title: ALKBH5 knockout, H3K9ac-ChIP, rep2

data_processing:
Raw reads were aligned to human hg38 reference genome using Bowtie2 (v2.4.5)
PCR duplication was removed by Picard (v2.27.3) MarkDuplicates
Unique reads were filtered by MAPQ > 1 using samtools (1.15.1) view with parameters ‘-hb -p 1’
For improving the quantification accuracy, a ChIP-seq normalization method, ChIPseqSpikeInFree, was employed to calculate the scale factors for all ChIP-seq samples.
Genome coverage bigwig files for Integrative Genomics Viewer visualization were generated by deeptools (v3.5.1)48 bamCoverage using scale factors for the normalization
Peaks were generated by macs2 (v2.2.7.1)49 callpeak with parameters ‘--BROAD --BROAD-CUTOFF -p’.
Peak annotation was carried out using Homer (v4.8.2) annotatePeaks.pl.
The overlap of ChIP-seq peaks was analyzed by bedtools (v2.30.0) intersect.
Heat maps were generated by deeptools (v3.5.1) computeMatrix and plotHeatmap.
ChIP–seq density was calculated by Homer (v4.8.2) analyzeRepeats.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
the cells were crosslinked with 1% formaldehyde at room temperature for 10 min with gentle shaking, and quenched with 125 mM glycine for 10 min. After washing with ice-cold PBS buffer for three times, the cells were resuspended in cell lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.5% NP-40, protease inhibitors) at 4°C on a rotator for 20 min. After centrifugation at 3000 g for 3 min, the pellets were resuspended in RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitors) and rotated at 4°C for 20 min, followed by a brief sonication on a Qsonica Sonicator q125 (42% amplitude, 10s on/10s off, 80 s). After incubation for another 20 min, cell lysate was sonicated on a Covaris S220 Sonicator for 6 min with a peak incident power of 140 W, a duty cycle of 10.1% and 200 cycles per burst at 4°C. After centrifugation at 4°C for 10 min, 50 µL of supernatant was saved as “Input” sample, and the rest of supernatant was subjected to IP experiment.
The DNA-sequencing library was prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions.

treatment_protocol: HEK293T and METTL3-/- cells were plated in 100 mm dishes at ~35% confluency a day before transfection. On the next day, the cells were transfected with empty vector, wild-type or D395A METTL3 plasmid.

value: ALKBH5 knockout

tag: chip antibody

value: H3K9ac (Abcam, #ab4441)


title: ALKBH5 knockout, H3K9ac-ChIP, rep1

status: Public on Dec 01 2025

type: SRA

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

country: USA

institute: UC-Riverside

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype


title: PAO1 at 25°C stationary replicate C

city: Atlanta

first: Rachel

middle: Evans

last: Robinson

state: GA

address: 1510 Clifton Road NE

department: Pediatrics

institute: Emory University

description: Library name: WT_25_stat_C

library_source: transcriptomic

data_processing:
Demultiplexing, quality control, and adaptor trimming using bcl-convert (v3.9.3) (this step only performed by SeqCenter)
Read mapping using bowtie2 (v2.4.5) to reference genome NC_002516.2) for P. aeruginosa PAO1
Raw read quantification using htseq-count (v2.0.2)
Differential gene expression analysis using DESeq2 (v1.38.3)
Assembly: NC_002516.2
Supplementary files format and content: Tab-delimited text file containing raw counts produced by htseq-count for all samples. Note, the first column provides the PA locus number (gene/transcript unique identifier corresponding to reference genome).

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: Bacterial

growth_protocol: Bacteria were grown at 37°C or 25°C, as indicated, in LB shaking at 200 rpm. Samples were collected first at exponential phase (OD ~ 0.5) and then again from the same cultures at stationary phase (OD ~2.0).

extract_protocol:
Standard TRI reagent protocol (phenol/chloroform based) for RNA extraction
Library construction was performed by SeqCenter (Pittsburgh, PA, USA) using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus depletion kit and 10 bp IDT for Illumina indices.

treatment_protocol: Cells were harvested by centrifugation and immediately used in RNA extraction protocol (below).

value: Bacterial

tag: strain

value: Wild-type

tag: temperature

tag: growth phase

value: stationary - OD ~ 2.0


title: 293T, 10min, RNA-seq rep1

data_processing:
Raw reads were aligned to human hg38 reference genome and supplemented with the sequences of the ERCC spike-in control using HISAT2 (v2.2.1) with parameters ‘-rna-strandness RF’
Reads on each gene were counted using featureCounts and then normalized to reads per kilo base per million mapped reads (RPKM)
Assembly: hg38
Supplementary files format and content: tab-delimited text files from featureCounts

extract_protocol:
total RNA was extracted using Trizol reagent. Nascent RNA was captured by using Click-iT Nascent RNA Capture Kit (Invitrogen).
Library preparation was conducted on-beads with SMARTer Stranded Total RNA-seq Kit v2 (Takara)

treatment_protocol: 5-ethynyluridine (EU) was added until its concentration reached 0.5 mM. The cells were harvested at 10, 20, 30, and 60 min later

value: WT

tag: treatment

tag: time

tag: molecule subtype

value: Nascent RNA


title: HC06

type: RNA

city: Houston

first: Cintia

middle: Sade

last: de Paiva

state: Texas

address: One Baylor Plaza

department: Ophthalmology

institute: Baylor College of Medicine

description: Age and sex matched control

hyb_protocol: Hybridization of the sample mixed with reporter codeset and capture probeset was done at 65°C for 20 h (according to manufacture's protocol)

scan_protocol: Samples were purified, immobilized on cartridges and scanned on the nCounter® SPRINT Profiler (nanoString Technologies)

data_processing: The raw RCC files were uploaded onto the nSolver software, raw counts were measured, stable houskeeping genes for normalization was identified using NormFinder, an excel plug-in software, and data were subsequently normalized to obtain normalized counts. The normalized counts were used for the final evaluations. The data was analyzed using ROSALIND (https://rosalind.bio/), which features a HyperScale architecture developed by ROSALIND, Inc. (San Diego, California, USA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes, and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library{Perkins, 2012 #1650}. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library{Hennig, 2024 #1651} that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. The hypergeometric distribution was used to analyze the enrichment of pathways, Gene Ontology, domain structure, and other ontologies. The topGO R library{A. Alexa, 2024 #1523}, was used to determine local similarities and dependencies between GO terms to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro{Mitchell, 2019 #1530}, NCBI{Geer, 2010 #1525}, MSigDB{Subramanian, 2005 #1532;Liberzon, 2011 #1536}, REACTOME{Fabregat, 2018 #1529}, and WikiPathways{Slenter, 2018 #1528}. Enrichment was calculated relative to a set of background genes relevant for the experiment.

source_name: Conunctival cells

label_protocol: Samples were then submitted to the Baylor College of Medicine Genomic and RNA Profiling core with the NanoString Human Immunology V2 panel (www.nanostring.com) for analysis. Five hundred ninety-four transcripts were quantified with the NanoString nCounter multiplexed target platform using the Human Immunology V2 panel. nCounts of mRNA transcripts were normalized using the geometric means of 15 housekeeping genes (ABCF1, ALAS1, EEF1G, G6PD, GAPDH, GUSB, HPRT1, OAZ1, POLR1B, POLR2A, PPIA, RPL19, SDHA, TBP, TUBB).

extract_protocol: A topical anesthetic was applied onto the eye immediately before collection. Samples of the temporal bulbar conjunctiva were collected using the EyePrim device (Opia Tech, Paris, France). Samples were ejected into tubes containing RNA lysis buffer and 1% 2-mercaptoethanol and immediately stored at -80°C. Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Valencia, California, USA) following the manufacturer's protocol. Samples were eluted into RNase-free water.

tag: Sex

value: F

tag: diagnosis

value: Control

tag: severity level

tag: age


title: HC05

description: Age and sex matched control


title: HC04

description: Age and sex matched control


title: Input_DMSO_Rep1

city: Boston

first: Mohamad Ali

last: Najia

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Library name: Input_DMSO_Rep1

data_processing:
ChIP-seq libraries were processed using the nf-core/chipseq pipeline v2.0.0 (https://doi.org/10.5281/zenodo.3240506) implemented in the NextFlow software package (v23.10.1). In brief, single-end reads were trimmed of adaptor sequences with trim-galore (v0.6.7) and aligned with BWA (v0.7.17-r1188) to the GRCh38 assembly of the human genome. Reads aligning to ENCODE blacklist sites (ENCFF356LFX) were omitted. Duplicate reads were removed with Picard (v2.27.4) with the MarkDuplicates tool. Peaks for H3K4me3 and H3K27ac ChIP-seq experiments were identified with MACS2 (v2.2.7.1) using the BAM files of the input ChIP-seq control and histone ChIP-seq samples with the following command line parameters: --keep-dup all --broad --broad-cutoff 0.1 --gsize 2701262066. We created bigwig files for visualization using bamCoverage from the deepTools package (v3.5.1) with the following command line options: --binSize 20 --normalizeUsing RPKM --smoothLength 60 --extendReads 150 --centerReads.  To identify genomic regions with differential H3K9me2 or H3K9me3 enrichment in JIB-04 treated cells, we performed window-based analyses using the csaw package (v1.34.0) in R due to the broad distribution of these histone marks on chromatin. Aligned reads were extended to 200 bp and counted into 2kb windows for each ChIP-seq library. Reads were also counted into 10kb bins, and the median average abundance of all bins was used as a global estimate of the background abundance. Windows were filtered to retain only those with a two-fold or greater increase in the average abundance above the scaled background estimate. Counts from the remaining windows were tested for significant ChIP signal enrichment using edgeR (v3.42.4). Briefly, an abundance-dependent trend in the NB dispersions was fitted to all windows, using the estimateDisp function. A GLM was fitted to the counts for each window using the trended NB dispersion. The quasi-likelihood (QL) dispersion was estimated from the GLM deviance. An abundance-dependent trend was robustly fitted to the QL dispersions across all windows, and the QL dispersion estimate for each window was shrunk to this trend. Finally, a P value for differential ChIP signal in each window was computed using the QL F-test.
Assembly: GRCh38
Supplementary files format and content: Counts matrix of NGS reads in a consensus set of H3K27ac peaks across all samples (tab-delimited text file)
Supplementary files format and content: Counts matrix of NGS reads in a consensus set of H3K4me3 peaks across all samples (tab-delimited text file)
Supplementary files format and content: bw files

growth_protocol: OCI-Ly1 cells were cultured in IMDM + 10% FBS + Penicillin-Streptomycin.

extract_protocol:
For ChIP-Seq experiments, 10 million OCI-Ly1 cells were fixed with 1% formaldehyde for 10 minutes at room temperature before termination with 0.125 M glycine. Cells were then lysed in ChIP buffer (0.6% SDS, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) and cross-linked chromatin was sonicated to obtain DNA fragments of 300-800 bp. Chromatin was then centrifuged (10 min, 4°C, 13,000 rpm) and the supernatant was diluted 6-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, and 167 mM NaCl) with protease inhibitors (Roche Diagnostics). Diluted chromatin was incubated with 5 μg of primary antibody overnight at 4°C with agitation. Antibodies were pelleted using 50 μL of Dynabeads (ThermoFisher Scientific). The beads were sequentially washed once with the ChIP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl), the ChIP wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), the ChIP wash buffer 3 (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris pH 8), and finally the ChIP wash buffer 4 (10 mM Tris-HCl, 1 mM EDTA). Chromatin was eluted using ChIP Elution Buffer (1% SDS, 100mM NaHCO3). The cross-link between protein and DNA was reversed by heat incubation (65°C, overnight), and proteins were then digested with proteinase K. DNA was recovered by phenol-chloroform extraction and ethanol precipitation in presence of 20 µg of glycogen (Sigma Aldrich).
ChIP-seq libraries were prepared using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB cat. no. E6040). Libraries were single-end indexed and sequenced on an Illumina HiSeq 2000 to generate 50 bp single end reads.

