title: H23 cells, cJun, cJun ChIP-seq

city: New York

first: Jin Suk

last: Park

address: 417 East 68th St

institute: MSKCC

description: Library name: Sample 5

data_processing:
For scRNA-seq, all processing of the resulting data was performed using the Scanpy package. For quality control, cells with less than 200 genes detected and genes expressed by less than 3 cells were filtered out. Based on the library distribution, cells with less than 1,000, greater than 5% mitochondrial RNA content or less than 5% ribosomal RNA content were excluded from analysis. Housekeeping genes MALAT1 and GM42418 were also removed, with 9,949 cells from freshly isolated KP tumor and 11,064 cells for day-7 KP tumoroids passing the filters.
Assembly: hg38, Mouse mm10
Supplementary files format and content: Matrix files, ProcessedPeaks

source_name: Cell line

extract_protocol:
To isolate primary LUAD cells, KP mice were euthanized and perfused with PBS through the left ventricle of the heart. Micro-dissected tumor tissues using a sterile scalpel were further dissociated by a mixture of dispase II (0.6 U/mL; D4693, Sigma Aldrich), collagenase type IV (0.166 U/mL; 17104019, Thermo Fisher Scientific), and DNase I (10 U/mL; 07900, STEMCELL Technologies) in Dulbecco’s Modified Eagle’s Medium (DMEM) containing gentamicin (2 μg/mL; 15710064, Gibco) at 37°C for 30-60 min. The cell suspension was filtered through 70 mm EASYstrainer (Greiner Bio-one) and spun at 300 g for 5 min at 4°C. The supernatant was aspirated, and red blood cells were lysed using RBC Lysis Buffer (eBioscience). Cells were then washed with PBS and spun at 300 g for 5 min at 4°C, re-suspended in ice-cold Fluorescence-Activated Cell Sorting (FACS) buffer [2% fetal bovine serum (FBS) in phosphate-buffered saline solution (PBS)], and strained through a 35 mm filter. Sorted GFP+ LUAD cells were seeded in a mixture of 50% Matrigel (Corning, Cat #: CB-40230C) and 50% LUAD media (Advanced DMEM/F12; 12634-010, Gibco), 2% of FBS, 2mM GlutaMAX (35050061, Gibco), 10 mM HEPES, 2 μg/mL of gentamicin, and 100 units/mL of penicillin/streptomycin).
Single-cell RNA-seq was performed on 10x Genomics Chromium platform. The scRNA-seq libraries were prepared based on the manufacturer’s protocol for 3’ end reading. The individual transcriptomes of encapsulated cells were barcoded during RT step and resulting cDNA purified with DynaBeads followed by amplification per manual guidelines. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to the sequencing adapters and indexed by PCR. The indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher). The raw sequencing data were then demultiplexed and aligned to the mouse genome using 10X CellRanger pipeline. This generated an output matrix of mRNA counts per cell for every gene. We used the filtered matrix for all downstream analysis. For ChIP-seq, For library construction and sequencing, DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. The KAPA HTP Library Preparation Kit (Kapa Biosystems, Cat #: KK8234) was used to prepare Illumina sequencing libraries with 0.02-5 ng of input DNA and 8-14 cycles of PCR.

value: Cell line

value: H23 cells

value: Lung adenocarcinoma

value: cJun (CST, 9165)


title: 2tj1B red H3K9me2 ChIP

status: Public on Apr 16 2026

type: SRA

city: Planegg

first: Luca

last: Salvi

state: Please select

address: Semmelweisstr. 3

country: Germany

institute: ViGeneron GmbH

library_source: genomic

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million or to background
Assembly: Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary files format and content: Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: cells were grown in liquid, rich YES medium

extract_protocol:
ChIP libraries: IP of crosslinked (1% formaldehyde, 15 min) sonycated lysate, followed by decrosslinking and protein and RNA degradation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). DNA sequencing via Illumina: Cells were lysed by bead beating and lysate was sonycated and RNAse-treated. DNA isolated via phenol-chloroform-isoamylalcohol purification followed by ethanol precipitation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). DNA sequencing via Nanopore: DNA extraction was performed with Genomic Tip 500/G kit (Qiagen) following the manufacturer’s instruction, but using Lallzyme MMX for lysis. Sequencing was performed using Oxford Nanopore (MinION). RNA sequencing: RNA was isolated applying the hot phenol method. Total RNA and polyA RNA Libraries made with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB). In the polyA library preparation, isolation of the polyA RNA from the total RNA was performed using polyT beads. Small RNA sequencing: strains with the endogenous Ago1 3xFLAG tagged were grown in YES and 2.5l of log phase cells were collected. Cells were resuspended in lysis buffer (50 mM HEPES pH 7.5, 1.5 M NaOAc, 5 mM MgCl2, 2 mM EDTA pH 8, 2 mM EGTA pH 8, 0.1% Nonidet P-40, 20% glycerol) supplemented with 1mM PMSF and Complete EDTA free Protease Inhibitor Cocktail (Roche), keeping a 1:1 ratio between the cell volume and the buffer. Cells were fragmented using glass beads and the bead beater as described for the ChIP protocol. The cell debris was eliminated by cetrifugation at 13000g and the crude lysate was incubated with 30μl of FLAG-M2 agarose resin (Sigma-Aldrich A2220) at 4°C for 2h with gentle rotation. The IP was washed five times with the lysis buffer and Ago1 was eluted from the resin mixing 1% SDS with 300 mM NaOAc and phenol-chloroform-isoamylalcohol (25:24:1, Roth). The sRNAs were concetrated by ethanol precipitation, run on an 18% polyacrylamide urea gel together with 22, 26 and 30 nt RNA markers and the bands of sizes between 20 and 30 nt were excised from the gel. A 3’ linker was ligated to the sRNAs (5 rAppCTGTAGGCACCATCAAT–N ′ H2 3’, NEB, reaction concentration 2μM). The 3' ligated products were purified on an 18% acrylamide urea gel with subsequent phenol-chloroform purification and ethanol purification. The 5' adaptor (5'-ACACUCUUUCCCUACACGACGCUC UUCCGAUCU-3', Metabion) ligation was performed, followed by reverse transcription (RT primer: 5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCGATTGATGGTGCCTACAG -3’, Metabion). The cDNA was amplified with 12-20 PCR cycles using the Phusion hot start II DNA polymerase kit (ThermoFisher) and the Illumina P5 5' primer (5' -AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC G -3') together with the Illumina P7 3' primer with inserted barcode (5'-CAA GCA GAA GAC GGC ATA CGA GAT XXXXXX GTG ACT GGA GTT CAG ACG TG -3'). The sRNA library was purified from an 8% polyacrylamide gel, ethanol precipitated and Single end sequencing was performed on an Illumina GAIIX sequencer.
Libraries were prepared using NEBnext Ultra Directional RNA or DNA Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer instruction.

tag: cell line

tag: genotype

tag: antibody used_for_ip

value: anti H3K9me2, Abcam 1220


title: Podocyte cell_HG_siRab3A_Rep_5_(20)

city: Valencia

first: Ana

last: Ortega

state: VALENCIA

address: Av. Menendez Pelayo 4

country: Spain

institute: Incliva Health Research Institute

description:
Library name: Sample_40_HG_si3_Biol_rep_5_(20)
Colum name in Counts_smallRNA.txt: HG_si27_20

library_source: transcriptomic

data_processing:
Small RNA levels were quantified with the featureCounts function from the Rsubread package from Bioconductor, R
Trimming was performed with Trim Galore!
Alignment to the GRCh38 reference genome was performed with STAR
Assembly: GRCh38
Supplementary files format and content: .txt files contain raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: podocyte AB8/13

growth_protocol: Conditionally immortalised human podocytes (cell line AB8/13) were cultured on collagen type I-coated (Gibco, Thermo-Fisher Scientific, Waltham, MA, USA) flasks or plates in the RPMI medium 1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (both from Biowest, Nuaillé, France), and 1% insulin-transferrin-selenium (ITS, Gibco, Thermo-Fisher Scientific, Waltham, MA, USA). They were maintained at 33 °C until reaching 80% confluence, then trypsinised and reseeded at 70% confluence for differentiation that was induced by incubating cells at 37 °C with 2% FBS for 10-14 days. All cultures were kept in a humidified incubator with 5% CO₂ and 95% air (BINDER, VWR International, Radnor, PA, USA). Differentiated podocytes were used to perform all experiments.

extract_protocol:
Total RNA, was isolated from podocyte-derived-EVs using the Total Exosome RNA and Protein Isolation kit (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer’s protocol. All RNA preparations were stored at −80 °C until further use.
Libraries were prepared from 6 μL of total RNA per sample using the Small RNA-Seq Library Prep Kit (Lexogen GmbH, Austria), following a protocol optimised for low-input samples. Individual libraries were normalised to 4 nM, pooled, and sequenced on the NextSeq 550 platform (Illumina, USA) using 150-cycle paired-end reads.

treatment_protocol: Podocytes were transiently transfected with siRNA targeting the RAB27A and the RAB3A gene using Lipofectamine 3000 (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) in serum-free Opti-MEM® Gibco, Thermo-Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol. As control, cells were transfected with a scrambled siRNA (scr) (Silencer™ Select Negative Control, Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). After 24 hours, the transfection medium was replaced with RPMI containing 1% penicillin-streptomycin and ITS. Cells were then treated with either normal glucose (NG; 5.5 mM) or high glucose (HG; 30 mM) concentrations (D-(+)-Glucose; Sigma Aldrich, St. Louis, MO, USA) and incubated for an additional 24 hours at 37 °C.

value: podocyte AB8/13

tag: cell type

value: renal podocyte

tag: sirna transfection

value: Rab27A transfected

tag: treatment

value: high glucose


title: Podocyte cell_NG_siRab3A_Rep_5_(20)

description:
Library name: Sample_39_NG_si3_Biol_rep_5_(20)
Colum name in Counts_smallRNA.txt: NG_si27_20

value: normal glucose


title: 1_rHA protein vaccine, follicular, D1

city: Gold Coast

first: Laurelle

last: Jackson

state: Queensland

address: 1 Parklands Dr, Southport

department: Pharmacy and Medical Sciences

country: Australia

institute: Griffith University

description:
Library name: DSP-1001660034485-B-A10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

data_processing:
GeoMx DSP sequencing data were processed using the NanoString GeoMx NGS Pipeline to generate digital count (DCC) files for each region of interest (ROI).
Assembly: Whole Transcriptome Atlas based on mm10
Supplementary files format and content: geomx_counts_matrix.txt
Supplementary files format and content: geomx_AOI_metadata.txt
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: lymph node

growth_protocol: Female BALB/c mice were maintained under specific pathogen-free conditions with ad libitum access to food and water. Animals were housed and handled in accordance with institutional animal ethics and biosafety guidelines. No in vitro cell culture growth conditions applied to this study, as tissues were collected directly from vaccinated animals for downstream spatial transcriptomic analyses.

