1B-KO IgG CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_ARID1B-KO_Sorafenib_IgG_rep1

tag: genotype


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t11hr Post-Splice BiolRep6

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

institute: Washington University in St. Louis

description: Library name: 3UTR.ActD.Eleven.Post.6

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38
Supplementary files format and content: counts.txt

source_name: kidney

growth_protocol: In Vitro: HEK cells were maintained in EMEMsupplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol Reagent and Zymo Clean and Concentrator Kit. 5ug of RNA per replicate were used for Library Preparation.
RNA libraries for RNA-seq were prepared using a targeted-RNA seq library preparation approach that followed similar paradigms to a Tru-Seq library construction for Illumina Sequencing.

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA. ActinomycinD:Transfection was induced on 24 hours after plating, and then on set of cells were harvested 48hours after.  5ug/mL ActinomycinD was added to the two remaining sets of cells, and one was harvested 5 hours post addition, and the final at 11 hours post addition.

tag: tissue

value: kidney

value: human embryonic kidney cells

value: WT

value: ISOMPRA Library Transfection


title: HepG2 ARID1B-KO ARID1B CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_ARID1B-KO_Sorafenib_ARID1B_rep1


title: HepG2 ARID1B-KO ARID1B CUT&RUN, Sorafenib, rep2

description: Library name: HepG2_ARID1B-KO_Sorafenib_ARID1B_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t11hr Post-Splice BiolRep5

description: Library name: 3UTR.ActD.Eleven.Post.5


title: HepG2 ARID1B-KO H3K4me3 CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_ARID1B-KO_Sorafenib_H3K4me3_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t11hr Post-Splice BiolRep4

description: Library name: 3UTR.ActD.Eleven.Post.4


title: HepG2 ARID1B-KO H3K27ac CUT&RUN, Sorafenib, rep2

description: Library name: HepG2_ARID1B-KO_Sorafenib_H3K27ac_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t11hr Post-Splice BiolRep2

description: Library name: 3UTR.ActD.Eleven.Post.2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t11hr Post-Splice BiolRep1

description: Library name: 3UTR.ActD.Eleven.Post.1


title: HepG2 ARID1B-KO IgG CUT&RUN, DMSO, rep2

description: Library name: HepG2_ARID1B-KO_DMSO_IgG_rep2

value: DMSO vehicle (0.1% v/v)


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t5hr Post-Splice BiolRep6

description: Library name: 3UTR.ActD.Five.Post.6


title: HepG2 ARID1B-KO IgG CUT&RUN, DMSO, rep1

description: Library name: HepG2_ARID1B-KO_DMSO_IgG_rep1


title: HepG2 ARID1B-KO ARID1B CUT&RUN, DMSO, rep2

description: Library name: HepG2_ARID1B-KO_DMSO_ARID1B_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t5hr Post-Splice BiolRep4

description: Library name: 3UTR.ActD.Five.Post.4


title: HepG2 ARID1B-KO ARID1B CUT&RUN, DMSO, rep1

description: Library name: HepG2_ARID1B-KO_DMSO_ARID1B_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t5hr Post-Splice BiolRep3

description: Library name: 3UTR.ActD.Five.Post.3


title: HepG2 ARID1B-KO H3K4me3 CUT&RUN, DMSO, rep2

description: Library name: HepG2_ARID1B-KO_DMSO_H3K4me3_rep2


title: HepG2 ARID1B-KO H3K4me3 CUT&RUN, DMSO, rep1

description: Library name: HepG2_ARID1B-KO_DMSO_H3K4me3_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t5hr Post-Splice BiolRep1

description: Library name: 3UTR.ActD.Five.Post.1


title: HepG2 ARID1B-KO H3K27ac CUT&RUN, DMSO, rep2

description: Library name: HepG2_ARID1B-KO_DMSO_H3K27ac_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Post-Splice BiolRep6

description: Library name: 3UTR.ActD.Zero.Post.6


title: HepG2 ARID1B-KO H3K27ac CUT&RUN, DMSO, rep1

description: Library name: HepG2_ARID1B-KO_DMSO_H3K27ac_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Post-Splice BiolRep5