treatment_protocol: Cells were treated with various doses of JIB-04 (Stem Cell Technologies cat. no. 73212) or 0.01% DMSO as a vehicle control.

value: DMSO


title: FTO knockout, H3K9ac-ChIP, rep1

value: FTO knockout


title: PAO1 at 25°C stationary replicate B

description: Library name: WT_25_stat_B


title: PAO1 at 25°C stationary replicate A

description: Library name: WT_25_stat_A


title: PLC_LV3

city: guangzhou

first: Zebing

last: Song

address: 250changgang road

country: China

institute: The Second Affiliated Hospital of Guangzhou Medical University

description:
Library name: sample12
PLC_LV3

data_processing:
HISAT2
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each Sample

extract_protocol:
RNA of HCC cells were extracted using Rneasy Mini Kit (74104, Qiagen, USA). The RNA samples were transported to Lianchuan Biotechnology Co., Ltd for libraries’ generation and sequencing.
Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform.

value: Hepatocellular Carcinoma Cell Line

value: Lenvatinib


title: HEK293T, H3K9ac-ChIP, rep2


title: PLC_LV1

description:
Library name: sample10
PLC_LV1


title: PLC_LV2

description:
Library name: sample11
PLC_LV2


title: ATD03

description: ATD = Aqueous tear deficient dry eye

value: ATD


title: HC03

description: Age and sex matched control


title: HEK293T, H3K9ac-ChIP, rep1


title: ALKBH5 knockout, Input


title: PAO1 at 37°C exponential replicate B

description: Library name: WT_37_exp_B

value: exponential - OD ~ 0.5


title: PAO1 at 37°C exponential replicate A

description: Library name: WT_37_exp_A


title: FTO knockout, H3K9ac-ChIP, rep2


title: FTO knockout, Input

description: Input-FTO


title: PLC_DMSO3

description:
Library name: sample9
PLC_DMSO3


title: PLC_DMSO1

description:
Library name: sample7
PLC_DMSO1


title: PLC_DMSO2

description:
Library name: sample8
PLC_DMSO2


title: PAO1 at 37°C exponential replicate C

description: Library name: WT_37_exp_C


title: PAO1 at 25°C exponential replicate B

description: Library name: WT_25_exp_B


title: ATD02

description: ATD = Aqueous tear deficient dry eye


title: 0.1% BIT 5H 8_10_17_A

city: Charlottesville

first: Jason

last: Papin

state: Virginia

address: 415 Lane Road Room 2041

department: Biomedical Engineering

institute: University of Virginia

data_processing:
Reads were aligned to the reference P. aeruginosa PA14 genome (NC_008463.1) using the BWA aligner with the MEM algorithm with default parameters
Aligned reads were tallied for each gene using FeatureCounts
Differential expression was then determined with DESeq2
Genome_build: PA14 (NC_008463.1)
Supplementary_files_format_and_content: The counts files contain a table with the raw gene counts for every gene in each condition and replicate
Supplementary_files_format_and_content: Differential expression files are csvs with the results from DeSeq: Logfold change results for each gene between different groups and different timepoints

source_name: Persister 5H rep 2

growth_protocol: A frozen stock of PA14 wild-type was streaked on an LB agar plate and grown overnight. Individual colonies were inoculated into a 50 mL flask containing 10 mL of LB and grown overnight with aeration. The overnight cultures were diluted in fresh LB in 500 mL flasks to an OD600 of 0.01 for a total volume of 50 mL and grown for 12 hours to reach stationary phase.

extract_protocol:
One millilitre samples for RNA-sequencing were collected immediately before exposure, 5 and 24 hours after exposure from the untreated and 10X MIC conditions. Samples were mixed with 2 mL of RNAprotect (Qiagen) to stabilize RNA and frozen at -80 C.
RNA libraries were prepared for sequencing using standard Illumina protocols. Ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit (Illumina). Libraries were sequenced on an Illumina HiSeq4000, 2x150bp configuration

treatment_protocol: The cultures were then subsequently exposed to BIT by removing 5 mL of the culture and adding 5mL of antimicrobial at various concentrations (PBS for the untreated condition, 0.2% BIT for the 10X MIC condition, 2% BIT for the 100X MIC condition, and 20% BIT for the 1000X MIC condition).  The flasks were returned to the incubator for 24 hours.

value: Persister


title: METTL3 knockout with mutated METTL3 rescue, H3K9Ac-ChIP, rep2

value: H3K9Ac (Abcam, #ab4441)


title: HEK293T, Input (Input-WT)

description: Input-WT


title: PAO1 at 25°C exponential replicate C

description: Library name: WT_25_exp_C


title: HC02

description: Age and sex matched control


title: ATD01

description: ATD = Aqueous tear deficient dry eye


title: HC01

description: Age and sex matched control


title: PAO1 at 25°C exponential replicate A

description: Library name: WT_25_exp_A


title: METTL3 knockout with mutated METTL3 rescue, H3K9Ac-ChIP, rep1


title: NRP2_48hr_rep2

city: CDMX

first: Addy

middle: Cecilia

last: Helguera-Repetto

state: CDMX

address: Montes Urales

department: Inmunobioquímica

country: Mexico

institute: Instituto Nacional de Perinatología "Isidro Espinosa de los Reyes"

description:
TB_083208_12
Gene expression 48hr post infection of THP-1 macrophages with bacilli of the NRP2 phase (replicate 2)

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing  1 uL of 25x Agilent Fragmentation Buffer and 5 uL of 10x Agilent Gene Expresion Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent-083208 M. tb THP1 infection (ID 083208_1492716586532) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner using AgilentHD_GX_1color protocol (Scan resolution 5um).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 11.5.1 (Agilent) using protocol GE1_1105_Oct12 and customed grid:FullGEML_083208_D_F_20160404) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mycobacterium tuberculosis

source_name: THP-1 infection, NRP2 phase, 48hr, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA of M. tuberculosis and 100 ng RNA of THP-1 macrophages using  the Low Input Quick Amp Labeling kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy Mini Kit column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: M. tuberculosis H37Rv was grown in Dubos broth (Difco™, USA). Aerobic bacteria were grown in agitation (180 rpm) at 37 °C and collected at the mid-log phase (OD600= 0.45) (Log phase). Then, the hypoxic dormant bacilli (NRP1 and NRP2 phases) were obtained by using the Wayne and Hayes model.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes differential lysis of bacilli of M. tuberculosis and THP-1 macrophages, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: THP-1 macrophages were infected with M. tuberculosis from either the Log phase of growth or the NRP1 or NRP2 latency phases in vitro (Model by Wayne and Hayes, 1996). The cultures were incubated for 24 or 48 hours at 37 ºC in a humidified incubator with 5% CO2

tag: phase

value: NRP2 48hr


title: Huh7_LV2

description:
Library name: sample5
Huh7_LV2


title: E. coli T4 phage infection, RNA004 chemistry

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

description: tRNA sequencing (RNA004)

library_source: other

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

molecule: other

organism: Escherichia coli

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004

value: T4 phage infection


title: NRP2_48hr_rep1

description:
TB_083208_11
Gene expression 48hr post infection of THP-1 macrophages with bacilli of the NRP2 phase (replicate 1)

source_name: THP-1 infection, NRP2 phase, 48hr, replicate 1


title: METTL3 knockout with wildtype METTL3 rescue, H3K9Ac-ChIP, rep2

value: Human embryonic kidney


title: Huh7_DMSO3

description:
Library name: sample3
Huh7_DMSO3


title: Huh7_LV1

description:
Library name: sample4
Huh7_LV1


title: NRP2_24hr_rep1

description:
TB_083208_9
Gene expression 24hr post infection of THP-1 macrophages with bacilli of the NRP2 phase (replicate 1)

source_name: THP-1 infection, NRP2 phase, 24hr, replicate 1

value: NRP2 24hr


title: METTL3 knockout with wildtype METTL3 rescue, H3K9Ac-ChIP, rep1


title: NRP2_24hr_rep2

description:
TB_083208_10
Gene expression 24hr post infection of THP-1 macrophages with bacilli of the NRP2 phase (replicate 2)

source_name: THP-1 infection, NRP2 phase, 24hr, replicate 2


title: E. coli, RNA002 chemistry

description: tRNA sequencing (RNA002)

source_name: strain MG1655

value: strain MG1655


title: METTL3 knockout, H3K9Ac-ChIP, rep2


title: D3.5 epiERa-/- Knockout Digested Uterus 32

city: Athens

first: Xiaoqin

last: Ye

state: Georgia

address: 501 D.W. Brooks Drive

department: Physiology and Pharmacology

institute: The University of Georgia

description:
Library name: DU-E32
Column name in geo_count.txt and geo_TPM.txt: DU-E32

data_processing:
The kallisto tool (v0.46.1) was applied to quantify the expression information from the sequencing data.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file "geo_tpm" contains transcript per million values for each sample.
Supplementary files format and content: tab delimited text file "geo_counts" contains the raw count values for each sample.

organism: Mus musculus

source_name: Digested uterus

extract_protocol:
For each uterus, ¼ of one uterine horn was fixed in 10% formalin and ¼ of the other uterine horn was flash-frozen on dry-ice, designated as “U” (uterus), the remaining ¾ uterine horns connected by the cervix were slit open, immersed in 0.5% dispase (REF#17105-041, gibco, Waltham, MA, USA) in 1xHBSS buffer without calcium or magnesium (REF#1415-052, gibco, Waltham, MA, USA) for 30 min in a 6-cm culture dish, modified from our previous procedure (3-5). To determine the effects of enzymatic digestion process on uterine gene expression, we collected a small piece of digested uterine tissue prior to being processed for LE isolation. The small piece of digested uterine tissue was frozen on dry-ice and designated as “DU” (digested uterus). The LE layer in the remaining uterine tissue was gently scraped. The dislodged LE sheets were collected into a 1.5 ml microcentrifuge tube using a 200 μl pipette tip under a dissection microscope, centrifuged at 2000g for 3 minutes. Upon the removal of the buffer, 1 ml of TRIzol (REF# 15596018, Invitrogen, Carlsbad, CA, USA) was added to the LE pellet, which was gently vortexed to disperse the LE pellet, and kept at -20oC. The U and DU tissues were carefully powdered in liquid N2 using a mortar and pestle, collected into a 1.5 ml microcentrifuge tube, in which 1 ml of TRIzol was added, and upon gentle vortexing to disperse the uterine powder, the tube was kept at -20oC. At the conclusion of tissue collection, the LE, DU, and U samples in TRIzol were processed as one batch per tissue for total RNA isolation.
A total amount 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.