extract_protocol:
Injection site muscle and draining lymph nodes were harvested, formalin-fixed, paraffin-embedded (FFPE), and sectioned for spatial transcriptomic analysis. For GeoMx DSP profiling, FFPE sections were deparaffinised, subjected to antigen retrieval and proteinase K digestion according to the manufacturer’s protocol for the GeoMx Whole Transcriptome Atlas assay. Regions of interest were selected based on guidance of morphology marker staining and histological evaluation, followed by UV photocleavage of indexing oligonucleotides for collection and sequencing.
For GeoMx DSP samples, photocleaved oligonucleotide tags released from selected regions of interest were collected and used for library preparation according to the NanoString GeoMx DSP Whole Transcriptome Atlas workflow. Sequencing libraries were generated by PCR amplification with sample-specific Illumina i5 and i7 dual-index primers, followed by purification and quantification prior to next-generation sequencing.

treatment_protocol: Groups of three female BALB/c mice per treatment group were immunised intramuscularly in the quadriceps with either AF03-adjuvanted recombinant haemagglutinin (rHA) protein vaccine or phosphate-buffered saline (PBS) control on Days 0 and 21. Blood was collected longitudinally on Days 0, 14, and 35 for serum-based immunogenicity analyses. For spatial transcriptomic profiling, injection site muscle and draining lymph nodes were collected on Days 1 and 7 following vaccination.

tag: tissue

value: lymph node

tag: time

value: healthy BALB/c mice

tag: region of_interest

value: Follicular

value: rHA protein vaccine


title: H23 cells, cJun, IgG ChIP-seq

state: NY

country: USA

description: Library name: Sample 6

tag: chip antibody


title: 1_No template control

description:
Library name: DSP-1001660034485-B-A01
Control with no template

source_name: No template control

value: No template control

value: control


title: sample TSA3

city: Chengdu

first: jia hao

last: lv

state: Sichuan

address: No. 1942, Huanhu North Road, Jianyang City, Chengdu, Sichuan Province

department: Institute of Sports Medicine and Health

country: China

institute: Chengdu Sport University

description:
Library name: TSA3
TSA3 skeletal muscle from tumor-bearing + exercise group, biological replicate 3

data_processing:
Raw reads in FASTQ format were processed using fastp (v0.20.1) to remove low-quality reads and obtain clean reads.
Clean reads were aligned to the Mus musculus reference genome using HISAT2 (v2.1.0).
Gene-level expression abundance was quantified as FPKM values, and read counts for each gene were obtained using HTSeq-count (v0.11.2).
PCA analysis was performed to evaluate biological replication among samples.
Differential expression analysis was performed using DESeq2, and genes with q value < 0.05 and fold change > 2 or < 0.5 were considered differentially expressed.
Assembly: GRCm39
Supplementary files format and content: counts.xls contains gene-level raw read counts for all samples.
Supplementary files format and content: fpkm.xls contains gene-level FPKM expression values for all samples.

molecule: polyA RNA

source_name: skeletal muscle

growth_protocol: Skeletal muscle tissues were collected from mice in four experimental groups: control group (NC), exercise group (N-A), CT26 tumor-bearing group (TS), and CT26 tumor-bearing plus exercise group (TSA), with four biological replicates in each group.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer, and RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
mRNA was enriched from total RNA and fragmented, followed by first-strand cDNA synthesis. Libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions, followed by end repair, A-tailing, adaptor ligation, PCR amplification, and sequencing.

treatment_protocol: Mice were assigned to four groups: control, exercise, CT26 tumor-bearing, and CT26 tumor-bearing plus exercise. Exercise-group mice received aerobic exercise intervention, tumor-bearing mice were inoculated with CT26 cells, and the combined group received both CT26 inoculation and aerobic exercise intervention.

value: skeletal muscle

value: wild type

value: tumor-bearing + exercise

tag: batch


title: sample TSA4

description:
Library name: TSA4
TSA4 skeletal muscle from tumor-bearing + exercise group, biological replicate 4


title: IRF9-IP

city: Taizhou

first: yin

last: yuan

state: jiangsu

address: 210 Yingchun Road, Hailing District, Taizhou City, Jiangsu Province

institute: Nanjing Medical University Affiliated Taizhou People's Hospital

description: Library name: Sample1

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Oral squamous cell carcinoma cell lines


title: H23 cells, CHD1, IgG ChIP-seq

description: Library name: Sample 4

value: Cell line

value: H23 cells

value: Lung adenocarcinoma


title: 2tj1C H3K9me2 ChIP

value: anti H3K9me2, Abcam 1220


title: 2tj1G H3K9me2 ChIP


title: 2tj1B H3K9me2 ChIP


title: sample TSA2

description:
Library name: TSA2
TSA2 skeletal muscle from tumor-bearing + exercise group, biological replicate 2


title: H23 cells, CHD1, CHD1 ChIP-seq

description: Library name: Sample 3


title: Podocyte cell_HG_siRab3A_Rep_4_(19)

description:
Library name: Sample_36_HG_si3_Biol_rep_4_(19)
Colum name in Counts_smallRNA.txt: HG_si27_19

value: podocyte AB8/13

value: renal podocyte

value: Rab27A transfected


title: 2tj1A red H3K9me2 ChIP


title: Podocyte cell_NG_siRab3A_Rep_4_(19)

description:
Library name: Sample_35_NG_si3_Biol_rep_4_(19)
Colum name in Counts_smallRNA.txt: NG_si27_19

value: normal glucose


title: sample TSA1

description:
Library name: TSA1
TSA1 skeletal muscle from tumor-bearing + exercise group, biological replicate 1


title: sample TS4

description:
Library name: TS4
TS4 skeletal muscle from tumor-bearing group, biological replicate 4

value: tumor-bearing


title: Podocyte cell_HG_scr_Rep_4_(19)

description:
Library name: Sample_34_HG_scr_Biol_rep_4_(19)
Colum name in Counts_smallRNA.txt: HG_scr_19

value: scramble transfected

value: high glucose


title: Cells in IP of patient P052 (PD3)

city: Chicago

first: Erting

last: Tang

state: IL

address: 5640 S Ellis Ave

institute: the University of Chicago

description:
Library name: P052
10x genomics

library_source: transcriptomic single cell

data_processing:
Alignment, filtering, counting, and demultiplexing of RNA-seq reads were performed using the Cell Ranger count (10x Genomics, version 7.1.0). For alignment, the GRCh38 reference genome was appended with the CAR transgene sequence of axicabtagene ciloleucel.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: T cells

extract_protocol:
Cryopreserved biospecimens were thawed and washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Antibody-stained cells were conjugated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) at 1:1000 dilution in PBS for 5 minutes at room temperature. Finally, cells were washed 3x in cold cell media (RPMI, 10% FBS) before sorting (BD Biosciences, FACSAria Fusion) for live cells.
Sorted cells were partitioned into droplets for single-cell RNA-seq via Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263). RNA-seq libraries were prepared according to manufacturer protocols. Libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via high-sensitivity D5000 screentapes (Agilent, 5067-5592), pooled, and sequenced (Illumina, Novaseq-6000).

value: T cells


title: Podocyte cell_NG_scr_Rep_4_(19)

description:
Library name: Sample_33_NG_scr_Biol_rep_4_(19)
Colum name in Counts_smallRNA.txt: NG_scr_19


title: Cells in IP of patient P032 (PD2)

description:
Library name: P032
10x genomics


title: NA_Knic_3

city: beijing

first: li

middle: yi

last: xiao

state: State...

address: road of xueyuan 38

institute: peking university

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed using fastp[2] (version 0.20.0). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA[3] (v0.7.12) and clean reads were aligned to the reference genome using BWA mem  -k 32 -T 30 -t 4 -M.
All peak calling was performed with MACS2  (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences were performed using findMotifsGenome.pl program in HOMER[5]( v4.9.1) software with ‘-len 8,10,12,14 -gc -size given -homer2 -dumpFasta’.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

source_name: Hela

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Take out the cryovial and shake it in 37°C water to quickly thaw it within 1-2min.Cells were centrifuged for 5 min at 600×g at 4 ℃ Cell activity was detected with LUNA-FL and counted.1 ml of 1 XHB buffer was added into the tissue sample, grinding and filtering, filtrate centrifuged at 4℃ 500×g for 5 min, supernatant was discarded, density gradient centrifugation for 10 min, nucleus suspension was obtained and counted with LUNA-FL.
CUT&Tag library was performed as described previously [1]. Briefly, the cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation. DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries.

treatment_protocol: Nicotinic acid treated for 24 hours

value: Hela

value: Human cervical cancer cells

value: pan-Knic (designed and prepared by PTM Biolabs Inc.)

value: NA treated 24hours


title: Podocyte cell_HG_scr_Rep_3_(18)

description:
Library name: Sample_30_HG_scr_Biol_rep_3_(18)
Colum name in Counts_smallRNA.txt: HG_scr_18


title: sample TS3

description:
Library name: TS3
TS3 skeletal muscle from tumor-bearing group, biological replicate 3

value: skeletal muscle

value: wild type


title: NA_Knic_2


title: sample NC3

description:
Library name: NC3
NC3 skeletal muscle from control group, biological replicate 3

value: control


title: 2tj1A H3K9me2 ChIP


title: 1tj1neo H3K9me2 ChIP


title: Podocyte cell_NG_siRab3A_Rep_3_(18)

description:
Library name: Sample_31_NG_si3_Biol_rep_3_(18)
Colum name in Counts_smallRNA.txt: NG_si27_18


title: Podocyte cell_HG_siRab3A_Rep_3_(18)

description:
Library name: Sample_32_HG_si3_Biol_rep_3_(18)
Colum name in Counts_smallRNA.txt: HG_si27_18


title: sample TS2

description:
Library name: TS2
TS2 skeletal muscle from tumor-bearing group, biological replicate 2


title: sample TS1

description:
Library name: TS1
TS1 skeletal muscle from tumor-bearing group, biological replicate 1


title: 1tj1 H3K9me2 ChIP


title: Cells in IP of patient P028 (PD1)

description:
Library name: P028
10x genomics


title: NA_Knic_1


title: sample NC2

description:
Library name: NC2
NC2 skeletal muscle from control group, biological replicate 2


title: Podocyte cell_NG_siRab3A_Rep_2_(17)

description:
Library name: Sample_27_NG_si3_Biol_rep_2_(17)
Colum name in Counts_smallRNA.txt: NG_si27_17


title: 1tj1neo red H3K9me2 ChIP


title: wt H3 ChIP

value: wt

value: anti H3, Abcam 176842


title: Podocyte cell_HG_scr_Rep_2_(17)

description:
Library name: Sample_26_HG_scr_Biol_rep_2_(17)
Colum name in Counts_smallRNA.txt: HG_scr_17

value: podocyte AB8/13


title: Podocyte cell_NG_scr_Rep_3_(18)

description:
Library name: Sample_29_NG_scr_Biol_rep_3_(18)
Colum name in Counts_smallRNA.txt: NG_scr_18

value: renal podocyte


title: 1tj1neo white H3K9me2 ChIP

value: anti H3K9me2, Abcam 1220


title: sample NC4

description:
Library name: NC4
NC4 skeletal muscle from control group, biological replicate 4


title: Ctrl_Knic_3


title: AA2

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq  PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the  library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were  generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Rockhopper was used to identify novel genes, operon, TSS, TTS and Cis-natural antisense transcripts. It can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can aid with elucidation of bacterial transcriptomes. Then, we extract upstream 700bp sequence of Transcription Start Site for predicting promoter using TDNN.(TimeDelayNeural Network)
According to the information of Transcription Start Site(Transcription terminal Site) and Translation start site(Translation terminal site), we extracted 5’UTR(3’UTR) sequences. Then,RBSfinder and TransTermH were used to predict SD sequence and terminator sequence respectively.Rockhopper was used to identify new intergenic region transcripts, and Blastx was compared with the nr library to annotate the newly predicted transgenic regions, and the unmarked transcripts were used as candidate non_x0002_coding sRNAs. RNA fold and Inta RNA were used to predict secondary structure and target gene respectively
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly  used method for estimating gene expression levels .
Assembly: GCF_001077475.1
Supplementary files format and content: tab delimited xls file includes raw counts and RPKM values for each sample

