title: G378W, mutant, replicate 3

city: Washington

first: Shaolei

last: Teng

state: District of Columbia

address: 415 College St. NW

department: Biology

institute: Howard University

description:
Library name: Sample 12
G378W, mutant, replicate 3

data_processing:
Libraries were quantified using Qubit and real-time PCR, and fragment size distribution was assessed using a bioanalyzer.
Qualified libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads. Data quality was ensured through raw read filtering, which removed adapter-containing reads, reads with >10% N content, or >50% low-quality bases.
Sequencing reads were trimmed and filtered by Novogene’s internal pipeline. FASTQC screened for the presence of over-represented sequences, the presence of adapters, and the overall base quality of the reads. Bowtie2 was used for short-read alignement.
Clean reads were used for de novo transcriptome assembly via Trinity, followed by quantification using RSEM -- Quantification of genes and Transcripts/isoforms.
Normalization and Statistical Analysis of DEGs
Assembly: Trinity software package was used to assemble the raw RNA-seq data without a reference genome
Supplementary files format and content: Table-delimated text file included count, TPM, FPKM for each sample

organism: Drosophila melanogaster

source_name: Whole Body

growth_protocol: Adult male and female Drosophila melanogaster were collected from wild-type and three CRISPR-engineered mutant lines (G378W, W621R, and deletion of residues 305–687 in the cysu gene). Flies were raised on standard cornmeal agar medium under controlled temperature (24 ± 1 °C) and light/dark cycle (12 h:12 h). RNA was extracted from pooled adult flies (day 1 post-eclosion).

extract_protocol:
Total RNA was extracted using the Quick-RNA Tissue/Insect Microprep Kit (Zymo Research, Cat # R2030) following the manufacturer’s instructions
Poly-A mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand synthesis. End repair, A-tailing, adaptor ligation, size selection, amplification, and purification steps were conducted to prepare libraries.

value: Whole Body

value: G378W Knockdown


title: Mouseb_4

status: Public on May 28 2025

type: SRA

city: SHANGHAI

first: Fudi

last: Wang

state: SHANGHAI

address: 320, YUEYANG ROAD

country: China

institute: Stanford University

description: Library name: Mouseb_4

library_source: transcriptomic

data_processing:
Quality control of the sequencing data was performed using FastQC (v0.11.8).
TrimGalore (v0.6.10) was employed for the trimming of sequence reads.
The RNA-seq reads were aligned to mm10 reference genome using the STAR software (v2.7.11b).
Raw read counts were subjected to variance stabilizing transformation (VST) using the DESeq2 (v1.44).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: BMDMs were prepared from three mice. At day4 of differentiation, 7x105 macrophages were seeded into 6-well plates.

extract_protocol:
Total RNA was extracted according to the protocol from manufacturer and qualified on a NanoDrop™ OneC Microvolume UV-Vis Spectrophotometer (Thermo Scientific™ 840274200).
Three biological replicates per treatment group with a total of 200 ng RNA per sample were sent to Novogene Co. (Sacramento, CA, USA) for sample quality control, library preparation, and sequencing.
Complementary DNA library construction and sequencing were performed for each sample on an Illumina Novaseq 6000 platform with paired-end 150-bp reads.

treatment_protocol: Cells were treated with 2µM thiothixene or DMSO for 24 hours at day 6. Drug-treated macrophages were washed with PBS once and cells were lysed with 0.5 ml TRIzol™ Reagent (ThermoFisher 15596026).

tag: tissue

value: Bone marrow

tag: cell line

value: BMDM

tag: cell type

value: Macrophage

tag: treatment

value: Thiothixene 2 µM


title: Colon Cancer_574

type: RNA

city: Palma

first: Ramon

middle: Maria

last: Rodriguez

state: Balearic Islands

address: Edificio S, Hospital Universitario Son Espases, Carretera de Valldemossa, 79

department: Oncology and hematology

country: Spain

institute: Institut d'Investigació Sanitària Illes Balears

description: Gene expression data from patiets with colon cancer

hyb_protocol: Samples were hybridized with GeneChip Human Clariom S Pico Arrays (Affymetrix, Thermo Fisher Scientific) and scanned at the Genomic Core Facility of the The Health Research Institute of the Balearic Islands (IdISBa)

scan_protocol: Array scanning was performed by using the GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix, Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software using default analysis settings.

label: biotin

organism: Homo sapiens

source_name: Human colon cancer

label_protocol: Double-stranded cDNA was generated from the amplified cRNA with the GeneChip Pico Reagent Kit (Affymetrix, Thermo Fisher Scientific) and then fragmented and biotin-labeled.

extract_protocol: RNeasy Plus Kit was used for extraction of total RNA according to the manufacturer's instructions.

tag: disease state

value: Human colon cancer

value: Colon

tag: age

tag: Sex

value: Male

tag: histological features diagnostic

tag: bmi

tag: unsaturated/saturated fa ratio

tag: ethnicity

value: White/Mediterranean


title: Mousea_4

description: Library name: Mousea_4


title: Caenorhabditis_elegans_embryo_secp-2(ths431)_H3K9me3_Input_seq

city: Guangzhou

first: shiyu

last: cai

address: No. 135 Xingang Xi Road, Haizhu District

institute: Sun Yat-sen University

description: Library name: secp-2(ths431)_H3K9me3_Input

library_source: genomic

data_processing:
The sequencing reads were processed using Trim Galore (v0.6.10 ) to remove adapters and filter out low-quality sequences.
Alignment was performed against the Caenorhabditis elegans reference genome (WS292 ) using Bowtie2.
Duplicate reads were removed using sambamba (v1.0.0 ). BAM files from replicates were merged with samtools (v1.19.2 ), and read counts were normalized using the RPKM (Reads Per Kilobase per Million mapped reads) method.the ChIP/input ratio was calculated using bamcompare.
Peak calling was performed with MACS2 (v3.0.1,--broad-cutoff 0.1)
Assembly: WBcel235 (WS292)
Supplementary files format and content: bigwig
Supplementary files format and content: broadPeak

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: embryo

extract_protocol:
worm embryos were crosslinked in 2% formaldehyde for 30 min. Crosslinking was quenched with 125 mM glycine for 5 min at room temperature and washed three times with M9 (3g/L KH2PO4, 6g/L Na2HPO4, 5g/L NaCl, 1 mM MgSO4). Crosslinked samples were suspended by FA buffer (50 mM Tris/HCl pH 7.5, 1 mM EDTA, 1 % Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl) with 1X complete protease inhibitor (Roche, 4693132001) and sonicated for three 8-min cycles (30 s on and 30 s off per cycle) with Diagenode Bioruptor on high amplitude. Lysates were precleared with protein A/G (Santa Cruz, SC-2003). 5% samples were saved for input. The rest of the lysate was immunoprecipitated with 2 μl of rabbit anti-H3K9me3 antibody (Millipore, 07-523) overnight at 4 °C. The next day, the samples were incubated with 20 μL protein A/G beads for 2h at 4 °C. Beads were extensively washed by FA  buffer two times, FA-500 buffer (50 mM Tris/HCl pH 7.5, 1 mM EDTA, 1 % Triton X-100, 0.1% sodium deoxycholate, 500 mM NaCl) two times, LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris/HCl pH 8.0) one time and TE buffe (10 mM Tris/HCl pH 8.0, 1 mM EDTA) 2 times. Washed samples were eluted with elution buffer (1% SDS, 100 mM NaHCO3) for 30 min at room temperature. The samples were de-crosslinked with 200 mM NaCl at 65 °C for 4 h. For input DNA, input samples were treated with RNase A (Thermofisher, EN0531) at 65 °C for 30 min. All DNA samples were purified by E.Z.N.A. Gel Extraction Kit (Omega, D2500).
ChIP-seq libraries were made using IVAHTS Universal DNA Library Prep Kit for lllumina V3 (Vazyme, ND607) according to the manufacturer’s instructions.

value: embryo

tag: genotype


title: Colon Cancer_573


title: Caenorhabditis_elegans_embryo_secp-1(ths593)_H3K9me3_ChIP_seq_R2

description: Library name: secp-1(ths593)_H3K9me3_ChIP_R2


title: Colon Cancer_567

value: Female


title: G378W, mutant, replicate 1

country: USA

description:
Library name: Sample 10
G378W, mutant, replicate 1

molecule: polyA RNA


title: N305-R687 Deletion, replicate 3

description:
Library name: Sample 9
N305-R687 Deletion, replicate 3

value: N305-R687 Knockdown


title: Colon Cancer_571


title: Colon Cancer_566


title: Mouse BMDC 100Q rep 3 (tRNA-seq)

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: Library name: Sample6

data_processing:
Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to mus musculus tRNA reference genome.
The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/, Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting IGV output.wig files were reformatted using custom Python scripts to obtain mutation rate and read coverage compatible with R for data visualization and analysis.
Assembly: mm39
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: .sam.tsv files with mutation, deletion, coverage for each gene position per sample

source_name: bone marrow

growth_protocol: Murine bone marrow-derived dendritic cells (BMDCs) were generated from 6-8 week-old C57BL/6 female mice. Bone marrow cells were collected from femora and tibiae and cultured at 37°C in RPMI-1640 (Gibco; AM9260G) supplemented with 10% v/v dialyzed fetal bovine serum (Gibco; 26400044), L-glutamine (2 mM; Gibco; 25030081), penicillin-streptomycin (Gibco; 15140122), MEM non-essential amino acids (Corning; MT25025CI), HEPES (10 mM; Gibco; 15630080), sodium pyruvate (1 mM; Corning; MT25000CI), and β-mercaptoethanol (55 µM; Gibco; 21985023). Recombinant murine GM-CSF (Peprotech 315–03-100μg) at 15 ng/mL was added to the complete RPMI medium. Cells were fed at days 2 and 4 with complete RPMI medium containing GM-CSF.

extract_protocol:
On day 5, total RNA was extracted from cells using TRIzol reagent (Thermo Fisher Scientific; 15596026)
MSR-seq (PMID 35513407)

treatment_protocol: Cells were plated in triplicate with either media alone (0Q) or supplemented with 100 nM queuine (100Q). Cells were fed at days 2 and 4 with complete RPMI medium containing GM-CSF ± queuine to maintain treatment concentration .