description: Library name: 3UTR.ActD.Zero.Post.5


title: HepG2 WT IgG CUT&RUN, Sorafenib, rep2

description: Library name: HepG2_WT_Sorafenib_IgG_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Post-Splice BiolRep4

description: Library name: 3UTR.ActD.Zero.Post.4


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t5hr Post-Splice BiolRep2

description: Library name: 3UTR.ActD.Five.Post.2


title: HepG2 WT IgG CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_WT_Sorafenib_IgG_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Post-Splice BiolRep3

description: Library name: 3UTR.ActD.Zero.Post.3


title: HepG2 WT ARID1B CUT&RUN, Sorafenib, rep2

description: Library name: HepG2_WT_Sorafenib_ARID1B_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Post-Splice BiolRep2

description: Library name: 3UTR.ActD.Zero.Post.2


title: HepG2 WT ARID1B CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_WT_Sorafenib_ARID1B_rep1


title: Trophoblast stem cells, Day4, WT RNA-seq, biol rep 1 [D4-WT6]

description: Day 4 Peg3 WT sample 1

value: Trophoblast stem cells

value: Day 4


title: Trophoblast stem cells, Day4, WT RNA-seq, biol rep 2 [D4-WT7]

description: Day 4 Peg3 WT sample 2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Post-Splice BiolRep1

description: Library name: 3UTR.ActD.Zero.Post.1


title: Trophoblast stem cells, Day4, Peg3 KO RNA-seq, biol rep 1 [D4-KO19]

description: Day 4 Peg3 KO sample 1


title: Trophoblast stem cells, Day2, WT RNA-seq, biol rep 3 [D2-WT9]

description: Day 2 Peg3 WT sample 3

value: Day 2


title: Trophoblast stem cells, Day2, WT RNA-seq, biol rep 4 [D2-WT17]

description: Day 2 Peg3 WT sample 4


title: HepG2 WT H3K4me3 CUT&RUN, Sorafenib, rep2

description: Library name: HepG2_WT_Sorafenib_H3K4me3_rep2


title: Trophoblast stem cells, Day2, Peg3 KO RNA-seq, biol rep 2 [D2-KO34]

description: Day 2 Peg3 KO sample 2


title: RKO cells, DMSO_2, Day1

description: Library name: RKO_DMSO_2

value: Human colorectal cancer cells

value: RKO

value: cell line

value: DMSO treatment

value: Day 1


title: HepG2 WT H3K4me3 CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_WT_Sorafenib_H3K4me3_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Pre-Splice BiolRep6

description: Library name: 3UTR.ActD.Zero.Pre.6


title: HepG2 WT H3K27ac CUT&RUN, Sorafenib, rep2

description: Library name: HepG2_WT_Sorafenib_H3K27ac_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Pre-Splice BiolRep4

description: Library name: 3UTR.ActD.Zero.Pre.4


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Pre-Splice BiolRep5

description: Library name: 3UTR.ActD.Zero.Pre.5


title: HepG2 WT H3K27ac CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_WT_Sorafenib_H3K27ac_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Pre-Splice BiolRep3

description: Library name: 3UTR.ActD.Zero.Pre.3


title: RKO cells, shDHODH_2, Day0

description: Library name: RKO_shDHODH_2

value: DHODH knockdown

value: Day 0


title: RKO cells, shDHODH_1, Day0

description: Library name: RKO_shDHODH_1


title: HepG2 WT IgG CUT&RUN, DMSO, rep2

description: Library name: HepG2_WT_DMSO_IgG_rep2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Pre-Splice BiolRep2

description: Library name: 3UTR.ActD.Zero.Pre.2


title: HepG2 WT IgG CUT&RUN, DMSO, rep1

description: Library name: HepG2_WT_DMSO_IgG_rep1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t0 Pre-Splice BiolRep1

description: Library name: 3UTR.ActD.Zero.Pre.1


title: HepG2 WT ARID1B CUT&RUN, DMSO, rep2

description: Library name: HepG2_WT_DMSO_ARID1B_rep2


title: HepG2 WT ARID1B CUT&RUN, DMSO, rep1

description: Library name: HepG2_WT_DMSO_ARID1B_rep1


title: PASLNB

description: Library name: Sample2

organism: Pseudomonas aeruginosa

value: biofilm

value: PA WT + AF slnA (mutant)