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa thalus

growth_protocol: Pseudomonas aeruginosa was cultured at 28℃ shaker in liquid LB.

extract_protocol:
RNA was extracted by using the RNeasy Plant Mini Kit for RNA extraction (Qiagen). 1 μg total RNA per sample was used for the library preparation
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was  purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations  under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized  using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And  in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the  second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase  activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to  prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U,  In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified  with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High_x0002_Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.

treatment_protocol: OD of bacterial solution was adjusted to 0.01, acetic acid was added to the treatment group, the working concentration of acetic acid was 0.04%, and the culture was held in a shaking table at 28℃ for 4 hours

tag: strain

value: Pseudomonas aeruginosa thalus

value: WT

value: 0.04%acetic acid


title: Podocyte cell_HG_siRab3A_Rep_2_(17)

description:
Library name: Sample_28_HG_si3_Biol_rep_2_(17)
Colum name in Counts_smallRNA.txt: HG_si27_17

value: Rab27A transfected

value: high glucose


title: 2tj1K DNA-seq

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million or to background
Assembly: Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary files format and content: Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv
Library strategy: DNA-seq


title: sample N-A2

description:
Library name: N-A2
N-A2 skeletal muscle from exercise group, biological replicate 2

value: exercise


title: 1tj1 H3 ChIP


title: sample N-A4

description:
Library name: N-A4
N-A4 skeletal muscle from exercise group, biological replicate 4


title: Podocyte cell_NG_scr_Rep_2_(17)

description:
Library name: Sample_25_NG_scr_Biol_rep_2_(17)
Colum name in Counts_smallRNA.txt: NG_scr_17

value: scramble transfected

value: normal glucose


title: sample N-A3

description:
Library name: N-A3
N-A3 skeletal muscle from exercise group, biological replicate 3


title: 2tj1E DNA-seq


title: Mock3

value: 0.00%acetic acid


title: 3tj1EL DNA-seq


title: Ctrl_Knic_1

value: Hela

value: Human cervical cancer cells

value: pan-Knic (designed and prepared by PTM Biolabs Inc.)


title: Podocyte cell_HG_siRab3A_Rep_5_(16)

description:
Library name: Sample_24_HG_si3_Biol_rep_1_(16)
Colum name in Counts_smallRNA.txt: HG_si27_16


title: AA1


title: AA3


title: 3tj1FM DNA-seq


title: Podocyte cell_NG_siRab3A_Rep_5_(16)

description:
Library name: Sample_23_NG_si3_Biol_rep_1_(16)
Colum name in Counts_smallRNA.txt: NG_si27_16


title: Podocyte cell_NG_scr_Rep_1_(16)

description:
Library name: Sample_21_NG_scr_Biol_rep_1_(16)
Colum name in Counts_smallRNA.txt: NG_scr_16


title: NEF,S1,snRNAseq

city: Melbourne

first: Andrew

middle: J

last: Fleetwood

address: 75 Commercial Road

institute: Baker Heart and Diabetes Institute

description:
Library name: NEF_RNA
10x Genomics

data_processing:
Raw FASTQ files were  processed using Cell Ranger ARC v2.0.2 (10X Genomics).
Analyses of pre-processed snRNA-seq and snATAC-seq data were performed in R v4.2.2 using Seurat v5.0.0 and v5.0.3  and, Signac v1.12.0
Assembly: Mus musculus: mm10-2020-A-2.0.0
Supplementary files format and content: processed data are available in .hd5 format.

molecule: nuclear RNA

source_name: Bone marrow

extract_protocol:
LSKs, cKit+ and monocytes were sorted from exNef and exGFP treated mice. Single cells were encapsulated in Gel-beads in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 3’ GEM Library and Gel Bead kit (Baker Heart and Diabetes Institute)
Transcriptomic (snRNA) and genomic (snATAC) libraries were prepared by loading 11,500 nuclei per lane and following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kits User Guide with all required proprietary kits and equipment including the 10xGenomics Chromium Controller (1000204, 10xGenomics), Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (PN- 1000283, 10xGenomics), Chromium Next GEM Chip J Single Cell Kit (PN-1000230, 10xGenomics) and Dual Index Kit TT Set A (PN-1000215, 10xGenomics). Libraries were pooled evenly and paired-end sequencing on an Illumina NovaSeq 6000 was performed.

value: Bone marrow

value: exNEF


title: sample N-A1

description:
Library name: N-A1
N-A1 skeletal muscle from exercise group, biological replicate 1

value: skeletal muscle

value: wild type


title: Podocyte cell_HG_siRab27A_Rep_5_(15)

description:
Library name: Sample_20_HG_si27_Biol_rep_5_(15)
Colum name in Counts_smallRNA.txt: HG_si27_15

value: podocyte AB8/13

value: renal podocyte


title: Mock1

value: Pseudomonas aeruginosa thalus

value: WT


title: 2tj1F DNA-seq


title: Mock2


title: 2tj1A DNA-seq


title: Podocyte cell_HG_scr_Rep_1_(16)

description:
Library name: Sample_22_HG_scr_Biol_rep_1_(16)
Colum name in Counts_smallRNA.txt: HG_scr_16


title: Podocyte cell_HG_scr_Rep_5_(15)

description:
Library name: Sample_18_HG_scr_Biol_rep_5_(15)
Colum name in Counts_smallRNA.txt: HG_scr_15


title: 2tj1D DNA-seq


title: sample NC1

description:
Library name: NC1
NC1 skeletal muscle from control group, biological replicate 1

value: control


title: HighFidelity_polyA_amplicon_11

city: Worcester

first: Athma

middle: A

last: pai

state: MA

address: 55 Lake Avenue North

department: RNA Therapeutics Institute

institute: UMass Chan Medical School

description:
Library name: 68B
Amplicon-seq of cDNA amplified from primers 68B_F and 68B_R

data_processing:
For amplicon sequencing, reads were aligned to the hg38 reference genome with ENSEMBL GRCh38.95 annotations using STAR with parameters described in methods section
Assembly: Grch38
Supplementary files format and content: SJ.out.tab

growth_protocol: K562 cells were grown in IMDM supplemented with 10% FBS. Cells lines were maintained at 37°C and 5% CO2 until 70% confluent.

extract_protocol:
For amplicon sequencing total RNA was extracted from either whole cells or nuclear fraction
For amplicon sequencing, RNA was reverse-transcribed into cDNA using the High-Capacity cDNA Reverse Transcription Kit. PCR reactions were carried out with Phire Hot Start II PCR Master Mix using 35 amplification cycles with an annealing temperature of 56 °C and a 15 s extension step. Amplified products were assessed on 2% agarose gels. Selected amplicons were submitted to Genewiz  for Amplicon-EZ next-generation sequencing and sequenced on an Illumina MiSeq platform using a 500-cycle paired-end configuration

value: chronic myeloid leukemia

tag: sample group


title: Podocyte cell_NG_scr_Rep_5_(15)

description:
Library name: Sample_17_NG_scr_Biol_rep_5_(15)
Colum name in Counts_smallRNA.txt: NG_scr_15


title: NEF,S1,snATACseq

description:
Library name: NEF_ATAC
10x Genomics

library_source: genomic single cell


title: 2tj1G DNA-seq


title: wt DNA-seq

value: wt


title: Podocyte cell_NG_siRab27A_Rep_5_(15)

description:
Library name: Sample_19_NG_si27_Biol_rep_5_(15)
Colum name in Counts_smallRNA.txt: NG_si27_15

value: Rab27A transfected


title: Podocyte cell_HG_siRab27A_Rep_4_(14)

description:
Library name: Sample_16_HG_si27_Biol_rep_4_(14)
Colum name in Counts_smallRNA.txt: HG_si27_14

value: high glucose


title: GFP,S1,snATACseq

description:
Library name: GFP_ATAC
10x Genomics

value: exGFP


title: HighFidelity_polyA_amplicon_10

description:
Library name: 67A
Amplicon-seq of cDNA amplified from primers 67A_F and 67A_R


title: GFP,S1,snRNAseq

description:
Library name: GFP_RNA
10x Genomics


title: Podocyte cell_HG_scr_Rep_4_(14)

description:
Library name: Sample_14_HG_scr_Biol_rep_4_(14)
Colum name in Counts_smallRNA.txt: HG_scr_14

value: scramble transfected


title: Podocyte cell_NG_siRab27A_Rep_4_(14)

description:
Library name: Sample_15_NG_si27_Biol_rep_4_(14)
Colum name in Counts_smallRNA.txt: NG_si27_14

value: normal glucose


title: 1tj1 DNA-seq


title: Aorta nuclei ATAC, VEDS, male

city: Baltimore

first: Leda

last: Restrepo

state: MD

address: 733 N Broadway, Miller Research Building

department: Human Genetics

institute: Johns Hopkins

description: Library name: v210-211_aorta_ATAC

data_processing:
FASTQ files were generated by the sequencing facility. FASTQ files were analyzed in aggregate per library. Reads were aligned to mm10 and accessible regions were called with MACS2. ENCODE mm10 blacklist regions were excluded. CPM-normalized signal tracks were generated.
Assembly: mm10 UCSC/GRCm38
Supplementary files format and content: Processed data include MACS2 peak calls in narrowPeak format.

source_name: Aorta

extract_protocol:
Aortic tissue was minced and nuclei were isolated using the Chromium Nuclei Isolation Kit (10x Genomics) according to the manufacturer’s protocol. Fresh nuclei were prepared and used immediately for library preparation.
ATAC-seq libraries were generated using the Chromium Single Cell ATAC workflow (10x Genomics) according to the manufacturer’s protocol, including transposition, barcoding, amplification, and library preparation on the Chromium instrument.

value: Aorta

value: Aortic nuclei

value: Disease


title: Aorta nuclei ATAC, WT, male

description: Library name: v134-135_aorta_ATAC


title: 1tj1 white Cbp1 ChIP

value: anti FLAG M2 affinity gel Sigma, n° A 2220


title: HighFidelity_polyA_amplicon_6

description:
Library name: 60B
Amplicon-seq of cDNA amplified from primers 60B_F and 60B_R


title: 1tj1 Cbp1 ChIP


title: HighFidelity_polyA_amplicon_8

description:
Library name: 65A
Amplicon-seq of cDNA amplified from primers 65A_F and 65A_R


title: NSCs, cko03, E14.5

city: Beijing

first: Xinrun

last: Wang

address: Dongdan

institute: PUMC

description: Library name: Sample_cko_03

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCm39 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8, similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: CSV files include rawcounts for each sample.

