title: AR_rep2

description:
Library name: Sample 14
Column name in raw_counts.txt: RA_rep2
Correspondence to fastq: DM_02


title: LID_1072676_PID_10571

status: Public on Apr 15 2026

type: SRA

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

country: USA

institute: Arizona State University

description:
Library name: LID_1072676_PID_10571
dog_id:17997926 precision cohort year 1. dog age at collection:5.95870408396076

library_source: genomic

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

molecule: genomic DNA

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

tag: tissue

value: feces metagenome

tag: batch


title: AM_rep1

city: Chicago

first: Francisco

last: Silva

state: Illinois

address: 420 E Superior street #9

department: Microbiology-Immunology

institute: Northwestern University

description:
Library name: Sample 10
Column name in raw_counts.txt: AM_rep1
Correspondence to fastq: DR_01

library_source: transcriptomic

data_processing:
Assembly: Filtered reads were aligned to the human reference genome UCSC hg38
Raw sequencing reads were quality-checked and trimmed to remove adapters and low-quality bases. Reads were aligned to the human reference genome, and gene-level counts were generated. Differential gene expression analysis was performed using standard statistical methods in R with an adjusted p-value < 0.05 and |log2 fold-change| ≥ 1.
Supplementary files format and content: Tab-delimited text files containing gene-level raw counts for all samples (raw_counts.txt) and corresponding sample metadata (Column_data.txt), including sample identifiers, conditions, and biological replicates.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from intestinal epithelial cells following 110 minutes of infection with Vibrio vulnificus strains or PBS control. Cells were lysed and RNA was isolated using a standard column-based RNA purification method according to the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA using a poly(A) selection protocol to enrich for mRNA, followed by fragmentation, cDNA synthesis, adapter ligation, and PCR amplification according to the manufacturer’s instructions.

tag: cell line

tag: cell type

value: Human Intestinal epithelial cells (IECs)

tag: genotype

value: Wild type

tag: treatment

value: Vibrio vulnificus intoxication

tag: group

value: AM


title: LID_1072684_PID_10571

description:
Library name: LID_1072684_PID_10571
dog_id:18123374 precision cohort year 1. dog age at collection:1.48773671001597


title: DAR_rep3

description:
Library name: Sample 9
Column name in raw_counts.txt: DAR_rep3
Correspondence to fastq: MCF_03

value: DAR


title: LID_1072679_PID_10571

description:
Library name: LID_1072679_PID_10571
dog_id:18013115 precision cohort year 1. dog age at collection:10.7908966461328


title: LID_1072719_PID_10569

description:
Library name: LID_1072719_PID_10569
dog_id:18103112 precision cohort year 1. dog age at collection:6.40209331508099


title: DAR_rep1

description:
Library name: Sample 7
Column name in raw_counts.txt: DAR_rep1
Correspondence to fastq: MCF_01


title: LID_1072718_PID_10569

description:
Library name: LID_1072718_PID_10569
dog_id:18041618 precision cohort year 1. dog age at collection:8.97313483915127


title: DRM_rep2

description:
Library name: Sample 5
Column name in raw_counts.txt: DRM_rep2
Correspondence to fastq: ABH_02

value: DRM


title: DRM_rep3

description:
Library name: Sample 6
Column name in raw_counts.txt: DRM_rep3
Correspondence to fastq: ABH_03


title: DAR_rep2

description:
Library name: Sample 8
Column name in raw_counts.txt: DAR_rep2
Correspondence to fastq: MCF_02


title: DAM_rep3

description:
Library name: Sample 3
Column name in raw_counts.txt: DAM_rep3
Correspondence to fastq: RID_03

value: DAM


title: LID_1072690_PID_10571

description:
Library name: LID_1072690_PID_10571
dog_id:18227999 precision cohort year 1. dog age at collection:3.67285535021675


title: DRM_rep1

description:
Library name: Sample 4
Column name in raw_counts.txt: DRM_rep1
Correspondence to fastq: ABH_01


title: LID_1072691_PID_10571

description:
Library name: LID_1072691_PID_10571
dog_id:18224261 precision cohort year 1. dog age at collection:3.17707620351357


title: LID_1072542_PID_10568

description:
Library name: LID_1072542_PID_10568
dog_id:26493279 precision cohort year 1. dog age at collection:5.02307209673739


title: LID_1072704_PID_10571

description:
Library name: LID_1072704_PID_10571
dog_id:18115676 precision cohort year 1. dog age at collection:7.15788272872462


title: LID_1072687_PID_10571

description:
Library name: LID_1072687_PID_10571
dog_id:18204149 precision cohort year 1. dog age at collection:3.17676249144422


title: LID_1072724_PID_10569

description:
Library name: LID_1072724_PID_10569
dog_id:18270308 precision cohort year 1. dog age at collection:2.26289071412275


title: DAM_rep1

description:
Library name: Sample 1
Column name in raw_counts.txt: DAM_rep1
Correspondence to fastq: RID_01


title: LID_1072697_PID_10571

description:
Library name: LID_1072697_PID_10571
dog_id:18144173 precision cohort year 1. dog age at collection:3.24537987679671


title: human fetal cells, d7TIC, hepaCAM+/MHCII-, rep4

city: Atlanta

first: Emily

middle: Jane

last: Hill

state: Georgia

address: 615 Michael Street

department: School of Medicine

institute: Emory University

description: Library name: Sample 112

data_processing:
Bulk sequencing of 40 million paired-end reads per sample was completed using the Illumina-based platform. FASTQ files were evaluated for quality using FastQC and then mapped to the human genome (hg19), using the Spliced Transcripts Alignment to a Reference (STAR) aligner with the paired-end option. The featureCounts package was used to generate a raw counts data matrix from mapped reads. After generating the filtered, raw counts data matrices, we used DESeq2 to normalize the matrices and perform differential gene expression-based statistics. scRNAseq: Fastq sequencing files were processed through CellRanger.
Assembly: hg19
Supplementary files format and content: Bulk RNAseq: tab-delimited/comma-delimited text file that includes raw counts for each sample and .bam files.
Supplementary files format and content: scRNAseq: matrix, barcode, and features files for each sample

source_name: human fetal cells

growth_protocol: Human cortical organoids (hCOs): Following 3D formation, hCOs were treated daily in neural induction media (DMEM/F12, KSR, NEAA, Glutamax, Pen/Strep, Beta-mercaptoethanol) supplemented with Dorsomorphin (Sigma, Cat. 142  P5499-25MG, 5 μM) and SB-431542 (Selleck Chemicals, Cat. S1067, 10 μM) for 6 days.  Following this treatment, hCOs were treated daily with neural media supplemented with EGF (R&D Systems, Cat. 236-EG-01M, 20 ng/mL) and FGF2 (R&D Systems, Cat. 233-FB-01M, 20 ng/mL) for 10 days, and every other day for days 16-24. At day 25, hCOs were treated every other day with neural media supplemented with BDNF (PeproTech, Cat. 450-02- 1mg, 20 ng/mL) and NT-3 (R&D Systems, Cat. 267-N3-005/CF, 20 ng/mL) to promote differentiation of progenitors. From day 43 onwards, hCOs were fed every 3 days with neural media only. hCOs were cultured in Neurobasal-A media supplemented with B27-A, 1% penicillin-streptomycin, and 1% GlutaMAX. hCOs were incubated in 10cm low-adherence cell culture dish at 37°C and 5% CO2.

extract_protocol:
Bulk RNAseq: RNA was extracted from the cells using a RNeasy Micro Kit (Qiagen, 74004) following the manufacturer’s instructions. scRNAseq: hCOs were dissociated and cells were prepared for library creation according to the 10X Genomics Chromium Next-GEM Single Cell 3' kit manufacturer's protocol (10X Genomics, 1000268). scRNAseq: hCOs were dissociated and cells were prepared for library creation according to the 10X Genomics Chromium Next-GEM Single Cell 3' kit manufacturer's protocol (10X Genomics, 1000268).
Bulk RNAseq: The SMART-Seq® v4 PLUS Kit (Takara Bio) was used following the manufacturer's instructions. scRNAseq: Libraries were created according to the 10X Genomics Chromium Next Gem Single Cell 3' kit manufacturer's protocol.

treatment_protocol: hCOs were treated with either control Neurobasal-A media or Neurobasal-A supplemented with TNF-α (30ng/mL, Cell Signaling Technology, 16769S), IL-1α (3ng/mL,Sigma-Aldrich, I2778), and C1q (400ng/mL, EMD Millipore, 204876).

value: human fetal cells

value: astrocyte

value: TIC


title: LID_1072726_PID_10569

description:
Library name: LID_1072726_PID_10569
dog_id:18257975 precision cohort year 1. dog age at collection:9.34822039698836


title: LID_1072707_PID_10571

description:
Library name: LID_1072707_PID_10571
dog_id:18115769 precision cohort year 1. dog age at collection:1.23899155829341


title: human fetal cells, d2IFNy, hepaCAM+/MHCII+, rep5

description: Library name: Sample 111

value: IFN-y


title: human fetal cells, d2IFNy, hepaCAM+/MHCII-, rep5

description: Library name: Sample 110


title: human fetal cells, d7TIC, hepaCAM+/MHCII+, rep3

description: Library name: Sample 113


title: LID_1072706_PID_10571

description:
Library name: LID_1072706_PID_10571
dog_id:18109334 precision cohort year 1. dog age at collection:1.23853524982888


title: LID_1072698_PID_10571

description:
Library name: LID_1072698_PID_10571
dog_id:18132161 precision cohort year 1. dog age at collection:2.82432124115902


title: DAM_rep2

description:
Library name: Sample 2
Column name in raw_counts.txt: DAM_rep2
Correspondence to fastq: RID_02


title: LID_1072695_PID_10571

description:
Library name: LID_1072695_PID_10571
dog_id:18236777 precision cohort year 1. dog age at collection:3.59326754886303


title: human fetal cells, d2IFNy, hepaCAM+/MHCII+, rep4

description: Library name: Sample 108


title: LID_1072727_PID_10569

description:
Library name: LID_1072727_PID_10569
dog_id:18257876 precision cohort year 1. dog age at collection:5.26340406114533


title: human fetal cells, d7con, hepaCAM+/MHCII-, rep5

description: Library name: Sample 109

value: control


title: LID_1072714_PID_10571

description:
Library name: LID_1072714_PID_10571
dog_id:18129386 precision cohort year 1. dog age at collection:3.16056354095368