value: bone marrow

value: dendritic cell

value: 100 nM queuine supplement


title: N305-R687 Deletion, replicate 2

description:
Library name: Sample 8
N305-R687 Deletion, replicate 2


title: Mouse BMDC 100Q rep 2 (tRNA-seq)

description: Library name: Sample5


title: Caenorhabditis_elegans_embryo_secp-1(ths593)_H3K9me3_Input_seq

description: Library name: secp-1(ths593)_H3K9me3_Input


title: Mouse BMDC 100Q rep 1 (tRNA-seq)

description: Library name: Sample4


title: Caenorhabditis_elegans_embryo_secp-1(ths593)_H3K9me3_ChIP_seq_R1

description: Library name: secp-1(ths593)_H3K9me3_ChIP_R1


title: G378W, mutant, replicate 2

description:
Library name: Sample 11
G378W, mutant, replicate 2


title: N305-R687 Deletion, replicate 1

description:
Library name: Sample 7
N305-R687 Deletion, replicate 1


title: W621R mutant, replicate 3

description:
Library name: Sample 6
W621R mutant, replicate 3

value: W621R Knockdown


title: W621R mutant, replicate 2

description:
Library name: Sample 5
W621R mutant, replicate 2

value: Whole Body


title: Caenorhabditis_elegans_embryo_set-25(ths172)_H3K9me3_ChIP_seq_R1

description: Library name: set-25(ths172)_H3K9me3_ChIP_R1


title: Mouse BMDC 0Q rep 2 (tRNA-seq)

description: Library name: Sample2

value: queuine-depleted media


title: Mouse BMDC 0Q rep 3 (tRNA-seq)

description: Library name: Sample3


title: Caenorhabditis_elegans_embryo_set-25(ths172)_H3K9me3_ChIP_seq_R2

description: Library name: set-25(ths172)_H3K9me3_ChIP_R2


title: Colon Cancer_562


title: Mouse BMDC 0Q rep 1 (tRNA-seq)

description: Library name: Sample1


title: Caenorhabditis_elegans_embryo_set-25(ths172)_H3K9me3_Input_seq

description: Library name: set-25(ths172)_H3K9me3_Input


title: W621R mutant, replicate 1

description:
Library name: Sample 4
W621R mutant, replicate 1


title: Colon Cancer_557-rep


title: Caenorhabditis_elegans_embryo_N2_H3K9me3_ChIP_seq_R2

description: Library name: N2_H3K9me3_ChIP_R2

value: WT


title: w1118 (control), replicate 3

description:
Library name: Sample 3
w1118 (control), replicate 3


title: Colon Cancer_556

description: Gene expression data from patiets with colon cancer


title: Hippocampus, P8-14 exposed, P21, rep 3

city: Maebashi

first: Izuki

last: Amano

state: Gunma

address: 3-9-22 Showa-machi

department: Department of Integrative Physiology, Graduate School of Medicine

country: Japan

institute: Gunma University

description: PFOS P8-14 03

data_processing:
BCL (base call) binaries were converted to FASTQ using the illumina package bcl2fastq. Removal of adapters and low-quality reads was performed using fastp (version 0.21.0). Reads after trimming were used for mapping to the mm10 reference genome and for read counting in the STAR (version 2.5.3a)-RSEM (version 1.3.3) pipeline.
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each Sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted following the instruction for RNeasy Lipid Tissue Mini Kit (QIAGEN).
Library preparation was performed using the TruSeq stranded mRNA kit (Illumina).

value: Hippocampus

value: PFOS P8-14


title: Caenorhabditis_elegans_embryo_N2_H3K9me3_ChIP_seq_R1

description: Library name: N2_H3K9me3_ChIP_R1


title: w1118 (control), replicate 2

description:
Library name: Sample 2
w1118 (control), replicate 2


title: Hippocampus, P8-14 exposed, P21, rep 2

description: PFOS P8-14 02


title: Colon Cancer_543


title: Colon Cancer_563


title: Colon Cancer_540


title: Caenorhabditis_elegans_embryo_N2_H3K9me3_Input_seq

description: Library name: N2_H3K9me3_Input


title: Colon Cancer_537


title: w1118 (control), replicate 1

description:
Library name: Sample 1
w1118 (control), replicate 1


title: Hippocampus, P8-14 exposed, P21, rep 1

description: PFOS P8-14 01


title: Sciatic nerve myeloid cells, PSNL surgery, 15 weeks after surgery, GEX

city: Glasgow

first: Paschalina

last: Chrysostomidou

address: University Avenue

country: United Kingdom

institute: University of Glasgow

description:
Library name: PSNL Chronic, GEX
10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned using the 10X Genomics Cell Ranger (version 6.0.0) “cellranger count” pipeline, using the pre-built mouse GRCm38 transcriptome reference and following guidance for “Feature Barcode Analysis” using TotalSeq-B antibodies. The following cell numbers were captured: 1,920 (acute crush), 2,471 (acute PSNL), 2,675 (chronic crush), 2,067 (chronic PSNL). Output files from Cell Ranger were analysed in R Studio (Version 2024.09.1) with Seurat (version 5.1.0).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: fastq files, filtered counts & seurat object

source_name: Sciatic Nerve

extract_protocol:
1 week or 15 weeks after surgery, mice were transcardially perfused with 10 ml PBS to remove leukocytes from circulating blood. Ligated, crushed or uninjured (sham) nerves were dissected and placed into a petri dish containing F12 medium (Gibco, #21765-029). Ligatures were removed with tweezers, if still present, and nerves were cut to 0.5 cm, ensuring equal lengths of nerve either side of the ligation/crush site. Following dissections, samples were transferred into wells of a standard 96-well PCR plate containing 51μl of the following digestion mix: 6.25 mg/ml collagenase type IA (Sigma Aldrich, #C9891), 0.2% Pronase (Millipore, #53702), 0.4% Hyaluronidase (ABNOVA, #P52330) in F12 medium. Spring scissors were used to chop the tissue into small pieces (50x chops, cleaning scissors between samples with 100% ethanol). After this manual dissociation, the plate was incubated on a shaking platform (220 rotations per minute) at 37°C for 30 minutes. The digestion mix was subsequently removed and replaced with 100μl of fluorescence-activated cell sorting (FACS) buffer: 0.4% BSA (Sigma-Aldrich, #A3983), 15 mM HEPES (Gibco, #15630080), 2mM EDTA (Invitrogen, #15575038) in Hank’s Buffered Saline Solution (HBSS, diluted from 10x, Gibco, #14175095). Samples were then further dissociated by pipetting up and down 50x, with the resulting single-cell solution filtered through a 35μm cap of a BD falcon tube with a cell strainer cap (BDBiosciences, # 352235). The plate was centrifuged at 1500 rotations per minute for 5 minutes at 4°C, after which supernatants were removed and resuspended in 50μl of the following staining mixture for 30 minutes at 4°C in a dark fridge: Fc block (BioLegend, #101302, 1:200), FITC-CD45 to stain leukocytes (BioLegend, #147709, 1:1200), PE-Cy7-CD11b to stain myeloid lineage cells (BioLegend, #101215, 1:1200) and, depending on the sample, one of four hashtag antibodies: TotalSeq-B0301-MHCI (BioLegend, #155831), TotalSeq-B0302-MHCI (BioLegend, #155833), TotalSeq-B0303-MHCI (BioLegend, #155835), TotalSeq-B0304-MHCI (BioLegend, #155837). At the acute time point, one week after surgery, the antibody staining mix also contained BUV395-Ly6G to stain neutrophils (BD Bioscience, #563978, 1:300). After staining, cells were centrifuged for 5 minutes at 1,500 rotations per minute at 4°C, after which the cell pellets were resuspended in 300μl FACS buffer and transferred to FACS tubes, adding DAPI to stain for dead cells (Invitrogen, #D1306, 1μl of a 1:2 dilution). Sorting was performed on a BD FACSAria II or BD FACSAria Fusion in the Advanced Cytometry Platform Core Facility of the Guy's and St Thomas' NHS Foundation Trust. Unstained cells, DAPI single stained cells and single stained control beads (BD™ CompBeads, BD Bioscience, #552845) were used for compensation. Cells were sorted into 1.5ml microcentrifuge tubes containing 4μl of 4% BSA (Sigma-Aldrich, #A3983) in PBS. All tubes were pre-coated for at least 1 hour with the same 4% BSA solution and placed on ice immediately following cell collection. The following samples were collected: for the 1-week time point, CD45+/CD11b+/Ly6G- live single cells from n = 2 sham (2,000 cells each), crush and PSNL mice (8,000 cells each); for the 15-week time point, as many CD45+/CD11b+ live single cells as possible were collected from n = 3 crush and n = 4 PSNL mice.
Hashed samples were combined as follows in two separate 10X runs: for the 1-week time point, one 10X well (acute crush) was filled with cells from 1x male sham, 1x male crush, 1x female crush mouse, while the other (acute PSNL) was filled with cells from 1x female sham, 1 male PSNL and 1 female PSNL mouse. A separate 10X run was performed for the 15-week time point, with one well (chronic crush) filled with 2x female crush and 1x male crush sample, and the other well (chronic PSNL) filled with 2x female and 2x male PSNL samples. Libraries were generated using the 10X Genomics Chromium Single Cell 3ʹ Feature Barcode Library & Gel Bead Kit (v3 Chemistry) according to manufacturer’s instructions and sequenced on an Illumina NextSeq 2000 P2 Flow Cell obtaining mean reads per cell of: 24,752 (acute crush well), 35,710 (acute PSNL well), 45,531 (chronic crush well), and 59,220 (chronic PSNL well).

treatment_protocol: Male and female C57BL/6JolaHsd mice underwent one of two models of nerve damage: partial sciatic nerve ligation (PSNL) or sciatic nerve crush. For both procedures, animals were anaesthetised under 2% isoflurane and pre-operatively administered 0.1mg/kg of the analgesic buprenorphine subcutaneously (s.c). After shaving the fur covering the left hip and leg region, the sciatic nerve was exposed via blunt dissection. For PSNL, roughly half of the nerve was tightly ligated with a suture (5.0 Vicryl suture, Ethicon, #W9982). For nerve crush, Watchmaker forceps (Dumont, #0304-5-PO) were placed horizontally around the nerve and pressed tightly for 10 seconds, the forceps were then placed vertically around the same section of nerve and again pressed tightly for 10 seconds. For sham surgeries the sciatic nerve was exposed but left untouched. In all cases, the wound was stapled shut with a Reflex 7mm metal wound clip (Fine Science Tools, #12032-07). Mice were transferred to a clean cage and left to recover in the animal unit. Animals were weighed and checked for autotomy daily for at least 3 days following surgery and wound clips were removed within 7 days of surgery.

value: Sciatic Nerve

value: pooled male and female

value: CD11b+ Myeloid cells

tag: surgery

value: PSNL

tag: library type

value: GEX

tag: batch

value: batch 2


title: Hippocampus, P1-7 exposed, P21, rep 3

description: PFOS P1-7 03

value: PFOS P1-7


title: Sciatic nerve myeloid cells, PSNL surgery, 15 weeks after surgery, CSP

description:
Library name: PSNL Chronic, CSP
10x Genomics

value: CSP

tag: hto

value: Ms.Hashtag_1 (PSNL F1),  Ms.Hashtag_2 (PSNL F2), Ms.Hashtag_3 (PSNL M1), Ms.Hashtag_4 (PSNL M2)


title: Hippocampus, P1-7 exposed, P21, rep 2

description: PFOS P1-7 02


title: CHIPseq-TY, CFAP20-KO + TY-CFAP20, rep3

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description:
Library name: CHIPseqTY_CFAP20KO-TYCFAP20_rep3
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20KO-CFAP20TY_average.txt