source_name: brain

growth_protocol: NSCs were maintained in DMEM/F12 supplemented with B27 and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain

tag: developmental stage

value: NSC

value: cko


title: HighFidelity_polyA_amplicon_9

description:
Library name: 66A
Amplicon-seq of cDNA amplified from primers 66A_F and 66A_R


title: Aorta nuclei ATAC, WT, female

description: Library name: v212-213_aorta_ATAC


title: Aorta nuclei ATAC, VEDS, female

description: Library name: v138-139_aorta_ATAC


title: HighFidelity_polyA_amplicon_4

description:
Library name: 57B
Amplicon-seq of cDNA amplified from primers 57B_F and 57B_R


title: NSCs, cko02, E14.5

description: Library name: Sample_cko_02


title: HighFidelity_polyA_amplicon_7

description:
Library name: 62B
Amplicon-seq of cDNA amplified from primers 62B_F and 62B_R


title: Podocyte cell_NG_siRab27A_Rep_3_(13)

description:
Library name: Sample_11_NG_si27_Biol_rep_3_(13)
Colum name in Counts_smallRNA.txt: NG_si27_13

value: podocyte AB8/13

value: renal podocyte


title: Podocyte cell_HG_scr_Rep_3_(13)

description:
Library name: Sample_10_HG_scr_Biol_rep_3_(13)
Colum name in Counts_smallRNA.txt: HG_scr_13


title: S8 HFD_MOM

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Library name: S8

data_processing:
The reads were trimmed for adapters and polyX tails using fastp.
The count table was generated by pseudo-aligning reads to the mouse transcriptome using kallisto and converting transcript counts to gene counts using tximport.
Assembly: GRCm39 (Ensembl version 104)
Supplementary files format and content: CSV file of gene counts

source_name: Pancreas

extract_protocol:
RNA extraction was performed using a RNeasy Micro Kit (Qiagen, Cat No. 74004).
RNA-seq libraries were made by using TruSeq Stranded mRNA kit.

value: Pancreas

value: beta cells


title: Podocyte cell_HG_siRab27A_Rep_3_(13)

description:
Library name: Sample_12_HG_si27_Biol_rep_3_(13)
Colum name in Counts_smallRNA.txt: HG_si27_13


title: S10 HFD_MOM

description: Library name: S10


title: Podocyte cell_NG_scr_Rep_4_(14)

description:
Library name: Sample_13_NG_scr_Biol_rep_4_(14)
Colum name in Counts_smallRNA.txt: NG_scr_14


title: HighFidelity_polyA_amplicon_2

description:
Library name: 53B
Amplicon-seq of cDNA amplified from primers 53B_F and 53B_R

value: chronic myeloid leukemia

value: WT


title: HighFidelity_polyA_amplicon_5

description:
Library name: 58A
Amplicon-seq of cDNA amplified from primers 58A_F and 58A_R


title: Podocyte cell_NG_scr_Rep_3_(13)

description:
Library name: Sample_9_NG_scr_Biol_rep_3_(13)
Colum name in Counts_smallRNA.txt: NG_scr_13


title: NSCs, cko01, E14.5

description: Library name: Sample_cko_01


title: NSCs, wt03, E14.5

description: Library name: Sample_wt_03

value: wt


title: S7 HFD

description: Library name: S7


title: S9 HFD_MOM

description: Library name: S9


title: S11 HFD_MOM

description: Library name: S11


title: HighFidelity_polyA_amplicon_3

description:
Library name: 54A
Amplicon-seq of cDNA amplified from primers 54A_F and 54A_R


title: 1tj1 red Cbp1 ChIP


title: HighFidelity_polyA_amplicon_1

description:
Library name: 52B
Amplicon-seq of cDNA amplified from primers 52B_F and 52B_R


title: NSCs, wt02, E14.5

description: Library name: Sample_wt_02


title: S6 HFD

description: Library name: S6


title: Low Fidelity_polyA_amplicon_3

description:
Library name: 44A
Amplicon-seq of cDNA amplified from primers 44A_F and 44A_R

value: Low Fidelity_polyA_amplicon


title: Podocyte cell_HG_siRab27A_Rep_2_(12)

description:
Library name: Sample_8_HG_si27_Biol_rep_2_(12)
Colum name in Counts_smallRNA.txt: HG_si27_12

value: Rab27A transfected

value: high glucose


title: NSCs, wt01, E14.5

description: Library name: Sample_wt_01


title: Podocyte cell_NG_siRab27A_Rep_2_(12)

description:
Library name: Sample_7_NG_si27_Biol_rep_2_(12)
Colum name in Counts_smallRNA.txt: NG_si27_12

value: normal glucose


title: LowFidelity_polyA_amplicon_2

description:
Library name: 42A
Amplicon-seq of cDNA amplified from primers 42A_F and 42A_R


title: S5 HFD

description: Library name: S5


title: Ctrl_Knic_2

value: Hela

value: Human cervical cancer cells

value: pan-Knic (designed and prepared by PTM Biolabs Inc.)


title: Podocyte cell_HG_scr_Rep_2_(12)

description:
Library name: Sample_6_HG_scr_Biol_rep_2_(12)
Colum name in Counts_smallRNA.txt: HG_scr_12

value: scramble transfected


title: LowFidelity_polyA_amplicon_1

description:
Library name: 36A
Amplicon-seq of cDNA amplified from primers 36A_F and 36A_R


title: S4 HFD

description: Library name: S4


title: PC-3-shRB1-2，ATAC

city: shenyang

first: Shouyi

state: Liaoning

address: No. 44 Xiaoheyan Road, Dadong District

institute: Liaoning Cancer Institute and Hospital

description: Library name: PC-3-shRB1-2，ATAC

data_processing:
ATAC-seq: Library construction, sequencing, and subsequent analysis were outsourced to Applied Protein Technology (Shanghai, China). CUT&TAG: Library construction, sequencing, and subsequent analysis were performed by Epibiotek Co., Ltd. (Guangzhou, China).
Assembly: hg38
Supplementary files format and content: bigWig

source_name: prostate cancer

growth_protocol: DMEM, 15% fetal bovine serum, 1x penicillin/streptomycin. Cells werecultured at 37C at 5% CO2

extract_protocol:
ATAC-seq: Briefly, fresh cultured cells were harvested, resuspended in PBS, and washed by centrifugation at 1000g for 5 minutes at 4°C. After removal of the PBS, 200 μL pre-cooled lysis buffer was added to the washed cells. The cells were gently pipetted to resuspend and incubated on ice for 10 minutes. The cells were then centrifuged at 500g for 10 minutes, and 1 mL washing buffer was added. After gentle mixing of the solution, the cells were centrifuged again at 500g for 10 minutes at 4°C to collect the nuclei. Next, 50 μL transposition reaction mix was added to the nuclear pellet, and the nuclei were resuspended. The mixture was gently pipetted to mix, then incubated at 37°C for 30 minutes and held at 4°C. DNA was purified with 2× DNA clean beads. To amplify the DNA, 15 PCR cycles were performed with P5 and P7 adapter primers, to generate the primary library. Finally, the ATAC-seq library was subjected to paired-end sequencing on the HiSeq 2500 platform (Illumina). CUT&TAG: The library preparation for CUT&TAG was performed according to the manufacturer’s instructions for the Epi™ Cut and Tag Kit (Epibiotek Co., Ltd., Guangzhou, China). In brief, magnetic beads were washed twice with binding buffer, and antibody buffer was prepared. Cells were resuspended in binding buffer and mixed with the magnetic beads, then incubated 10 minutes at room temperature under gentle rotation. After addition of antibody buffer, the primary antibodies were incubated at room temperature for 2 hours. The reaction was then centrifuged at 500 rpm, the supernatant was discarded, and the beads were washed with antibody buffer. The secondary antibody (IgG) was added and incubated at room temperature for 1 hour under gentle rotation. After incubation, the beads were washed twice with antibody buffer. Tn5 buffer was prepared and mixed with pAG-Tn5 Mix, then incubated at room temperature for 1 hour under gentle rotation. The reaction was then washed twice with 500 μL Tn5 Buffer, and tagmentation buffer was then added and incubated at 37°C for 1 hour. After incubation, 10% SDS was added and incubated at 55°C for 10 minutes, and DNA was purified with 1.8× DNA Clean Beads. The DNA was then amplified with 25 μL 2× AmpliMix, 2.5 μL N5 primer, and 2.5 μL N7 primer; thoroughly mixed by vortexing; and centrifuged. PCR amplification was performed with the following cycling conditions: stage 0: 72°C for 3 minutes; stage 1: 98°C for 30 seconds; stage 2: 98°C for 15 seconds, 60°C for 20 seconds, 72°C for 8 seconds (14 cycles); and stage 3: 72°C for 2 minutes. After amplification, DNA was purified with 1× DNA Clean Beads, and the library was quality-checked with a Bioptic Qsep100 Analyzer to ensure that the size distribution met the theoretical expectations.
ATAC-seq: Library construction, sequencing, and subsequent analysis were outsourced to Applied Protein Technology (Shanghai, China). CUT&TAG: Library construction, sequencing, and subsequent analysis were performed by Epibiotek Co., Ltd. (Guangzhou, China).

value: prostate cancer

value: Human prostate cancer epithelial cells


title: Podocyte cell_NG_scr_Rep_2_(12)

description:
Library name: Sample_5_NG_scr_Biol_rep_2_(12)
Colum name in Counts_smallRNA.txt: NG_scr_12

value: podocyte AB8/13


title: S3 CONTROL

description: Library name: S3


title: HighFidelity_nuclear_amplicon_11

description:
Library name: 26A
Amplicon-seq of cDNA amplified from primers 26A_F and 26A_R


title: S2 CONTROL

description: Library name: S2


title: HighFidelity_nuclear_amplicon_12

description:
Library name: 29A
Amplicon-seq of cDNA amplified from primers 29A_F and 29A_R


title: PC-3-shRB1-1，ATAC

description: Library name: PC-3-shRB1-1，ATAC


title: PC_3_shLHX2，ATAC

description: Library name: PC_3_shLHX2，ATAC


title: HighFidelity_nuclear_amplicon_10

description:
Library name: 25A
Amplicon-seq of cDNA amplified from primers 25A_F and 25A_R


title: PC_3_Vec，ATAC

description: Library name: PC_3_Vec，ATAC

value: control


title: Podocyte cell_HG_siRab27A_Rep_1_(11)

description:
Library name: Sample_4_HG_si27_Biol_rep_1_(11)
Colum name in Counts_smallRNA.txt: HG_si27_11

value: renal podocyte


title: S1 CONTROL

description: Library name: S1

value: Pancreas

value: beta cells


title: PC3_203_2，ATAC

description: Library name: PC3_203_2，ATAC

value: overexpress LHX2-003


title: Podocyte cell_HG_scr_Rep_1_(11)

description:
Library name: Sample_2_HG_scr_Biol_rep_1_(11)
Colum name in Counts_smallRNA.txt: HG_scr_11


title: HighFidelity_nuclear_amplicon_9

description:
Library name: 24A
Amplicon-seq of cDNA amplified from primers 24A_F and 24A_R

value: chronic myeloid leukemia

value: WT


title: Podocyte cell_NG_siRab27A_Rep_1_(11)

description:
Library name: Sample_3_NG_si27_Biol_rep_1_(11)
Colum name in Counts_smallRNA.txt: NG_si27_11

value: Rab27A transfected


title: PC3_203_1，ATAC

description: Library name: PC3_203_1，ATAC


title: MLEC_CSE-KO_Cre-pos_2_ATAC

city: Mannheim

first: Fredy

middle: Andres

last: Delgado Lagos

address: Ludolf-Krehl- Straße 13-17

department: Vascular Dysfunction

institute: UMM, Heidelberg University

description: Library name: Sample 5

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 99) with STAR 2.7.3a (Dobin et al., STAR: ultrafast universal RNA-seq aligner). Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq). Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded. Remaining peaks were unified to represent a common set of regions for all samples. The raw count matrix was normalized with DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 99. Contrasts were created with DESeq2 based on the normalized count peak matrix with all size factors set to one. Peaks were classified as significantly differential at average count > 10 and -1 < log2FC > 1.
Assembly: mm10
Supplementary files format and content: tab-seperated txt file

source_name: lung endothelial cells

extract_protocol:
50.000 cells were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina).
Cells were pelleted and resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and was incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform (Illumina) using P3 flowcell with 2x 38bp paired-end setup.