title: human fetal cells, d7con, hepaCAM+/MHCII-, rep4

description: Library name: Sample 106


title: human fetal cells, d2IFNy, hepaCAM+/MHCII-, rep4

description: Library name: Sample 107


title: human fetal cells, d2IFNy, hepaCAM+/MHCII+, rep3

description: Library name: Sample 105


title: LID_1072729_PID_10569

description:
Library name: LID_1072729_PID_10569
dog_id:18290036 precision cohort year 1. dog age at collection:6.26368925393566


title: LID_1072722_PID_10571

description:
Library name: LID_1072722_PID_10571
dog_id:18115583 precision cohort year 1. dog age at collection:9.73745151722564


title: human fetal cells, d7TIC, hepaCAM+/MHCII-, rep3

description: Library name: Sample 102


title: human fetal cells, d2IFNy, hepaCAM+/MHCII-, rep3

description: Library name: Sample 104


title: LID_1072740_PID_10571

description:
Library name: LID_1072740_PID_10571
dog_id:18236669 precision cohort year 1. dog age at collection:5.42208532968287


title: LID_1072737_PID_10571

description:
Library name: LID_1072737_PID_10571
dog_id:18243572 precision cohort year 1. dog age at collection:1.26169290440338


title: LID_1072734_PID_10571

description:
Library name: LID_1072734_PID_10571
dog_id:18254063 precision cohort year 1. dog age at collection:10.5118925393566


title: human fetal cells, d7TIC, hepaCAM+/MHCII+, rep1

description: Library name: Sample 97


title: LID_1072744_PID_10571

description:
Library name: LID_1072744_PID_10571
dog_id:13727074 precision cohort year 1. dog age at collection:17.0939520115598


title: LID_1072741_PID_10571

description:
Library name: LID_1072741_PID_10571
dog_id:18243479 precision cohort year 1. dog age at collection:3.24587421096661


title: human fetal cells, d7TIC, hepaCAM+/MHCII-, rep1

description: Library name: Sample 96


title: human fetal cells, d2IFNy, hepaCAM+/MHCII+, rep2

description: Library name: Sample 100


title: LID_1072735_PID_10569

description:
Library name: LID_1072735_PID_10569
dog_id:18253793 precision cohort year 1. dog age at collection:9.84375237660659


title: LID_1072728_PID_10569

description:
Library name: LID_1072728_PID_10569
dog_id:18283805 precision cohort year 1. dog age at collection:6.84850558977869


title: LID_1072746_PID_10571

description:
Library name: LID_1072746_PID_10571
dog_id:13802224 precision cohort year 1. dog age at collection:2.10666210358202


title: human fetal cells, d2IFNy, hepaCAM+/MHCII-, rep1

description: Library name: Sample 94


title: human fetal cells, d7TIC, hepaCAM+/MHCII+, rep2

description: Library name: Sample 101


title: human fetal cells, d2IFNy, hepaCAM+/MHCII-, rep2

description: Library name: Sample 99


title: LID_1072738_PID_10569

description:
Library name: LID_1072738_PID_10569
dog_id:18258137 precision cohort year 1. dog age at collection:2.84593885466575


title: human fetal cells, d7con, hepaCAM+/MHCII-, rep1

description: Library name: Sample 93


title: hCO, d31tic, d55 withdrawal, rep4

description: Library name: Sample 92

source_name: human cortical organoid

value: human cortical organoid

value: TIC withdrawal


title: human fetal cells, d7con, hepaCAM+/MHCII-, rep2

description: Library name: Sample 98


title: human fetal cells, d2IFNy, hepaCAM+/MHCII+, rep1

description: Library name: Sample 95


title: LID_1072742_PID_10571

description:
Library name: LID_1072742_PID_10571
dog_id:18264287 precision cohort year 1. dog age at collection:0.677513499125409


title: LID_1072755_PID_10571

description:
Library name: LID_1072755_PID_10571
dog_id:13770661 precision cohort year 1. dog age at collection:3.35278348163358


title: human fetal cells, d7con, hepaCAM+/MHCII-, rep3

description: Library name: Sample 103


title: hCO, d31con, d55 withdrawal, rep3

description: Library name: Sample 89

value: control withdrawal


title: LID_1072750_PID_10571

description:
Library name: LID_1072750_PID_10571
dog_id:13482361 precision cohort year 1. dog age at collection:6.39128450832763


title: LID_1072736_PID_10569

description:
Library name: LID_1072736_PID_10569
dog_id:18264224 precision cohort year 1. dog age at collection:4.18189596167009


title: LID_1072761_PID_10571

description:
Library name: LID_1072761_PID_10571
dog_id:21171601 precision cohort year 1. dog age at collection:3.37990531599361


title: hCO, d31tic, d36 withdrawal, rep4

description: Library name: Sample 88


title: LID_1072739_PID_10569

description:
Library name: LID_1072739_PID_10569
dog_id:18241394 precision cohort year 1. dog age at collection:4.84211727127538


title: hCO, d31con, d55 withdrawal, rep4

description: Library name: Sample 90


title: hCO, d31tic, d55 withdrawal, rep3

description: Library name: Sample 91


title: LID_1072745_PID_10569

description:
Library name: LID_1072745_PID_10569
dog_id:13699297 precision cohort year 1. dog age at collection:2.66775039926991


title: LID_1072758_PID_10571

description:
Library name: LID_1072758_PID_10571
dog_id:13816288 precision cohort year 1. dog age at collection:7.86159593885467


title: hCO, d31tic, d36 withdrawal, rep3

description: Library name: Sample 87


title: LID_1072771_PID_10571

description:
Library name: LID_1072771_PID_10571
dog_id:21472357 precision cohort year 1. dog age at collection:3.34131873146247


title: LID_1072563_PID_10568

description:
Library name: LID_1072563_PID_10568
dog_id:26661327 precision cohort year 1. dog age at collection:5.41963267168606


title: LID_1072747_PID_10569

description:
Library name: LID_1072747_PID_10569
dog_id:13563940 precision cohort year 1. dog age at collection:13.7999087383071


title: hCO, d31con, d36 withdrawal, rep3

description: Library name: Sample 85


title: hCO, d31con, d36 withdrawal, rep4

description: Library name: Sample 86


title: LID_1072749_PID_10569

description:
Library name: LID_1072749_PID_10569
dog_id:13644619 precision cohort year 1. dog age at collection:5.16467031713438


title: hCO, d31tic, d17 withdrawal, rep4

description: Library name: Sample 84


title: hCO, d31con, d17 withdrawal, rep3

description: Library name: Sample 81


title: hCO, d31con, d17 withdrawal, rep4

description: Library name: Sample 82


title: hCO, d31tic, d17 withdrawal, rep3

description: Library name: Sample 83


title: LID_1072751_PID_10569

description:
Library name: LID_1072751_PID_10569
dog_id:13766875 precision cohort year 1. dog age at collection:2.51174994296144


title: LID_1072752_PID_10569

description:
Library name: LID_1072752_PID_10569
dog_id:13436302 precision cohort year 1. dog age at collection:8.38751996349532


title: hCO, d31tic, d0 withdrawal, rep3

description: Library name: Sample 79

value: d31 TIC


title: LID_1072778_PID_10571

description:
Library name: LID_1072778_PID_10571
dog_id:21285793 precision cohort year 1. dog age at collection:10.6489847136664

value: feces metagenome


title: LID_1072782_PID_10571

description:
Library name: LID_1072782_PID_10571
dog_id:21560997 precision cohort year 1. dog age at collection:2.43777093315081


title: hCO, d31con, d0 withdrawal, rep3

description: Library name: Sample 77

value: d31 control


title: hCO, d31con, d0 withdrawal, rep4

description: Library name: Sample 78


title: LID_1072756_PID_10569

description:
Library name: LID_1072756_PID_10569
dog_id:13790419 precision cohort year 1. dog age at collection:11.1030686744239


title: hCO, d31tic, d55 withdrawal, rep2

description: Library name: Sample 76


title: hCO, d31tic, d0 withdrawal, rep4

description: Library name: Sample 80


title: LID_1072565_PID_10568

description:
Library name: LID_1072565_PID_10568
dog_id:26661429 precision cohort year 1. dog age at collection:1.46874287018024


title: hCO, d31tic, d55 withdrawal, rep1

description: Library name: Sample 75


title: LID_1072757_PID_10569

description:
Library name: LID_1072757_PID_10569
dog_id:13612195 precision cohort year 1. dog age at collection:3.90839607574721


title: hCO, d31con, d55 withdrawal, rep2

description: Library name: Sample 74


title: hCO, d31tic, d36 withdrawal, rep2

description: Library name: Sample 72


title: LID_1072790_PID_10571

description:
Library name: LID_1072790_PID_10571
dog_id:21649071 precision cohort year 1. dog age at collection:2.53911894440642


title: LID_1072759_PID_10569

description:
Library name: LID_1072759_PID_10569
dog_id:13766971 precision cohort year 1. dog age at collection:2.51463039014374


title: LID_1072789_PID_10571

description:
Library name: LID_1072789_PID_10571
dog_id:21648978 precision cohort year 1. dog age at collection:5.24446725986767


title: hCO, d31con, d36 withdrawal, rep2

description: Library name: Sample 70


title: LID_1072791_PID_10571

description:
Library name: LID_1072791_PID_10571
dog_id:21669021 precision cohort year 1. dog age at collection:2.70950452505894


title: LID_1072792_PID_10571

description:
Library name: LID_1072792_PID_10571
dog_id:21756783 precision cohort year 1. dog age at collection:1.72319187770933


title: hCO, d31con, d55 withdrawal, rep1

description: Library name: Sample 73


title: LID_1072754_PID_10569

description:
Library name: LID_1072754_PID_10569
dog_id:13721899 precision cohort year 1. dog age at collection:9.09403756939691


title: hCO, d31con, d36 withdrawal, rep1

description: Library name: Sample 69


title: LID_1072581_PID_10568

description:
Library name: LID_1072581_PID_10568
dog_id:26769480 precision cohort year 1. dog age at collection:3.23197581565138


title: hCO, d31tic, d17 withdrawal, rep2

description: Library name: Sample 68


title: 16day,Torin2,mRNA-seq,rep3

city: weifang

first: yongqi

last: liu

state: shandong

address: 699 Binhu Road, Xiashan District

country: China

institute: Peking University Institute of Advanced Agricultural Sciences

description:
Library name: Torin2_T16d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.