library_source: other

data_processing:
Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using bwa-mem tools (BWA (Version 0.7.17) and a combined reference genome containing GCA_000001405.15_GRCh38 (Li, 2013) and D.melanogaster genome BDGP6 to quantify spike-in counts. Only uniquely mapping and high-quality reads (> q30) were included in the analyses. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into stranded TagDirectories with fixed 200 bp fragment length using HOMER tools (Version 4.8.2). UCSC genome tracks were generated using HOMER tools.
OK-seq data in untreated RPE1 cells was downloaded from Chen et al. 2019 (datasets GSM3130725 and GSM3130726). Sequences were trimmed using TrimGalore (Version 0.6.5), and aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Replication initiation zones were subsequently defined using the replication fork directionality analysis R toolkit (OKseqHMM; available on https://github.com/CL-CHEN-Lab/OK-Seq), with read coverage threshold 6 for GSM3130725 and 1 for GSM3130726, and smoothing window size 15 kb. Initiation zones present in both datasets were identified using mergePeaks of HOMER tools (Version 4.8.2), with -d given. Origins were defined as the center of initiation zones. For all origins, their nearest TSS was defined using annotatePeaks of HOMER tools, together with the distance between the TSS and the origin. Here, a negative distance represents an origin upstream of the TSS (co-directional transcription relative to replication), while a positive distance represents an origin downstream of a TSS (head-on transcription relative to replication). To allow for clean transcription versus replication analyses, we further selected only origins for which their nearest TSS was not preceded by another gene within 5kb upstream of the TSS. This resulted in a list of 2,040 origins. A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings.
Read-density profiles around TSS or origin coordinates were defined using the AnnotatePeaks.pl tool of HOMER using normalization of the deduplicated reads to the number of identified Drosophila spike-in reads. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019).
Assembly: Hg38 | BDGP6
Supplementary files format and content: ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_WT_average.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of 3000 actively transcribed genes (defined by BrU-seq in WT cells) with a minimal size of 3 kb; data is average of 3 ChIPs in WT cells
Supplementary files format and content: ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20KO-CFAP20TY_average.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of 3000 actively transcribed genes (defined by BrU-seq in WT cells) with a minimal size of 3 kb; data is average of 3 ChIPs in CFAP20-KO + TY-CFAP20 cells
Supplementary files format and content: TSScoordinates_InclBrUseqInWTmock.txt: tab-delimited text file containing coordinates of 9944 TSSs, including BrUseq signal in WT cells
Supplementary files format and content: OriginCenter_OKseq_Select5kbUpstreamTSSempty.txt: tab-delimited text file containing coordinates of a set of origins, defined as described
Supplementary files format and content: ChIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_TYCFAP20resc_rep1_FragLength200_SpikeNorm.txt: tab-delimited text file containing the read-density/10M reads at the indicated distance from a set of origins, defined as described
Supplementary files format and content: ChIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_TYCFAP20resc_rep2_FragLength200_SpikeNorm.txt: tab-delimited text file containing the read-density/10M reads at the indicated distance from a set of origins, defined as described
Supplementary files format and content: ChIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_TYCFAP20resc_rep3_FragLength200_SpikeNorm.txt: tab-delimited text file containing the read-density/10M reads at the indicated distance from a set of origins, defined as described
Supplementary files format and content: ChIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_WT_rep1_FragLength200_SpikeNorm.txt: tab-delimited text file containing the read-density/10M reads at the indicated distance from a set of origins, defined as described
Supplementary files format and content: ChIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_WT_rep2_FragLength200_SpikeNorm.txt: tab-delimited text file containing the read-density/10M reads at the indicated distance from a set of origins, defined as described
Supplementary files format and content: ChIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_WT_rep3_FragLength200_SpikeNorm.txt: tab-delimited text file containing the read-density/10M reads at the indicated distance from a set of origins, defined as described

molecule: other

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO + TY-CFAP20

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 in DMEM GlutaMAX (Gibco), supplemented with 10% fetal calf serum (Avantor, VWR) and penicillin/streptomycin (Sigma).

extract_protocol:
Attached cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed once with PBS followed by incubation with 1% FA for 20 min at RT. Fixation was stopped by the addition of glycine in PBS to a final concentration of 0.1 M for 3 min at RT. This was followed by washing with cold PBS and collection of the cells in 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), and 20 mM Hepes (pH 7.6) in miliQ. Chromatin was pelleted by centrifugation for 5 min at 400 × g and incubated in 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) in miliQ for 10 min at 4 °C. Chromatin was again pelleted by centrifugation and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6) in miliQ) to a final concentration of 15 × 10^6 cells/mL. Chromatin was sonicated to approximately one nucleosome using the Bioruptor Pico (Diagenode), 8 cycles of 30s ON/30 s OFF in a 4°C water bath. ChIP was performed using 84 μg of WT chromatin and 60 ug of CFAP20-KO + TY-CFAP20 chromatin + 74 and 53 ng of Drosophila spike-in chromatin, respectively (Active Motif, 53083) with 5.7 ug of TY antibody (Diagenode; C15200054) and 1 μg spike-in antibody (Active Motif, 61686) by overnight incubation at 4 °C. Protein-chromatin-pull down followed with 20 ul protein A Dynabeads (Thermo Fisher; 10001D) per sample. ChIP samples were extensively washed and purified using Qiagen MinElute kit.
Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NovaSeq X, using paired-end sequencing with 151 bp from each end.
ChIP-seq

treatment_protocol: Cells were grown to 80-90% confluency

tag: genome used_to_map_to

value: Hg38 | BDGP6 (spike-in)

value: untreated

tag: pulldown antibody

value: Mouse anti-TY (Diagenode; C15200054)

tag: type of_material

value: ChIP DNA


title: CHIPseq-TY, CFAP20-KO + TY-CFAP20, rep1

description:
Library name: CHIPseqTY_CFAP20KO-TYCFAP20_rep1
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20KO-CFAP20TY_average.txt

tag: cell line

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO + TY-CFAP20


title: Colon Cancer_535

value: Human colon cancer

tag: tissue

value: Colon

value: Female

value: White/Mediterranean


title: Colon Cancer_533

tag: disease state

value: Male


title: Hippocampus, P1-7 exposed, P21, rep 1

description: PFOS P1-7 01

value: Hippocampus

value: WT

tag: treatment


title: CHIPseq-TY, WT, rep3

description:
Library name: CHIPseqTY_WT_rep3
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_WT_average.txt

source_name: RPE1 iCas9 p53/puro-dKO WT

value: RPE1 iCas9 p53/puro-dKO WT


title: Sciatic nerve myeloid cells, PSNL or Sham surgery, 1 week after surgery, CSP

description:
Library name: PSNL Acute, CSP
10x Genomics

value: Sciatic Nerve

tag: Sex

value: pooled male and female

tag: cell type

value: CD11b+ Myeloid cells

value: PSNL or sham

value: HTO_AHH01_TotalSeqB (PSNL SHAM F), HTO_AHH02_TotalSeqB (PSNL F), HTO_AHH03_TotalSeqB (PSNL M)

value: batch 1


title: Colon Cancer_530

tag: age

tag: histological features diagnostic

tag: bmi


title: Colon Cancer_522

tag: unsaturated/saturated fa ratio

tag: ethnicity


title: Hippocampus, control, P21, rep 3

description: Control 03

tag: genotype

value: sham


title: Hippocampus, control, P21, rep 2

description: Control 02


title: Sciatic nerve myeloid cells, Crush surgery, 15 weeks after surgery, GEX

description:
Library name: Crush Chronic, GEX
10x Genomics

tag: surgery

value: crush

tag: library type

value: GEX

tag: batch

value: batch 2


title: CHIPseq-TY, WT, rep1

description:
Library name: CHIPseqTY_WT_rep1
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_WT_average.txt

tag: genome used_to_map_to

value: Hg38 | BDGP6 (spike-in)

value: untreated

tag: pulldown antibody

value: Mouse anti-TY (Diagenode; C15200054)

value: ChIP DNA


title: Sciatic nerve myeloid cells, Crush or Sham surgery, 1 week after surgery, GEX

description:
Library name: Crush Acute, GEX
10x Genomics

value: crush or sham


title: Colon Cancer_517

value: Human colon cancer

value: Colon

value: Female

value: White/Mediterranean


title: DH5α_1000_10

city: Shenzhen

first: Yuanyuan

last: Kang

address: No. 6 Pingshan 1st Road, Taoyuan Street, Nanshan District

department: School of Civil and Environmental Engineering

institute: Harbin Institue of Technology

description: Library name: DH5α_1000_10

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the A.baylyi ADP1 reference genome (NC_005966.1) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Assembly: NC_017316.1, GCF_000982435.1, NC_006827.2
Supplementary files format and content: Excel file includes FPKM values for each sample
Supplementary files format and content: Excel file includes LOG2FC values for each sample

organism: Enterococcus faecalis

source_name: Bacteria

growth_protocol: Liquid brain heart infusion (BHI) medium at 37 °C

extract_protocol:
Total RNA was extracted using the Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed the donor ( E. faecalis OG1RF) and intrageneric recipient or intergeneric recipient at a 1:1 ratio in BHI, and  incubation in triplicate for 2 h in 0.1 mg/L 20 nm PS, 1 mg/L 20 nm PS, 10 mg/L 20 nm PS, 0.1 mg/L 120 nm PS, 1 mg/L 120 nm PS, 10 mg/L 120 nm PS, 0.1 mg/L 1000 nm PS, 1 mg/L 1000 nm PS, 10 mg/L 1000 nm PS, at 25 °C

value: Bacteria

value: intergeneric conjugation under the exposure of 10 mg/L 1000 nm PS


title: Sciatic nerve myeloid cells, Crush surgery, 15 weeks after surgery, CSP

description:
Library name: Crush Chronic, CSP
10x Genomics

value: Sciatic Nerve

value: pooled male and female

value: CD11b+ Myeloid cells

value: CSP

tag: hto

value: Ms.Hashtag_1 (CRUSH F1), Ms.Hashtag_2 (CRUSH F2), Ms.Hashtag_3 (CRUSH M1)


title: Lean_Visceral_fat, bio rep 4

city: Boston

first: Heather

last: Faust

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hopsital

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_16

data_processing:
Reads were mapped to the GRCh38.93 transcriptome using kallisto 0.42.4 and transcriptional levels of genes were quantified with the log2(TPM + 1) (transcripts per kilobase million) metric.
Aligned reads were imported into Deseq2 using tximport
Removed outlier samples based on total reads mapped per sample and heatmap of count matrix.
Deseq2 was used to quantify differentially expressed genes
Assembly: GRCh38.93
Supplementary files format and content: .xls file of raw count matrix

source_name: visceral fat

growth_protocol: Primary human synovial fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 10% CO2 at 37C

extract_protocol:
10K were lysed in 25uL  pf TCL buffer with 1% BME and submitted for sequencing.
Full-length cDNA and sequencing libraries were performed using Illumina Smart-seq2 protocol. Libraries were sequenced on MiSeq from Illumina to generate 35 base paired-end reads

value: Freshly isolated OT-I T cells

tag: tissue

value: visceral fat

value: Lean (std chow)

tag: time

value: 8 weeks


title: CHIPseq-TY, CFAP20-KO + TY-CFAP20, rep2

description:
Library name: CHIPseqTY_CFAP20KO-TYCFAP20_rep2
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20KO-CFAP20TY_average.txt

tag: cell line

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO + TY-CFAP20

value: Hg38 | BDGP6 (spike-in)

tag: treatment

value: untreated

value: Mouse anti-TY (Diagenode; C15200054)

tag: type of_material

value: ChIP DNA


title: Hippocampus, control, P21, rep 1

description: Control 01

value: Hippocampus

value: WT

value: sham


title: Colon Cancer_518

tag: disease state

value: Human colon cancer

value: Colon

tag: age

tag: Sex

value: Male

value: White/Mediterranean


title: DH5α_1000_1

description: Library name: DH5α_1000_1

tag: cell type

value: Bacteria

value: intergeneric conjugation under the exposure of 1 mg/L 1000 nm PS


title: Sciatic nerve myeloid cells, Crush or Sham surgery, 1 week after surgery, CSP

description:
Library name: Crush Acute, CSP
10x Genomics

value: Sciatic Nerve

value: pooled male and female

value: CD11b+ Myeloid cells

value: crush or sham

value: CSP

value: HTO_AHH01_TotalSeqB (CRUSH SHAM M), HTO_AHH02_TotalSeqB (CRUSH F), HTO_AHH03_TotalSeqB (CRUSH M)

value: batch 1


title: Lean_Visceral_fat, bio rep 3

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_15

value: Freshly isolated OT-I T cells

value: visceral fat

value: Lean (std chow)

value: 8 weeks


title: Sciatic nerve myeloid cells, PSNL or Sham surgery, 1 week after surgery, GEX