value: lung endothelial cells


title: Podocyte cell_NG_scr_Rep_1_(11)

description:
Library name: Sample_1_NG_scr_Biol_rep_1_(11)
Colum name in Counts_smallRNA.txt: NG_scr_11

value: normal glucose


title: HighFidelity_nuclear_amplicon_8

description:
Library name: 23B
Amplicon-seq of cDNA amplified from primers 23B_F and 23B_R


title: HighFidelity_nuclear_amplicon_7

description:
Library name: 22B
Amplicon-seq of cDNA amplified from primers 22B_F and 22B_R


title: MLEC_CSE-KO_Cre-pos_3_ATAC

description: Library name: Sample 6


title: LLC, Dot1l_sgRNA#2_rep1, RNA-seq

first: Siyuan

last: Xu

address: No.131, Dongan Road, Shanghai

institute: Fudan Unversity

description: Library name: LLC_Dot1l_sgRNA#2_rep1

data_processing:
RNA-seq reads within FASTQ files were trimmed using trim_galore with default parameters.
Trimmed reads were aligned to the human reference genome hg38 or mm10 using HISAT2 version 2.2.1 with default parameters
SAMtools version 1.9 was applied to transform SAM into the BAM format.
FeautureCounts version 0.6.1 was used to calculate the read counts of each transcript. TEtranscripts version 2.2.3 was applied to calculate the read counts of transposable elements.
DESeq2 package version 1.36.0 was used for differential expression analysis.
Assembly: hg38 or mm10
Supplementary files format and content: Raw counts for each sample

source_name: LLC

growth_protocol: HuH-7, Hepa1-6, Hep53.4, and LLC cell lines were maintained in 89% DMEM medium , 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured at 37°C with 5% (v/v) of CO2.

extract_protocol:
RNA was harvested using RNeasy Mini Kit from QIAGEN. About 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacture’s protocol.

treatment_protocol: HuH-7 cells were treated with EPZ-5676 for 7 days.

value: LLC

value: Lung carcinoma


title: PC3_201_1，ATAC

description: Library name: PC3_201_1，ATAC

value: overexpress LHX2-001


title: LLC, Dot1l_sgRNA#1_rep2, RNA-seq

description: Library name: LLC_Dot1l_sgRNA#1_rep2


title: LLC, Dot1l_sgRNA#2_rep2, RNA-seq

description: Library name: LLC_Dot1l_sgRNA#2_rep2


title: LLC, Dot1l_sgRNA#1_rep1, RNA-seq

description: Library name: LLC_Dot1l_sgRNA#1_rep1


title: PC3_201_2，ATAC

description: Library name: PC3_201_2，ATAC


title: PC3_Vec_2，ATAC

description: Library name: PC3_Vec_2，ATAC


title: HighFidelity_nuclear_amplicon_6

description:
Library name: 21A
Amplicon-seq of cDNA amplified from primers 21A_F and 21A_R


title: MLEC_CSE-KO_Cre-pos_1_ATAC

description: Library name: Sample 4


title: LLC, sgNeg2_rep1, RNA-seq

description: Library name: LLC_Dot1l_Neg2_rep1


title: HighFidelity_nuclear_amplicon_5

description:
Library name: 20A
Amplicon-seq of cDNA amplified from primers 20A_F and 20A_R


title: HighFidelity_nuclear_amplicon_4

description:
Library name: 19A
Amplicon-seq of cDNA amplified from primers 19A_F and 19A_R


title: Lung tissue scRNA-seq from con3(Rat No.3 from Blank control group)

first: Boyue

address: No.11 BeiSanHuanDongLu, ChaoYang District

institute: Dongzhimen Hospital

description:
Library name: con3
10x Genomics

data_processing:
Raw FASTQ files were processed using Cell Ranger (v4.3.0) for alignment, barcode processing, and UMI quantification against the GRCh38 human reference genome.
Assembly: Rnor 6.0
Supplementary files format and content: 10x Genomics filtered gene-barcode matrices containing UMI counts for each gene in each cell (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).

organism: Rattus norvegicus

source_name: Lung tissue

extract_protocol:
Fresh rat lung tissues were minced into approximately 1 mm³ fragments, washed three times with ice-cold PBS, and enzymatically dissociated using the MACS Tumor Dissociation Kit for 30 min at room temperature. The resulting cell suspension was filtered through 70 um and 40 um cell strainers, followed by centrifugation (4°C, 300 × g, 10 min). After removal of the supernatant, red blood cells were lysed using red blood cell lysis buffer for 10 min at 4 °C. The remaining cells were washed twice with DPBS containing 0.04% BSA. Cell suspensions were adjusted to a final concentration of 1,000 cells/uL and samples with cell viability > 80% were considered qualified for subsequent analysis.
Single-cell RNA libraries were constructed using DNBelab C Series High-Throughput Single-Cell RNA Library Prep Kit (V3.0). Cells were encapsulated with barcoded beads using DNBelab C-TaiM 4 droplet generation system, followed by reverse transcription at 42°C for 90 min. After magnetic bead-based purification of reverse transcription products, cDNA was PCR-amplified and purified. Sequencing libraries were constructed through cDNA fragmentation, end repair, adapter ligation, and indexing PCR, then sequenced on MGISEQ-2000RS platform with paired-end sequencing.

value: Lung tissue

value: Cells in lung tissue


title: Lung tissue scRNA-seq from con2(Rat No.2 from Blank control group)

description:
Library name: con2
10x Genomics


title: Hep53.4, Dot1l_sgRNA#2_rep2, RNA-seq

description: Library name: Hep53.4_Dot1l_sgRNA#2_rep2

value: Hepatocellular carcinoma


title: MLEC_WT_Cre-neg_2_ATAC

description: Library name: Sample 2


title: HighFidelity_nuclear_amplicon_3

description:
Library name: 18A
Amplicon-seq of cDNA amplified from primers 18A_F and 18A_R


title: Hep53.4, Dot1l_sgRNA#2_rep1, RNA-seq

description: Library name: Hep53.4_Dot1l_sgRNA#2_rep1


title: HighFidelity_nuclear_amplicon_2

description:
Library name: 16B
Amplicon-seq of cDNA amplified from primers 16B_F and 16B_R


title: MLEC_WT_Cre-neg_3_ATAC

description: Library name: Sample 3


title: MLEC_WT_Cre-neg_1_ATAC

description: Library name: Sample 1


title: Lung tissue scRNA-seq from con1(Rat No.1 from Blank control group)

description:
Library name: con1
10x Genomics


title: HighFidelity_nuclear_amplicon_1

description:
Library name: 15B
Amplicon-seq of cDNA amplified from primers 15B_F and 15B_R


title: Hep53.4, Dot1l_sgRNA#1_rep2, RNA-seq

description: Library name: Hep53.4_Dot1l_sgRNA#1_rep2


title: LLC, sgNeg2_rep2, RNA-seq

description: Library name: LLC_Dot1l_Neg2_rep2


title: MLEC_CSE-KO_Cre-pos_H3K9ac_3

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner). Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq). Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 109.
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix
Library strategy: CUT&Run

extract_protocol:
For Cut’n’Run library preparation, precipitated DNA samples was purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).
10ul of DNA per sample was used as input for SMARTer® ThruPLEX® DNA-Seq Kit following manufacture’s protocol (Takara Bio). Sequencing was performed on NextSeq2000 platform (Illumina) using P3 flowcell with 2x 36bp paired-end setup.


title: Lung tissue scRNA-seq from mod3(Rat No.3 from ARDS model group)

description:
Library name: mod3
10x Genomics


title: MLEC_CSE-KO_Cre-pos_H3K9ac_1

description: Library name: Sample 4


title: LowFidelity_nuclear_amplicon_7

description:
Library name: 7A
Amplicon-seq of cDNA amplified from primers 7A_F and 7A_R


title: MLEC_CSE-KO_Cre-pos_H3K9ac_2

description: Library name: Sample 5


title: Lung tissue scRNA-seq from mod2(Rat No.2 from ARDS model group)

description:
Library name: mod2
10x Genomics


title: Hep53.4, sgNeg2_rep2, RNA-seq

description: Library name: Hep53.4_Dot1l_Neg2_rep2


title: LowFidelity_nuclear_amplicon_6

description:
Library name: 6A
Amplicon-seq of cDNA amplified from primers 6A_F and 6A_R


title: Lung tissue scRNA-seq from mod1(Rat No.1 from ARDS model group)

description:
Library name: mod1
10x Genomics


title: PC3_Vec_1，ATAC

description: Library name: PC3_Vec_1，ATAC

value: prostate cancer

value: Human prostate cancer epithelial cells


title: Hep53.4, Dot1l_sgRNA#1_rep1, RNA-seq

description: Library name: Hep53.4_Dot1l_sgRNA#1_rep1


title: LowFidelity_nuclear_amplicon_5

description:
Library name: 5A
Amplicon-seq of cDNA amplified from primers 5A_F and 5A_R


title: Hepa1-6, Dot1l_sgRNA#2_rep2, RNA-seq

description: Library name: Hepa1-6_Dot1l_sgRNA#2_rep2


title: Hep53.4, sgNeg2_rep1, RNA-seq

description: Library name: Hep53.4_Dot1l_Neg2_rep1


title: MLEC_WT_Cre-neg_H3K9ac_2

description: Library name: Sample 2


title: LowFidelity_nuclear_amplicon_4

description:
Library name: 4A
Amplicon-seq of cDNA amplified from primers 4A_F and 4A_R


title: Lung tissue scRNA-seq from cas2(Rat No.2 from YQHYJDF group)

description:
Library name: cas2
10x Genomics


title: MLEC_WT_Cre-neg_H3K9ac_1

description: Library name: Sample 1


title: MLEC_WT_Cre-neg_H3K9ac_3

description: Library name: Sample 3


title: LowFidelity_nuclear_amplicon_3

description:
Library name: 3A
Amplicon-seq of cDNA amplified from primers 3A_F and 3A_R


title: Lung tissue scRNA-seq from cas1(Rat No.1 from YQHYJDF group)

description:
Library name: cas1
10x Genomics


title: Hepa1-6, Dot1l_sgRNA#1_rep2, RNA-seq

description: Library name: Hepa1-6_Dot1l_sgRNA#1_rep2


title: MLEC_CSE-KO_Cre-pos_3_RNA

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 99) with STAR 2.7.3a (Dobin et al., STAR: ultrafast universal RNA-seq aligner). Alignments were filtered to remove: duplicates with Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: tab-seperated txt file