data_processing:
Raw data QC: FastQC v0.11.9 for read quality assessment.
Alignment: Reads were mapped to the tomato genome (SL4.0) using HISAT2 v2.2.1.
Quantification: Gene expression counts generated with featureCounts v2.0.1.
Differential analysis: DESeq2 v1.30.1 for normalization and identification of DEGs (|log₂FC| ≥ 1.0, adjusted p < 0.05).
Assembly: S_lycopersicum_chromosomes.4.00
Supplementary files format and content: gene FPKM and log2 fold-change/p-value matrices for differential expression analysis.

organism: Solanum lycopersicum

source_name: callus

growth_protocol: Plant materials: Sterilized tomato seeds (cv. Micro-Tom) were germinated on 1/2 MS medium in darkness for 3 days, then transferred to long-day conditions (16-h light/8-h dark) at 25°C and 70% humidity.Callus induction: Cotyledons from 6-day-old seedlings were excised and cultured on SIM medium (MS salts, 3% sucrose, 1 mg/L Zeatin, 0.1 mg/L IAA) under 50 µmol m⁻² s⁻¹ light intensity.

extract_protocol:
RNA extraction: Total RNA was extracted using RNAprep Pure Plant Kit (TIANGEN) for tomato samples or TRIzol (Invitrogen) for human cell controls. RNA quality was assessed using Qubit 4.
Library preparation: mRNA-seq libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme). Libraries were sequenced on DNBSEQ-T7 or MGISEQ-2000RS platforms with paired-end 150 bp reads.

treatment_protocol: Wounding and systemin treatment: Cotyledons were placed on SIM medium (control) or SIM supplemented with 100 nM systemin peptide.Chemical treatments: Torin2 (1 µM) was applied to callus tissues at specific time points.

value: callus


title: 16day,Torin2,mRNA-seq,rep2

description:
Library name: Torin2_T16d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d31tic, d36 withdrawal, rep1

description: Library name: Sample 71


title: hCO, d31con, d17 withdrawal, rep1

description: Library name: Sample 65


title: LID_1072766_PID_10569

description:
Library name: LID_1072766_PID_10569
dog_id:21264289 precision cohort year 1. dog age at collection:3.31394022359115


title: hCO, d31con, d17 withdrawal, rep2

description: Library name: Sample 66


title: hCO, d31tic, d0 withdrawal, rep2

description: Library name: Sample 64


title: 14day,Torin2,mRNA-seq,rep3

description:
Library name: Torin2_T14d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 16day,Torin2,mRNA-seq,rep1

description:
Library name: Torin2_T16d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 14day,Torin2,mRNA-seq,rep2

description:
Library name: Torin2_T14d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d31con, d0 withdrawal, rep2

description: Library name: Sample 62


title: 14day,Torin2,mRNA-seq,rep1

description:
Library name: Torin2_T14d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d31tic, d17 withdrawal, rep1

description: Library name: Sample 67


title: hCO, d31tic, d0 withdrawal, rep1

description: Library name: Sample 63


title: 12day,Torin2,mRNA-seq,rep3

description:
Library name: Torin2_T12d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 12day,Torin2,mRNA-seq,rep2

description:
Library name: Torin2_T12d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con d21withdrawal, rep4

description: Library name: Sample 58


title: hCO, d7tic d21withdrawal, rep4

description: Library name: Sample 60


title: 12day,Torin2,mRNA-seq,rep1

description:
Library name: Torin2_T12d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 10day,Torin2,mRNA-seq,rep1

description:
Library name: Torin2_T10d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d31con, d0 withdrawal, rep1

description: Library name: Sample 61


title: hCO, d7con d21withdrawal, rep3

description: Library name: Sample 57


title: 10day,Torin2,mRNA-seq,rep3

description:
Library name: Torin2_T10d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic d21withdrawal , rep3

description: Library name: Sample 59


title: 10day,Torin2,mRNA-seq,rep2

description:
Library name: Torin2_T10d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic d14withdrawal , rep3

description: Library name: Sample 55


title: 9day,Torin2,mRNA-seq,rep3

description:
Library name: Torin2_T9d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic d14withdrawal, rep4

description: Library name: Sample 56


title: 9day,Torin2,mRNA-seq,rep2

description:
Library name: Torin2_T9d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 9day,Torin2,mRNA-seq,rep1

description:
Library name: Torin2_T9d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con d14withdrawal, rep4

description: Library name: Sample 54


title: hCO, d7con d14withdrawal, rep3

description: Library name: Sample 53


title: 16day,mock,mRNA-seq,rep3

description:
Library name: Mock_M16d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic d7withdrawal, rep4

description: Library name: Sample 52


title: 16day,mock,mRNA-seq,rep1

description:
Library name: Mock_M16d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic d7withdrawal , rep3

description: Library name: Sample 51


title: 14day,mock,mRNA-seq,rep3

description:
Library name: Mock_M14d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 16day,mock,mRNA-seq,rep2

description:
Library name: Mock_M16d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con d7withdrawal, rep3

description: Library name: Sample 49


title: hCO, d7tic withdrawal, rep4

description: Library name: Sample 48

value: d7 TIC


title: 14day,mock,mRNA-seq,rep2

description:
Library name: Mock_M14d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 14day,mock,mRNA-seq,rep1

description:
Library name: Mock_M14d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic withdrawal, rep3

description: Library name: Sample 47


title: hCO, d7con withdrawal, rep4

description: Library name: Sample 46

value: d7 control


title: hCO, d7con d7withdrawal, rep4

description: Library name: Sample 50


title: 12day,mock,mRNA-seq,rep2

description:
Library name: Mock_M12d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 12day,mock,mRNA-seq,rep3

description:
Library name: Mock_M12d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con withdrawal, rep3

description: Library name: Sample 45


title: hCO, d7tic d21withdrawal , rep1

description: Library name: Sample 43


title: hCO, d7tic d21withdrawal, rep2

description: Library name: Sample 44


title: 12day,mock,mRNA-seq,rep1

description:
Library name: Mock_M12d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 10day,mock,mRNA-seq,rep1

description:
Library name: Mock_M10d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con d21withdrawal, rep1

description: Library name: Sample 41


title: 9day,mock,mRNA-seq,rep3

description:
Library name: Mock_M9d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 9day,mock,mRNA-seq,rep2

description:
Library name: Mock_M9d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 10day,mock,mRNA-seq,rep2

description:
Library name: Mock_M10d_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 16day,pi-2,mRNA-seq,rep3

description:
Library name: T16dpi-2_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con d14withdrawal, rep2

description: Library name: Sample 38


title: 9day,mock,mRNA-seq,rep1

description:
Library name: Mock_M9d_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con d7withdrawal, rep2

description: Library name: Sample 34


title: 16day,pi-2,mRNA-seq,rep2

description:
Library name: T16dpi-2_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 16day,DCL2,mRNA-seq,rep2

description:
Library name: T16ddcl2_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 16day,DCL2,mRNA-seq,rep3

description:
Library name: T16ddcl2_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 10day,mock,mRNA-seq,rep3

description:
Library name: Mock_M10d_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7con d21withdrawal, rep2

description: Library name: Sample 42


title: hCO, d7tic d7withdrawal, rep2

description: Library name: Sample 36


title: 16day,pi-2,mRNA-seq,rep1

description:
Library name: T16dpi-2_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic d7withdrawal , rep1

description: Library name: Sample 35


title: hCO, d7tic d14withdrawal, rep2

description: Library name: Sample 40


title: hCO, d7con d7withdrawal, rep1

description: Library name: Sample 33


title: EPFL8-mutant,mRNA-seq,rep2

description:
Library name: epfl8-mutant_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic withdrawal, rep2

description: Library name: Sample 32


title: EPFL8-mutant,mRNA-seq,rep1

description:
Library name: epfl8-mutant_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: EPFL8,mRNA-seq,rep3

description:
Library name: EPFL8_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: EPFL8-mutant,mRNA-seq,rep3

description:
Library name: epfl8-mutant_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d84tic, rep5

description: Library name: Sample 28


title: hCO, d7con d14withdrawal, rep1

description: Library name: Sample 37


title: hCO, d7tic d14withdrawal , rep1

description: Library name: Sample 39


title: hCO, d7con withdrawal, rep2

description: Library name: Sample 30


title: EPFL8,mRNA-seq,rep2

description:
Library name: EPFL8_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d7tic withdrawal, rep1

description: Library name: Sample 31


title: hCO, d7con withdrawal, rep1

description: Library name: Sample 29


title: hCO, d84con, rep2

description: Library name: Sample 26


title: 16day,DCL2,mRNA-seq,rep1

description:
Library name: T16ddcl2_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d84tic, rep4

description: Library name: Sample 27


title: CK,mRNA-seq,rep2

description:
Library name: CK_rep2
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d31tic, rep4

description: Library name: Sample 23


title: hCO, d31con, rep2

description: Library name: Sample 22


title: hCO, d31tic, rep5

description: Library name: Sample 24


title: CK,mRNA-seq,rep3

description:
Library name: CK_rep3
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: hCO, d84con, rep1

description: Library name: Sample 25


title: 10x scRNA-seq of RSI hindlimb

city: KunMing

first: Xue

last: Lv

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology, CAS

library_source: transcriptomic single cell

data_processing:
Split-seq data were pre-processed by dropEst 0.8.6, 10x data were pre-processed by cellranger 6.1.1
Assembly: PRJNA1048078
Supplementary files format and content: tab-delimited text file including raw matrix of geneXcell
Supplementary files format and content: tab-delimited text file including gene names, cell barcodes and counts matrix.

organism: Rhinolophus sinicus

source_name: limb

extract_protocol:
Each sample was homogenized using Dounce homogenizers (Wheaton) with a loose pestle for 10 rounds followed by 20 rounds with a tight pestle.  The resulting homogenate was processed to obtain a uniform nuclear solution.  Subsequently, the nuclear extract was filtered through a 40 μm cell strainer (Corning) into 1.5 ml tubes, which were then centrifuged to isolate the nuclei.
The purified nuclei were then diluted to 1×106 nuclei/ml after quantification using a hemocytometer.  The nuclei were evenly distributed among 48 wells of a 96-well plate, with each well containing 9,000 ~ 12,000 nuclei.  Subsequently, random hexamer and anchored poly(dT)15 barcoded reverse transcription (RT) primers were added to each of the 48 wells, respectively.  The cells were then combined and split twice.  Following this, the second- and third-round barcodes were attached.
16 libraries were generated and subjected to sequencing on the Illumina platform to produce 150 bp pair-end reads.