description:
Library name: PSNL Acute, GEX
10x Genomics

value: PSNL or sham

value: GEX


title: Colon Cancer_512

description: Gene expression data from patiets with colon cancer

value: Human colon cancer

value: Colon

value: Male

tag: histological features diagnostic

tag: bmi

tag: unsaturated/saturated fa ratio

tag: ethnicity


title: Colon Cancer_510

value: Female

value: White/Mediterranean


title: Lean_Visceral_fat, bio rep 2

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_14


title: Sample 1003 CD45+ cells, TCR

city: New York

first: Ning

last: Yao

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Sample_1003_TCR
10X Genomics

data_processing:
FASTQ sequencing reads were processed using the Cell Ranger pipeline, which extracts cell barcodes, unique molecular identifiers (UMIs), and cDNA or antibody barcodes. It aligns cDNA reads to the human GRCh38 reference genome and generates gene and antibody UMI count matrices.
Assembly: mm10
Supplementary files format and content: Raw count matrices: matrix.mtx.gz, Barcode files: barcode.tsv.gz , Feature files: features.tsv.gz
Supplementary files format and content: TCR sequencing: TCR_contig.csv
Library strategy: TCR-seq

source_name: Spleen

extract_protocol:
Mice bearing bilateral E0771 breast cancer tumors (5*105 cells/mouse, in 100 uL PBS) were excised following 2 treatments of IT isotype control of 2141-V11. Tumors were excised and homogenized using the genlteMACs dissociation (mouse tumor dissociation kit, Miltenyi) according to the manufacturer's recommendations, then CD45+ immune cells were sorted for analysis.
Single cells were encapsulated into nanoliter-scale Gel Beads-in-emulsion (GEMs) using Chromium Controller (10X Genomics) following manufacture’s protocol. Chromium Single Cell 5’ Library & Gel Bead, Single Cell V(D)J Enrichment Kit, Mouse T Cell, and Single Cell 5' Feature Barcode kits were used to prepare single cell 5’ RNA, single cell TCR, and single cell surface protein libraries following manufacture’s protocol. The quality and quantity of the libraries were assessed with Agilent TapeStation (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).

value: Spleen

value: CD45+ cells

value: Untreated (Control #1, #2)

tag: library type

value: TCR


title: Colon Cancer_513


title: CHIPseq-TY, WT, rep2

description:
Library name: CHIPseqTY_WT_rep2
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_WT_average.txt

value: RPE1 iCas9 p53/puro-dKO WT

tag: genome used_to_map_to

value: Hg38 | BDGP6 (spike-in)

value: untreated

value: Mouse anti-TY (Diagenode; C15200054)

value: ChIP DNA


title: Colon Cancer_505


title: DH5α_120_10

description: Library name: DH5α_120_10

value: Bacteria

value: intergeneric conjugation under the exposure of 10 mg/L 120 nm PS


title: Lean_Visceral_fat, bio rep 1

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_13

value: Freshly isolated OT-I T cells

value: visceral fat

value: Lean (std chow)

value: 8 weeks


title: Sample 1003 CD45+ cells, HTO

description:
Library name: Sample_1003_HTO
10X Genomics

data_processing:
FASTQ sequencing reads were processed using the Cell Ranger pipeline, which extracts cell barcodes, unique molecular identifiers (UMIs), and cDNA or antibody barcodes. It aligns cDNA reads to the human GRCh38 reference genome and generates gene and antibody UMI count matrices.
Assembly: mm10
Supplementary files format and content: Raw count matrices: matrix.mtx.gz, Barcode files: barcode.tsv.gz , Feature files: features.tsv.gz
Supplementary files format and content: TCR sequencing: TCR_contig.csv
Library strategy: CITE-seq

molecule: protein

value: HTO

value: Total Seq C Hashtag 1, Total Seq C Hashtag 2


title: Colon Cancer_504

value: Human colon cancer

value: Colon

value: Male

value: White/Mediterranean


title: DH5α_120_1

description: Library name: DH5α_120_1

value: intergeneric conjugation under the exposure of 1 mg/L 120 nm PS


title: Lean_LN, bio rep 4

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_12

source_name: lymph nodes

value: lymph nodes


title: Sample 1003 CD45+ cells, GEX

description:
Library name: Sample_1003_GEX
10X Genomics

value: Spleen

value: CD45+ cells

value: Untreated (Control #1, #2)

value: mRNA


title: DH5α_120_0.1

description: Library name: DH5α_120_0.1

value: Bacteria

value: intergeneric conjugation under the exposure of 0.1 mg/L 120 nm PS


title: DH5α_20_10

description: Library name: DH5α_20_10

value: intergeneric conjugation under the exposure of 10 mg/L 20 nm PS


title: Colon Cancer_501

value: Female


title: Sample 1002 CD45+ cells, TCR

description:
Library name: Sample_1002_TCR
10X Genomics

source_name: Lymph node

value: Lymph node

value: Untreated (Control #2)

value: TCR


title: Lean_LN, bio rep 3

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_11

value: Freshly isolated OT-I T cells

value: Lean (std chow)

value: 8 weeks


title: Sample 1002 CD45+ cells, HTO

description:
Library name: Sample_1002_HTO
10X Genomics

value: HTO

value: Total Seq C Hashtag 2


title: Lean_LN, bio rep 2

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_10

value: lymph nodes


title: Sample 1002 CD45+ cells, GEX

description:
Library name: Sample_1002_GEX
10X Genomics


title: Colon Cancer_496

value: Human colon cancer

value: Colon

value: Male

value: White/Mediterranean


title: Lean_LN, bio rep 1

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_9


title: DH5α_20_1

description: Library name: DH5α_20_1

value: Bacteria

value: intergeneric conjugation under the exposure of 1 mg/L 20 nm PS


title: DH5α_20_0.1

description: Library name: DH5α_20_0.1

value: intergeneric conjugation under the exposure of 0.1 mg/L 20 nm PS


title: Colon Cancer_499


title: HFD_Visceral_fat, bio rep 4

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_8

value: visceral fat

value: High fat diet (60% kcal fat)


title: DH5α_NA

description: Library name: DH5α_NA

value: intergeneric conjugation


title: Sample 1001 CD45+ cells, TCR

description:
Library name: Sample_1001_TCR
10X Genomics

source_name: Tumor

value: Tumor

value: CD45+ cells

value: Untreated (Control #1)

value: TCR


title: Sample 1001 CD45+ cells, HTO

description:
Library name: Sample_1001_HTO
10X Genomics

value: HTO

value: Total Seq C Hashtag 1


title: Sample 1001 CD45+ cells, GEX

description:
Library name: Sample_1001_GEX
10X Genomics

value: mRNA


title: OG1RS_1000_10

description: Library name: OG1RS_1000_10

value: Intrageneric conjugation under the exposure of 10 mg/L 1000 nm PS


title: HFD_Visceral_fat, bio rep 2

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_6

value: Freshly isolated OT-I T cells

value: 8 weeks


title: Colon Cancer_485

description: Gene expression data from patiets with colon cancer

value: Human colon cancer

value: Colon

value: Male

value: White/Mediterranean


title: OG1RS_1000_1

description: Library name: OG1RS_1000_1

value: Bacteria

value: Intrageneric conjugation under the exposure of 1 mg/L 1000 nm PS


title: OG1RS_1000_0.1

description: Library name: OG1RS_1000_0.1

value: Intrageneric conjugation under the exposure of 0.1 mg/L 1000 nm PS


title: Sample 1011 CD45+ cells, HTO

description:
Library name: Sample_1011_HTO
10X Genomics

value: Spleen

value: Spleen (Treated spleen #3)

value: Total Seq C Hashtag 3


title: HFD_LN, bio rep 4

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_4

value: lymph nodes

value: High fat diet (60% kcal fat)


title: Colon Cancer_474

value: Female


title: Colon Cancer_478


title: Colon Cancer_489


title: Colon Cancer_488


title: Sample 1011 CD45+ cells, GEX

description:
Library name: Sample_1011_GEX
10X Genomics

value: CD45+ cells

value: mRNA


title: Colon Cancer_469


title: HFD_Visceral_fat, bio rep 3

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_7

value: Freshly isolated OT-I T cells

value: visceral fat


title: HFD_LN, bio rep 3

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_3

value: 8 weeks


title: Colon Cancer_463

value: Human colon cancer

value: Colon


title: Sample 1010 CD45+ cells, TCR

description:
Library name: Sample_1010_TCR
10X Genomics

value: Spleen (Treated spleen #1,#2)

value: TCR


title: OG1RS_120_1

description: Library name: OG1RS_120_1

value: Bacteria

value: Intrageneric conjugation under the exposure of 1 mg/L 120 nm PS


title: HFD_LN, bio rep 2

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_2


title: Sample 1011 CD45+ cells, TCR

description:
Library name: Sample_1011_TCR
10X Genomics

value: Spleen


title: Sample 1010 CD45+ cells, HTO

description:
Library name: Sample_1010_HTO
10X Genomics

value: HTO

value: Total Seq C Hashtag 1, Total Seq C Hashtag 2


title: OG1RS_20_10

description: Library name: OG1RS_20_10

value: Intrageneric conjugation under the exposure of 10 mg/L 20 nm PS


title: HFD_Visceral_fat, bio rep 1

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_5

value: High fat diet (60% kcal fat)


title: HFD_LN, bio rep 1

description:
Takara SMART-Seq v4 Ultra low Input RNA kit, NovaSeq (PE150)
Sample_1

value: lymph nodes


title: Sample 1010 CD45+ cells, GEX

description:
Library name: Sample_1010_GEX
10X Genomics

value: CD45+ cells


title: Colon Cancer_477

value: Female

value: White/Mediterranean


title: Young,Lymphoma,scRNA,rep3

city: Tampa

first: Rebecca

last: Hesterberg

address: 12902 Magnolia Dr.

institute: Moffitt Cancer Center

description: 10x Genomics

data_processing:
A reference genome was built using the GRCm38 mouse transcriptome using the mkref module of Cell Ranger (v6.1.2, 10X Genomics).
Raw sequencing reads from single cells were aligned against the customized mouse reference and processed using count module of Cell Ranger.
Gene-barcode matrices containing only barcodes with UMI counts passing threshold were imported to Seurat (PMID: 25867923) for further analysis.
Genes detected in less than 3 cells were excluded; cells with less than 200 genes detected or greater than 10% mitochondrial UMIs were also filtered out.
Doublets were detected using Scrublet (PMID: 30954476), DoubletFinder (PMID: 30954475), scDblFinder (PMID: 35814628), and doubletCells implemented in scran (PMID: 27909575), assuming 0.08% doublet rate for every 1,000 sequenced cells. Cells identified as doublets by at least two algorithms were removed from further analysis.
Assembly: mm10
Supplementary files format and content: 10X standard processed files of barcodes.tsv.gz. features.tsv.gz and matrix.mtx.gz from filtered_feature_bc_matrix

source_name: spleen

extract_protocol:
RNA was extracted according to manufacturer’s protocol (Macherey-Nagel) and quantified immediately. RNA was then converted to cDNA using manufacturers’ protocol (Bio Rad)
The cDNA libraries were then completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 3’ Reagent Kit version 3.1, and approximately 30,000 to 40,000  sequencing reads per cell were generated on the Illumina NovaSeq 6000 instrument using the S2-100 flow cell.  Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v6.1.2 software.