tag: tissue

value: Digested uterus

value: epiERa-/- (Esr1f/-Wnt7aCre/+)

value: Female

tag: day of_pregnancy

value: Day 3.5 post coitum


title: NRP1_48hr_rep1

description:
TB_083208_7
Gene expression 48hr post infection of THP-1 macrophages with bacilli of the NRP1 phase (replicate 1)

source_name: THP-1 infection, NRP1 phase, 48hr, replicate 1

value: NRP1 48hr


title: Huh7_DMSO2

description:
Library name: sample2
Huh7_DMSO2

value: WT

value: DMSO


title: D3.5 epiERa-/- Knockout Digested Uterus 35

description:
Library name: DU-E35
Column name in geo_count.txt and geo_TPM.txt: DU-E35


title: METTL3 knockout, H3K9Ac-ChIP, rep1

tag: chip antibody


title: NRP1_24hr_rep2

description:
TB_083208_6
Gene expression 24hr post infection of THP-1 macrophages with bacilli of the NRP1phase (replicate 2)

source_name: THP-1 infection, NRP1 phase, 24hr, replicate 2

value: NRP1 24hr


title: SjD01

description: SjD KCS = Sjӧgren disease keratoconjunctivitis sicca

value: F

value: SJD KCS


title: Huh7_LV3

description:
Library name: sample6
Huh7_LV3

tag: cell line

value: Hepatocellular Carcinoma Cell Line

value: Lenvatinib


title: Huh7_DMSO1

description:
Library name: sample1
Huh7_DMSO1

tag: cell type


title: HEK293T, H3K9Ac-ChIP, rep1

value: H3K9Ac (Abcam, #ab4441)


title: MCF7_CD44LOW_WM_2

city: London

first: Heena

last: Dhiman

address: 72 Du Cane Road

country: United Kingdom

institute: Imperial College London

description: Library name: MCF7_CD44LOW_WM_2

data_processing:
Trimming of adapters and low quality bases was performed using Trim-Galore v0.4.0
Reads were mapped to the mouse mm10 genome using Bowtie v2.2.9 (PMID: 22388286)
Reads with MAPQ lower than 10 were excluded from further analyses, and duplicated reads were removed (samtools v1.3.1, PMID: 33590861)
Accessible regions were identified using MACS v1.4.1 (PMID: 18798982) with the following parameters: --format=BAM --gsize=hs --bw=300 --nomodel --nolambda --shiftsize=150
Assembly: hg38
Supplementary files format and content: List of peaks called with MACS (BED format)

source_name: MCF7 CD44low facs-sorted

growth_protocol: MCF7 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal calf serum (FCS). Long-term oestrogen-deprived cells (LTED) were derived from MCF7 after one year oestrogen deprivation as previously described and were maintained in phenol-red free DMEM containing 10% charcoal stripped fetal calf serum (SFCS) (PMID: 26610607). Both media were supplemented with 2 mM L-glutamine, 100 units/mL penicillin and streptomycin. 10−8 M estradiol (E2758 Sigma) was added routinely to MCF7. LTED were maintained in phenol-red free DMEM containing 10% charcoal stripped foetal calf serum (SFCS), supplemented with 2 mM L-glutamine and 100 units/mL penicillin and streptomycin.

extract_protocol:
After sorting based on CD44 expression (FITC, BD Pharmingen) using a FACS Aria III (BD Biosciences) (Hong et al. 2019), 5 x 104 CD44high and CD44low cells were resuspended in 200 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630) and immediately centrifuged at 500 g for 10 minutes at 4°C. The nuclei were resuspended in a transposition reaction mix containing transposase (Illumina) and incubated at 37°C for 30 minutes. The DNA was purified using a Qiagen MinElute Kit (Qiagen).
Library preparation for next-generation sequencing was carried out following the manufacturer's instructions (New England Biolabs). Libraries were pooled and sequenced on an Illumina HiSeq 2000.

treatment_protocol: MCF7 cells were either growth in E2-supplemented medium, or treated with E2-depleted medium for 2 days, and sorted into CD44high and CD44low subpopulation.

value: MCF7 CD44low facs-sorted

value: E2 starvation for 2 days

tag: replicate


title: HEK293T, H3K9Ac-ChIP, rep2

value: Human embryonic kidney


title: D0.5 epiERa-/- Knockout Digested Uterus 27

description:
Library name: DU-E27
Column name in geo_count.txt and geo_TPM.txt: DU-E27

tag: genotype

value: Day 0.5 post coitum


title: MCF7_CD44LOW_WM_1

description: Library name: MCF7_CD44LOW_WM_1


title: METTL3 knockout, Input


title: NRP1_24hr_rep1

description:
TB_083208_5
Gene expression 24hr post infection of THP-1 macrophages with bacilli of the NRP1 phase (replicate 1)

source_name: THP-1 infection, NRP1 phase, 24hr, replicate 1


title: NRP1_48hr_rep2

description:
TB_083208_8
Gene expression 48hr post infection of THP-1 macrophages with bacilli of the NRP1 phase (replicate 2)

source_name: THP-1 infection, NRP1 phase, 48hr, replicate 2


title: D0.5 epiERa-/- Knockout Digested Uterus 25

description:
Library name: DU-E25
Column name in geo_count.txt and geo_TPM.txt: DU-E25

value: Digested uterus


title: HEK293T, Input


title: LOG_48hr_rep2

description:
TB_083208_4
Gene expression 48hr post infection of THP-1 macrophages with bacilli of the Log phase (replicate 2)

source_name: THP-1 infection, Log phase, 48hr, replicate 2

value: LOG 48hr


title: D3.5 epiERa-/- Knockout Digested Uterus 34

description:
Library name: DU-E34
Column name in geo_count.txt and geo_TPM.txt: DU-E34

value: epiERa-/- (Esr1f/-Wnt7aCre/+)

value: Female


title: METTL3-KO, m6A-IP, rep2

description: caRNA

data_processing:
Raw reads were aligned to human hg38 reference genome and spike-in genomes (NEB) using HISAT2 (v2.2.1) with parameters ‘--rna-strandness RF’
Strand-specific reads were separated by using samtools (1.15.1) view with specific flags 99, 147, 83 and 163.
m6A Peaks on each strand were called by using macs2 (v2.2.7.1) callpeak with parameters ‘--nomodel –keepdup 5 -q 0.01’.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include intervals and fold-change of m6A peaks

extract_protocol:
The chromosome fractions of parental and METTL3-/- HEK293T cells were extracted and chromosome-associated RNA (caRNA) was isolated with TRIZOL reagent. The resulting caRNA was treated with Turbo DNA-free Kit (Invitrogen) and RiboMinu Human/Mouse Transcriptome Isolation Kit (Thermo Scientific), successively, to remove residual genomic DNA and rRNA by following the manufacturer’s protocols.
m6A immunoprecipitation was performed with EpiMark® N6-Methyladenosine Enrichment Kit (NEB). m6A-seq Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocol

value: METTL3 knockout


title: D3.5 Esr1f/- Control Digested Uterus 16

description:
Library name: DU-CE16
Column name in geo_count.txt and geo_TPM.txt: DU-CE16

value: Day 3.5 post coitum


title: MCF7_CD44HIGH_WM_1

description: Library name: MCF7_CD44HIGH_WM_1

source_name: MCF7 CD44high facs-sorted

value: MCF7 CD44high facs-sorted


title: LOG_24hr_rep2

description:
TB_083208_2
Gene expression 24hr post infection of THP-1 macrophages with bacilli of the Log phase (replicate 2)

source_name: THP-1 infection, Log phase, 24hr, replicate 2

value: LOG 24hr


title: MCF7_CD44LOW_RM_3

description: Library name: MCF7_CD44LOW_RM_3

value: E2 supplemented


title: D3.5 Esr1f/- Control Digested Uterus 14

description:
Library name: DU-CE14
Column name in geo_count.txt and geo_TPM.txt: DU-CE14


title: METTL3-KO, m6A-IP, rep1

description: caRNA


title: MCF7_CD44LOW_RM_2

description: Library name: MCF7_CD44LOW_RM_2


title: MCF7_CD44LOW_RM_1

description: Library name: MCF7_CD44LOW_RM_1


title: 293T, m6A-IP, rep1

description: caRNA

value: WT


title: LOG_24hr_rep1

description:
TB_083208_1
Gene expression 24hr post infection of THP-1 macrophages with bacilli of the Log phase (replicate 1)

source_name: THP-1 infection, Log phase, 24hr, replicate 1


title: D0.5 Esr1f/- Control Digested Uterus 9

description:
Library name: DU-CE9
Column name in geo_count.txt and geo_TPM.txt: DU-CE9


title: D0.5 epiERa-/- Knockout Digested Uterus 26

description:
Library name: DU-E26
Column name in geo_count.txt and geo_TPM.txt: DU-E26


title: D0.5 Esr1f/- Control Digested Uterus 5

description:
Library name: DU-CE5
Column name in geo_count.txt and geo_TPM.txt: DU-CE5


title: TPKM intrahepatic pig mass 4, from TPKM3 cells autologous injection (hydrogel injection site), biol rep 2

city: Chicago

first: Lobna

last: Elkhadragy

state: Illinois

address: 2201 W Campbell Park Dr,

department: Radiology

institute: University of Illinois at Chicago

description: Library name: TPKM3G4

data_processing:
Sequence reads were trimmed for adaptor sequence and/or low-quality sequence using Trimmomatic v0.36.
Trimmed sequence reads were mapped to Sscrofa11.1 using STAR v2.7.11b
Read count quantification and normalization were performed using RSEM v1.3.3.
Assembly: Sscrofa11.1
Supplementary files format and content: csv files contain raw counts, FPKM and TPM values for each sample

organism: Sus scrofa

source_name: Intrahepatic pig mass

growth_protocol: Primary hepatocytes were suspended in hepatocyte plating medium. Cells developed by hepatocyte gene alterataion were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and Penicillin-Streptomycin in humidified incubator with 5% CO2 at 37C.