value: limb


title: CK,mRNA-seq,rep1

description:
Library name: CK_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: 10x scRNA-seq of RSI forelimb


title: EPFL8,mRNA-seq,rep1

description:
Library name: EPFL8_rep1
Total RNA was extracted from the samples, and qualified RNA samples were used to construct cDNA libraries, which were then subjected to high-throughput sequencing.


title: scRNA-seq of Rhinolophus sinicus-random


title: hCO, d31con, rep1

description: Library name: Sample 21


title: hCO, d7tic, rep4

description: Library name: Sample 19


title: hCO, d7tic, rep5

description: Library name: Sample 20


title: hCO, d1tic, rep5

description: Library name: Sample 16


title: scRNA-seq of Rhinolophus sinicus-dT


title: hCO, d7con, rep2

description: Library name: Sample 18


title: LID_1067268_PID_10530

description:
Library name: LID_1067268_PID_10530
dog_id:19370913 precision cohort year 1. dog age at collection:3.25940185565442


title: LID_1067879_PID_10530

description:
Library name: LID_1067879_PID_10530
dog_id:19519551 precision cohort year 1. dog age at collection:7.03855806525211


title: LID_1067240_PID_10530

description:
Library name: LID_1067240_PID_10530
dog_id:17728184 precision cohort year 1. dog age at collection:2.06513803331052


title: LID_1067859_PID_10530

description:
Library name: LID_1067859_PID_10530
dog_id:19273425 precision cohort year 1. dog age at collection:2.81034679443304


title: hCO, d1tic, rep4

description: Library name: Sample 15


title: hCO, d7con, rep1

description: Library name: Sample 17


title: MFS1_VGLL3_3

city: Stockholm

first: Mireia

last: Cruz De los Santos

address: Karolinska NKS J6:20

department: Oncology Pathology

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 21
column name in gene_count.txt and gene_fpkm.txt: MFS1_YAP1_3

data_processing:
Raw FASTQ files were processed with fastp to remove adapter sequences, reads containing poly-N, and low-quality reads. Quality metrics including Q20, Q30, and GC content were calculated. All downstream analyses were conducted using clean, high-quality reads.
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.0.5), selected for its splice-aware alignment capabilities. Read counts per gene were generated using featureCounts (v1.5.0-p3), and expression levels were calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: gene_count.txt (the readcount list with the annotation of each gene), samples can be identified by "title" column
Supplementary files format and content: gene_fpkm.txt (the FPKM list with the annotation of each gene), samples can be identified by "title" column.

source_name: Sarcoma ex vivo tumor spheroids

growth_protocol: Patient-derived sarcoma cells were collected from surgically excised tumor samples at Karolinska Hospital (Solna, Sweden) under approved ethical permits (2013/1979-31 and 2022-05409-01). Tumor tissue was cut into approximately 2 mm fragments and dissociated using the Tumor Dissociation Kit (Miltenyi, 130-095-929) together with the gentleMACS Octo Dissociator (Miltenyi, 130-096-427). Tumor cells were then enriched using the human Tumor Cell Isolation Kit (Miltenyi, 130-108-339), following the manufacturer’s instructions.Negatively selected sarcoma cells were cultured in DMEM supplemented with Glutamax-I (Gibco, 61965-026), 1% penicillin/streptomycin (Gibco, 15140-122), 10% heat-inactivated FBS (Gibco, A5256701), 1× Sodium Pyruvate (Gibco, 11360-039), and 1× Primocin (InvivoGen, NC9392943). For the stable knock down production from patient-derived cell lines,  lentiviral particles were produced in HEK293T cells by transfection with Lipofectamine 3000 (Invitrogen, L3000001), using third-generation packaging plasmids (Addgene #12253, #12251, and #8454) together with either scrambled shRNA control (SHC016, Sigma), shRNA targeting YAP#1 (Addgene #42540), shVGLL3#1 (Vector Builder, VB231101-1341xmh). Following transfection, lentivirus-containing supernatants were collected and mixed at a 1:1 ratio with DMEM supplemented with 10% FBS, 1× Sodium Pyruvate, and 5 μg/mL Polybrene (Sigma, TR-1003-G) to transduce patient-derived cells. Cells were incubated overnight and subsequently selected with 2 μg/mL puromycin (Gibco, A1113803) prior to use in downstream experiments. For spheroid generation, patient-derived cells were harvested and transferred into spheroid medium consisting of DMEM/F-12 (1:1) (Gibco, 31330-038), 1% penicillin/streptomycin, 1× Glutamax (Gibco, 35050-061), and 20% heat-inactivated FBS. Approximately 5,000–10,000 cells per well were seeded in Nunclon Sphera 96-well U-bottom plates (Thermo Fisher Scientific, 174929). An additional 100 µL per well of cold spheroid medium containing 4% Geltrex (Gibco, A14132-02) was then added. The cultures were incubated for three days at 37°C in a humidified 5% CO₂ environment to allow spheroid formation.

extract_protocol:
After treatment, a minimum of 24 spheroids were collected for each condition and transferred into Eppendorf tubes. They were rinsed twice with 1× PBS (Gibco, 14190-144) and then centrifuged at 500 g for 4 minutes. RNA extraction was performed by lysing the spheroids using the PureLink RNA Mini Kit (Invitrogen, 12183018A), following the manufacturer’s protocol, along with on-column DNase treatment using the PureLink DNase kit (Invitrogen, 12185010). The concentration and purity of the isolated RNA were assessed based on absorbance readings at 260/280 nm using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies).
Total RNA samples were submitted to NovoGene for Human mRNA Sequencing. Library preparation and sequencing were carried out by NovoGene using their standard mRNA-seq workflow. Briefly, polyadenylated mRNA was enriched from total RNA using oligo(dT)-attached magnetic beads and then fragmented. First-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand synthesis to generate double-stranded cDNA. Libraries were constructed through end repair, A-tailing, adapter ligation, PCR amplification, and purification. Final libraries underwent quality assessment at NovoGene prior to sequencing by Qubit and real-time PCR for quantification and bioanalyzer size distribution detection.
Quantified libraries were pooled and Sequencing was performed by NovoGene on an Illumina NovaSeq X Plus platform using paired-end 150 bp (PE150) reads.

treatment_protocol: Once the spheroids were formed, the medium was replaced with 200 µL of spheroid medium containing entinostat (Selleckchem, S1053). Control groups received the same volume of DMSO (Sigma, D2650) to match the solvent used for the drug treatments. The spheroids were then incubated for 24 hours at 37°C in a humidified environment with 5% CO₂.

value: Sarcoma ex vivo tumor spheroids

value: Myxofibrosarcoma

value: DMSO


title: LID_1067882_PID_10530

description:
Library name: LID_1067882_PID_10530
dog_id:19490541 precision cohort year 1. dog age at collection:18.0327971708875


title: LID_1067872_PID_10530

description:
Library name: LID_1067872_PID_10530
dog_id:19548776 precision cohort year 1. dog age at collection:3.03547798311659


title: LID_1067896_PID_10530

description:
Library name: LID_1067896_PID_10530
dog_id:19649129 precision cohort year 1. dog age at collection:1.97769792379649


title: MFS1_VGLL3_2

description:
Library name: Sample 20
column name in gene_count.txt and gene_fpkm.txt: MFS1_YAP1_2


title: MFS1_VGLL3_1

description:
Library name: Sample 19
column name in gene_count.txt and gene_fpkm.txt: MFS1_YAP1_1


title: LID_1067889_PID_10530

description:
Library name: LID_1067889_PID_10530
dog_id:19613249 precision cohort year 1. dog age at collection:9.46883793444368


title: LID_1067918_PID_10530

description:
Library name: LID_1067918_PID_10530
dog_id:19907747 precision cohort year 1. dog age at collection:5.0014830025097


title: MFS1_YAP1_2

description:
Library name: Sample 17
column name in gene_count.txt and gene_fpkm.txt: MFS1_VGLL3_2


title: LID_1067930_PID_10530

description:
Library name: LID_1067930_PID_10530
dog_id:20195045 precision cohort year 1. dog age at collection:6.29277891854894


title: LID_1067925_PID_10530

description:
Library name: LID_1067925_PID_10530
dog_id:19960415 precision cohort year 1. dog age at collection:4.09952277739752


title: LID_1067913_PID_10530

description:
Library name: LID_1067913_PID_10530
dog_id:19886225 precision cohort year 1. dog age at collection:2.747376226329


title: MFS1_SCR_2

description:
Library name: Sample 14
column name in gene_count.txt and gene_fpkm.txt: MFS1_SCR_2

value: shSCR


title: MFS1_YAP1_1

description:
Library name: Sample 16
column name in gene_count.txt and gene_fpkm.txt: MFS1_VGLL3_1


title: MFS1_SCR_1

description:
Library name: Sample 13
column name in gene_count.txt and gene_fpkm.txt: MFS1_SCR_1


title: MFS1_YAP1_3

description:
Library name: Sample 18
column name in gene_count.txt and gene_fpkm.txt: MFS1_VGLL3_3


title: CBOS1_ENT_3

description:
Library name: Sample 12
column name in gene_count.txt and gene_fpkm.txt: CBOS1_ENT_3

value: Chondroblastic osteosarcoma

value: WT

value: Entinostat 1µM


title: LID_1067915_PID_10530

description:
Library name: LID_1067915_PID_10530
dog_id:19908059 precision cohort year 1. dog age at collection:2.83755418663016


title: LID_1067937_PID_10530

description:
Library name: LID_1067937_PID_10530
dog_id:20285042 precision cohort year 1. dog age at collection:2.36208076659822


title: MFS1_SCR_3

description:
Library name: Sample 15
column name in gene_count.txt and gene_fpkm.txt: MFS1_SCR_3


title: LID_1068343_PID_10530

description:
Library name: LID_1068343_PID_10530
dog_id:20327930 precision cohort year 1. dog age at collection:7.56878850102669


title: LID_1068915_PID_10531

description:
Library name: LID_1068915_PID_10531
dog_id:21123697 precision cohort year 1. dog age at collection:7.37719598448551


title: CBOS1_ENT_1

description:
Library name: Sample 10
column name in gene_count.txt and gene_fpkm.txt: CBOS1_ENT_1


title: CBOS1_ENT_2

description:
Library name: Sample 11
column name in gene_count.txt and gene_fpkm.txt: CBOS1_ENT_2


title: LID_1067931_PID_10530

description:
Library name: LID_1067931_PID_10530
dog_id:20195138 precision cohort year 1. dog age at collection:6.46015856719142