value: spleen

value: T & NK cells

value: lymphoma transplant


title: OG1RS_20_1

description: Library name: OG1RS_20_1

value: Intrageneric conjugation under the exposure of 1 mg/L 20 nm PS


title: Sample 1009 CD45+ cells, TCR

description:
Library name: Sample_1009_TCR
10X Genomics

source_name: Lymph nodes

value: Lymph nodes

value: Mixed treatment (Treated lymph nodes injected sites #3, non-injected sites #1)


title: Colon Cancer_454

value: Human colon cancer

value: Colon


title: Colon Cancer_462

value: Male


title: OG1RS_120_10

description: Library name: OG1RS_120_10

value: Bacteria

value: Intrageneric conjugation under the exposure of 10 mg/L 120 nm PS


title: DH5α_1000_0.1

description: Library name: DH5α_1000_0.1

value: intergeneric conjugation under the exposure of 0.1 mg/L 1000 nm PS


title: OG1RS_120_0.1

description: Library name: OG1RS_120_0.1

value: Intrageneric conjugation under the exposure of 0.1 mg/L 120 nm PS


title: Young,Lymphoma,scRNA,rep2

description: 10x Genomics


title: Sample 1009 CD45+ cells, HTO

description:
Library name: Sample_1009_HTO
10X Genomics

value: HTO

value: Total Seq C Hashtag 1, Total Seq C Hashtag 3


title: OG1RS_20_0.1

description: Library name: OG1RS_20_0.1

value: Intrageneric conjugation under the exposure of 0.1 mg/L 20 nm PS


title: Colon Cancer_451

value: White/Mediterranean


title: Young,Lymphoma,scRNA,rep1

description: 10x Genomics

value: spleen


title: Colon Cancer_447

value: Female


title: OG1RS_NA

description: Library name: OG1RS_NA

value: Intrageneric conjugation


title: Sample 1009 CD45+ cells, GEX

description:
Library name: Sample_1009_GEX
10X Genomics

value: CD45+ cells

value: mRNA


title: Young,Ctrl,scRNA,rep3

description: 10x Genomics

value: T & NK cells

value: non-tumor-bearing control


title: UC9_stool_UC

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

description:
Library name: UC9_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC9

data_processing:
FASTQ files produced by Illumina Miseq were uploaded to the Illumina BAseSpace Sequence Hub. Read classification was performed using the 16S Metagenomics app (ver 1.1.0) whithin the Illumina BaseSpace Sequence Hub, based on the Greengenes May 2013 (v13.8) database curated by Illumina, and OTU counts of bacterial reads were caluculated.
Assembly: Greengene v13.8 database curated by Illumina
Supplementary files format and content: Csv file of Family-Level Taxonomy Table
Library strategy: 16S rRNA-seq

organism: human gut metagenome

source_name: Stool sample

extract_protocol:
DNA extraction from oral specimens Oral bacteria were collected from the periodontal pockets and tongue tissue during oral care. In the edentulous jaw, we collected bacteria only from the tongue, whereas in the case of the teeth, we collected bacteria from the periodontal pockets. The QIAamp DNA Mini Kit (Qiagen) was used to extract genomic DNA from the oral samples. Fecal samples were collected by the participants themselves following the manufacturer's instructions. DNA was extracted from 200 mg of stool using a QIAamp DNA Stool Mini Kit (Qiagen).
After determining the concentration of genomic DNA extracted from the samples using Nanodrop one (Thermo Fisher Scientific), 6.25 ng DNA was added to 25 μl of 2x KAPA HS HiFi ready mix (KAPA Biosystem). The DNA mixture was amplified using a PCR thermal cycler (C1000 Touch Thermal Cycler, Bio-Rad) programmed with an initial denaturation of 3 minutes at 95°C, followed by 25 cycles of denaturation at 95°C for 30 seconds, annealing at the temperature of 72°C for 30 seconds, and extension at 72°C for 30 seconds with the following primer pair for the V3-V4 region of 16S rRNA. Forward primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, 16S amplicon Reverse primer: TCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAAT CCA. The barcode and adaptor sequence were inserted into the products by the Nextera XT Index Kit (Illumina) using a C1000 Touch Thermal Cycler (Bio-rad) programmed with an initial denaturation of 3 min at 95°C, followed by 8 cycles of denaturation at 95°C for 30 sec, annealing at the temperature of 55°C for 30 sec, and extension at 72°C for 5 min. Product concentrations were confirmed using a Qubit (Thermo Fisher Scientific). The libraries were pooled to equal molecular amounts and analyzed on an Illumina Mi-Seq DNA sequencer with a 300 bp paired-end cycle sequencing kit (Illumina).

value: Stool sample

value: Urothelial carcinoma


title: Sample 1008 CD45+ cells, TCR

description:
Library name: Sample_1008_TCR
10X Genomics

value: Lymph nodes

value: Treated lymph nodes injected sites #2

value: TCR


title: Young,Ctrl,scRNA,rep2

description: 10x Genomics


title: Sample 1008 CD45+ cells, HTO

description:
Library name: Sample_1008_HTO
10X Genomics

value: Total Seq C Hashtag 2


title: Young,Ctrl,scRNA,rep1

description: 10x Genomics


title: UC8_stool_UC

description:
Library name: UC8_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC8


title: UC6_stool_UC

description:
Library name: UC6_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC6


title: Sample 1008 CD45+ cells, GEX

description:
Library name: Sample_1008_GEX
10X Genomics


title: Aged,Lymphoma,scRNA,rep3

description: 10x Genomics

value: lymphoma transplant


title: Aged,Lymphoma,scRNA,rep2

description: 10x Genomics


title: UC56_stool_UC

description:
Library name: UC56_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC56


title: Colon Cancer_436

description: Gene expression data from patiets with colon cancer

value: Human colon cancer

value: Colon


title: UC55_stool_UC

description:
Library name: UC55_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC55


title: Aged,Lymphoma,scRNA,rep1

description: 10x Genomics


title: Sample 1007 CD45+ cells, HTO

description:
Library name: Sample_1007_HTO
10X Genomics

value: Mixed treatment (Treated lymph nodes injected sites #1, non-injected sites #2)

value: HTO

value: Total Seq C Hashtag 1, Total Seq C Hashtag 2


title: Colon Cancer_432

value: Female

value: White/Mediterranean


title: UC5_stool_UC

description:
Library name: UC5_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC5


title: Colon Cancer_434

value: Male


title: Aged,Ctrl,scRNA,rep3

description: 10x Genomics

value: spleen

value: T & NK cells


title: UC49_stool_UC

description:
Library name: UC49_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC49

value: Stool sample


title: Colon Cancer_445


title: Colon Cancer_427


title: Sample 1006 CD45+ cells, TCR

description:
Library name: Sample_1006_TCR
10X Genomics

value: Tumor

value: CD45+ cells

value: Mixed treatment (Treated tumor injected sites #3, non-injected sites #1)


title: Colon Cancer_431


title: Colon Cancer_440


title: Aged,Ctrl,scRNA,rep2

description: 10x Genomics

value: non-tumor-bearing control


title: Colon Cancer_421


title: Sample 1006 CD45+ cells, HTO

description:
Library name: Sample_1006_HTO
10X Genomics

value: Total Seq C Hashtag 1, Total Seq C Hashtag 3


title: Sample 1007 CD45+ cells, TCR

description:
Library name: Sample_1007_TCR
10X Genomics

value: Lymph nodes

value: TCR


title: Aged,Ctrl,scRNA,rep1

description: 10x Genomics


title: Colon Cancer_407

value: Human colon cancer

value: Colon


title: UC46_stool_UC

description:
Library name: UC46_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC46

value: Urothelial carcinoma


title: Sample 1006 CD45+ cells, GEX

description:
Library name: Sample_1006_GEX
10X Genomics

value: mRNA


title: UC45_stool_UC

description:
Library name: UC45_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC45


title: Sample 1005 CD45+ cells, TCR

description:
Library name: Sample_1005_TCR
10X Genomics

value: Mixed treatment (Treated tumor injected sites #2, non-injected sites #3)


title: UC43_stool_UC

description:
Library name: UC43_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC43


title: Sample 1005 CD45+ cells, HTO

description:
Library name: Sample_1005_HTO
10X Genomics

value: HTO

value: Total Seq C Hashtag 2, Total Seq C Hashtag 3


title: UC40_stool_UC

description:
Library name: UC40_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC40


title: 7-5mgkg_Rep6

city: La Jolla

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Data was analyzed using Rosalind software.

organism: Rattus norvegicus

source_name: Cardiac, IR surgery

label_protocol: To evaluate the downstream genetic changes due to Keap1i-PLP administration, RNA samples were analyzed by the NanoString nCounter MAX analysis system, with an nCounter rat custom cardiac codeset, allowing for multiplexed assessment of 380 genes. Manufacturer’s instructions were followed for all samples. In brief, RNA sample concentrations were measured on Qubit 3.0 fluorometer with a Qubit RNA HS Assay kit. Hybridization buffer (70 µL) was mixed with an Immunology Panel Reporter CodeSet solution, with 8 µL of the master mix was mixed in a separate reaction vessel with 50-100 ng of RNA per tissue sample and RNA-free water up to 13 µL total.

growth_protocol: All procedures in this study were approved by the Committee on Animal Research at the University of California San Diego, and according to guidelines established by the Association for the Assessment and Accreditation of Laboratory Animal Care. Female Sprague Dawley rats (225-250g, Envigo) underwent ischemia–reperfusion surgery via left-thoracotomy and temporary occlusion of the left coronary artery for 35 minutes,

extract_protocol: RNA from liquid nitrogen, flash frozen LV tissue was isolated using the Qiagen RNeasy Fibrous Tissue Mini kit and quantified on a NanoDrop spectrophotometer (ThermoFisher).

treatment_protocol: Animals were intravenously injected with either saline, scrambled PLP, or 3mg/kg Keap1i-PLP or 7.5 mg/kg Keap1i-PLP.

tag: strain

value: Sprague-Dawley

value: female

value: heart

value: IV injection of 7.5mg/kg Keap1i-PLP


title: 3mgkg_Rep5

value: IV injection of 3mg/kg Keap1i-PLP


title: Sample 1007 CD45+ cells, GEX

description:
Library name: Sample_1007_GEX
10X Genomics

value: CD45+ cells

value: Mixed treatment (Treated lymph nodes injected sites #1, non-injected sites #2)


title: Colon Cancer_404

source_name: Human colon cancer

value: Female

value: White/Mediterranean


title: Colon Cancer_403


title: UC48_stool_UC

description:
Library name: UC48_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC48

value: Stool sample


title: UC4_stool_UC

description:
Library name: UC4_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC4


title: 7-5mgkg_Rep5


title: Sample 1004 CD45+ cells, TCR

description:
Library name: Sample_1004_TCR
10X Genomics

value: Tumor

value: Mixed treatment (Treated tumor injected sites #1, non-injected sites #2)

value: TCR


title: 7-5mgkg_Rep3


title: 7-5mgkg_Rep4


title: UC34_stool_UC

description:
Library name: UC34_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC34

value: Urothelial carcinoma


title: Sample 1004 CD45+ cells, HTO

description:
Library name: Sample_1004_HTO
10X Genomics

tag: hto

value: Total Seq C Hashtag 1, Total Seq C Hashtag 2


title: Colon Cancer_400

description: Gene expression data from patiets with colon cancer

value: Human colon cancer

tag: tissue

value: Colon


title: UC33_stool_UC

description:
Library name: UC33_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC33


title: Colon Cancer_406

value: Male


title: Colon Cancer_402


title: Colon Cancer_398


title: UC30_stool_UC

description:
Library name: UC30_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC30


title: X2409-KO-Saline

city: Montreal

first: Simon-Pierre

last: Gravel

state: QC

address: 2940 ch. de la polytechnique

department: Faculty of pharmacy

country: Canada

institute: University of Montreal

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed sequences were aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
Gene expressions were obtained from STAR both as readcounts and TPM values as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in FPKM and TPM values, for these stranded RNA libraries
DESeq2 version 1.30.1 was then used to normalize gene readcounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include DESEQ2 normalized counts for each sample

source_name: Suprarenal aorta

growth_protocol: Mice were fed with a regular chow diet and used at 8 weeks of age