extract_protocol:
RNA extraction was performed using Direct-zol RNA Miniprep Plus kit (Zymo).
RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one 10B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina). The quality-scores line in fastq files use an ASCII offset of 33 known as Sanger scores

value: Intrahepatic pig mass

value: sgTP53; sgPTEN; sgCDKN2A; c-myc overexpression


title: D3.5 Esr1f/- Control Digested Uterus 11

description:
Library name: DU-CE11
Column name in geo_count.txt and geo_TPM.txt: DU-CE11


title: TPKM intrahepatic pig mass 3, from TPKM3 cells autologous injection (hydrogel injection site), biol rep 1

description: Library name: TPKM3G3


title: 293T, m6A-IP, rep2

description: caRNA


title: MCF7_CD44HIGH_RM_3

description: Library name: MCF7_CD44HIGH_RM_3


title: MCF7_CD44HIGH_RM_2

description: Library name: MCF7_CD44HIGH_RM_2


title: MCF7_CD44HIGH_WM_2

description: Library name: MCF7_CD44HIGH_WM_2


title: D0.5 Esr1f/- Control Digested Uterus 8

description:
Library name: DU-CE8
Column name in geo_count.txt and geo_TPM.txt: DU-CE8


title: LOG_48hr_rep1

description:
TB_083208_3
Gene expression 48hr post infection of THP-1 macrophages with bacilli of the Log phase (replicate 1)

source_name: THP-1 infection, Log phase, 48hr, replicate 1


title: TPKM intrahepatic pig mass 2, from TPKM3 cells autologous injection (gelatin sponge injection site), biol rep 2

description: Library name: TPKM3G2


title: MCF7_CD44HIGH_RM_1

description: Library name: MCF7_CD44HIGH_RM_1


title: METTL3-KO, Input, rep2

description: caRNA


title: 293T, Input, rep2

description: caRNA


title: METTL3-KO, Input, rep1

description: caRNA


title: LTED_CD44LOW_3

description: Library name: LTED_CD44LOW_3

source_name: LTED CD44low facs-sorted

value: LTED CD44low facs-sorted


title: D3.5 epiERa-/- Knockout Uterus 37

description:
Library name: U-E37
Column name in geo_count.txt and geo_TPM.txt: U-E37

source_name: Uterus

value: Uterus


title: 293T, Input, rep1

description: caRNA


title: TKM subcutaneous xenograft mouse tumors from TKM3 cells injection, biol rep 3

description: Library name: TKM3S

source_name: Subcutaneous xenograft tumor

value: Subcutaneous xenograft tumor

value: sgTP53; sgCDKN2A; c-myc overexpression


title: LTED_CD44LOW_2

description: Library name: LTED_CD44LOW_2


title: D3.5 epiERa-/- Knockout Uterus 35

description:
Library name: U-E35
Column name in geo_count.txt and geo_TPM.txt: U-E35


title: TKM subcutaneous xenograft mouse tumors from TKM2 cells injection, biol rep 2

description: Library name: TKM2S


title: 700-47_BLT_G872_LN_SP_ART

city: Jupiter

first: Susana

middle: T

last: Valente

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description: Library name: 700-47

data_processing:
FastQC
STAR alignment to custom genome consisting of the concatenation of human genome (GRCh38.p14), the mouse genome (GRCm39) and the HIV-1 genome (NC_001802.1).
featureCounts used to map transcripts to genes
Transcripts per million (TPMs) were determined by normalizing counts to gene length (in kb) and then by library size.
Differential gene expression analysis was conducted using DESeq2
Assembly: custom genome consisting of the concatenation of human genome (GRCh38.p14), the mouse genome (GRCm39) and the HIV-1 genome (NC_001802.1).
Supplementary files format and content: tab-delimited text format featureCounts table
Supplementary files format and content: tab-delimited text format transcripts per million (TPM) tables for each tissue

organism:
Homo sapiens
Mus musculus

source_name: Lymph Node

growth_protocol: Humanized BLT mice were generated and maintained as previously described by the Garcia Lab

extract_protocol:
Cell-associated RNA was extracted from mononuclear cells isolated from the liver, lung, spleen and lymph nodes of BLT mice treated as above using the Qiagen QIAmp viral RNA Mini Kit.
DNase-treated total RNA (100 ng input for the liver, lung, and spleen samples, 50 ng for the lymph node samples) was depleted of ribosomal RNA and library constructed using NEBNext Ultra II Directional RNA kit

treatment_protocol: ART was administered to humanized BLT mice via irradiated Teklad chow diet containing emtricitabine (1,500 mg kg-1), tenofovir disoproxil fumarate 1,560 mg kg-1) and raltegravir (600 mg kg-1) (Research Diets). 200mg SP pellets were subcutaneously implanted into the back of shaved, anaesthetized humanized mice BLT mice.

value: Lymph Node

value: Mononuclear cells (MNCs)

value: SP+ART


title: LTED_CD44LOW_1

description: Library name: LTED_CD44LOW_1


title: D3.5 epiERa-/- Knockout Uterus 34

description:
Library name: U-E34
Column name in geo_count.txt and geo_TPM.txt: U-E34

value: epiERa-/- (Esr1f/-Wnt7aCre/+)


title: D0.5 Esr1f/- Control Digested Uterus 1

description:
Library name: DU-CE1
Column name in geo_count.txt and geo_TPM.txt: DU-CE1

value: Digested uterus

value: Female

value: Day 0.5 post coitum


title: D3.5 epiERa-/- Knockout Uterus 33

description:
Library name: U-E33
Column name in geo_count.txt and geo_TPM.txt: U-E33

value: Day 3.5 post coitum


title: 700-45_BLT_G872_LN_SP_ART

description: Library name: 700-45


title: D3.5 epiERa-/- Knockout Uterus 32

description:
Library name: U-E32
Column name in geo_count.txt and geo_TPM.txt: U-E32


title: TPM subcutaneous xenograft mouse tumors from TPM2 cells injection, biol rep 2

description: Library name: TPM2S

value: sgTP53; sgPTEN; c-myc overexpression


title: TPM subcutaneous xenograft mouse tumors from TPM3 cells injection, biol rep 3

description: Library name: TPM3S


title: 700-42_BLT_G862_LN_ART

description: Library name: 700-42

value: ART


title: 700-43_BLT_G863_LN_SP_ART

description: Library name: 700-43


title: TPKM intrahepatic pig mass 1, from TPKM3 cells autologous injection (gelatin sponge injection site), biol rep 1

description: Library name: TPKM3G1


title: TKM subcutaneous xenograft mouse tumors from TKM1 cells injection, biol rep 1

description: Library name: TKM1S


title: LTED_CD44HIGH_3

description: Library name: LTED_CD44HIGH_3

source_name: LTED CD44high facs-sorted

value: LTED CD44high facs-sorted


title: LTED_CD44HIGH_1

description: Library name: LTED_CD44HIGH_1


title: TPM subcutaneous xenograft mouse tumors from TPM1 cells injection, biol rep 1

description: Library name: TPM1S


title: LTED_CD44HIGH_2

description: Library name: LTED_CD44HIGH_2


title: 700-40_BLT_G594_LN_ART

description: Library name: 700-40


title: D0.5 epiERa-/- Knockout Uterus 26

description:
Library name: U-E26
Column name in geo_count.txt and geo_TPM.txt: U-E26


title: CBX5-NC-2

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
To process RNA-seq raw data, first obtain the FASTQ files from sequencing providers . Perform quality control using FastQC, and trim low-quality reads and adapter sequences with tools like Trimmomatic or Cutadapt. Align the cleaned reads to a reference genome using HISAT2 , utilizing an appropriate annotation file (GTF/GFF). Quantify transcript abundance with StringTie or count reads per gene with featureCounts.
Assembly: hg38 or mm39
Supplementary files format and content: tab-delimited text files include read count values for each Sample, bw

source_name: liver

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.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: liver

value: hepatocellular carcinoma

value: siNC


title: TPKM clone 10 subcutaneous xenograft mouse tumors

description: Library name: TPKM1C10S

value: sgTP53; sgPTEN; sgCDKN2A; c-myc overexpression


title: D0.5 epiERa-/- Knockout Uterus 25

description:
Library name: U-E25
Column name in geo_count.txt and geo_TPM.txt: U-E25

value: Uterus


title: 700-37_BLT_G241_LN_ART

description: Library name: 700-37


title: CBX5-NC-1


title: TPKM clone 7 subcutaneous xenograft mouse tumors

description: Library name: TPKM1C7S

value: Subcutaneous xenograft tumor


title: 700-36_BLT_G873_Spleen_SP_ART

description: Library name: 700-36

source_name: Spleen

value: Spleen


title: D0.5 epiERa-/- Knockout Uterus 21

description:
Library name: U-E21
Column name in geo_count.txt and geo_TPM.txt: U-E21


title: CBX5-Si-3


title: TPKM clone 6 subcutaneous xenograft mouse tumors

description: Library name: TPKM1C6S


title: D0.5 epiERa-/- Knockout Uterus 27

description:
Library name: U-E27
Column name in geo_count.txt and geo_TPM.txt: U-E27


title: 700-35_BLT_G872_Spleen_SP_ART

description: Library name: 700-35

value: Mononuclear cells (MNCs)


title: D3.5 Esr1f/- Control Uterus 16

description:
Library name: U-CE16
Column name in geo_count.txt and geo_TPM.txt: U-CE16


title: CBX5-NC-3


title: D3.5 Esr1f/- Control Uterus 14

description:
Library name: U-CE14
Column name in geo_count.txt and geo_TPM.txt: U-CE14


title: D3.5 Esr1f/- Control Uterus 13

description:
Library name: U-CE13
Column name in geo_count.txt and geo_TPM.txt: U-CE13


title: 700-32_BLT_G867_Spleen_SP_ART

description: Library name: 700-32

value: SP+ART


title: 700-39_BLT_G592_LN_SP_ART

description: Library name: 700-39

value: Lymph Node


title: 700-31_BLT_G863_Spleen_SP_ART

description: Library name: 700-31


title: CBX5-Si-1


title: IP_DBD2

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to human reference genome hg19 by Bowtie.
Only uniquely mapped reads were kept for down-stream analyses.
PCR duplicates were removed by samTools.
BigWig files were generated by deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files normalized to RPKM

extract_protocol:
Genomic DNA was isolated by PureLink™ Genomic DNA Mini Kit (Thermo) according to the manufacturer’s protocol.  1 μg diluted gDNA was sonicated to ~150 bp by the Bioruptor Pico sonication device following the manufacturer’s instructions.
Sonicated gDNA was denatured at 95ºC for 10 min and chilled on ice. 10 μL of denatured DNA was stored as input. Half of the gDNA was rotated with 3 μg 6mA antibody (NEB, E1610S) or 1 μg IgG antibody in 1× IP buffer [10 mM Tris-HCl, 150 mM NaCl, 0.1% (v/v) Igepal CA-630] at 4°C overnight. 40 μL of Protein A magnetic beads was washed twice in 0.5 mL of 1× IP buffer and then pre-blocked in 0.5 mL 1× IP buffer with 0.5 mg/mL BSA for 2 hours. Then, the incubated DNA-antibody mixture was added to pre-blocked beads washed with 1× IP buffer and rotated at 4°C for 2 hours. The beads were washed five times with 1× IP buffer. IP product was eluted twice by adding 50 μL elution buffer [20 mM 6mA  monophosphate in 1× IP buffer] to beads and rotating at 4°C for 1 hour. IP product was purified by ethanol precipitation. The library was prepared using KAPA HiFi Kit for Illumina and sequenced by the University of Chicago Genomics  Facility.