title: LID_1068924_PID_10531

description:
Library name: LID_1068924_PID_10531
dog_id:21215386 precision cohort year 1. dog age at collection:3.47826830937714


title: CBOS1_DMSO_2

description:
Library name: Sample 8
column name in gene_count.txt and gene_fpkm.txt: CBOS1_DMSO_2


title: LID_1068356_PID_10530

description:
Library name: LID_1068356_PID_10530
dog_id:20383832 precision cohort year 1. dog age at collection:8.16603924252795


title: CBOS1_DMSO_3

description:
Library name: Sample 9
column name in gene_count.txt and gene_fpkm.txt: CBOS1_DMSO_3


title: CBOS1_DMSO_1

description:
Library name: Sample 7
column name in gene_count.txt and gene_fpkm.txt: CBOS1_DMSO_1


title: MFS1_ENT_3

description:
Library name: Sample 6
column name in gene_count.txt and gene_fpkm.txt: MFS1_ENT_3


title: LID_1068351_PID_10530

description:
Library name: LID_1068351_PID_10530
dog_id:20345177 precision cohort year 1. dog age at collection:1.49334550155905


title: LID_1068349_PID_10530

description:
Library name: LID_1068349_PID_10530
dog_id:20355179 precision cohort year 1. dog age at collection:12.1606395923644


title: LID_1068346_PID_10530

description:
Library name: LID_1068346_PID_10530
dog_id:20355086 precision cohort year 1. dog age at collection:3.41241729409081


title: MFS1_ENT_2

description:
Library name: Sample 5
column name in gene_count.txt and gene_fpkm.txt: MFS1_ENT_2


title: MFS1_ENT_1

description:
Library name: Sample 4
column name in gene_count.txt and gene_fpkm.txt: MFS1_ENT_1


title: LID_1068367_PID_10530

description:
Library name: LID_1068367_PID_10530
dog_id:20423711 precision cohort year 1. dog age at collection:7.04004106776181


title: LID_1068360_PID_10530

description:
Library name: LID_1068360_PID_10530
dog_id:20384018 precision cohort year 1. dog age at collection:2.24642558369458


title: MFS1_DMSO_2

description:
Library name: Sample 2
column name in gene_count.txt and gene_fpkm.txt: MFS1_DMSO_2


title: MFS1_DMSO_3

description:
Library name: Sample 3
column name in gene_count.txt and gene_fpkm.txt: MFS1_DMSO_3


title: LID_1068372_PID_10530

description:
Library name: LID_1068372_PID_10530
dog_id:20469926 precision cohort year 1. dog age at collection:9.84091946155601


title: MFS1_DMSO_1

description:
Library name: Sample 1
column name in gene_count.txt and gene_fpkm.txt: MFS1_DMSO_1


title: THP-1 FOLR2 KO cells replicate 3

city: Indianapolis

first: David

middle: M

last: Aronoff

state: Indiana

address: 545 Barnhill Dr. EH 305

department: Department of Medicine

institute: Indiana University School of Medicine

description: Library name: KO_exp3

data_processing:
Demultiplexing, barcode processing and sequence alignment was performed with Cell Ranger Multi (V4.0.10) pipeline.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated value files and matrix files from Cell Ranger

molecule: cytoplasmic RNA

growth_protocol: THP-1 WT or FOLR2 KO cells were passaged and PMA treated in RPMI +10% FBS +1% antibiotic/antimycotic at 37C with 5% humidity.

extract_protocol:
After harvesting PMA treated cells, cells were cultured in 12-well tissue culture plates in RPMI lacking FBS or A/A for 4 hours at 37C and 5% humidity. Cells were harvested from plates and dead cells were removed with a Miltenyi dead cell removal kit. Cells were then fixed for sequencing using the 10x Genomics FLEX protocol.
Single cell suspension was sequenced on the Illumina NovaSeq X Plus platform.

value: FOLR2 KO

value: Unstimulated


title: LID_1068940_PID_10531

description:
Library name: LID_1068940_PID_10531
dog_id:21450712 precision cohort year 1. dog age at collection:1.3374971480721


title: THP-1 FOLR2 KO cells replicate 2

description: Library name: KO_exp2


title: THP-1 FOLR2 KO cells replicate 4

description: Library name: KO_exp4


title: LID_1068974_PID_10531

description:
Library name: LID_1068974_PID_10531
dog_id:21548892 precision cohort year 1. dog age at collection:2.43767586888737


title: THP-1 WT cells replicate 4

description: Library name: WT_exp4


title: LID_1068966_PID_10531

description:
Library name: LID_1068966_PID_10531
dog_id:21492735 precision cohort year 1. dog age at collection:5.68483344741045


title: LID_1068380_PID_10530

description:
Library name: LID_1068380_PID_10530
dog_id:20528063 precision cohort year 1. dog age at collection:9.35902920374173


title: LID_1068379_PID_10530

description:
Library name: LID_1068379_PID_10530
dog_id:20543144 precision cohort year 1. dog age at collection:1.53441706593657


title: THP-1 WT cells replicate 3

description: Library name: WT_exp3


title: LID_1068976_PID_10531

description:
Library name: LID_1068976_PID_10531
dog_id:21560811 precision cohort year 1. dog age at collection:11.6098847821127


title: THP-1 FOLR2 KO cells replicate 1

description: Library name: KO_exp1


title: LID_1067256_PID_10537

description:
Library name: LID_1067256_PID_10537
dog_id:19383141 precision cohort year 1. dog age at collection:3.09208875199635


title: LID_1068378_PID_10530

description:
Library name: LID_1068378_PID_10530
dog_id:20511344 precision cohort year 1. dog age at collection:8.68594569929272


title: LID_1067933_PID_10537

description:
Library name: LID_1067933_PID_10537
dog_id:20199092 precision cohort year 1. dog age at collection:1.29420488250057


title: THP-1 WT cells replicate 1

description: Library name: WT_exp1


title: stereo,6day

description:
Library name: stereo_6d
Tomato callus Spatial Transcriptomics sequencing data

data_processing:
Alignment: Raw reads were mapped to the tomato genome (SL4.0, ITAG4.1) using BSTMatrix (v2.4) for BMKMANU data, SAW (v8.0) for Stereo-Seq, and CellRanger (v7.0.0) for 10x Genomics.
Clustering: Seurat (v5.1.0) filtered cells (>30 genes/cell), normalized counts, and performed PCA/Harmony-based batch correction. UMAP/Louvain clustering identified cell states.
Trajectory & Networks: Monocle2/3 inferred pseudo-time trajectories. RNA velocity (velocyto/dynamo) and co-expression networks (hdWGCNA) analyzed developmental dynamics.
Spatial Visualization: Custom Python scripts mapped gene expression to cell masks using histological images.
Assembly: S_lycopersicum_chromosomes.4.00
Supplementary files format and content: The clustering analysis results were saved as an RDS file containing clustering information for subsequent analysis and data sharing.
Library strategy: Spatial Transcriptomics

extract_protocol:
Total RNA was extracted from tomato callus tissues using the RNAprep Pure Plant Kit (TIANGEN). For spatial transcriptomics, RNA was isolated from cryosectioned or FFPE-embedded tissues (10-µm sections) after permeabilization (14 min for BMKMANU; 30 min Triton X-100 for ISSeq). RNA integrity was verified via Qubit 4.0.
BMKMANU S1000/S3000 RNA-Seq: Libraries were prepared using BMKMANU S1000/S3000 Gene Expression Assay Kits (ST03002). Tissue sections were permeabilized, reverse-transcribed, and amplified with cDNA denaturation and purification steps. Final libraries were sequenced on Illumina NovaSeq.BGI Stereo-Seq: cDNA was synthesized on Stereo-Seq chips after methanol fixation and FB/ssDNA staining. Amplified cDNA was fragmented and ligated with adapters for DNBSEQ-T10 sequencing.


title: LID_1068957_PID_10531

description:
Library name: LID_1068957_PID_10531
dog_id:21291913 precision cohort year 1. dog age at collection:7.48638679747509


title: LID_1067269_PID_10537

description:
Library name: LID_1067269_PID_10537
dog_id:19330503 precision cohort year 1. dog age at collection:1.32436877329074


title: stereo,12day

description:
Library name: stereo_12d
Tomato callus Spatial Transcriptomics sequencing data


title: 16day,mRNA-seq,rep3

description:
Library name: T16d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V46 RNA - seq Library Prep Kit for MGI.


title: 16day,mRNA-seq,rep2

description:
Library name: T16d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V45 RNA - seq Library Prep Kit for MGI.


title: THP-1 WT cells replicate 2

description: Library name: WT_exp2


title: LID_1068391_PID_10530

description:
Library name: LID_1068391_PID_10530
dog_id:20581568 precision cohort year 1. dog age at collection:3.05361624458134


title: LID_1067927_PID_10537

description:
Library name: LID_1067927_PID_10537
dog_id:19973510 precision cohort year 1. dog age at collection:3.44005247547342


title: stereo,2day4day

description:
Library name: stereo_2d4d
Tomato callus Spatial Transcriptomics sequencing data


title: 15day,mRNA-seq,rep3

description:
Library name: T15d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V43 RNA - seq Library Prep Kit for MGI.


title: 16day,mRNA-seq,rep1

description:
Library name: T16d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V44 RNA - seq Library Prep Kit for MGI.


title: LID_1067858_PID_10537

description:
Library name: LID_1067858_PID_10537
dog_id:19254444 precision cohort year 1. dog age at collection:3.14151266255989


title: LID_1067870_PID_10537

description:
Library name: LID_1067870_PID_10537
dog_id:19597913 precision cohort year 1. dog age at collection:6.4652064795802


title: 15day,mRNA-seq,rep2

description:
Library name: T15d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V42 RNA - seq Library Prep Kit for MGI.


title: LID_1068981_PID_10531

description:
Library name: LID_1068981_PID_10531
dog_id:21582471 precision cohort year 1. dog age at collection:5.94552817704768


title: LID_1068990_PID_10531

description:
Library name: LID_1068990_PID_10531
dog_id:21630483 precision cohort year 1. dog age at collection:3.62331736253708


title: 15day,mRNA-seq,rep1

description:
Library name: T15d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V41 RNA - seq Library Prep Kit for MGI.


title: LID_1067903_PID_10537

description:
Library name: LID_1067903_PID_10537
dog_id:19682120 precision cohort year 1. dog age at collection:7.48950490531599


title: LID_1067902_PID_10537

description:
Library name: LID_1067902_PID_10537
dog_id:19682213 precision cohort year 1. dog age at collection:2.40252110426648


title: 14day,mRNA-seq,rep2

description:
Library name: T14d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V39 RNA - seq Library Prep Kit for MGI.