value: Coculture


title: PAB

description: Library name: Sample1

value: PA WT

value: Monoculture


title: PAWTB

description: Library name: Sample3

value: PA WT + AF WT


title: WTPAF

description: Library name: Sample7

value: AF WT + PA WT


title: HepG2 WT H3K4me3 CUT&RUN, DMSO, rep2

description: Library name: HepG2_WT_DMSO_H3K4me3_rep2

value: WT

value: DMSO vehicle (0.1% v/v)


title: HepG2 WT H3K4me3 CUT&RUN, DMSO, rep1

description: Library name: HepG2_WT_DMSO_H3K4me3_rep1


title: GSK3B knockout RKO Input ChIP-Seq 1

city: Suzhou

first: Xiaoqin

last: Yang

address: NO. 199 Renai Road

institute: Soochow University

description: Library name: GSK3B knockout RKO Input ChIP-Seq 1

data_processing:
Reads were aligned to the reference genome (hg38) using Bowtie2. Subsequently, duplicates, multi mapping reads, and low quality alignments were removed using SAMtools. Mitochondrial reads, chromosome Y alignments, and ENCODE blacklisted genomic regions were excluded. Peaks were called using MACS3 with the settings -f BAMPE -B --nomodel --SPMR --keep-dup 1. For histone modification ChIP-Seq, peak calling was performed  with --broad option enabled.
Assembly: hg38
Supplementary files format and content: BigWig (except for Input sample)

source_name: RKO cell

extract_protocol:
The chromatin immunoprecipitation (ChIP) protocol was performed to analyze histone modifications. Briefly, cells were collected and treated with 1% formaldehyde for 10 minutes at room temperature to induce crosslinking. After sonication, an anti-H3K27ac antibody was used for immunoprecipitation, and then the DNA was extracted and purified using the Universal DNA Purification Kit.
The ChIP-seq library was prepared using the ChIP-Seq DNA sample preparation kit (NEBNext Ultra II DNA) according to the manufacturer’s instructions. Then, these H3K27ac ChIP-Seq libraries were quantified using Qubit fluorometric assay (ThermoFisher) and sequenced on an Illumina Novaseq 6000 sequencer (Illumina, San Diego, California, United States) using the PE150 strategy.

value: RKO cell


title: Trophoblast stem cells, Day0, Peg3 KO RNA-seq, biol rep 1 [D0-KO19]

description: Day 0 Peg3 KO sample 1

value: Trophoblast stem cells

value: Peg3 KO

value: stem (Day 0)


title: HepG2 WT H3K27ac CUT&RUN, DMSO, rep2

description: Library name: HepG2_WT_DMSO_H3K27ac_rep2


title: HepG2 WT H3K27ac CUT&RUN, DMSO, rep1

description: Library name: HepG2_WT_DMSO_H3K27ac_rep1


title: GSK3B wild-type RKO Input ChIP-Seq 1

description: Library name: GSK3B wild-type RKO Input ChIP-Seq 1


title: GSK3B knockout RKO H3K27ac ChIP-Seq 1

description: Library name: GSK3B knockout RKO H3K27ac ChIP-Seq 1


title: SLNF

description: Library name: Sample4

value: AF slnA (mutant)


title: HepG2 ARID1B-KO RNA-seq, Sorafenib, rep2

description: Library name: HepG2_ARID1B-KO_Sorafenib_RNAseq_rep2

data_processing:
Quantification: Salmon (default parameters) against GRCh38/Ensembl 109. Gene-level summarization: tximeta v1.24.0 + tximport. Differential expression: DESeq2 v1.46.0, design ~genotype+treatment+genotype:treatment, apeglm shrinkage. Genes <10 counts in >=3 samples excluded.
Assembly: GRCh38 / Ensembl release 109
Supplementary files format and content: Per-sample Salmon quant.sf (tab-delimited: Name, Length, EffectiveLength, TPM, NumReads). Shared: DESeq2 raw count matrix, normalized count matrix, sample metadata table.

growth_protocol: HepG2 (CVCL_0027) maintained at 37°C, 5% CO2 in DMEM/10% FBS/1% P-S.