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 300ng of total RNA was used as input for VaZyme_VAHTS Universal Stranded mRNA-seq - V6 (Vazyme). Sequencing was performed on the NextSeq500 platform (Illumina) using P3 flowcell with 75bp single-end setup.

value: CSE-KO


title: Hepa1-6, Dot1l_sgRNA#2_rep1, RNA-seq

description: Library name: Hepa1-6_Dot1l_sgRNA#2_rep1


title: Hepa1-6, Dot1l_sgRNA#1_rep1, RNA-seq

description: Library name: Hepa1-6_Dot1l_sgRNA#1_rep1


title: MLEC_CSE-KO_Cre-pos_2_RNA

description: Library name: Sample 5


title: Hepa1-6, sgNeg2_rep2, RNA-seq

description: Library name: Hepa1-6_Dot1l_Neg2_rep2


title: MLEC_CSE-KO_Cre-pos_1_RNA

description: Library name: Sample 4


title: MIF_3_Dex_Rep1

city: Athens

first: Zhihua

last: Hua

state: Ohio

address: 22 Richland Ave

department: Department of Environmental and Plant Biology

institute: Ohio University

description: Library name: Sample 5

data_processing:
Adapter and low-quality sequences were removed from the raw FASTQ sequencing data using fastp (phred>=20, minimum length=30; Chen et al., Bioinformatics (2018)34:i884–i890).  The resulting valid sequences were aligned to the Arabidopsis thaliana Col-0 reference genome (TAIR10; www.arabidopsis.org) using STAR (Dobin et al., Bioinformatics (2013)29:15-21) to identify accepted hits of each locus.  HTSeq was then used to calculate an absolute expression level (counts) of each locus based on the accepted hits (Anders et al., Bioinformatics (2014)31:166-169).
Assembly: Arabidopsis thaliana reference genome TAIR10
Supplementary files format and content: Gene expression count tables generated from HTSeq are provided in CSV format, containing gene identifiers and corresponding raw read counts for each RNA-Seq sample.

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Seeds harvested at the same time from plants grown under an identical environmental condition were for RNA-Seq analysis.  Dried seeds were vapor-phase surface sterilized for 3 to 5 h in the presence of 100 ml NaOCl (bleach) supplemented with 3 ml HCl.  Seeds were stratified in water at 4°C for three days in dark before being planted on 1/2 MS medium plus 1% (w/v) sucrose supplemented with 10 μM dexamethasone.  Seedlings were grown horizontally for 7 days under a long-day photoperiod (16-h white light (120 μmol m-2 s-1)/8-h darkness at 21°C and 19°C, respectively).

extract_protocol:
Total RNA was isolated from whole seedlings using the NucleoSpin RNA Plus kit (Macherey-Nagel) according to the manufacturer’s instructions.
Poly(A)-selected mRNA-Seq libraries were constructed and sequenced on an Illumina NovaSeq 6000 platform by Novogene following their standard Illumina library preparation and sequencing protocols.

treatment_protocol: Seedlings were grown on medium supplemented with 10 μM dexamethasone for inducible expression during the 7-day growth period.

value: whole seedlings

value: Transgenic plants

value: Dex (10 μM)


title: prt-16hyt1-1, 7-d-old continuous light grown seedlings, Biological replicate 4

city: Nottingham

first: Michael

last: Holdsworth

address: University of Nottingham, University Park

country: United Kingdom

institute: University of Nottingham

data_processing:
Sequence reads were trimmed for adaptor sequences and low quality sequences using default parameters of skewer v0.2.2 Trimmed sequenes were mapped to Arabidopsis thaliana genome (TAIR10) using default parameters of hisat2 v2.1.0 Only uniquely mapped were used for further downstream analysis. Read counts for each gene are calculated using featureCounts v1.6.0. Supplementary files format and content: rawcounts.tx
Assembly: TAIR10
Supplementary files format and content: The file is tab seperated and following are the column names pattern.
Supplementary files format and content: <GeneId><GeneName><SampleRep1><SampleRep2><SampleRep3><SampleRep4>

source_name: 7-d-old total seedlings

growth_protocol: Seeds were sterilised and grown on 1/2 MS agar plates without sucrose for 7 days in continuous light conditions

extract_protocol:
Total RNA was extracted using RNAeasy minikit and sent for RNA sequencing
RNA was extracted using RNeasy plant mini kit Qiagen as per manufacturer’s instructions. RNA was sent to Deep-Seq Next Generation Sequencing Facility (University of Nottingham) for further analysis. RNA concentrations were measured using the Qubit Fluorometer and the Qubit RNA BR Assay Kit (ThermoFisher Scientific; Q10211) and RNA integrity was assessed using the Agilent 4200 TapeStation and the Agilent RNA Screentape (Agilent; 5067-5576). Poly(A) selection was performed on 1 μg of total RNA, using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490L). Indexed sequencing libraries were then prepared using the NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (NEB; E7420) and NEBNext Multiplex Oligos for Illumina, Index Primer Sets 2, 3 and 4 (NEBNext; E7500S, E7710S and E7730S). PolyA selection, cDNA synthesis and library generation were carried out using the Biomek 4000 Automated Laboratory Workstation (Beckman Coulter). Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (ThermoFisher Scientific; Q32854). Library fragment-length distributions were analysed using the Agilent TapeStation 4200 and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent; 5067-5584 and 5067-5585). Libraries were pooled in equimolar amounts and final library quantification performed using the KAPA Library Quantification Kit for Illumina (Roche; KK4824). The library pool was sequenced on the Illumina NextSeq500 using two NextSeq500 High Output 150 cycle kits

treatment_protocol: 7 days old seedlings of mutant lines were harvested untreated

value: 7-d-old total seedlings


title: MIF_3_Dex_Rep2

description: Library name: Sample 6


title: MIF_1_Dex_Rep2

description: Library name: Sample 4


title: MLEC_WT_Cre-neg_3_RNA

description: Library name: Sample 3

value: WT


title: Lung tissue scRNA-seq from cas3(Rat No.3 from YQHYJDF group)

description:
Library name: cas3
10x Genomics


title: LowFidelity_nuclear_amplicon_2

description:
Library name: 2A
Amplicon-seq of cDNA amplified from primers 2A_F and 2A_R

value: chronic myeloid leukemia


title: MLEC_WT_Cre-neg_2_RNA

description: Library name: Sample 2

value: lung endothelial cells


title: KP cells, Day 7

city: New York

first: Jin Suk

last: Park

address: 417 East 68th St

institute: MSKCC

description:
Library name: Sample 2
10x Genomics

data_processing:
For scRNA-seq, all processing of the resulting data was performed using the Scanpy package. For quality control, cells with less than 200 genes detected and genes expressed by less than 3 cells were filtered out. Based on the library distribution, cells with less than 1,000, greater than 5% mitochondrial RNA content or less than 5% ribosomal RNA content were excluded from analysis. Housekeeping genes MALAT1 and GM42418 were also removed, with 9,949 cells from freshly isolated KP tumor and 11,064 cells for day-7 KP tumoroids passing the filters.
Assembly: hg38, Mouse mm10
Supplementary files format and content: Matrix files, ProcessedPeaks

source_name: Lung

extract_protocol:
To isolate primary LUAD cells, KP mice were euthanized and perfused with PBS through the left ventricle of the heart. Micro-dissected tumor tissues using a sterile scalpel were further dissociated by a mixture of dispase II (0.6 U/mL; D4693, Sigma Aldrich), collagenase type IV (0.166 U/mL; 17104019, Thermo Fisher Scientific), and DNase I (10 U/mL; 07900, STEMCELL Technologies) in Dulbecco’s Modified Eagle’s Medium (DMEM) containing gentamicin (2 μg/mL; 15710064, Gibco) at 37°C for 30-60 min. The cell suspension was filtered through 70 mm EASYstrainer (Greiner Bio-one) and spun at 300 g for 5 min at 4°C. The supernatant was aspirated, and red blood cells were lysed using RBC Lysis Buffer (eBioscience). Cells were then washed with PBS and spun at 300 g for 5 min at 4°C, re-suspended in ice-cold Fluorescence-Activated Cell Sorting (FACS) buffer [2% fetal bovine serum (FBS) in phosphate-buffered saline solution (PBS)], and strained through a 35 mm filter. Sorted GFP+ LUAD cells were seeded in a mixture of 50% Matrigel (Corning, Cat #: CB-40230C) and 50% LUAD media (Advanced DMEM/F12; 12634-010, Gibco), 2% of FBS, 2mM GlutaMAX (35050061, Gibco), 10 mM HEPES, 2 μg/mL of gentamicin, and 100 units/mL of penicillin/streptomycin).
Single-cell RNA-seq was performed on 10x Genomics Chromium platform. The scRNA-seq libraries were prepared based on the manufacturer’s protocol for 3’ end reading. The individual transcriptomes of encapsulated cells were barcoded during RT step and resulting cDNA purified with DynaBeads followed by amplification per manual guidelines. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to the sequencing adapters and indexed by PCR. The indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher). The raw sequencing data were then demultiplexed and aligned to the mouse genome using 10X CellRanger pipeline. This generated an output matrix of mRNA counts per cell for every gene. We used the filtered matrix for all downstream analysis. For ChIP-seq, For library construction and sequencing, DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. The KAPA HTP Library Preparation Kit (Kapa Biosystems, Cat #: KK8234) was used to prepare Illumina sequencing libraries with 0.02-5 ng of input DNA and 8-14 cycles of PCR.

value: Lung

value: KP cells

value: Lung adenocarcinoma


title: LowFidelity_nuclear_amplicon_1

description:
Library name: 1A
Amplicon-seq of cDNA amplified from primers 1A_F and 1A_R


title: Hepa1-6, sgNeg2_rep1, RNA-seq

description: Library name: Hepa1-6_Dot1l_Neg2_rep1


title: WT_Dex_Rep2

description: Library name: Sample 2

value: Wild Type


title: prt6-1hyt1-1, 7-d-old continuous light grown seedlings, Biological replicate 2


title: KP cells, Day 0

description:
Library name: Sample 1
10x Genomics


title: MLEC_WT_Cre-neg_1_RNA

description: Library name: Sample 1


title: prt6-1hyt1-1, 7-d-old continuous light grown seedlings, Biological replicate 1


title: prt6-1hyt1-1, 7-d-old continuous light grown seedlings, Biological replicate 3


title: WT_Dex_Rep1

description: Library name: Sample 1


title: LID_1065733_PID_10499

status: Public on Apr 15 2026

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

description:
Library name: LID_1065733_PID_10499
dog_id:17149979 precision cohort year 1. dog age at collection:3.29762719598449

data_processing:
bcl2fastq
Supplementary files format and content: sumamrized to species level

organism: Canis lupus familiaris

source_name: feces metagenome

extract_protocol:
For each fecal sample, a lysate was prepared using the following procedure: The fecal collection tube was thawed and vortexed to homogenize the fecal sample in the storage solution. A small aliquot (∼200 µL) of the fecal slurry was removed using a fresh 1 mL serological pipette and transferred to a 2 mL tube pre-filled with garnet shards and a 6 mm zirconium bead (Benchmark Scientific, D1033-30G). To this tube, 365 µL of PowerBead solution (Qiagen, #12955-4-bs) and 20 µL of 20% sodium dodecyl sulfate (SDS) were added. The tubes were subjected to bead-beating using a TissueLyzer instrument for 45 seconds at 30 cycles per second. The resulting fecal homogenate was treated twice with Protein Precipitation Solution (MP Biomedical, product no. 116560203) to remove proteins.
metagenomic library prep doi: dx.doi.org/10.17504/protocols.io.rm7vzbob4vx1/v1