tag: antibody

value: 6mA antibody

tag: technology


title: D3.5 Esr1f/- Control Uterus 11

description:
Library name: U-CE11
Column name in geo_count.txt and geo_TPM.txt: U-CE11

value: Female


title: TPKM clone 4 subcutaneous xenograft mouse tumors

description: Library name: TPKM1C4S


title: TPKM clone 3 subcutaneous xenograft mouse tumors

description: Library name: TPKM1C3S


title: D3.5 Esr1f/- Control Uterus 12

description:
Library name: U-CE12
Column name in geo_count.txt and geo_TPM.txt: U-CE12


title: TPKM clone 2 subcutaneous xenograft mouse tumors

description: Library name: TPKM1C2S


title: IP_DBD1


title: IP_WT2


title: TPKM subcutaneous xenograft mouse tumors from TPKM4 cells injection, biol rep 3

description: Library name: TPKM4S2


title: D0.5 Esr1f/- Control Uterus 9

description:
Library name: U-CE9
Column name in geo_count.txt and geo_TPM.txt: U-CE9

value: Day 0.5 post coitum


title: CBX5-Si-2

tag: treatment


title: 700-29_BLT_G671_Spleen_ART

description: Library name: 700-29


title: IP_WT1


title: 700-33_BLT_G868_Spleen_ART

description: Library name: 700-33


title: TPKM clone 5 subcutaneous xenograft mouse tumors

description: Library name: TPKM1C5S


title: IgG_DBD2

value: IgG antibody


title: D0.5 Esr1f/- Control Uterus 5

description:
Library name: U-CE5
Column name in geo_count.txt and geo_TPM.txt: U-CE5


title: TXM cells (from Pig #1)

description: Library name: TXM1

source_name: Cell line developed by hepatocyte gene alteration

value: Edited hepatocytes

value: sgTP53; sgAXIN1; c-myc overexpression


title: 700-30_BLT_G862_Spleen_ART

description: Library name: 700-30

value: ART


title: 700-26_BLT_G587_Spleen_ART

description: Library name: 700-26


title: IgG_DBD1


title: TPKM subcutaneous xenograft mouse tumors from TPKM2 cells injection, biol rep 1

description: Library name: TPKM2S


title: D0.5 Esr1f/- Control Uterus 8

description:
Library name: U-CE8
Column name in geo_count.txt and geo_TPM.txt: U-CE8


title: 700-25_BLT_G241_Spleen_ART

description: Library name: 700-25


title: D0.5 Esr1f/- Control Uterus 3

description:
Library name: U-CE3
Column name in geo_count.txt and geo_TPM.txt: U-CE3


title: 700-27_BLT_G592_Spleen_SP_ART

description: Library name: 700-27


title: TPK cells (from Pig #2)

description: Library name: TPK

value: Cell line developed by hepatocyte gene alteration

value: sgTP53; sgPTEN; sgCDKN2A


title: IgG_WT1


title: 700-22_BLT_G871_Lung_ART

description: Library name: 700-22

source_name: Lung

value: Lung


title: TKM cells (from Pig #3), biol rep 3

description: Library name: TKM3

value: sgTP53; sgCDKN2A; c-myc overexpression


title: IgG_WT2


title: 700-24_BLT_G873_Lung_SP_ART

description: Library name: 700-24


title: TPKM subcutaneous xenograft mouse tumors from TPKM3 cells injection, biol rep 2

description: Library name: TPKM3S

value: sgTP53; sgPTEN; sgCDKN2A; c-myc overexpression


title: D0.5 Esr1f/- Control Uterus 2

description:
Library name: U-CE2
Column name in geo_count.txt and geo_TPM.txt: U-CE2

value: Uterus


title: D3.5 epiERa-/- Knockout Luminal Epithelium 37

description:
Library name: LE-E37
Column name in geo_count.txt and geo_TPM.txt: LE-E37

source_name: Luminal epithelium

value: Luminal epithelium

value: epiERa-/- (Esr1f/-Wnt7aCre/+)

value: Day 3.5 post coitum


title: D0.5 Esr1f/- Control Uterus 1

description:
Library name: U-CE1
Column name in geo_count.txt and geo_TPM.txt: U-CE1


title: PK cells (from Pig #2)

description: Library name: PK

value: sgPTEN; sgCDKN2A


title: 700-21_BLT_G868_Lung_ART

description: Library name: 700-21

value: Mononuclear cells (MNCs)


title: TKM cells (from Pig #2), biol rep 2

description: Library name: TKM2


title: D3.5 epiERa-/- Knockout Luminal Epithelium 36

description:
Library name: LE-E36
Column name in geo_count.txt and geo_TPM.txt: LE-E36

value: Female


title: TKM cells (from Pig #1), biol rep 1

description: Library name: TKM1


title: D3.5 epiERa-/- Knockout Luminal Epithelium 35

description:
Library name: LE-E35
Column name in geo_count.txt and geo_TPM.txt: LE-E35


title: TPM cells (from Pig #3), biol rep 3

description: Library name: TPM3

value: sgTP53; sgPTEN; c-myc overexpression


title: 700-19_BLT_G863_Lung_SP_ART

description: Library name: 700-19

value: SP+ART


title: M0 THP-1 cells treated with osimertinib (100 nM) for 16 h, biological replicate 3

city: Gangnam-gu

first: Yoon Soo

last: Chang

state: Seoul

address: #413 63-gil 20 Eonju-ro

department: Internal Medicine

country: South Korea

institute: Yonsei University College of Medicine

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC). Affymetrix Power Tools (affymetrix-power-tools.html) was used for analysis.

label: biotin

source_name: M0-polarized THP-1 cells

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified incubator with 5% CO2 and split regularly to maintain logarithmic growth.

extract_protocol: Total RNA was extracted from M0-polarized THP-1 cells using Trizol according to the manufacturer's instructions. RNA quantity and purity were assessed by spectrophotometry, and RNA integrity was evaluated by microfluidic analysis before array hybridization.

treatment_protocol: THP-1 cells were differentiated to an M0 macrophage-like state by treatment with phorbol 12-myristate 13-acetate (PMA) as described in the associated manuscript. M0-polarized THP-1 cells were then treated with vehicle, cisplatin (0.5 μM), or osimertinib (100 nM) for 16 hours prior to RNA extraction.

tag: polarization

value: Osimertinib


title: D3.5 epiERa-/- Knockout Luminal Epithelium 34

description:
Library name: LE-E34
Column name in geo_count.txt and geo_TPM.txt: LE-E34


title: TPM cells (from Pig #1), biol rep 1

description: Library name: TPM1

value: Edited hepatocytes


title: D3.5 epiERa-/- Knockout Luminal Epithelium 32

description:
Library name: LE-E32
Column name in geo_count.txt and geo_TPM.txt: LE-E32


title: 700-16_BLT_G594_Lung_ART

description: Library name: 700-16

value: ART


title: 700-17_BLT_G671_Lung_ART

description: Library name: 700-17


title: D3.5 epiERa-/- Knockout Luminal Epithelium 31

description:
Library name: LE-E31
Column name in geo_count.txt and geo_TPM.txt: LE-E31


title: TPM cells (from Pig #2), biol rep 2

description: Library name: TPM2

value: Cell line developed by hepatocyte gene alteration


title: 700-15_BLT_G592_Lung_SP_ART

description: Library name: 700-15


title: TPKM clone 10 cells, isolated from TPKM1 cell pool

description: Library name: TPKM1C10


title: TPKM clone 9 cells, isolated from TPKM1 cell pool

description: Library name: TPKM1C9


title: 700-13_BLT_G241_Lung_ART

description: Library name: 700-13


title: D0.5 epiERa-/- Knockout Luminal Epithelium 27

description:
Library name: LE-E27
Column name in geo_count.txt and geo_TPM.txt: LE-E27

value: Day 0.5 post coitum


title: 700-14_BLT_G587_Lung_ART

description: Library name: 700-14

value: Lung


title: TPKM clone 8 cells, isolated from TPKM1 cell pool

description: Library name: TPKM1C8


title: D0.5 epiERa-/- Knockout Luminal Epithelium 26

description:
Library name: LE-E26
Column name in geo_count.txt and geo_TPM.txt: LE-E26


title: 700-20_BLT_G867_Lung_SP_ART

description: Library name: 700-20


title: D0.5 epiERa-/- Knockout Luminal Epithelium 25

description:
Library name: LE-E25
Column name in geo_count.txt and geo_TPM.txt: LE-E25


title: M0 THP-1 cells treated with osimertinib (100 nM) for 16 h, biological replicate 1


title: M0 THP-1 cells treated with cisplatin (0.5 μM) for 16 h, biological replicate 1

value: Cisplatin


title: 700-12_BLT_G873_Liver_SP_ART

description: Library name: 700-12

source_name: Liver

value: Liver


title: TPKM clone 5 cells, isolated from TPKM1 cell pool

description: Library name: TPKM1C5

value: sgTP53; sgPTEN; sgCDKN2A; c-myc overexpression


title: D0.5 epiERa-/- Knockout Luminal Epithelium 24

description:
Library name: LE-E24
Column name in geo_count.txt and geo_TPM.txt: LE-E24

value: Luminal epithelium


title: WT_SPI2_rep2

city: Würzburg

first: Alexander

last: Westermann

address: Josef-Schneider Straße 2

country: Germany

institute: HIRI

description: Library name: WT_SPI2_rep2

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11/v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422 (Illumina)
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT)
Alignment of trimmed read pairs to Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 genome using map_single_fragments.py fom the RILseq software (Melamed et al., 2018) v0.82 (https://github.com/asafpr/RILseq; see https://github.com/yairra/RILseq for latest versions) with default parameters. BWA (Li, 2013) v0.7.17 was used for read alignment with the RILseq software.
Mapping of chimeric fragments with map_chimeric_fragments.py from the RILseq software with default parameters but including a transcript file (TF) based on an ad hoc annotation of Salmonella Typhimurium strain SL1344 described in (Holmqvist et al., 2016) (parameter: -t TF)
Overrepresented interacting regions were identified using the RILseq_significant_regions.py script from the RILseq software with default parameters except for including a BioCyc data folder for Salmonella (--bc_dir), the chromosome ID mapping --BC_chrlist NC_016810.1,NC_016810,NC_017718.1,NC_017718,NC_017719.1,NC_017719,NC_017720.1,NC_017720) and parameters for excluding rRNA interactions (--ribozero --rrna_list rRNA,RRNA). The resulting significant interacting regions (S-chimeras) were reannotated using the Salmonella ad hoc annotation described above.
Assembly: GCF_000210855.2
Supplementary files format and content: Character (TAB) separated value files containing counts of statistically significant chimeras

organism: Salmonella enterica

growth_protocol: Raw macrophages were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C. Salmonella were cultivated in LB or SPI-2-inducing minimal medium.

extract_protocol:
Trizol
RIL-seq library preparation was conducted using the sRNA NEBNext kit for Illumina. 3 µL of RNA were mixed with 1 µL of 3’ SR Adaptor (1:10 diluted) and incubated at 70°C for 2 min. 6.5 µL of 3’ ligation mix (5 µL of 3’ ligation buffer, 1.5 µL of 3’ enzyme mix) were added and incubated at 25°C for 1 h. 2.75 µL of SR mix (2.5 µL of water, 0.25 µL of SR RT primer) were added to reactions and incubated for three subsequential steps (75°C for 5 min, 37°C for 15 min, 25°C for 15 min). Pre-denatured 5’ adaptor (1:10 diluted) was added to each tube together with 5’ ligation mix (0.5 µL of 5’ ligation reaction buffer, 1.25 µL 5’ ligation enzyme mix) and samples were incubated at 25°C for 1 hour. For first-strand cDNA synthesis, 5 µL of cDNA mix were added (4 µL first-strand buffer, 0.5 µL murine RNase inhibitor, 0.5 µL SuperScript II RT). The reactions were incubated at 50°C for 1 h followed by 15 min at 70°C. 10 µL of cDNA were PCR-amplified with barcoded NEB index primer and SR primer in a 50 µL reaction (25 µL LongAmp Taq 2x mix, 12.5 µL nuclease-free water, 1.25 µL SR primer, 1.25 µL index primer).

treatment_protocol: Infection was carried out following the protocol of PMID: 26789254 with the indicated Salmonella Typhimurium (SL1344) strain. At 20 hours post-infection, cells were harvested and bacterial RNA subjected to RIL-seq as described in PMID: 35063132. Salmonella was cultivated in LB to an OD600 of 2.0, followed by two successive washes with Phosphate-Buffered Saline (PBS). Subsequently, the bacteria were inoculated at a ratio of 1:50 and transferred to SPI-2 medium (170mM MES, 5mM KCl, 7.5mM (NH4)2SO4, 0.5mM K2SO4, 1mM KH2PO4, 8µM MgCl2, 38mM Glycerol,  bacto casamino acid 0.1% and pH of 5.8). This cultivation was conducted at 37 °C with constant shaking at 220 rpm until the cultures attained an OD600 of 0.3.