extract_protocol:
Total RNA from the suprarenal aorta was extracted using the RNeasy Mini Kit (No. 74106, Qiagen).
Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific)

treatment_protocol: Wild-type and KO mice were treated with saline or angiotensin II (Ang II) (500 to 1000 ng/min/kg) s.c. with constant infusion using osmotic pumps for 24 h

value: Suprarenal aorta

tag: genotype

value: IKKb knockout

value: Saline 24h


title: Colon Cancer_396


title: Colon Cancer_394


title: Sample 1005 CD45+ cells, GEX

description:
Library name: Sample_1005_GEX
10X Genomics

value: Mixed treatment (Treated tumor injected sites #2, non-injected sites #3)

value: mRNA


title: UC3_stool_UC

description:
Library name: UC3_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC3


title: X2406-KO-Saline


title: X2403-KO-Saline


title: UC29_stool_UC

description:
Library name: UC29_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC29


title: Colon Cancer_393


title: UC27_stool_UC

description:
Library name: UC27_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC27


title: 3mgkg_Rep3

value: Sprague-Dawley

value: female

value: heart

value: IV injection of 3mg/kg Keap1i-PLP


title: 7-5mgkg_Rep2

value: IV injection of 7.5mg/kg Keap1i-PLP


title: X2401-KO-Saline


title: UC25_stool_UC

description:
Library name: UC25_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC25

value: Stool sample


title: X2386-KO-Ang2

value: Angiotensin II (500 to 1000 ng/min/kg) 24h


title: UC2_stool_UC

description:
Library name: UC2_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC2

value: Urothelial carcinoma


title: 3mgkg_Rep2


title: 3mgkg_Rep1


title: 7-5mgkg_Rep1


title: Sample 1004 CD45+ cells, GEX

description:
Library name: Sample_1004_GEX
10X Genomics

value: Tumor

value: CD45+ cells

value: Mixed treatment (Treated tumor injected sites #1, non-injected sites #2)


title: X2385-KO-Ang2


title: Colon Cancer_391

value: Human colon cancer

value: Colon

value: Female

value: White/Mediterranean


title: Colon Cancer_389


title: Colon Cancer_380


title: X2384-KO-Ang2

value: Suprarenal aorta

value: IKKb knockout


title: UC18_stool_UC

description:
Library name: UC18_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC18


title: 3mgkg_Rep4

value: Sprague-Dawley


title: Colon Cancer_375

value: Male


title: Scrambled_Rep4

value: female

value: heart

value: IV injection of scrambled PLP


title: Scrambled_Rep5


title: X2383-KO-Ang2


title: UC14_stool_UC

description:
Library name: UC14_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC14

value: Stool sample


title: Scrambled_Rep3


title: UC13_stool_UC

description:
Library name: UC13_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC13


title: X2380-KO-Ang2

value: Angiotensin II (500 to 1000 ng/min/kg) 24h


title: Colon Cancer_373


title: Colon Cancer_374


title: X2378-WT-Saline

value: Wild-type

value: Saline 24h


title: UC12_stool_UC

description:
Library name: UC12_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC12

value: Urothelial carcinoma


title: Scrambled_Rep6


title: UC11_stool_UC

description:
Library name: UC11_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC11


title: Colon Cancer_377


title: X2376-WT-Saline


title: Scrambled_Rep1


title: UC10_stool_UC

description:
Library name: UC10_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC10


title: Scrambled_Rep2


title: Colon Cancer_372


title: X2373-WT-Saline


title: C9_stool_Healthy

description:
Library name: C9_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C9

value: Healthy


title: Saline_Rep4

value: IV injection of saline


title: Colon Cancer_371

description: Gene expression data from patiets with colon cancer

value: Human colon cancer

value: Colon


title: C8_stool_Healthy

description:
Library name: C8_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C8


title: Saline_Rep3


title: X2370-WT-Saline


title: Saline_Rep1


title: C7_stool_Healthy

description:
Library name: C7_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C7


title: Colon Cancer_368

value: Female

value: White/Mediterranean


title: Saline_Rep2


title: B16Nid1 CD11b_cells 3

city: Granada

first: Juan Carlos

last: Rodriguez-Manzaneque

state: Granada

address: Avda de la Ilustración 114

institute: GENYO. Centre for Genomics and Oncological Research

description:
Library name: CD11b-B16Nid1_3
Column name in Allsamples_FPKM.txt: B16Nid1_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software, removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Assembly: Quiality filtered using FacstQ files were aligned against the mouse genome GRCm38 using Hisat v2.0.5
Supplementary files format and content: Processed data file contains FPKM of each mapped gene calculated using featureCounts v1.50-p3

source_name: Primary CD11b+ cells isolated from tumour tissue

extract_protocol:
Frozen pieces of tumors (approximately 5-8 mg) were mechanically disrupted with metallic beads on TissueLyser LT (Qiagen, Netherlands). CD11b+ cells were isolated by magnetic separation in a Automacs Pro Separator.  Then, total RNA was extracted from  samples using NucleoSpin RNAII kit (Macherery-Nagel).
For sequencing total bulk-tumor, mRNA-seq libraries were generated according to the manufacturer’s instructions of the TruSeq stranded mRNA Library Prep kit (20020595, Illumina). For sequencing CD11b+ cells, mRNAseq libriaries were generated according Novogene protocols and sequenced on Illumina Novaseq X platform


title: X2359-WT-Ang2

value: Suprarenal aorta


title: Colon Cancer_369


title: C6_stool_Healthy

description:
Library name: C6_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C6


title: X2358-WT-Ang2


title: B16Nid1 CD11b_cells 2

description:
Library name: CD11b-B16Nid1_2
Column name in Allsamples_FPKM.txt: B16Nid1_2

value: Primary CD11b+ cells isolated from tumour tissue


title: Colon Cancer_370

value: Male


title: X2372-WT-Saline


title: X2356-WT-Ang2


title: C5_stool_Healthy

description:
Library name: C5_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C5


title: Colon Cancer_365


title: X2352-WT-Ang2


title: C4_stool_Healthy

description:
Library name: C4_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C4


title: B16F1 CD11b_cells 3

description:
Library name: CD11b-B16F1_3
Column name in Allsamples_FPKM.txt: B16F1_3


title: Colon Cancer_363


title: C3_stool_Healthy

description:
Library name: C3_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C3


title: X2350-WT-Ang2


title: Colon Cancer_358


title: Colon Cancer_353


title: C21_stool_Healthy

description:
Library name: C21_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C21


title: pDCs_IMQ-16h_rep3_R18

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

data_processing:
Reads were aligned to the murine reference genome version mm10 with Gencode vM19 annotations using STAR (PMID: 23104886; version 2.6.1a) in 2-pass mode. Reads per gene were obtained via STAR (ReadsPerGene.out.tab).
Assembly: mm10
Supplementary files format and content: ReadsPerGene.out.tab (STAR)
Supplementary files format and content: For each gene, raw counts quantifications for each sample, along with symbol (GeneSymbol) and Ensembl (ENSMUSGID) identifiers are provided. The type of gene (GeneType) based on the reference GENCODE annotation is also provided (e.g. protein_coding, lncRNA, etc).

source_name: Bone-marrow derived plasmacytoid dendritic cells (pDCs)

growth_protocol: Bone marrow (BM) has been isolated from wild-type C57BL/6 mice as previously described (PMID: 22251703). Tibiae and femurs were flushed with RPMI-1640 (Gibco). BM cells have been supplemented in culture with Flt3L (80 ng/mL, Peprotech) and kept differentiating for 7-days till harvest for downstream applications in medium, as previously described (PMID: 22251703). pDCs were enriched with IMag-Streptavidin beads (BD Biosciences) conjugated to B220 with a routine purity of 80% (FACS purity check gating B220+ Cd11b- CD11cint). Cells were seeded in 96 wells plates (1 x 10^6).

extract_protocol:
Harvest of the cells have been done at indicated time points (0h, 6h and 16h). After harvest, pDCs were put in QIAzolTM Lysis Reagent (QIAGEN) and further processed for RNA extraction with miRNeasy Micro Kit according to the manufacturer’s instructions (QIAGEN). Samples were then further purified before downstream application with RNeasy® MinElute® Cleanup Kit to eliminate traces of contaminants, according to the manufacturer’s instructions (QUIAGEN). cDNA synthesis was performed with SuperScript First-Strand Synthesis SystemTM (Invitrogen) according to the manufacturer’s instructions.
Sequencing libraries were prepared using the NEBNext rRNA depletion kit (human/mouse/rat) and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs). Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen). Pooled libraries were sequenced on a NextSeq500 instrument (Illumina) in 2x75bp paired-end sequencing mode.

treatment_protocol: pDCs were stimulated with IMQ (2.5µg/mL) for 6 or 16 hours.

value: wild-type

value: IMQ

tag: time


title: B16F1 CD11b_cells 1

description:
Library name: CD11b-B16F1_1
Column name in Allsamples_FPKM.txt: B16F1_1


title: C20_stool_Healthy

description:
Library name: C20_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C20


title: B16F1 CD11b_cells 2

description:
Library name: CD11b-B16F1_2
Column name in Allsamples_FPKM.txt: B16F1_2


title: pDCs_IMQ-16h_rep2_R17

value: Bone-marrow derived plasmacytoid dendritic cells (pDCs)

tag: treatment


title: Colon Cancer_350


title: B16Nid1 CD11b_cells 1

description:
Library name: CD11b-B16Nid1_1
Column name in Allsamples_FPKM.txt: B16Nid1_1


title: C2_stool_Healthy

description:
Library name: C2_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C2

value: Stool sample


title: Rx rhLCV positive R.335

first: Victor

last: Tkachev

address: 55 Fruit Street

department: Center for Transplantation Sciences

institute: Mass General Research Institute

description: Library name: R.335

data_processing:
GEX libraries were aligned using the ‘Cellranger multi’ pipeline (v6.0.1). Samples were aggregated with the ‘Cellranger aggr’ pipeline with arguments ‘--normalize=none --nosecondary’. Our reference transcriptome was created with the Cellranger makeref command, and used genome assembly Mmul_10 as the reference genome and Ensembl v105 as the reference set of genomic annotations for the NHP samples.
Assembly: Mmul_10; Ensembl v105
Supplementary files format and content: rds file containing QC'd scRNAseq Seurat object with scVI batch-integrated latent space. Y chromosome, Immunoglobulin, and TCR genes not related to MAIT or gamma-delta populations were removed.

organism: Macaca mulatta

source_name: primary

extract_protocol:
Samples were thawed, sorted for CD3+ CD20- cells, and prepared for single-cell sequencing.
All products used in the preparation of these samples, excluding the NHP TCR-specific custom primer set18, are available from 10x Genomics. Samples in this publication were prepared using the Next GEM 5’ v2 Gel Beads with the i7 Multiplex Plate (Single Index) or the Next GEM Single Cell 5’ v2 Sample Index Plate TT (Dual Index). GEMs were generated using v2 Gel Beads and the v1 Target Enrichment kit utilizing the off-the-shelf human/mouse T-cell Mix 1 and 2 premixed primers for the human samples and substituting the provided primers with custom-designed primers as previously described18 for NHP samples.

value: blood

value: T cells

tag: batch


title: C19_stool_Healthy

description:
Library name: C19_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C19

tag: disease state


title: pDCs_LAL-16h_rep3_R15

value: LAL


title: pDCs_LAL-16h_rep2_R14


title: Rx rhLCV negative R.333

description: Library name: R.333


title: Rx rhLCV negative R.332

description: Library name: R.332


title: Colon Cancer_347

description: Gene expression data from patiets with colon cancer

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software using default analysis settings.