value: feces metagenome


title: LID_1065734_PID_10499

description:
Library name: LID_1065734_PID_10499
dog_id:17135534 precision cohort year 1. dog age at collection:2.46229751311887


title: MIF_1_Dex_Rep1

description: Library name: Sample 3


title: LID_1066330_PID_10498

description:
Library name: LID_1066330_PID_10498
dog_id:15225484 precision cohort year 1. dog age at collection:12.4203741729409


title: LID_1066333_PID_10498

description:
Library name: LID_1066333_PID_10498
dog_id:15157462 precision cohort year 1. dog age at collection:8.89938398357289


title: LID_1066329_PID_10498

description:
Library name: LID_1066329_PID_10498
dog_id:13726981 precision cohort year 1. dog age at collection:4.09519735341091


title: LID_1066332_PID_10498

description:
Library name: LID_1066332_PID_10498
dog_id:15431494 precision cohort year 1. dog age at collection:4.47835196592897


title: LID_1065730_PID_10499

description:
Library name: LID_1065730_PID_10499
dog_id:17150165 precision cohort year 1. dog age at collection:5.96477869039471


title: LID_1065731_PID_10499

description:
Library name: LID_1065731_PID_10499
dog_id:17168393 precision cohort year 1. dog age at collection:5.49960073009354


title: LID_1065732_PID_10499

description:
Library name: LID_1065732_PID_10499
dog_id:17159126 precision cohort year 1. dog age at collection:4.21486424823181


title: LID_1065725_PID_10499

description:
Library name: LID_1065725_PID_10499
dog_id:17174123 precision cohort year 1. dog age at collection:2.24349760438056


title: LID_1065726_PID_10499

description:
Library name: LID_1065726_PID_10499
dog_id:17155007 precision cohort year 1. dog age at collection:6.0497376226329


title: LID_1065724_PID_10499

description:
Library name: LID_1065724_PID_10499
dog_id:17143493 precision cohort year 1. dog age at collection:1.04728116206556


title: LID_1065727_PID_10499

description:
Library name: LID_1065727_PID_10499
dog_id:17155100 precision cohort year 1. dog age at collection:6.6815537303217


title: LID_1065729_PID_10499

description:
Library name: LID_1065729_PID_10499
dog_id:17227784 precision cohort year 1. dog age at collection:2.06544223895353


title: LID_1065722_PID_10499

description:
Library name: LID_1065722_PID_10499
dog_id:17155193 precision cohort year 1. dog age at collection:2.8844398813598


title: LID_1065728_PID_10499

description:
Library name: LID_1065728_PID_10499
dog_id:17150072 precision cohort year 1. dog age at collection:13.1345919841813


title: LID_1065717_PID_10499

description:
Library name: LID_1065717_PID_10499
dog_id:17224130 precision cohort year 1. dog age at collection:5.06613620807666


title: LID_1065718_PID_10499

description:
Library name: LID_1065718_PID_10499
dog_id:17183768 precision cohort year 1. dog age at collection:5.72048254620123


title: LID_1065713_PID_10499

description:
Library name: LID_1065713_PID_10499
dog_id:16325281 precision cohort year 1. dog age at collection:4.37634040611453


title: LID_1065714_PID_10499

description:
Library name: LID_1065714_PID_10499
dog_id:16316689 precision cohort year 1. dog age at collection:1.62451517225645


title: LID_1065712_PID_10499

description:
Library name: LID_1065712_PID_10499
dog_id:16319377 precision cohort year 1. dog age at collection:4.70741691383375


title: LID_1065720_PID_10499

description:
Library name: LID_1065720_PID_10499
dog_id:17234477 precision cohort year 1. dog age at collection:1.15140885238421


title: LID_1065708_PID_10499

description:
Library name: LID_1065708_PID_10499
dog_id:16333606 precision cohort year 1. dog age at collection:4.71024412502852


title: LID_1065711_PID_10499

description:
Library name: LID_1065711_PID_10499
dog_id:16333531 precision cohort year 1. dog age at collection:1.20893223819302


title: LID_1065709_PID_10499

description:
Library name: LID_1065709_PID_10499
dog_id:16292506 precision cohort year 1. dog age at collection:6.86265115217887


title: LID_1065719_PID_10499

description:
Library name: LID_1065719_PID_10499
dog_id:17149886 precision cohort year 1. dog age at collection:4.2971138489619


title: LID_1065706_PID_10499

description:
Library name: LID_1065706_PID_10499
dog_id:16330006 precision cohort year 1. dog age at collection:2.87862194843714


title: LID_1065703_PID_10499

description:
Library name: LID_1065703_PID_10499
dog_id:16345531 precision cohort year 1. dog age at collection:9.38116967069739


title: LID_1065704_PID_10499

description:
Library name: LID_1065704_PID_10499
dog_id:16330192 precision cohort year 1. dog age at collection:9.37440109514031


title: LID_1065701_PID_10499

description:
Library name: LID_1065701_PID_10499
dog_id:16319443 precision cohort year 1. dog age at collection:9.70702144649783


title: LID_1065716_PID_10499

description:
Library name: LID_1065716_PID_10499
dog_id:17231693 precision cohort year 1. dog age at collection:6.81850330823637


title: LID_1065694_PID_10499

description:
Library name: LID_1065694_PID_10499
dog_id:16412914 precision cohort year 1. dog age at collection:6.98305954825462


title: LID_1065705_PID_10499

description:
Library name: LID_1065705_PID_10499
dog_id:16330099 precision cohort year 1. dog age at collection:4.29195185945699


title: LID_1065702_PID_10499

description:
Library name: LID_1065702_PID_10499
dog_id:16321336 precision cohort year 1. dog age at collection:4.03661875427789


title: LID_1065693_PID_10499

description:
Library name: LID_1065693_PID_10499
dog_id:16399105 precision cohort year 1. dog age at collection:1.3921590995513


title: LID_1065689_PID_10499

description:
Library name: LID_1065689_PID_10499
dog_id:16393561 precision cohort year 1. dog age at collection:2.39393680127766


title: LID_1065686_PID_10499

description:
Library name: LID_1065686_PID_10499
dog_id:16456045 precision cohort year 1. dog age at collection:2.73345881816108


title: LID_1065687_PID_10499

description:
Library name: LID_1065687_PID_10499
dog_id:16455622 precision cohort year 1. dog age at collection:11.3110027378508


title: LID_1065685_PID_10499

description:
Library name: LID_1065685_PID_10499
dog_id:16393654 precision cohort year 1. dog age at collection:1.0549851699749


title: LID_1065696_PID_10499

description:
Library name: LID_1065696_PID_10499
dog_id:16358230 precision cohort year 1. dog age at collection:3.21533006312267


title: LID_1065691_PID_10499

description:
Library name: LID_1065691_PID_10499
dog_id:16393468 precision cohort year 1. dog age at collection:8.22553045859001


title: LID_1065692_PID_10499

description:
Library name: LID_1065692_PID_10499
dog_id:16398058 precision cohort year 1. dog age at collection:2.62651152178873


title: LID_1065688_PID_10499

description:
Library name: LID_1065688_PID_10499
dog_id:16455952 precision cohort year 1. dog age at collection:5.73137881207696


title: LID_1065700_PID_10499

description:
Library name: LID_1065700_PID_10499
dog_id:16350208 precision cohort year 1. dog age at collection:6.5041067761807


title: LID_1065682_PID_10499

description:
Library name: LID_1065682_PID_10499
dog_id:16394305 precision cohort year 1. dog age at collection:3.53562057951175


title: LID_1065683_PID_10499

description:
Library name: LID_1065683_PID_10499
dog_id:16455715 precision cohort year 1. dog age at collection:4.73222298273633


title: LID_1065680_PID_10499

description:
Library name: LID_1065680_PID_10499
dog_id:16456156 precision cohort year 1. dog age at collection:1.56479580196213


title: LID_1065676_PID_10499

description:
Library name: LID_1065676_PID_10499
dog_id:16451062 precision cohort year 1. dog age at collection:4.56793292265572


title: LID_1065684_PID_10499

description:
Library name: LID_1065684_PID_10499
dog_id:16401403 precision cohort year 1. dog age at collection:15.0592250361244


title: LID_1065674_PID_10499

description:
Library name: LID_1065674_PID_10499
dog_id:16483957 precision cohort year 1. dog age at collection:6.66532626055213


title: LID_1065690_PID_10499

description:
Library name: LID_1065690_PID_10499
dog_id:16394212 precision cohort year 1. dog age at collection:5.22478895733516


title: LID_1065663_PID_10499

description:
Library name: LID_1065663_PID_10499
dog_id:16759456 precision cohort year 1. dog age at collection:10.9618982432124


title: LID_1065664_PID_10499

description:
Library name: LID_1065664_PID_10499
dog_id:16718053 precision cohort year 1. dog age at collection:3.36886835500799


title: LID_1065679_PID_10499

description:
Library name: LID_1065679_PID_10499
dog_id:16386139 precision cohort year 1. dog age at collection:4.29766522168986


title: LID_1065650_PID_10499

description:
Library name: LID_1065650_PID_10499
dog_id:16517374 precision cohort year 1. dog age at collection:10.0827059091946


title: LID_1065647_PID_10499

description:
Library name: LID_1065647_PID_10499
dog_id:16659364 precision cohort year 1. dog age at collection:7.93851243440566


title: LID_1065656_PID_10499

description:
Library name: LID_1065656_PID_10499
dog_id:16480774 precision cohort year 1. dog age at collection:3.74623545516769


title: LID_1065657_PID_10499

description:
Library name: LID_1065657_PID_10499
dog_id:16480669 precision cohort year 1. dog age at collection:6.83195490151342


title: LID_1065648_PID_10499

description:
Library name: LID_1065648_PID_10499
dog_id:16497988 precision cohort year 1. dog age at collection:13.2472621492129


title: LID_1065649_PID_10499

description:
Library name: LID_1065649_PID_10499
dog_id:16533415 precision cohort year 1. dog age at collection:6.16946155601186


title: LID_1065677_PID_10499

description:
Library name: LID_1065677_PID_10499
dog_id:16393318 precision cohort year 1. dog age at collection:8.89373716632443


title: LID_1065660_PID_10499

description:
Library name: LID_1065660_PID_10499
dog_id:16759198 precision cohort year 1. dog age at collection:7.20730663928816


title: LID_1065645_PID_10499

description:
Library name: LID_1065645_PID_10499
dog_id:16659658 precision cohort year 1. dog age at collection:10.5994334169899


title: LID_1065644_PID_10499

description:
Library name: LID_1065644_PID_10499
dog_id:16701250 precision cohort year 1. dog age at collection:16.3952772073922


title: LID_1065646_PID_10499

description:
Library name: LID_1065646_PID_10499
dog_id:16642726 precision cohort year 1. dog age at collection:3.26557152635181


title: LID_1065652_PID_10499

description:
Library name: LID_1065652_PID_10499
dog_id:16533511 precision cohort year 1. dog age at collection:7.42069739143661