title: LID_1068403_PID_10530

description:
Library name: LID_1068403_PID_10530
dog_id:20722607 precision cohort year 1. dog age at collection:6.70088980150582


title: 14day,mRNA-seq,rep1

description:
Library name: T14d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V38 RNA - seq Library Prep Kit for MGI.


title: 14day,mRNA-seq,rep3

description:
Library name: T14d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V40 RNA - seq Library Prep Kit for MGI.


title: 13day,mRNA-seq,rep3

description:
Library name: T13d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V37 RNA - seq Library Prep Kit for MGI.


title: LID_1069000_PID_10531

description:
Library name: LID_1069000_PID_10531
dog_id:21668928 precision cohort year 1. dog age at collection:3.45950262377367


title: LID_1067259_PID_10537

description:
Library name: LID_1067259_PID_10537
dog_id:19419867 precision cohort year 1. dog age at collection:4.26683778234086


title: LID_1067263_PID_10537

description:
Library name: LID_1067263_PID_10537
dog_id:19421478 precision cohort year 1. dog age at collection:7.1828656171572


title: 13day,mRNA-seq,rep2

description:
Library name: T13d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V36 RNA - seq Library Prep Kit for MGI.


title: LID_1067238_PID_10537

description:
Library name: LID_1067238_PID_10537
dog_id:17706659 precision cohort year 1. dog age at collection:2.97714655106852


title: 12day,mRNA-seq,rep1

description:
Library name: T12d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V32 RNA - seq Library Prep Kit for MGI.


title: 12day,mRNA-seq,rep2

description:
Library name: T12d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V33 RNA - seq Library Prep Kit for MGI.


title: 12day,mRNA-seq,rep3

description:
Library name: T12d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V34 RNA - seq Library Prep Kit for MGI.


title: LID_1067898_PID_10537

description:
Library name: LID_1067898_PID_10537
dog_id:19660169 precision cohort year 1. dog age at collection:17.2335158567191


title: 11day,mRNA-seq,rep3

description:
Library name: T11d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V31 RNA - seq Library Prep Kit for MGI.


title: LID_1069008_PID_10531

description:
Library name: LID_1069008_PID_10531
dog_id:21745695 precision cohort year 1. dog age at collection:2.6303331051791


title: LID_1069004_PID_10531

description:
Library name: LID_1069004_PID_10531
dog_id:21702108 precision cohort year 1. dog age at collection:10.2105293178188


title: LID_1067919_PID_10537

description:
Library name: LID_1067919_PID_10537
dog_id:19938485 precision cohort year 1. dog age at collection:13.0095254391969


title: 11day,mRNA-seq,rep2

description:
Library name: T11d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V30 RNA - seq Library Prep Kit for MGI.


title: 13day,mRNA-seq,rep1

description:
Library name: T13d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V35 RNA - seq Library Prep Kit for MGI.


title: LID_1067229_PID_10537

description:
Library name: LID_1067229_PID_10537
dog_id:17730353 precision cohort year 1. dog age at collection:4.23123431439653


title: LID_1068409_PID_10530

description:
Library name: LID_1068409_PID_10530
dog_id:20799155 precision cohort year 1. dog age at collection:1.15902349988592


title: 10day,mRNA-seq,rep3

description:
Library name: T10d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V28 RNA - seq Library Prep Kit for MGI.


title: LID_1067899_PID_10537

description:
Library name: LID_1067899_PID_10537
dog_id:19660262 precision cohort year 1. dog age at collection:1.48323066392882


title: 10day,mRNA-seq,rep2

description:
Library name: T10d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V27 RNA - seq Library Prep Kit for MGI.


title: LID_1067265_PID_10537

description:
Library name: LID_1067265_PID_10537
dog_id:19490820 precision cohort year 1. dog age at collection:4.19279032626055


title: 10day,mRNA-seq,rep1

description:
Library name: T10d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V26 RNA - seq Library Prep Kit for MGI.


title: LID_1067253_PID_10537

description:
Library name: LID_1067253_PID_10537
dog_id:19366602 precision cohort year 1. dog age at collection:9.92048825005704


title: LID_1069147_PID_10531

description:
Library name: LID_1069147_PID_10531
dog_id:21821106 precision cohort year 1. dog age at collection:2.39673169062286


title: LID_1067934_PID_10537

description:
Library name: LID_1067934_PID_10537
dog_id:20267435 precision cohort year 1. dog age at collection:5.30739029583999


title: 11day,mRNA-seq,rep1

description:
Library name: T11d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V29 RNA - seq Library Prep Kit for MGI.


title: LID_1067916_PID_10537

description:
Library name: LID_1067916_PID_10537
dog_id:19907873 precision cohort year 1. dog age at collection:5.0362765229295


title: LID_1067214_PID_10537

description:
Library name: LID_1067214_PID_10537
dog_id:17796587 precision cohort year 1. dog age at collection:2.66532626055213


title: 4day,mRNA-seq,rep3

description:
Library name: T4d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V19 RNA - seq Library Prep Kit for MGI.


title: LID_1068411_PID_10530

description:
Library name: LID_1068411_PID_10530
dog_id:20811335 precision cohort year 1. dog age at collection:3.16335843029888


title: 8day,mRNA-seq,rep3

description:
Library name: T8d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V25 RNA - seq Library Prep Kit for MGI.


title: 6day,mRNA-seq,rep1

description:
Library name: T6d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V20 RNA - seq Library Prep Kit for MGI.


title: LID_1067279_PID_10537

description:
Library name: LID_1067279_PID_10537
dog_id:19269519 precision cohort year 1. dog age at collection:10.3117727583847


title: 6day,mRNA-seq,rep2

description:
Library name: T6d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V21 RNA - seq Library Prep Kit for MGI.


title: 8day,mRNA-seq,rep1

description:
Library name: T8d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V23 RNA - seq Library Prep Kit for MGI.


title: 2day,mRNA-seq,rep3

description:
Library name: T2d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V16 RNA - seq Library Prep Kit for MGI.


title: 8day,mRNA-seq,rep2

description:
Library name: T8d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V24 RNA - seq Library Prep Kit for MGI.


title: LID_1068431_PID_10530

description:
Library name: LID_1068431_PID_10530
dog_id:20977387 precision cohort year 1. dog age at collection:2.35894364590463


title: LID_1069158_PID_10531

description:
Library name: LID_1069158_PID_10531
dog_id:21877884 precision cohort year 1. dog age at collection:3.66438512434406


title: 4day,mRNA-seq,rep2

description:
Library name: T4d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V18 RNA - seq Library Prep Kit for MGI.


title: 2day,mRNA-seq,rep2

description:
Library name: T2d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V15 RNA - seq Library Prep Kit for MGI.


title: 6day,mRNA-seq,rep3

description:
Library name: T6d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V22 RNA - seq Library Prep Kit for MGI.


title: 4day,mRNA-seq,rep1

description:
Library name: T4d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V17 RNA - seq Library Prep Kit for MGI.


title: LID_1069156_PID_10531

description:
Library name: LID_1069156_PID_10531
dog_id:21862542 precision cohort year 1. dog age at collection:1.74235683321926


title: LID_1069167_PID_10531

description:
Library name: LID_1069167_PID_10531
dog_id:21865005 precision cohort year 1. dog age at collection:2.41042094455852


title: LID_1067246_PID_10537

description:
Library name: LID_1067246_PID_10537
dog_id:17707001 precision cohort year 1. dog age at collection:3.30595482546201


title: 1day,mRNA-seq,rep2

description:
Library name: T1d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V12 RNA - seq Library Prep Kit for MGI.


title: 2day,mRNA-seq,rep1

description:
Library name: T2d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V14 RNA - seq Library Prep Kit for MGI.


title: LID_1068430_PID_10530

description:
Library name: LID_1068430_PID_10530
dog_id:20956876 precision cohort year 1. dog age at collection:6.77452657996806


title: LID_1069169_PID_10531

description:
Library name: LID_1069169_PID_10531
dog_id:21877698 precision cohort year 1. dog age at collection:1.32717316906229


title: 1day,mRNA-seq,rep3

description:
Library name: T1d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V13 RNA - seq Library Prep Kit for MGI.


title: LID_1067277_PID_10537

description:
Library name: LID_1067277_PID_10537
dog_id:19313058 precision cohort year 1. dog age at collection:3.15820594722032


title: 1day,mRNA-seq,rep1

description:
Library name: T1d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V11 RNA - seq Library Prep Kit for MGI.


title: 0day,mRNA-seq,rep3

description:
Library name: T0d-rep3
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V10 RNA - seq Library Prep Kit for MGI.

source_name: cotyledon

value: cotyledon


title: LID_1069174_PID_10531

description:
Library name: LID_1069174_PID_10531
dog_id:21960969 precision cohort year 1. dog age at collection:5.74771845767739


title: LID_1068922_PID_10530

description:
Library name: LID_1068922_PID_10530
dog_id:21188959 precision cohort year 1. dog age at collection:6.13130276066621


title: 0day,mRNA-seq,rep2

description:
Library name: T0d-rep2
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V9 RNA - seq Library Prep Kit for MGI.


title: LID_1069176_PID_10531

description:
Library name: LID_1069176_PID_10531
dog_id:22001225 precision cohort year 1. dog age at collection:6.59428473648186


title: LID_1067261_PID_10537

description:
Library name: LID_1067261_PID_10537
dog_id:19490634 precision cohort year 1. dog age at collection:3.61305042208533


title: LID_1069181_PID_10531

description:
Library name: LID_1069181_PID_10531
dog_id:22043135 precision cohort year 1. dog age at collection:6.18032740132329


title: Trachemys scripta elegans female 2 dissection 2

city: Memphis

first: Troy

last: Camarata

state: TN

address: 1003 Monroe Avenue

department: Biomedical Sciences

institute: Baptist University College of Osteopathic Medicine

description:
Library name: B3
Turtle_Individual_Methylation.xlsx

data_processing:
Sequence quality and adapter trimming were performed using Fastqc and Fastp.
Sequence reads were aligned to the mouse or red-eared slider genome using Bismark.
Methylated cytosines were determined using MethyKit R package. MethylKit performed a Fisher’s test on the pooled sample and control groups, and an FDR-corrected P value threshold of ≤0.05 was considered significant for identifying differentially methylated cytosines (DMCs).
Assembly: T. scripta elegans: CAS_Tse_1.0; M. musculus: GRCm38
Supplementary files format and content: Quality control statistics for all sequenced samples in worksheet files
Supplementary files format and content: Genomic location, base calling, gene ID, reference ID, methylation location for each sample in worksheet files

organism: Trachemys scripta elegans

source_name: adult kidney cortex

extract_protocol:
Genomic DNA was extracted using the Monarch Genomic DNA Extraction Kit (New England Biolabs) following manufacturer’s instructions including proteinase K and RNase A incubations. For mice, outer cortical tissue was dissected in cold PBS followed by genomic DNA extraction. For adult turtle kidneys, surface convolutions or medullary tissue were dissected in cold PBS followed by extraction of genomic DNA.
Firstly, the genomic DNA spiked with lambda DNA were fragmented to 200-400 bp. The DNA fragments were bisulfite treatedto generate single strand DNA (ssDNA). During the bisulfite conversion, unmethylated cytosine were converted into uracil, whilemethylated cytosine staid unchanged. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis. Thelibrary was ready after size selection and PCR amplification.