tag: age


title: C17_stool_Healthy

description:
Library name: C17_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C17


title: Colon Cancer_346-rep

tag: Sex


title: C16_stool_Healthy

description:
Library name: C16_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C16


title: pDCs_LAL-16h_rep1_R13

tag: cell type


title: Colon Cancer_345

tag: histological features diagnostic


title: Rx rhLCV positive R.331

description: Library name: R.331


title: Colon Cancer_348


title: Colon Cancer_343

tag: bmi


title: Colon Cancer_342


title: pDCs_IMQ-6h_rep3_R12


title: NoRx rhLCV negative R.329

description: Library name: R.329

value: placebo


title: C15_stool_Healthy

description:
Library name: C15_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C15

value: Healthy


title: pDCs_IMQ-6h_rep2_R11


title: NoRx rhLCV negative R.328

description: Library name: R.328


title: pDCs_IMQ-16h_rep1_R16


title: Rx rhLCV positive R.334

description: Library name: R.334


title: Colon Cancer_341


title: Colon Cancer_340


title: pDCs_IMQ-6h_rep1_R10


title: C14_stool_Healthy

description:
Library name: C14_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C14


title: C18_stool_Healthy

description:
Library name: C18_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C18


title: Rx rhLCV positive R.321

description: Library name: R.321


title: C13_stool_Healthy

description:
Library name: C13_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C13


title: pDCs_LAL-6h_rep3_R09


title: Colon Cancer_336


title: NoRx rhLCV negative R.312

description: Library name: R.312


title: Colon Cancer_335


title: C12_stool_Healthy

description:
Library name: C12_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C12


title: NoRx rhLCV negative R.255

description: Library name: R.255


title: pDCs_LAL-6h_rep2_R08


title: Colon Cancer_332


title: C11_stool_Healthy

description:
Library name: C11_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C11


title: NoRx rhLCV negative R.235

description: Library name: R.235


title: C10_stool_Healthy

description:
Library name: C10_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C10


title: NoRx rhLCV negative R.234

description: Library name: R.234


title: C1_stool_Healthy

description:
Library name: C1_stool
Column name in stool_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C1


title: pDCs_LAL-0h_rep2_R05


title: NoRx rhLCV negative R.232

description: Library name: R.232


title: pDCs_LAL-0h_rep3_R06


title: NM_4

city: Raleigh

first: Ramsey

middle: S

last: Lewis

state: North Carolina

address: 101 Derieux Pl

department: Crop and Soil Sciences Department

institute: North Carolina State University

description: Library name: Samlple 16

data_processing:
Raw sequencing reads (in FASTA format) were quality-checked using FastQC (Andrews, 2010) and were trimmed to remove poor quality bases (> Q30) using fastq-mcf (Aronesty, 2011).
Reads were mapped against tobacco K326 genome assembly Nitab4.5 using hisat2 version 2.1.0
Reads mapped to gene assembly were manipulated using samtools  for sorting/indexing
RNA-seq read counts mapping to transcript sequences of annotated gene models were extracted from sorted and indexed BAM files using the multicov function of the Bedtools package (version v2.23.0; Quinlan et al., 2010)
Assembly: Tobacco K326 enome assembly Ntab (ASM71507v2)
Supplementary files format and content: tab-delimited text files include raw count values for each sample

organism: Nicotiana tabacum

source_name: Root

growth_protocol: Tobaco genotype K326, K326 nic1/nic2, K326 myc2a and K326 nic1/nic2/myc2a were grown in a greenhouse pot experiment for the purpose of generating root transcriptome data. Three to five plants of each genotype were grown in 1.9 L soil-filled pots suspended in water in 18.9 L buckets. The lower two to four cm of the pots were immersed in water to promote root growth out of the holes in the bottom of the pots to permit efficient collection of clean root tissues for RNA extraction.

extract_protocol:
Root samples were collected and frozen and ground in liquid nitrogen, and RNA was purified using Plant Rneasy mini kit of Qiagen.
total RNA samples was used for RNA-seq library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA)  followed the protocol for long size insertions.

treatment_protocol: Plants were decapitated (topped) when 50 percent of the plants were flowering in order to stimulate alkaloid biosynthesis. .Root tissues were collected from each plant 18 hours after decapitation.

value: Root

value: K326 nic1/nic2/myc2a


title: pDCs_LAL-0h_rep1_R04


title: NoRx rhLCV negative R.227

description: Library name: R.227


title: PANC-1-CGN cell CGN IP2

first: Yuling

last: Su

state: State...

address: Guangzhou University City, Panyu District, Guangzhou City

institute: South China univerisity of technology

data_processing:
Date preprocessing. Adaptor and low-quality bases were trimmed with Trimmomatic tools (version: 0.36), and the clean reads underwent rRNA deleting through RNAcentral to obtain effective reads. Genomic alignment (version from UCSC genome browser) was performed using hisat2 (version:2.1.0) to get uniquely mapping reads.
Expression calculation. Effective reads from the input sample were utilized for RNA-seq analysis; the read count values of each transcript were calculated by HTSeq (version: 0.6.0), followed by estimating the TPM (Transcripts Per Kilobase of exon model per Million mapped reads) values.
Peaks calling and motif identification. Piranha (version 1.2.1) was employed to perform peak calling, followed by Hommer (version 4.8) for peak annotation. The nucleotides in the Peaks region were used for the detection of the consensus motif by STREME (version: 5.5.1, https://meme-suite.org/meme/tools/streme) and MEME (version:5.5.1, https://meme-suite.org/meme/tools/meme). Motif central enrichment was performed by CentriMo (version:5.5.1). Raw data are available in the GEO database.The RIP RNA was assessed by Agilent 2200 TapeStation (Agilent Technologies, USA) and Qubit (Thermo Fisher Scientific, USA). The RIP RNA was fragmented to approximately 200bp and underwent first-strand and second-strand cDNA synthesis, followed by adaptor ligation and enrichment with a low-cycle according to the instructions of NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation and Qubit® (Life Technologies, USA). It was subsequently sequenced on Illumina (Illumina, USA) platform with pair-end 150bp at Ribobio Co. Ltd (Ribobio, China).
Assembly: hg38

source_name: cell line

extract_protocol:
CGN-specific antibodies captured the target protein to increase the enrichment of CGN protein-RNA complex. Subsequently, the complex's protein and RNA were analyzed and detected. RNA was isolated from the complex, and gene-specific analysis techniques (such as PCR, qRT-PCR) or high-throughput sequencing were employed to analyze both the quantity and type of RNA present.
The RIP RNA was assessed by Agilent 2200 TapeStation (Agilent Technologies, USA) and Qubit (Thermo Fisher Scientific, USA). The RIP RNA was fragmented to approximately 200bp and underwent first-strand and second-strand cDNA synthesis, followed by adaptor ligation and enrichment with a low-cycle according to the instructions of NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation and Qubit® (Life Technologies, USA). It was subsequently sequenced on Illumina (Illumina, USA) platform with pair-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: cell line

tag: cell line

value: Human epithelial cell

value: KRAS G12D mutation

value: CGN IP


title: NM_3

description: Library name: Sample 15

value: Root tissues were collected from each plant 18 hours after decapitation.


title: pDCs_UT-0h_rep3_R03


title: Colon Cancer_328

first: Ramon

last: Rodriguez

address: Edificio S, Hospital Universitario Son Espases, Carretera de Valldemossa, 79

institute: Institut d'Investigació Sanitària Illes Balears

extract_protocol: RNeasy Plus Kit was used for extraction of total RNA according to the manufacturer's instructions.

value: Human colon cancer

value: Colon

value: Male

tag: ethnicity

value: White/Mediterranean


title: Colon Cancer_330


title: NM_2

description: Library name: Sample 14


title: Colon Cancer_327


title: pDCs_UT-0h_rep2_R02

value: Bone-marrow derived plasmacytoid dendritic cells (pDCs)

value: wild-type


title: PANC-1-CGN cell CGN IP1


title: Colon Cancer_326

value: Female


title: pDCs_LAL-6h_rep1_R07

value: LAL


title: NM_1

description: Library name: Sample 13


title: PANC-1-CGN cell input2

value: total cell


title: pDCs_UT-0h_rep1_R01


title: Colon Cancer_331


title: M_5

description: Library name: Sample 12

value: K326 myc2a


title: Colon Cancer_322


title: PANC-1-CGN cell input1


title: Colon Cancer_323


title: MS1 Zmiz1 shRNA #3

city: new orleans

first: Rajan

last: K C

state: LA

address: 6602 Freret St

department: Cell and Molecular Biology

institute: Tulane University

description:
Zmiz1-shRNA-3
MS1 Zmiz1 control_vs_comparison.deseq.counts.csv

data_processing:
Illumina Nextseq500/550
Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1) using the BaseSpace sequence hub.
The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1) using the BaseSpace sequence hub.
Assembly: mm10
Supplementary files format and content: Comma separated spreadsheet file with raw counts for every gene for every sample.

source_name: Pancreas

growth_protocol: MS1 mouse pancreas ECs (CRL-2279; ATCC) were cultured in DMEM medium supplemented with 5% fetal bovine serum (FBS) and Antibiotic-Antimycotic (Thermofisher, 15240062).

extract_protocol:
Total RNA was extracted from Wildtype and Zmiz1KO P7 iRECs and control and Zmiz1 shRNA treated MS1 using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732).
RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 0.5 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).
RNA sequencing using Illumina Nextseq 500/550 system.

treatment_protocol: 100μg of tamoxifen (Sigma, T5648) was administered orally to newborn pups from Zmiz1fl/fl;Cdh5-CreERT2 and Zmiz1fl/fl mating and retinal endothelial isolation was performed at postnatal day 7.

value: Pancreas

value: Endothelial Cells

value: Zmiz1 knockdown

tag: developmental stage


title: M_4

description: Library name: Sample 11

value: Root


title: MS1 Zmiz1 shRNA #2

description:
Zmiz1-shRNA-2
MS1 Zmiz1 control_vs_comparison.deseq.counts.csv


title: Input in TKO rep2

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

description:
Library name: Input_TKO_rep2
Input_TKO_rep2

data_processing:
Trim adapter and low quality reads using Trim_galore
Map reads on mouse genome by Bowtie2
Remove PCR duplicates by Picard
Assembly: mm10
Supplementary files format and content: bigWig

source_name: TKO

growth_protocol: Mouse embryonic fibroblasts were maintained in Dulbecco's modified Eagle's medium (Nacalai tesque, 08458-16) containing 10% fetal bovine serum (Biosera, FB1061), MEM Non-Essential medium and 2-Mercaptoethanol (Nacalai tesque, 21417-52).

extract_protocol:
ChIP DNA was extracted by Native ChIP protocol
At least 2 × 105 cells were lysed in 50 µl Buffer 1 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl (pH7.5), 0.3 M Sucrose, 0.5 mM DTT, and protease inhibitors (Nacalai tesque, 04080-11), then were added 50 µl Buffer2 (Buffer 1 + 1% NP40) to the sample. After the incubation for 10 min on ice, the sample was added 800 µl Buffer 3 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl (pH7.5), 1.2 M Sucrose, 0.5 mM DTT, and protease inhibitors). After centrifugation at 9000 rpm for 10 min at 4°C, the sample was added 100 µl MNase buffer (0.32 M Sucrose, 50 mM Tris-HCl (pH7.5), 4 mM MgCl2, 1 mM CaCl2, and phenylmethylsulfonyl fluoride (PMSF)) followed by incubation for 20 min at 37 °C with 0.3 U MNase (TAKARA, 2910 A). After the incubation, the reaction was stopped by 10 µl 0.5 M EDTA. After centrifugation at 15,000 rpm for 10 min at 4°C, the supernatant was added 900 µl Incubation buffer (50 mM NaCl, 20 mM Tris-HCl (pH7.5), 5 mM EDTA, 0.01% NP40, ad PMSF). In all, 10% of the sample was used for input, and the remains proceeded the following procedure. The sample was mixed with the antibody-beads complex which was formed by incubation of 20 µl protein A/G beads (Santa Cruz, sc-2003) with antibody in Incubation buffer on ice for 1 h. After rotating for overnight at 4°C, the complex was washed by 500 µl Wash buffer A (75 mM NaCl, 50 mM Tris-HCl (pH7.5), 10 mM EDTA, and 0.01% NP40), 500 µl Wash buffer B (100 mM NaCl, 50 mM Tris-HCl (pH7.5), 10 mM EDTA, and 0.01% NP40), and 500 µl wash buffer C (175 mM, 50 mM Tris-HCl (pH7.5), 10 mM EDTA, and 0.01% NP40). The ChIP DNA was eluted by RNase and Protease treatment followed by DNA purification using PCR purification kit (QIAGEN).