extract_protocol:
1x10^6 cells pelleted (500xg, 1 min). Total RNA isolated with Monarch Total RNA Miniprep Kit (NEB T1010) with on-column DNase I digestion.
KAPA mRNA HyperPrep Kit (Roche #08098123702) from 750 ng total RNA. Fragmentation 6 min 94°C. Adapter ligation 7 µM stock. 9 PCR cycles. Paired-end 75 bp on Illumina NextSeq 100.

value: sorafenib 5 µM, 48 h


title: HepG2 ARID1B-KO RNA-seq, Sorafenib, rep3

description: Library name: HepG2_ARID1B-KO_Sorafenib_RNAseq_rep3


title: GSK3B wild-type RKO H3K27ac ChIP-Seq 1

description: Library name: GSK3B wild-type RKO H3K27ac ChIP-Seq 1


title: HepG2 ARID1B-KO RNA-seq, Sorafenib, rep1

description: Library name: HepG2_ARID1B-KO_Sorafenib_RNAseq_rep1


title: WSU-DLCL2_DOT1Li_Rep3

city: Amsterdam

first: Rachele

last: Niccolai

address: Plesmanlaan 121

department: Tumor Biology and Immunology

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Sample8.3

data_processing:
FASTQ files were produced by BCL Convert using demultiplexing.
Sample distribution was based on indexing using IDT UDI indexes.
Seqpurge was used for adapter trimming.
RNA-seq data were aligned with STAR against reference genome GRCh38, and reads were counted and annotated per gene using GenSum (https://www.github.com/NKI-GCF/gensum) against Ensembl GRCh38.107.
DESeq2 package was used to normalize read counts and to obtain the differential gene expression of RNA-seq samples.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files includes raw counts for each sample

growth_protocol: SUDHL10, WSU-DLCL2, and SUDHL4 were maintained in IMDM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen).
RNA-seq libraries were prepared using the xGen polyA+ stranded RNA library kit, according to manufacturer’s protocol.

treatment_protocol: SUDHL10, WSU-DLCL2, and SUDHL4 GCB-DLBCL cell lines were treated for six days with the following concentrations of EPZ-5676 (DOT1Li): 100 nM for SUDHL10; and 250 nM for WSU-DLCL2 and SUDHL4; and the following concentration of GSK343 (EZH2i): 5 µM for SUDHL4. At day 3, 5x10^4 cells/ml were reseeded with fresh medium and inhibitors.

value: GCB-DLBCL


title: GSK3B knockout RKO ATAC-Seq 1

description: Library name: GSK3B knockout RKO ATAC-Seq 1

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina, San Diego, California, United States) using the PE150 strategy.
The original ATAC-Seq reads were trimmed of adapter sequences using fastp. The trimmed reads were then aligned to the reference genome (hg38) using Bowtie2. Subsequently, duplicates, multi mapping reads, and low quality alignments were removed using SAMtools. Mitochondrial reads, chromosome Y alignments, and ENCODE blacklisted genomic regions were excluded. Peaks were called using MACS3 with the settings -f BAMPE -B --nomodel --SPMR --keep-dup 1.
Assembly: hg38
Supplementary files format and content: BigWig

source_name: RKO cells

extract_protocol:
ATAC sequencing service was provided by CloudSeq Biotech (Shanghai, China) with GenSeq® ATAC kit (GenSeq Inc.). Briefly, cells were lysed using cold lysis buffer. After lysis, nuclei were collected by centrifuging at 500 g for 10 min at 4℃. The pellet was transposed with transposome and tags were added on both sides of fragmented genomic DNA according to the manufacturer's instruction.
After tagmentation, the purified tagged DNA was used for PCR amplification with GenSeq® 2×HiFi PCR Mix (GenSeq Inc.). The libraries were quantified using Qubit fluorometric assay (ThermoFisher).

value: RKO cells


title: HepG2 ARID1B-KO RNA-seq, DMSO, rep2

description: Library name: HepG2_ARID1B-KO_DMSO_RNAseq_rep2


title: HepG2 ARID1B-KO RNA-seq, DMSO, rep3

description: Library name: HepG2_ARID1B-KO_DMSO_RNAseq_rep3