value: Salmonella

tag: infection condition

value: SPI-2 medium

tag: timepoint post_infection

tag: biological replicate


title: 700-11_BLT_G872_Liver_SP_ART

description: Library name: 700-11


title: M0 THP-1 cells treated with cisplatin (0.5 μM) for 16 h, biological replicate 3


title: TPKM clone 4 cells, isolated from TPKM1 cell pool

description: Library name: TPKM1C4


title: 700-10_BLT_G871_Liver_ART

description: Library name: 700-10


title: D0.5 epiERa-/- Knockout Luminal Epithelium 23

description:
Library name: LE-E23
Column name in geo_count.txt and geo_TPM.txt: LE-E23

value: epiERa-/- (Esr1f/-Wnt7aCre/+)

tag: Sex


title: WT_SPI2_rep1

description: Library name: WT_SPI2_rep1


title: TPKM cells (from Pig #4), biol rep 4

description: Library name: TPKM4


title: 700-8_BLT_G867_Liver_SP_ART

description: Library name: 700-8

value: Mononuclear cells (MNCs)


title: M0 THP-1 cells treated with vehicle, biological replicate 3

value: Vehicle


title: Hfq_SPI2_rep2

description: Library name: Hfq_SPI2_rep2


title: M0 THP-1 cells treated with osimertinib (100 nM) for 16 h, biological replicate 2


title: D0.5 epiERa-/- Knockout Luminal Epithelium 21

description:
Library name: LE-E21
Column name in geo_count.txt and geo_TPM.txt: LE-E21

value: Female


title: M0 THP-1 cells treated with cisplatin (0.5 μM) for 16 h, biological replicate 2


title: D3.5 Esr1f/- Control Luminal Epithelium 16

description:
Library name: LE-CE16
Column name in geo_count.txt and geo_TPM.txt: LE-CE16

value: Day 3.5 post coitum


title: D0.5 epiERa-/- Knockout Luminal Epithelium 22

description:
Library name: LE-E22
Column name in geo_count.txt and geo_TPM.txt: LE-E22


title: 700-7_BLT_G863_Liver_SP_ART

description: Library name: 700-7

value: SP+ART


title: M0 THP-1 cells treated with vehicle, biological replicate 2


title: TPKM cells (from Pig #2), biol rep 2

description: Library name: TPKM2

value: Edited hepatocytes


title: M0 THP-1 cells treated with vehicle, biological replicate 1


title: D3.5 Esr1f/- Control Luminal Epithelium 15

description:
Library name: LE-CE15
Column name in geo_count.txt and geo_TPM.txt: LE-CE15


title: 700-6_BLT_G862_Liver_ART

description: Library name: 700-6

value: ART


title: 700-9_BLT_G868_Liver_ART

description: Library name: 700-9


title: TPKM clone 2 cells, isolated from TPKM1 cell pool

description: Library name: TPKM1C2

value: Cell line developed by hepatocyte gene alteration


title: MyD88 3wks_2: Colon_3wks colonized_rep2

city: Hamilton

first: Premysl

last: Bercik

state: ON

address: 1280 Main St W

country: Canada

institute: McMaster University

description: Colonic tissue from germ-free MyD88-/- Ticam-/- mice (10-14 weeks) colonized with E.coli HA108

hyb_protocol: Procedures were performed according to the manufacturer’s protocol (Nanostring Technologies, Seattle, WA, USA)

scan_protocol: Sample Cartridges are placed in the Digital Analyzer for data collection. Color codes on the surface of the cartridge are counted and tabulated for each target molecule.

data_processing: Collected data were imported into nSolver software (Nanostring Technologies). Data were normalized to the geometric means of positive and negative controls.

label: color-coded barcode technology

source_name: Colon tissues

label_protocol: The protocol followed was according to manufacturer's intructions (color-coded barcode technology)

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Toronto, Canada) and DNase digestion during purification was carried out using the RNase-free DNase (Qiagen). The RNA samples were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA). The RNA concentrations were then adjusted to 20 ng/µl. The quality of the isolated RNA was checked with Agilent RNA 6000 Nano Assay kit reagents using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Germ-free mice were mono-colonized with 109 CFU of E. coli HA107 via intragastric gavage three times weekly for two weeks

tag: strain

value: MyD88-/- Ticam-/-

tag: age

value: 10-14 weeks

value: Colon


title: TPKM cells (from Pig #1), biol rep 1

description: Library name: TPKM1


title: MyD88 3wks_1: Colon_3wks colonized_rep1

description: Colonic tissue from germ-free MyD88-/- Ticam-/- mice (10-14 weeks) colonized with E.coli HA107

tag: tissue


title: 700-5_BLT_G671_Liver_ART

description: Library name: 700-5

value: Liver


title: D3.5 Esr1f/- Control Luminal Epithelium 14

description:
Library name: LE-CE14
Column name in geo_count.txt and geo_TPM.txt: LE-CE14

tag: day of_pregnancy


title: TPKM cells (from Pig #3), biol rep 3

description: Library name: TPKM3

value: sgTP53; sgPTEN; sgCDKN2A; c-myc overexpression


title: Hfq_SPI2_rep1

description: Library name: Hfq_SPI2_rep1


title: normal hepatocytes control (from Pig #5), biol rep 3

description: Library name: PGHEP5

source_name: Normal hepatocytes

value: Normal hepatocytes

value: Primary hepatocytes

value: WT


title: normal hepatocytes control (from Pig #4), biol rep 2

description: Library name: PGHEP4


title: 700-4_BLT_G594_Liver_ART

description: Library name: 700-4


title: D0.5 Esr1f/- Control Luminal Epithelium 8

description:
Library name: LE-CE8
Column name in geo_count.txt and geo_TPM.txt: LE-CE8

value: Luminal epithelium

value: Day 0.5 post coitum


title: MyD88 GF_2: Colon_GF_rep2

description: Colonic tissue from germ-free MyD88-/- Ticam-/- mice (10-14 weeks)


title: 700-3_BLT_G592_Liver_SP_ART

description: Library name: 700-3

value: Mononuclear cells (MNCs)


title: D0.5 Esr1f/- Control Luminal Epithelium 9

description:
Library name: LE-CE9
Column name in geo_count.txt and geo_TPM.txt: LE-CE9

value: Female


title: MyD88 GF_1: Colon_GF_rep1


title: SW 4wks_2: Colon_4wks colonized_rep2

description: Colonic tissue from germ-free NIH swiss mice (10-14 weeks) colonized with E.coli HA110

value: Swiss Webster


title: D0.5 Esr1f/- Control Luminal Epithelium 7

description:
Library name: LE-CE7
Column name in geo_count.txt and geo_TPM.txt: LE-CE7


title: normal hepatocytes control (from Pig #3), biol rep 1

description: Library name: PGHEP3


title: SW 4wks_1: Colon_4wks colonized_rep1

description: Colonic tissue from germ-free NIH swiss mice (10-14 weeks) colonized with E.coli HA109


title: normal liver control (from Pig #5), biol rep 3

description: Library name: PG5L

source_name: Normal liver tissue

value: Normal liver tissue


title: SW 2wks_2: Colon_2wks colonized_rep2

description: Colonic tissue from germ-free NIH swiss mice (10-14 weeks) colonized with E.coli HA108


title: 700-1_BLT_G241_Liver_ART

description: Library name: 700-1


title: D0.5 Esr1f/- Control Luminal Epithelium 6

description:
Library name: LE-CE6
Column name in geo_count.txt and geo_TPM.txt: LE-CE6


title: NIR_36ug_6

city: Hsinchu

first: Hsin mei

last: Lee

address: Guangfu Rd.

country: Taiwan

institute: National Tsing Hua University

description: Library name: NIR_36ug_6

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: mm_GRChm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: Tumor

growth_protocol: Murine PDAC Ak4.4 cells were orthotopically implanted in the pancrea of 6-8-week-old female FVB mice. 10^5 Ak4.4 cells were injected in the pancrea through a 28-gauge needle.

extract_protocol:
The integrity of RNA extracted from the treatment and control groups using the RNeasy Kit (Qiagen) was evaluated with the RNA Nano6000 assay kit (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: The experimental design involved orthotopically implanted murine PDAC (Ak4.4) cells in FVB mice, followed by IV administration of TAM-cGAMPnp on day 15. Subsequent transcriptome analysis of the tumors was performed after 24-hour circulation.

value: Tumor

value: PDAC


title: normal liver control (from Pig #2), biol rep 1

description: Library name: PG2L


title: SW 2wks_1: Colon_2wks colonized_rep1

description: Colonic tissue from germ-free NIH swiss mice (10-14 weeks) colonized with E.coli HA107


title: D3.5 Esr1f/- Control Luminal Epithelium 11

description:
Library name: LE-CE11
Column name in geo_count.txt and geo_TPM.txt: LE-CE11

value: Day 3.5 post coitum


title: D0.5 Esr1f/- Control Luminal Epithelium 4

description:
Library name: LE-CE4
Column name in geo_count.txt and geo_TPM.txt: LE-CE4


title: D0.5 Esr1f/- Control Luminal Epithelium 5

description:
Library name: LE-CE5
Column name in geo_count.txt and geo_TPM.txt: LE-CE5


title: NIR_36ug_2

description: Library name: NIR_36ug_2


title: NIR_36ug_1

description: Library name: NIR_36ug_1


title: 1101_B27_3D_D15

city: Auburn

first: Michael

middle: W

last: Greene

state: AL

address: 260 Lem Morrison Dr

institute: Auburn University

description:
Library name: Sample 18
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture

data_processing:
Sequencing reads were aligned to the human GRCh38 and mouse GRCm38 reference genomes and counted with STAR. The alignment and resulting counts table obtained from STAR was split into mouse and human tables based on Ensemble IDs and then used for downstream analyses.
Human and mouse mapped raw counts obtained from STAR were used for differential expression analysis with the R package DESeq2. False discovery rates (FDR) p value less than 0.05 were considered significantly differentially expressed and genes with log2 fold change greater than 1.5 were used for downstream gene set analyses.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: tab-delimited text file with htseq gene counts for each Sample.

molecule: polyA RNA

source_name: 3D engineered CRC tissue

growth_protocol: 3D engineered CRC tissues were maintained in culture for 29 days in a standard incubator with a temperature of 37 °C and 5% CO2. The culture media were changed every 2-3 days. Media for all experiments was composed of DMEM  containing 10% (v/v) fetal bovine serum (FBS), 1% (v/v) penicillin-streptomycin solution , and 2 mM glutaGRO™ Supplement.  PDX xenografts were established and propagated in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NOD-SCID) mice.

extract_protocol:
3D engineered CRC tissues and in vivo tumors were flash frozen in liquid nitrogen, and then stored at -80C.  RNA was isolated using RNeasy Plus Micro Kit (Qiagen).
Illumina TruSeq RNA Stranded RNA Kit with Ribo-Zero Gold was used for the construction of sequencing libraries.