value: adult kidney cortex

tag: Sex

value: female

value: Mixed

tag: tissue type

value: Manual dissected cortical tissue


title: Trachemys scripta elegans female 1 dissection 2

description:
Library name: B2
Turtle_Individual_Methylation.xlsx


title: LID_1069184_PID_10531

description:
Library name: LID_1069184_PID_10531
dog_id:22058822 precision cohort year 1. dog age at collection:2.26853753137121

value: feces metagenome


title: 0day,mRNA-seq,rep1

description:
Library name: T0d-rep1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V8 RNA - seq Library Prep Kit for MGI.


title: Trachemys scripta elegans male 1 dissection 2

description:
Library name: B1
Turtle_Individual_Methylation.xlsx

value: male


title: Trachemys scripta elegans male 1 dissection 1

description:
Library name: A1
Turtle_Individual_Methylation.xlsx


title: Trachemys scripta elegans female 2 dissection 1

description:
Library name: A3
Turtle_Individual_Methylation.xlsx


title: LID_1067868_PID_10537

description:
Library name: LID_1067868_PID_10537
dog_id:19598006 precision cohort year 1. dog age at collection:6.88221537759525


title: LID_1069186_PID_10531

description:
Library name: LID_1069186_PID_10531
dog_id:22058600 precision cohort year 1. dog age at collection:2.3504639136056


title: LID_1068937_PID_10530

description:
Library name: LID_1068937_PID_10530
dog_id:21450526 precision cohort year 1. dog age at collection:2.67052627576242


title: Trachemys scripta elegans female 1 dissection 1

description:
Library name: A2
Turtle_Individual_Methylation.xlsx


title: LID_1067278_PID_10537

description:
Library name: LID_1067278_PID_10537
dog_id:19300614 precision cohort year 1. dog age at collection:5.32099399193855


title: LID_1067864_PID_10537

description:
Library name: LID_1067864_PID_10537
dog_id:19257525 precision cohort year 1. dog age at collection:3.14134154688569


title: LID_1067226_PID_10537

description:
Library name: LID_1067226_PID_10537
dog_id:17728091 precision cohort year 1. dog age at collection:2.5034413263366


title: LID_1067885_PID_10537

description:
Library name: LID_1067885_PID_10537
dog_id:19561451 precision cohort year 1. dog age at collection:2.37223362993384


title: LID_1069185_PID_10531

description:
Library name: LID_1069185_PID_10531
dog_id:22058501 precision cohort year 1. dog age at collection:2.51745379876797


title: LID_1067271_PID_10537

description:
Library name: LID_1067271_PID_10537
dog_id:19251663 precision cohort year 1. dog age at collection:5.80532740132329


title: LID_1067264_PID_10537

description:
Library name: LID_1067264_PID_10537
dog_id:19419771 precision cohort year 1. dog age at collection:6.09571070043349


title: LID_1067239_PID_10537

description:
Library name: LID_1067239_PID_10537
dog_id:17643539 precision cohort year 1. dog age at collection:5.57023347783101


title: LID_1067267_PID_10537

description:
Library name: LID_1067267_PID_10537
dog_id:19371507 precision cohort year 1. dog age at collection:3.59311544604152


title: Tumor tissue from the KLN205 anti-PD-1 antibody model-02

type: RNA

city: Hiroshima

first: Masahiko

last: Sumii

address: 1-2-3 Kasumi, Minami-ku,

country: Japan

institute: Hiroshima University Hospital

description: Gene expression data from tumor tissue in anti-PD-1 antibody group

hyb_protocol: 2.3 µg of single-strand DNA was incubated in GeneChip® Hybridization Oven 645 (Affymeterix) using the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher). Hybridized with Clariom S Array, mouse (Termo Fisher).

scan_protocol: The arrays were then stained and washed in a GeneChip® Fluidics Station 450 (Affymetrix) and scanned in a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: A CEL file is automatically created after scanning. CELL files were analyzed with Transcriptome Analysis Console (TAC) ver. 4.0 to create a text file of expression levels.

label: biotin

organism: Mus musculus

source_name: Tumor tissue with anti-PD-1 antibody treatment

label_protocol: Using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher), 250 ng of total RNA to cRNA was processed into biotin-labeled single-stranded DNA.

growth_protocol: KLN205 cells (1×10^6) were suspended in 50 µL of RPMI-1640 medium mixed with 100 µL of Matrigel Basement Membrane Matrix (Corning) and subcutaneously injected into the left flank of mice

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: IgG2a isotype control antibody or an aPD-1 antibody were intraperitoneally injected every three days at a dose of 250 μg.

value: subcutaneous tumor

value: with anti-PD-1 antibody treatment


title: LID_1067245_PID_10537

description:
Library name: LID_1067245_PID_10537
dog_id:17701877 precision cohort year 1. dog age at collection:1.47419005247547


title: Tumor tissue from the KLN205 Control model-04

description: Gene expression data from tumor tissue in Control group

source_name: Tumor tissue without anti-PD-1 antibody treatment

value: without anti-PD-1 antibody treatment; control


title: LID_1069212_PID_10531

description:
Library name: LID_1069212_PID_10531
dog_id:22367348 precision cohort year 1. dog age at collection:2.07092744695414


title: Tumor tissue from the KLN205 Control model-02


title: LID_1069215_PID_10531

description:
Library name: LID_1069215_PID_10531
dog_id:22392695 precision cohort year 1. dog age at collection:4.31873146246863


title: Tumor tissue from the KLN205 anti-PD-1 antibody model-03


title: Tumor tissue from the KLN205 Control model-03


title: LID_1068973_PID_10530

description:
Library name: LID_1068973_PID_10530
dog_id:21546198 precision cohort year 1. dog age at collection:6.10122442771313


title: WTplusW782_3

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine (IRB)

description: Library name: Sample 29

data_processing:
We used FastQC v0.11.9 to assess the quality of the reads.
Adapters sequences were removed using Trimmomatic v0.39
Reads were subsequently mapped to the mouse genome using HISAT2 v2.1.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

growth_protocol: U-2932 cells were kept in culture using  complete medium (RPMI, 10% FBS, 1% Penicillin-Streptomycin, 1% MEM NEAA, 1% GlutaMAX, 1% Sodium pyruvate, 0.1% 2-mercaptoethanol, all from Gibco).

extract_protocol:
Total RNA was extracted from sorted cells with Monarch® Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s instruction. Quality controls were performed on Bioanalyzer 2100 using RNA Integrity Number (RIN) > 8 (Agilent Technologies, Santa Clara, CA, USA) and Qubit V4 (Invitrogen Thermo Fisher Scientific, Waltham, MA, USA).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) was employed with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis with the addition of barcode sequences. The sequencing of the pre-pools was performed using the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads.

treatment_protocol: U-2932 cells were transfected with different RFX7-encoding constructs using the NEON system.

value: Diffuse large B-cell Lymphoma


title: LID_1067250_PID_10537

description:
Library name: LID_1067250_PID_10537
dog_id:19490727 precision cohort year 1. dog age at collection:3.19640276827135


title: Tumor tissue from the KLN205 anti-PD-1 antibody model-01


title: WTplusW782_2

description: Library name: Sample 28


title: Tumor tissue from the LLC Control model-02

growth_protocol: LLC cells (1×10^6) were suspended in 50 µL of RPMI-1640 medium mixed with 100 µL of Matrigel Basement Membrane Matrix (Corning) and subcutaneously injected into the left flank of mice


title: Tumor tissue from the LLC Control model-03


title: LID_1067901_PID_10537

description:
Library name: LID_1067901_PID_10537
dog_id:19682027 precision cohort year 1. dog age at collection:4.40349075975359


title: LID_1067895_PID_10537

description:
Library name: LID_1067895_PID_10537
dog_id:19648991 precision cohort year 1. dog age at collection:2.22966575404974


title: Tumor tissue from the LLC anti-PD-1 antibody model-03


title: WTplusW782_1

description: Library name: Sample 27


title: Tumor tissue from the LLC Control model-01


title: Tumor tissue from the LLC anti-PD-1 antibody model-02


title: LID_112447_PID_10501

description:
Library name: LID_112447_PID_10501
dog_id:18921113 precision cohort year 1. dog age at collection:2.48203285420945


title: WTplusQ688_2

description: Library name: Sample 25


title: LID_112461_PID_10501

description:
Library name: LID_112461_PID_10501
dog_id:14083465 precision cohort year 1. dog age at collection:4.32152635181383


title: WT_3

description: Library name: Sample 23


title: WTplusQ688_1

description: Library name: Sample 24


title: WTplusQ688_3

description: Library name: Sample 26


title: WT_2

description: Library name: Sample 22


title: LID_112460_PID_10501

description:
Library name: LID_112460_PID_10501
dog_id:14111776 precision cohort year 1. dog age at collection:14.6571127081907


title: Tumor tissue from the LLC anti-PD-1 antibody model-01


title: LID_112429_PID_10501

description:
Library name: LID_112429_PID_10501
dog_id:18760688 precision cohort year 1. dog age at collection:7.53593429158111


title: WT_1

description: Library name: Sample 21


title: LID_112371_PID_10501

description:
Library name: LID_112371_PID_10501
dog_id:18596717 precision cohort year 1. dog age at collection:4.91535477983117


title: Q688_3

description: Library name: Sample 17


title: LID_112419_PID_10501

description:
Library name: LID_112419_PID_10501
dog_id:18783266 precision cohort year 1. dog age at collection:1.87374515172256