title: LID_1065639_PID_10499

description:
Library name: LID_1065639_PID_10499
dog_id:16718185 precision cohort year 1. dog age at collection:3.28648566430907


title: LID_1065643_PID_10499

description:
Library name: LID_1065643_PID_10499
dog_id:16675744 precision cohort year 1. dog age at collection:2.69267624914442


title: LID_1065641_PID_10499

description:
Library name: LID_1065641_PID_10499
dog_id:16659457 precision cohort year 1. dog age at collection:8.43440565822496


title: LID_111986_PID_10500

description:
Library name: LID_111986_PID_10500
dog_id:17864249 precision cohort year 1. dog age at collection:6.09844855122063


title: LID_1065654_PID_10499

description:
Library name: LID_1065654_PID_10499
dog_id:16485742 precision cohort year 1. dog age at collection:7.99874515172256


title: LID_111981_PID_10500

description:
Library name: LID_111981_PID_10500
dog_id:17834588 precision cohort year 1. dog age at collection:3.33327629477527


title: LID_111983_PID_10500

description:
Library name: LID_111983_PID_10500
dog_id:17879378 precision cohort year 1. dog age at collection:11.2703627652293


title: LID_111980_PID_10500

description:
Library name: LID_111980_PID_10500
dog_id:17834714 precision cohort year 1. dog age at collection:3.2565594341775


title: LID_111977_PID_10500

description:
Library name: LID_111977_PID_10500
dog_id:17828180 precision cohort year 1. dog age at collection:3.75233858088068


title: LID_111979_PID_10500

description:
Library name: LID_111979_PID_10500
dog_id:17818991 precision cohort year 1. dog age at collection:5.49931553730322


title: LID_1065642_PID_10499

description:
Library name: LID_1065642_PID_10499
dog_id:16650841 precision cohort year 1. dog age at collection:1.76967830253251


title: LID_111976_PID_10500

description:
Library name: LID_111976_PID_10500
dog_id:17879240 precision cohort year 1. dog age at collection:4.54363449691992


title: LID_111992_PID_10500

description:
Library name: LID_111992_PID_10500
dog_id:17832338 precision cohort year 1. dog age at collection:2.33333333333333


title: LID_1065640_PID_10499

description:
Library name: LID_1065640_PID_10499
dog_id:16654321 precision cohort year 1. dog age at collection:8.55133470225873


title: LID_111982_PID_10500

description:
Library name: LID_111982_PID_10500
dog_id:17819084 precision cohort year 1. dog age at collection:7.41516465130428


title: LID_111974_PID_10500

description:
Library name: LID_111974_PID_10500
dog_id:17864699 precision cohort year 1. dog age at collection:2.18075519050878


title: LID_111963_PID_10500

description:
Library name: LID_111963_PID_10500
dog_id:17537783 precision cohort year 1. dog age at collection:11.7796030116359


title: LID_111943_PID_10500

description:
Library name: LID_111943_PID_10500
dog_id:17477177 precision cohort year 1. dog age at collection:2.18896874287018


title: LID_111952_PID_10500

description:
Library name: LID_111952_PID_10500
dog_id:17324120 precision cohort year 1. dog age at collection:3.17157198266028


title: LID_111935_PID_10500

description:
Library name: LID_111935_PID_10500
dog_id:17334410 precision cohort year 1. dog age at collection:4.00718685831622


title: LID_111975_PID_10500

description:
Library name: LID_111975_PID_10500
dog_id:17876027 precision cohort year 1. dog age at collection:2.34747889573352


title: LID_111937_PID_10500

description:
Library name: LID_111937_PID_10500
dog_id:17521772 precision cohort year 1. dog age at collection:1.26893680127766


title: LID_111954_PID_10500

description:
Library name: LID_111954_PID_10500
dog_id:17643074 precision cohort year 1. dog age at collection:5.96149897330595


title: LID_111964_PID_10500

description:
Library name: LID_111964_PID_10500
dog_id:17600072 precision cohort year 1. dog age at collection:5.62514259639516


title: LID_111944_PID_10500

description:
Library name: LID_111944_PID_10500
dog_id:17505263 precision cohort year 1. dog age at collection:9.52081336983801


title: LID_111927_PID_10500

description:
Library name: LID_111927_PID_10500
dog_id:17019707 precision cohort year 1. dog age at collection:6.8616244581337


title: LID_111924_PID_10500

description:
Library name: LID_111924_PID_10500
dog_id:17081183 precision cohort year 1. dog age at collection:5.52347136664385


title: LID_111931_PID_10500

description:
Library name: LID_111931_PID_10500
dog_id:17021852 precision cohort year 1. dog age at collection:2.27626625598905


title: LID_111932_PID_10500

description:
Library name: LID_111932_PID_10500
dog_id:17021741 precision cohort year 1. dog age at collection:5.860141455624


title: LID_111923_PID_10500

description:
Library name: LID_111923_PID_10500
dog_id:17029964 precision cohort year 1. dog age at collection:3.86173853524983


title: LID_111920_PID_10500

description:
Library name: LID_111920_PID_10500
dog_id:17098454 precision cohort year 1. dog age at collection:10.5175393566051


title: LID_111907_PID_10500

description:
Library name: LID_111907_PID_10500
dog_id:17223944 precision cohort year 1. dog age at collection:7.05991900524755


title: LID_111917_PID_10500

description:
Library name: LID_111917_PID_10500
dog_id:17076131 precision cohort year 1. dog age at collection:6.86504677161761


title: LID_111916_PID_10500

description:
Library name: LID_111916_PID_10500
dog_id:17114480 precision cohort year 1. dog age at collection:1.36778462240475


title: LID_111906_PID_10500

description:
Library name: LID_111906_PID_10500
dog_id:17275976 precision cohort year 1. dog age at collection:2.90654232261008


title: LID_111919_PID_10500

description:
Library name: LID_111919_PID_10500
dog_id:17098547 precision cohort year 1. dog age at collection:3.12023728040155


title: LID_111283_PID_10500

description:
Library name: LID_111283_PID_10500
dog_id:16728355 precision cohort year 1. dog age at collection:6.36744239105635


title: LID_111282_PID_10500

description:
Library name: LID_111282_PID_10500
dog_id:16726996 precision cohort year 1. dog age at collection:1.20049053159936


title: LID_111900_PID_10500

description:
Library name: LID_111900_PID_10500
dog_id:17254559 precision cohort year 1. dog age at collection:0.734827743554643


title: LID_111279_PID_10500

description:
Library name: LID_111279_PID_10500
dog_id:16622320 precision cohort year 1. dog age at collection:3.01808122290669


title: LID_111926_PID_10500

description:
Library name: LID_111926_PID_10500
dog_id:17029868 precision cohort year 1. dog age at collection:7.44256217202829


title: LID_111281_PID_10500

description:
Library name: LID_111281_PID_10500
dog_id:16669375 precision cohort year 1. dog age at collection:9.69066088675945


title: LID_111276_PID_10500

description:
Library name: LID_111276_PID_10500
dog_id:16709986 precision cohort year 1. dog age at collection:3.95197353410906


title: LID_111280_PID_10500

description:
Library name: LID_111280_PID_10500
dog_id:16668595 precision cohort year 1. dog age at collection:1.93685831622177


title: LID_111273_PID_10500

description:
Library name: LID_111273_PID_10500
dog_id:16035112 precision cohort year 1. dog age at collection:9.80264658909423


title: LID_111270_PID_10500

description:
Library name: LID_111270_PID_10500
dog_id:15984169 precision cohort year 1. dog age at collection:3.62143509012092


title: LID_111269_PID_10500

description:
Library name: LID_111269_PID_10500
dog_id:16036330 precision cohort year 1. dog age at collection:9.72079625827059


title: LID_111262_PID_10499

description:
Library name: LID_111262_PID_10499
dog_id:16023097 precision cohort year 1. dog age at collection:6.38300821355236


title: LID_111278_PID_10500

description:
Library name: LID_111278_PID_10500
dog_id:16673392 precision cohort year 1. dog age at collection:9.1868012776637


title: LID_111271_PID_10500

description:
Library name: LID_111271_PID_10500
dog_id:15984106 precision cohort year 1. dog age at collection:5.28553502167465


title: LID_111260_PID_10499

description:
Library name: LID_111260_PID_10499
dog_id:15999211 precision cohort year 1. dog age at collection:9.27138945927447


title: LID_111263_PID_10500

description:
Library name: LID_111263_PID_10500
dog_id:16027219 precision cohort year 1. dog age at collection:4.71846718381626


title: LID_111264_PID_10500

description:
Library name: LID_111264_PID_10500
dog_id:15974539 precision cohort year 1. dog age at collection:11.368925393566


title: LID_111258_PID_10499

description:
Library name: LID_111258_PID_10499
dog_id:16083733 precision cohort year 1. dog age at collection:4.23119628869116


title: LID_111268_PID_10500

description:
Library name: LID_111268_PID_10500
dog_id:15962722 precision cohort year 1. dog age at collection:2.94461556011864


title: LID_111261_PID_10499

description:
Library name: LID_111261_PID_10499
dog_id:16005943 precision cohort year 1. dog age at collection:2.88398357289528


title: LID_111257_PID_10499

description:
Library name: LID_111257_PID_10499
dog_id:16079779 precision cohort year 1. dog age at collection:7.06471975055137


title: LID_111266_PID_10500

description:
Library name: LID_111266_PID_10500
dog_id:15983974 precision cohort year 1. dog age at collection:10.2299794661191


title: LID_111224_PID_10499

description:
Library name: LID_111224_PID_10499
dog_id:16178209 precision cohort year 1. dog age at collection:3.33909232641266


title: LID_111255_PID_10499

description:
Library name: LID_111255_PID_10499
dog_id:15962629 precision cohort year 1. dog age at collection:3.28507871321013


title: LID_111209_PID_10499

description:
Library name: LID_111209_PID_10499
dog_id:16872980 precision cohort year 1. dog age at collection:7.63700661647274


title: LID_111256_PID_10499

description:
Library name: LID_111256_PID_10499
dog_id:16036393 precision cohort year 1. dog age at collection:1.55110654802647


title: LID_111213_PID_10499

description:
Library name: LID_111213_PID_10499
dog_id:16863260 precision cohort year 1. dog age at collection:1.56991406190585


title: LID_111254_PID_10499

description:
Library name: LID_111254_PID_10499
dog_id:16035175 precision cohort year 1. dog age at collection:8.88852764468781


title: LID_111272_PID_10500

description:
Library name: LID_111272_PID_10500
dog_id:16003159 precision cohort year 1. dog age at collection:6.21328618145867


title: LID_111208_PID_10499

description:
Library name: LID_111208_PID_10499
dog_id:16873076 precision cohort year 1. dog age at collection:4.15195071868583


title: LID_111211_PID_10499

description:
Library name: LID_111211_PID_10499
dog_id:16882196 precision cohort year 1. dog age at collection:13.1540611453342


title: LID_111206_PID_10498

description:
Library name: LID_111206_PID_10498
dog_id:16882067 precision cohort year 1. dog age at collection:3.90788272872462


title: LID_111201_PID_10498

description:
Library name: LID_111201_PID_10498
dog_id:16895168 precision cohort year 1. dog age at collection:4.32454939539128