tag: batch

value: Batch 27

value: 3D engineered CRC tissue

tag: pdx model

value: In vitro

tag: crc stage

value: Stage IV


title: SW GF_3: Colon_GF_rep3

description: Colonic tissue from germ-free NIH swiss mice (10-14 weeks)

value: 10-14 weeks

value: Colon


title: SW GF_2: Colon_GF_rep2


title: 1101_B27_T

description:
Library name: Sample 17
in vivo subcutaneously grown PDX CRC tumor

source_name: PDX tumor

value: PDX tumor

value: In vivo


title: D0.5 Esr1f/- Control Luminal Epithelium 3

description:
Library name: LE-CE3
Column name in geo_count.txt and geo_TPM.txt: LE-CE3

value: Luminal epithelium


title: 700-2_BLT_G587_Liver_ART

description: Library name: 700-2

value: Liver

tag: cell type

value: ART


title: 1101_B16_Tumor

description:
Library name: Sample 16
in vivo subcutaneously grown PDX CRC tumor

value: Batch 16


title: Control_2

description: Library name: Control_2

tag: cell line


title: Control_1

description: Library name: Control_1


title: D0.5 Esr1f/- Control Luminal Epithelium 2

description:
Library name: LE-CE2
Column name in geo_count.txt and geo_TPM.txt: LE-CE2

tag: genotype

value: Female

value: Day 0.5 post coitum


title: Control_4

description: Library name: Control_4

value: Tumor


title: normal liver control (from Pig #3), biol rep 2

description: Library name: PG3L

value: Normal liver tissue

value: WT


title: 1101_B10_4509

description:
Library name: Sample 14
in vivo subcutaneously grown PDX CRC tumor

value: Batch 10


title: 1101_B26_Tumor

description:
Library name: Sample 15
in vivo subcutaneously grown PDX CRC tumor

value: Batch 26


title: D0.5 Esr1f/- Control Luminal Epithelium 1

description:
Library name: LE-CE1
Column name in geo_count.txt and geo_TPM.txt: LE-CE1


title: Batch 3 mouse 1

city: South San Francisco

first: Kimberle

last: Shen

state: CA

address: 1 Dna way

institute: Genentech

library_source: transcriptomic single cell

data_processing:
cellranger7.0
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

source_name: brain (hippocampus)

extract_protocol:
Miltenyi neural dissociation kit for brain dissociation
10X 3'

value: brain (hippocampus)

value: Injected


title: SW GF_1: Colon_GF_rep1

value: Swiss Webster

value: 10-14 weeks


title: APOE3

city: Durham

first: Gurpreet

last: Baht

state: North Carolina

address: 300 North Duke Street

department: Orthopaedic

institute: Duke University

description: Library name: sample6

data_processing:
fastp toolkit
Raw RNA-seq reads were processed using the fastp toolkit to remove sequencing adapters and trim low-quality bases from the 3′ ends. Quality control metrics were also generated to assess read quality before downstream analysis.
Cleaned reads were then aligned to the GRCm39 mouse reference genome using the HISAT2 aligner with default parameters.
The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools.
Gene-level read counts were quantified from the sorted BAM files using featureCounts with the corresponding Ensembl GTF annotation file.
Assembly: GRCm39
Supplementary files format and content: tab-delimited test file includes raw counts for each sample

source_name: Bone Marrow Stromal Cells (BMSCs)

growth_protocol: Bone marrow stromal cells (BMSCs) were maintained in α-Minimum Essential Medium (α-MEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics (penicillin/streptomycin) in a humidified atmosphere containing 5% CO₂ at 37 °C.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen) following the manufacturer’s instructions. 500ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the KAPA HyperPrep Kit following the manufacturer’s protocol.

treatment_protocol: BMSCs were differentiated into osteoblasts in osteogenic medium consisting of α-MEM supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin/streptomycin, 30 μM ascorbic acid, 10 nM dexamethasone, and 8 mM β-glycerophosphate. Recombinant ApoE (100 ng/mL) was added two days after induction of osteogenic differentiation and maintained throughout the duration of the differentiation period.

value: Bone Marrow Stromal Cells (BMSCs)

value: Recombinant ApoE with osteoblast differentiation


title: SW 4wks_2: Brain_4wks colonized_rep2

description: Brain (hippocampus and amygdala) tissue from germ-free NIH swiss mice (10-14 weeks)

source_name: Brain tissues

value: Brain


title: APOE2

description: Library name: sample5


title: SW 4wks_1: Brain_4wks colonized_rep1


title: SW 4wks_3: Brain_4wks colonized_rep3


title: B26_1101_D15_3D

description:
Library name: Sample 13
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture

value: 3D engineered CRC tissue

value: In vitro

value: Stage IV


title: SW GF_3: Brain_GF_rep3


title: Batch 2 mouse 2


title: APOE1

description: Library name: sample4


title: 1101_B16_3D_D15

description:
Library name: Sample 12
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture

value: Batch 16


title: 1101_B10_3D_D15

description:
Library name: Sample 11
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture


title: 1001_B29_T

description:
Library name: Sample 10
in vivo subcutaneously grown PDX CRC tumor

value: Batch 29

value: PDX tumor

value: In vivo

value: Stage III-B


title: Batch 2 mouse 1

value: WT


title: VEH3

description: Library name: sample3

value: control with osteoblast differentiation


title: VEH2

description: Library name: sample2


title: VEH1

description: Library name: sample1


title: Batch 1 mouse 2

value: brain (hippocampus)


title: Batch 1 mouse 1

value: Injected


title: SW GF_2: Brain_GF_rep2

value: Swiss Webster


title: SW GF_1: Brain_GF_rep1

value: 10-14 weeks


title: 1001_B28_T

description:
Library name: Sample 9
in vivo subcutaneously grown PDX CRC tumor

value: Batch 28


title: 000-621

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

description: Expression value derived from nCounter Digital Analyzer

hyb_protocol: Purified total RNA was processed using the Nanostring nCounter v3.0a array.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Nanostring)

data_processing: Nanostring nCounter v3.0a arrays were normalized using the top 100 genes without background subtraction using the geometric mean in the nSolver Analysis Software.v3 (Nanostring). The log2 count normalized matrices of microRNAs in the Nanostring arrays were batch-adjusted using theComBat function in the sva package (version 3.46.0) and used for all subsequent analyses.

source_name: Asthma Female

extract_protocol:
Whole blood was collected in PaxGene RNA tubes
Total RNA from whole blood samples was isolated using a column-based system (total-RNA kit; Norgen)

value: Whole blood

tag: disease

value: Asthma

value: Female

tag: endotype

value: low


title: 1001_B4_4501

description:
Library name: Sample 8
in vivo subcutaneously grown PDX CRC tumor

value: Batch 4


title: adult brain ATAC-seq, control CT0 repeat-2

city: Ann Arbor

first: Swathi

last: Yadlapalli

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Library name: ATACseq_control_CT0_Rep2

data_processing:
Refer to the published ATACseq protocol (Yuan et al. PLoS Genetics 2024, doi:  10.1371/journal.pgen.1011278).
Assembly: dm6
Supplementary files format and content: bigwig of ATAC-seq scores

organism: Drosophila melanogaster

source_name: adult brain

growth_protocol: Flies were raised on standard cornmeal/yeast media and maintained at room temperature (20 to 22 °C) under a 12h:12h LD schedule. The following flies used in the study were previously described, obtained from the Bloomington Stock Center, or developed for this study: Clk-GAL4 (BDSC#93198), UAS-mor-RNAi (BDSC#34919).

extract_protocol:
Flies of genotype ClkGAL4>UAS-tetR-GFP-NLS was used for a bright GFP marker specific to clock neurons and DAPI was used as a viability marker. A small population of cells were heated at 60C for 5min and used as a dead cell (DAPI+) control. Live clock neurons are defined by GFP+ and DAPI- gating. We followed previously published ATACseq protocol for fruit fly (Yuan et al. PLoS Genetics 2024, doi:  10.1371/journal.pgen.1011278).
We followed previously published ATACseq protocol for fruit fly (Yuan et al. PLoS Genetics 2024, doi:  10.1371/journal.pgen.1011278).

treatment_protocol: Flies were entrained to Light-Dark (LD) cycles where they were exposed to 12-hour Light-Dark (LD) cycles for 5 days before sample collection. The initiation of the light phase is labeled as Zeitgeber Time (ZT) 0, while ZT12 signifies the beginning of the dark period. For the control/mor-RNAi samples, we collected samples on the second day after releasing into Dark-Dark free-running condition (DD2).

value: adult brain

value: non-clock cells

value: mor-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-mor-RNAi BDSC#34919;)

tag: treatment

value: constant condition second day (CT)


title: Bone Marrow Derived Macrophages, LL2 NRF2 KO Conditioned Media, 100nM CDDO-ME, Replicate 3

city: Indianapolis

first: Ana

middle: S

last: Leal

state: IN

address: 980 W Walnut St

department: Department of Medicine

institute: Indiana University

description: Library name: N1D8_ME_4

data_processing:
Reads were filtered for adapter-related content, containing undetermined bases >10%, and Qscores <=5
Filtered reads were mapped to Mus musculus GRCm39 using Kallisto for pseudo alignment.
Tximport v1.30.0 R package was used to calculate length-scaled transcripts per mission and convert to count-level data (gene counts per million).
Assembly: Mus musculus GRCm39
Supplementary files format and content: .csv file containing length-scaled TPM data of gene-level counts

source_name: Bone Marrow Derived Macrophage

growth_protocol: Lewis lung carcinoma (LL2) cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Complete-DMEM) in a humified incubator with 5% atmospheric CO2 at 37°C. Bone marrow-derived macrophage (BMDM) were isolated from C57BL/6 mice. Femurs and tibias were harvested under sterile conditions and bone marrow flushed out using Complete-DMEM with 20 ng/mL recombinant M-CSF. The suspension of progenitor cells was split evenly and approximately 500K cells/well plated into 6-well plates in 2mL media. Cells were incubated at 5% CO2 at 37°C for 5 days, washed 3x in PBS, and fresh 2mL Complete-DMEM with 20 ng/mL M-CSF added. After 48 hours, macrophages were ready for use.