value: TKO

value: MEF


title: Colon Cancer_321

city: Palma


title: Input in TKO rep1

description:
Library name: Input_TKO_rep1
Input_TKO_rep1


title: MS1 Zmiz1 shRNA #1

description:
Zmiz1-shRNA-1
MS1 Zmiz1 control_vs_comparison.deseq.counts.csv


title: M_3

description: Library name: Sample 10

value: Root tissues were collected from each plant 18 hours after decapitation.


title: Colon Cancer_320

value: Human colon cancer


title: MS1 Ctrl shRNA #3

description:
NonSilencing-shRNA-3
MS1 Zmiz1 control_vs_comparison.deseq.counts.csv

value: Wildtype


title: M_2

description: Library name: Sample 9


title: Colon Cancer_317

description: Gene expression data from patiets with colon cancer

value: Colon

value: Male


title: Input in Setdb1 KO

description:
Library name: Input_Setdb1KO
Input_Setdb1KO

source_name: Setdb1 KO

value: Setdb1 KO


title: M_1

description: Library name: Sample 8


title: MS1 Ctrl shRNA #2

description:
NonSilencing-shRNA-2
MS1 Zmiz1 control_vs_comparison.deseq.counts.csv


title: Colon Cancer_316

value: White/Mediterranean


title: N_3

description: Library name: Sample 7

value: K326 nic1/nic2


title: MS1 Ctrl shRNA #1

description:
NonSilencing-shRNA-1
MS1 Zmiz1 control_vs_comparison.deseq.counts.csv


title: H3K27me3 ChIP-seq in TKO rep1

description:
Library name: K27me3_TKO_rep1
K27me3_TKO_rep1


title: P7 Zmiz1KO iRECs #3

description:
Zmiz1-iRECs-P7-MUT-3
Zmiz1iRECSWT_vs_Zmiz1iRECSMUT.genes.deseq.counts.csv

source_name: Retina

value: Retina

value: Zmiz1 knockout


title: P7 Zmiz1KO iRECs #2

description:
Zmiz1-iRECs-P7-MUT-2
Zmiz1iRECSWT_vs_Zmiz1iRECSMUT.genes.deseq.counts.csv


title: N_1

description: Library name: Sample 5


title: H3K9me2 ChIP-seq in 5KO rep2

description:
Library name: K9me2_5KO_rep2
K9me2_5KO_rep2


title: H3K9me2 ChIP-seq in 5KO rep1

description:
Library name: K9me2_5KO_rep1
K9me2_5KO_rep1


title: Colon Cancer_314


title: CK_4

description: Library name: Sample 4


title: P7 Zmiz1KO iRECs #1

description:
Zmiz1-iRECs-P7-MUT-1
Zmiz1iRECSWT_vs_Zmiz1iRECSMUT.genes.deseq.counts.csv


title: Colon Cancer_311

value: Female


title: Colon Cancer_313


title: Colon Cancer_309


title: P7 wildtype iRECs #3

description:
Zmiz1-iRECs-P7-WT-3
Zmiz1iRECSWT_vs_Zmiz1iRECSMUT.genes.deseq.counts.csv


title: CK_3

description: Library name: Sample 3


title: H3K9me2 ChIP-seq in TKO rep2

description:
Library name: K9me2_TKO_rep2
K9me2_TKO_rep2


title: H3K9me2 ChIP-seq in TKO rep1

description:
Library name: K9me2_TKO_rep1
K9me2_TKO_rep1


title: H3K27me3 ChIP-seq in TKO rep2

description:
Library name: K27me3_TKO_rep2
K27me3_TKO_rep2


title: Colon Cancer_305


title: N_2

description: Library name: Sample 6


title: CK_2

description: Library name: Sample 2


title: CK_1

description: Library name: Sample 1


title: P7 wildtype iRECs #2

description:
Zmiz1-iRECs-P7-WT-2
Zmiz1iRECSWT_vs_Zmiz1iRECSMUT.genes.deseq.counts.csv


title: H3K9me3 ChIP-seq in TKO

description:
Library name: K9me3_TKO
K9me3_TKO


title: P7 wildtype iRECs #1

description:
Zmiz1-iRECs-P7-WT-1
Zmiz1iRECSWT_vs_Zmiz1iRECSMUT.genes.deseq.counts.csv


title: Colon Cancer_315


title: H3K9me3 ChIP-seq in Setdb1 KO

description:
Library name: K9me3_Setdb1KO
K9me3_Setdb1KO


title: Colon Cancer_303

description: Gene expression data from patiets with colon cancer


title: F1 Landsberg erecta X Columbia, WT, replicate 2

status: Public on May 27 2025

city: Buenos Aires

first: Ariel

last: Chernomoretz

address: Av Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

description:
Library name: LerXCol_23
Column name in processed data file: LerXCol_23_alleleCol and LerXCol_23_alleleLer
F1_LerXCol_raw_counts.csv

data_processing:
Before carrying out read mapping, the TrimGalore wrapper was used to remove adapter sequences with Curadapt and to check read quality with FastQC.
The STAR v2.7.9a (Dobin et al. 2013) aligner was used. STAR’s “2-pass” method improved sensitivity in detecting novel junctions that were not aligned to the coordinates of isoforms present in the genome annotation.
The TAIR10 reference genome was used for reads from the Col-0 accession, while an established strategy (Winkelmüller et al. 2021) was employed for Ler. A pseudo-reference genome was generated by utilizing the single nucleotide variant (SNP) and insertion/deletion (Indel) data of Ler obtained from the 1001 Genomes Project website, starting from the Col-0 genome. The pseudogene function incorporated in the GEAN software was employed to infer the sequence of the pseudo-genome by replacing the reference allele with the alternative allele of Ler.
Assembly: TAIR10
Supplementary files format and content: csv files include raw counts matrix. For F1 samples, it was included raw counts for Col-0 and Ler genome mapping. Only reads that could be unambiguously assigned to one parent were considered.

organism: Arabidopsis thaliana

source_name: entire seedlings

growth_protocol: Plants were cultivated on soil at 22°C under long-day (LD; 16-h light/8-h dark cycles; 80 μmol·m-2 s-1 of white light) conditions.

extract_protocol:
Seeds were sown on MS medium containing 0.8% m/v agar, stratified for four days in the dark at 4°C, and then transferred to continuous white light at 22°C. After nine days of growth, entire seedlings were collected and total RNA was purified using the QIAGEN RNeasy Plant Mini Kit following the manufacturer’s protocol.
cDNA libraries were generated based on the Illumina TruSeq RNA Sample Preparation Guide. Polyadenylated mRNA was extracted from 3 μg of total RNA and then fragmented. Reverse transcriptase SuperScript II (SSII RT) (Thermo Fisher Scientific, Waltham, MA, USA) and random hexamers were used to synthesize cDNA. Finally, specific adapters were added to each sample and the libraries were sequenced on the Illumina GAIIx platform with 100 bp reads. Reads were analyzed using version 1.3 of the Illumina pipeline and underwent quality filtration using standard Illumina procedures.

treatment_protocol: The prmt5-5 mutant isolated in the Col-0 background was backcrossed for 7 generations with WT plants of the Ler accession, checking for the presence of the mutant allele after each cross. To generate hybrid backgrounds of WT plants (F1 Col-0 x Ler) and prmt5-5 mutant plants (F1 prmt5-5 Col x prmt5-5 Ler), multiple crosses were conducted involving WT and prmt5-5 mutant plants from the Col-0 and Ler accessions.

value: entire seedlings

value: WT

tag: accession


title: F1 Columbia X Landsberg erecta, prmt5-5, replicate 1

description:
Library name: prmt5_ColXprmt5_Ler_25
Column name in processed data file: prmt5_ColXprmt5_Ler_25_alleleCol and prmt5_ColXprmt5_Ler_25_alleleLer
F1_ColXLer_raw_counts.csv


title: F1 Landsberg erecta X Columbia, prm5-5, replicate 3

description:
Library name: prmt5_LerXprmt5_Col_32
Column name in processed data file: prmt5_LerXprmt5_Col_32_alleleCol and prmt5_LerXprmt5_Col_32_alleleLer
F1_LerXCol_raw_counts.csv


title: F1 Landsberg erecta X Columbia, prm5-5, replicate 1

description:
Library name: prmt5_LerXprmt5_Col_29
Column name in processed data file: prmt5_LerXprmt5_Col_29_alleleCol and prmt5_LerXprmt5_Col_29_alleleLer
F1_LerXCol_raw_counts.csv


title: F1 Columbia X Landsberg erecta, prmt5-5, replicate 3

description:
Library name: prmt5_ColXprmt5_Ler_28
Column name in processed data file: prmt5_ColXprmt5_Ler_28_alleleCol and prmt5_ColXprmt5_Ler_28_alleleLer
F1_ColXLer_raw_counts.csv


title: F1 Landsberg erecta X Columbia, prm5-5, replicate 2

description:
Library name: prmt5_LerXprmt5_Col_30
Column name in processed data file: prmt5_LerXprmt5_Col_30_alleleCol and prmt5_LerXprmt5_Col_30_alleleLer
F1_LerXCol_raw_counts.csv


title: F1 Landsberg erecta X Columbia, WT, replicate 3

description:
Library name: LerXCol_24
Column name in processed data file: LerXCol_24_alleleCol and LerXCol_24_alleleLer
F1_LerXCol_raw_counts.csv


title: F1 Landsberg erecta X Columbia, WT, replicate 1

description:
Library name: LerXCol_21
Column name in processed data file: LerXCol_21_alleleCol and LerXCol_21_alleleLer
F1_LerXCol_raw_counts.csv


title: Colon Cancer_302


title: F1 Columbia X Landsberg erecta, WT, replicate 3

description:
Library name: ColXLer_20
Column name in processed data file: ColXLer_20_alleleCol and ColXLer_20_alleleLer
F1_ColXLer_raw_counts.csv


title: F1 Columbia X Landsberg erecta, WT, replicate 2

description:
Library name: ColXLer_19
Column name in processed data file: ColXLer_19_alleleCol and ColXLer_19_alleleLer
F1_ColXLer_raw_counts.csv


title: F1 Columbia X Landsberg erecta, WT, replicate 1

description:
Library name: ColXLer_18
Column name in processed data file: ColXLer_18_alleleCol and ColXLer_18_alleleLer
F1_ColXLer_raw_counts.csv


title: Landsberg erecta accession, prmt5-5, replicate 3

description:
Library name: prmt5_Ler_16
Column name in processed data file: prmt5_Ler_16
parental_raw_counts.csv

value: Ler


title: Colon Cancer_301


title: Landsberg erecta accession, prmt5-5, replicate 1

description:
Library name: prmt5_Ler_13
Column name in processed data file: prmt5_Ler_13
parental_raw_counts.csv