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

treatment_protocol: LL2 lung cancer cells (WT, KEAP1 KO, and NRF2 KO) were split 1:4 into fresh Complete-DMEM. An additional plate of Complete-DMEM without cancer cells was included as a control. After 48 hours, conditioned media (CM) was harvested and cleared through centrifugation at 500 x g for 5 minutes. Cleared cancer CM was added to naïve macrophages totaling 75% CM, 25% Complete-DMEM. 100nM CDDO-Me or vehicle control was added to macrophages and incubated for 24 hours. RNA was harvested for 3 independent samples in each treatment group.

value: Bone Marrow Derived Macrophage

value: Macrophage

value: LL2 NRF2 KO Conditioned Media, 100nM CDDO-Me


title: Bone Marrow Derived Macrophages, LL2 NRF2 KO Conditioned Media, 100nM CDDO-ME, Replicate 2

description: Library name: N1D8_ME_3


title: adult brain ATAC-seq, control CT0 repeat-1

description: Library name: ATACseq_control_CT0_Rep1


title: 1001_B17

description:
Library name: Sample 6
in vivo subcutaneously grown PDX CRC tumor

value: Batch 17

value: PDX tumor

value: In vivo

value: Stage III-B


title: 000-617

value: high


title: 1001_B21_Tumor

description:
Library name: Sample 7
in vivo subcutaneously grown PDX CRC tumor

value: Batch 21


title: Bone Marrow Derived Macrophages, LL2 NRF2 KO Conditioned Media, 100nM CDDO-ME, Replicate 1

description: Library name: N1D8_ME_1


title: adult brain ATAC-seq, mor-RNAi CT12 repeat-3

description: Library name: ATACseq_morRNAi_CT12_Rep3

value: clock neurons ClkGAL4


title: 1001_B11_4512

description:
Library name: Sample 5
in vivo subcutaneously grown PDX CRC tumor

value: Batch 11


title: 000-598

source_name: Asthma Male

value: Whole blood

value: Asthma

value: Male


title: Bone Marrow Derived Macrophages, LL2 KEAP1 KO Conditioned Media, 100nM CDDO-ME, Replicate 3

description: Library name: K3F10_ME_4

value: LL2 KEAP1 KO Conditioned Media, 100nM CDDO-Me


title: adult brain ATAC-seq, mor-RNAi CT0 repeat-3

description: Library name: ATACseq_morRNAi_CT0_Rep3

value: adult brain

value: mor-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-mor-RNAi BDSC#34919;)


title: T. thermophila RNA004 chemistry

first: Laura

last: White

address: 12801 E 17th Avenue RC1S

institute: University of Colorado

description: tRNA sequencing (RNA004)

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004

value: Tetrahymena thermophila


title: T. thermophila RNA002 chemistry

description: tRNA sequencing (RNA002)


title: Bone Marrow Derived Macrophages, LL2 KEAP1 KO Conditioned Media, 100nM CDDO-ME, Replicate 2

description: Library name: K3F10_ME_3

value: Bone Marrow Derived Macrophage

value: Macrophage


title: 1001_B29_3D_D15

description:
Library name: Sample 4
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture

value: Batch 29

value: 3D engineered CRC tissue

value: In vitro


title: adult brain ATAC-seq, mor-RNAi CT12 repeat-2

description: Library name: ATACseq_morRNAi_CT12_Rep2

value: constant condition second day (CT)


title: Bone Marrow Derived Macrophages, LL2 KEAP1 KO Conditioned Media, 100nM CDDO-ME, Replicate 1

description: Library name: K3F10_ME_1


title: 000-595

source_name: Control Male

value: Control


title: 000-593

value: high


title: 1001_B28_3D_D15

description:
Library name: Sample 3
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture

value: Batch 28

value: Stage III-B


title: adult brain ATAC-seq, mor-RNAi CT0 repeat-2

description: Library name: ATACseq_morRNAi_CT0_Rep2

value: clock neurons ClkGAL4


title: adult brain ATAC-seq, mor-RNAi CT12 repeat-1

description: Library name: ATACseq_morRNAi_CT12_Rep1


title: Bone Marrow Derived Macrophages, LL2 WT Conditioned Media, 100nM CDDO-ME, Replicate 3

description: Library name: WT_ME_4

value: LL2 WT Conditioned Media, 100nM CDDO-Me


title: B17_1001_D15_3D

description:
Library name: Sample 2
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture

value: Batch 17


title: 1001_B11_3D_D15

description:
Library name: Sample 1
3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture

value: Batch 11


title: 000-601

value: Whole blood

value: Asthma

value: Male


title: adult brain ATAC-seq, mor-RNAi CT0 repeat-1

description: Library name: ATACseq_morRNAi_CT0_Rep1

value: adult brain

value: mor-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-mor-RNAi BDSC#34919;)


title: Early-passage HUVECs, Rep F

city: Madrid

first: Fátima

middle: Milhano

last: Santos

address: Av. de los Reyes Católicos, 2 4 planta izquierda, Moncloa - Aravaca

country: Spain

institute: IIS-FJD

description:
Library name: Celula-F
miRNA amplification

data_processing:
Raw FASTQ files were quality-filtered and trimmed to remove low-quality bases, sequencing adapters, and poly-A tails. Read quality was assessed with FastQC v0.11.9, ensuring high %Q20 scores, absence of Ns, and removal of adapters and poly-A sequences.
Trimmed sequence reads were mapped to the hg38/GRCh38 reference genome using miRDeep2. Next, miRNA identifiers were assigned using the mature and precursor miRNA database from miRBase.
Assembly: hg38/GRCh38
Supplementary files format and content: individual tab-delimited text files include raw counts.

source_name: HUVECs

growth_protocol: First-passage cryopreserved HUVECs were cultured and serially passaged until reaching senescence, following the replicative senescence protocol. Cells studied within 2–8 passages (early passage; PD < 20) were regarded as early passage ECs, whereas those passaged 28–38 times (PD > 96) were regarded as senescent ECs.

extract_protocol:
Total RNA was extracted from the cell pellets using the MagMAX™ mirVana™ Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's instructions for ECs.
Libraries of small RNA were constructed using NEXTFlex Small RNA-Seq Kit v4 (Illumina Compatible) (PerkinElmer, Waltham, MA, USA), according to the manufacturer’s guidelines. Size selection was performed targeting fragments that were 150–180 bp in size using BluePippin (Sage Science, Beverly, Massachusetts, USA). Size‐selected libraries were then PCR amplified with indexed sequencing primers, and finally sequenced on a NovaSeq X Plus System (Illumina, San Diego, California, USA) for 150x2 cycles in high‐output mode with target coverage of 20 M reads for each library.

value: HUVECs

value: Endothelial cells

value: WT


title: Bone Marrow Derived Macrophages, LL2 WT Conditioned Media, 100nM CDDO-ME, Replicate 2

description: Library name: WT_ME_3

value: Bone Marrow Derived Macrophage

value: Macrophage


title: Bone Marrow Derived Macrophages, LL2 WT Conditioned Media, 100nM CDDO-ME, Replicate 1

description: Library name: WT_ME_1


title: 000-588

source_name: Control Female

value: Control

value: Female


title: 000-579


title: Early-passage HUVECs, Rep E

description:
Library name: Celula-E
miRNA amplification


title: 7040

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

data_processing:
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline,  which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads in a minimum of five samples per group.
The annotation was performed using the annotatePeak function in the default mode of the R ChIPseeker (version 1.32.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file includes information about differential methylated positions with q-values less than 0.01 and methylation  differences greater than the absolute value of 25 and their annotations.
Library strategy: Enzymatic methyl-seq (EM-seq)

organism: Bos taurus

source_name: Blood

growth_protocol: The cows were raised in the same conditions on the farm

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction
DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines

value: Blood

value: Subfertile


title: 7095


title: Bone Marrow Derived Macrophages, Control Media, 100nM CDDO-ME, Replicate 3

description: Library name: ME_4

value: Control Media, 100nM CDDO-Me


title: 000-571

value: high


title: Senescent HUVECs, Rep C

description:
Library name: Celula-C
miRNA amplification


title: 000-489

value: low


title: Early-passage HUVECs, Rep D

description:
Library name: Celula-D
miRNA amplification


title: 7022


title: Bone Marrow Derived Macrophages, Control Media, 100nM CDDO-ME , Replicate 1

description: Library name: ME_1


title: Bone Marrow Derived Macrophages, Control Media, 100nM CDDO-ME, Replicate 2

description: Library name: ME_3


title: 000-487

value: Whole blood


title: 7014


title: Bone Marrow Derived Macrophages, LL2 NRF2 KO Conditioned Media, Vehicle Treatment, Replicate 3

description: Library name: N1D8_V_4

value: LL2 NRF2 KO Conditioned Media, Vehicle


title: 000-640

value: Asthma

value: Male


title: 6121


title: Senescent HUVECs, Rep A

description:
Library name: Celula-A
miRNA amplification


title: Senescent HUVECs, Rep B

description:
Library name: Celula-B
miRNA amplification


title: 6030


title: 000-576


title: 000-634


title: 4098

value: Fertile


title: 000-636


title: Early-passage EVs, Rep F

description:
Library name: Vesicula-F
3’ mRNA amplification

data_processing:
Raw FASTQ files were quality-filtered and trimmed to remove low-quality bases, sequencing adapters, and poly-A tails. Read quality was assessed with FastQC v0.11.9, ensuring high %Q20 scores, absence of Ns, and removal of adapters and poly-A sequences.
Trimmed sequence reads were mapped to the GRCh38 reference genome using STAR v2.7.10. After alignment, duplicate reads were removed using UMI-tools, based on unique molecular identifiers (UMIs) associated with each original fragment.
Gene-level counts were computed with HTSeq-count v2.0.2, using the corresponding NCBI GTF annotation.
Assembly: GRCh38
Supplementary files format and content: individual tab-delimited text files include raw counts.

source_name: HUVECs derived Evs

extract_protocol:
Total RNA was extracted from the cell pellets using the MagMAX™ mirVana™ Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's instructions for ECs. EVs were processed using the Total Exosome RNA and Protein Isolation Kit (Invitrogen), following the manufacturer's recommendations.
Dual-indexed mRNA libraries were prepared using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Lexogen GmbH, Vienna, Austria), according to the user guide. According to the manufacturer's recommendations, 250 ng of starting material was used for cellular RNA analysis, while a low-input protocol (<10ng total) was used for EVs. Library quality was evaluated using the QiaXcel Advanced System (Qiagen), while the quantity was measured using a Quantus Fluorometer (Promega Corporation).

value: HUVECs derived Evs

value: Endothelial cells derived Evs


title: Bone Marrow Derived Macrophages, LL2 NRF2 KO Conditioned Media, Vehicle Treatment, Replicate 2

description: Library name: N1D8_V_3


title: Bone Marrow Derived Macrophages, LL2 NRF2 KO Conditioned Media, Vehicle Treatment, Replicate 1

description: Library name: N1D8_V_1


title: 4044


title: Early-passage EVs, Rep E

description:
Library name: Vesicula-E
3’ mRNA amplification

value: WT


title: Bone Marrow Derived Macrophages, LL2 KEAP1 KO Conditioned Media, Vehicle Treatment, Replicate 2

description: Library name: K3F10_V_3

value: Bone Marrow Derived Macrophage

value: LL2 KEAP1 KO Conditioned Media, Vehicle


title: Bone Marrow Derived Macrophages, LL2 KEAP1 KO Conditioned Media, Vehicle Treatment, Replicate 3

description: Library name: K3F10_V_4

value: Macrophage


title: 4050


title: 000-629

description: Expression value derived from nCounter Digital Analyzer

value: Female


title: Senescent EVs, Rep B

description:
Library name: Vesicula-B
3’ mRNA amplification


title: Bone Marrow Derived Macrophages, LL2 KEAP1 KO Conditioned Media, Vehicle Treatment, Replicate 1

description: Library name: K3F10_V_1


title: Senescent EVs, Rep C

description:
Library name: Vesicula-C
3’ mRNA amplification


title: 000-630


title: 3131

value: Blood


title: 4035


title: Bone Marrow Derived Macrophages, LL2 WT Conditioned Media, Vehicle Treatment, Replicate 3

description: Library name: WT_V_4

value: LL2 WT Conditioned Media, Vehicle


title: 000-627


title: 000-626


title: Bone Marrow Derived Macrophages, LL2 WT Conditioned Media, Vehicle Treatment, Replicate 2

description: Library name: WT_V_3


title: Senescent EVs, Rep A

description:
Library name: Vesicula-A
3’ mRNA amplification


title: 3067


title: 000-633