title: W782_3

description: Library name: Sample 20


title: LID_112414_PID_10501

description:
Library name: LID_112414_PID_10501
dog_id:18783062 precision cohort year 1. dog age at collection:2.2081336983801


title: LID_112351_PID_10501

description:
Library name: LID_112351_PID_10501
dog_id:17720474 precision cohort year 1. dog age at collection:4.5539299566507


title: LID_112423_PID_10501

description:
Library name: LID_112423_PID_10501
dog_id:18894743 precision cohort year 1. dog age at collection:1.80792265571526


title: W782_2

description: Library name: Sample 19


title: LID_112381_PID_10501

description:
Library name: LID_112381_PID_10501
dog_id:18624860 precision cohort year 1. dog age at collection:3.17419575633128


title: LID_112345_PID_10501

description:
Library name: LID_112345_PID_10501
dog_id:17777201 precision cohort year 1. dog age at collection:10.4601015286334


title: NLS_2

description: Library name: Sample 13


title: LID_112465_PID_10501

description:
Library name: LID_112465_PID_10501
dog_id:14067958 precision cohort year 1. dog age at collection:3.89997338200624


title: W782_1

description: Library name: Sample 18


title: Q688_1

description: Library name: Sample 15


title: NLS_3

description: Library name: Sample 14


title: Q688_2

description: Library name: Sample 16


title: LID_112453_PID_10501

description:
Library name: LID_112453_PID_10501
dog_id:18976172 precision cohort year 1. dog age at collection:3.1534052019165


title: LID_112446_PID_10501

description:
Library name: LID_112446_PID_10501
dog_id:18957269 precision cohort year 1. dog age at collection:1.31798996121378


title: LID_112323_PID_10501

description:
Library name: LID_112323_PID_10501
dog_id:17886788 precision cohort year 1. dog age at collection:3.10580652521104


title: NLS_1

description: Library name: Sample 12


title: Elderly6

city: Pamplona

first: Itziar

last: Cenzano

state: Navarra

address: Avenida de Pio XII, 55

country: Spain

institute: CIMA Universidad de Navarra

description:
Library name: Old_6_S1
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v6.1.1 (10x Genomics) with the human genome GRCh38. Downstream analysis, including quality control, clustering, differential expression, and pathway analysis, was conducted in R v4.1.3 using Seurat v4.3.0.
Assembly: GRCh38
Supplementary files format and content: HDF5 files

molecule: polyA RNA

source_name: Bone Marrow

extract_protocol:
Human BM endothelial cells (EC) and mesenchymal stromal cells (MSC) were isolated by mechanical dissociation, enzymatic digestion (0.3% collagenase I, dispase 5 U/ml, 15 min, 37°C), ACK-mediated RBC lysis, and filtration. Cells were stained in PBS + 2% FBS + 2 mM EDTA with lineage (CD3, CD19, CD45, CD64) and population-specific markers, and dead cells were excluded by TO-PRO-3. EC were defined as TO-PRO-3⁻/Lin⁻/CD45⁻/CD235⁻/CD16⁻/CD56⁻/CD9⁺/CD31⁺ and MSC as TO-PRO-3⁻/Lin⁻/CD45⁻/CD235⁻/CD16⁻/CD56⁻/CD31⁻/CD271⁺. Sorting was performed using a BD FACSAria II into PBS + 0.05% UltraPure BSA. Viability was assessed with AO/PI on a Nexcelom Cellometer.
scRNA-seq was performed using the Single Cell 3’ Reagent Kits v3.1 (10X Genomics) according to the manufacturer’s instructions. Approximately 10,000 cells were loaded at a concentration of 1,000 cells/µL on a Chromium Controller instrument (10X Genomics) to generate single-cell gel bead-in-emulsions (GEMs). Each cell was encapsulated with primers containing a fixed Illumina Read one sequence, followed by a cell-identifying 16 bp 10X barcode, a 10 bp Unique Molecular Identifier (UMI), and a poly-dT sequence. A subsequent reverse transcription yielded full-length, barcoded cDNA. This cDNA was then released from the GEMs, PCR-amplified, and purified with magnetic beads (SPRIselect, Beckman Coulter). Enzymatic Fragmentation and Size Selection optimized cDNA size before library construction. Illumina adaptor sequences were added, and the resulting library was amplified via end repair, A-tailing, adaptor ligation, and PCR. Libraries' quality control and quantification were performed using Qubit 3.0 Fluorometer (Life Technologies) and Agilent’s 4200 TapeStation System (Agilent), respectively. Sequencing was performed in a NextSeq2000 (Illumina) (Read 1: 28cycles, i7 Index: 10cycles, i5 Index:10 Read 2: 90cycles) at an average depth of 45,000 reads/cell.

value: Bone Marrow

value: EC and MSC

tag: age


title: LID_112457_PID_10501

description:
Library name: LID_112457_PID_10501
dog_id:14079643 precision cohort year 1. dog age at collection:8.90172256445357


title: LID_112427_PID_10501

description:
Library name: LID_112427_PID_10501
dog_id:18760595 precision cohort year 1. dog age at collection:5.37303216974675


title: Elderly4

description:
Library name: Old_4_S1
10X Genomics


title: LID_112459_PID_10501

description:
Library name: LID_112459_PID_10501
dog_id:14118622 precision cohort year 1. dog age at collection:2.65983154612518


title: LID_112389_PID_10501

description:
Library name: LID_112389_PID_10501
dog_id:18650033 precision cohort year 1. dog age at collection:6.17493725758613


title: Elderly7

description:
Library name: Old_7_S1
10X Genomics


title: Elderly5

description:
Library name: Old_5_S1
10X Genomics


title: LID_112462_PID_10501

description:
Library name: LID_112462_PID_10501
dog_id:14028271 precision cohort year 1. dog age at collection:11.1415126625599


title: Elderly2

description:
Library name: Old_2_S1
10X Genomics


title: LID_112390_PID_10501

description:
Library name: LID_112390_PID_10501
dog_id:18619076 precision cohort year 1. dog age at collection:8.1720282911248


title: Elderly3

description:
Library name: Old_3MSC_S1
10X Genomics


title: LID_112415_PID_10501

description:
Library name: LID_112415_PID_10501
dog_id:18807452 precision cohort year 1. dog age at collection:3.38221537759525


title: Elderly1

description:
Library name: Old_1_S1
10X Genomics


title: Young5

description:
Library name: Young_5_S1
10X Genomics


title: Young3

description:
Library name: Young_3_S1
10X Genomics


title: LID_112329_PID_10501

description:
Library name: LID_112329_PID_10501
dog_id:17951351 precision cohort year 1. dog age at collection:5.69849418206708


title: Young4

description:
Library name: Young_4_S1
10X Genomics


title: LID_112361_PID_10501

description:
Library name: LID_112361_PID_10501
dog_id:17674397 precision cohort year 1. dog age at collection:1.96437942048825


title: Young2

description:
Library name: Young_bn2_S2
10X Genomics


title: LID_112337_PID_10501

description:
Library name: LID_112337_PID_10501
dog_id:17731295 precision cohort year 1. dog age at collection:2.64864248231805


title: LID_112396_PID_10501

description:
Library name: LID_112396_PID_10501
dog_id:18798080 precision cohort year 1. dog age at collection:4.12970568104038


title: LID_112373_PID_10501

description:
Library name: LID_112373_PID_10501
dog_id:18618674 precision cohort year 1. dog age at collection:3.58495893223819


title: Young1

description:
Library name: Young_bn1_S1
10X Genomics


title: LID_112535_PID_10502

description:
Library name: LID_112535_PID_10502
dog_id:16455820 precision cohort year 1. dog age at collection:4.31308464522017


title: NT046

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

description: Library name: Sample 34

data_processing:
Adapter-trimmed reads in the FASTQ format wereused as inputs, wherein demultiplexing was performed using BaseSpace default settings
The trimmed FASTQ were aligned using STAR to the mouse genome (mm10)
Reads were quantified in TPM format using Salmon
Read count matrices generated above were processed for differential expression using DESeq
Read count matrices were subjected to further downstream analysis using iGEAK
Assembly: mm10
Supplementary files format and content: tab delimited raw counts with genes in rows and samples in columns

source_name: glioma tumor cells

growth_protocol: Primary murine cell lines were grown in NeuroCult basal medium containing 10% NeuroCult Proliferation Supplement (Stemcell Technologies, #05702) and supplemented with 2µg/mL heparin (Stemcell Technologies #07980) plus growth factors (Shenandoah Biotech #PB-500-20) including 20ng/mL Epidermal Growth Factor (EGF; #200-53), 20ng/mL Fibroblast Growth Factor-basic (FGF; #200-12), 10ng/mL PDGF-AA (#200-54) and 10ng/mL PDGF-BB (#200-58). Cultures were grown as neurosphere suspensions in ultra-low attachment PrimeSurface cell culture plates (SBio # #MS-90900).

extract_protocol:
RNA was isolated using the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, #D7003)
RNA libraries were prepared for bulk sequencing using standard Illumina protocols

value: glioma tumor cells

value: sgRNA Nf1, Pten, Trp53


title: LID_112479_PID_10502

description:
Library name: LID_112479_PID_10502
dog_id:14216617 precision cohort year 1. dog age at collection:8.34602441250285


title: NT044

description: Library name: Sample 32

value: IDH1R132H+PIK3CAE545K+sgRNA Cic, Fubp1, Cdkn2a


title: NT045

description: Library name: Sample 33


title: NT047

description: Library name: Sample 35


title: LID_112347_PID_10501

description:
Library name: LID_112347_PID_10501
dog_id:17795285 precision cohort year 1. dog age at collection:3.2513118868355


title: NT043

description: Library name: Sample 31


title: NT035

description: Library name: Sample 29

value: IDH1R132H+PIK3CAE545K+sgRNA Cic, Fubp1, Trp53


title: NT042

description: Library name: Sample 30


title: LID_112477_PID_10502

description:
Library name: LID_112477_PID_10502
dog_id:14422420 precision cohort year 1. dog age at collection:3.54406228610541


title: LID_112527_PID_10502

description:
Library name: LID_112527_PID_10502
dog_id:15554455 precision cohort year 1. dog age at collection:13.1776180698152


title: LID_112550_PID_10502

description:
Library name: LID_112550_PID_10502
dog_id:19049462 precision cohort year 1. dog age at collection:6.16946155601186


title: LID_112601_PID_10502

description:
Library name: LID_112601_PID_10502
dog_id:19144437 precision cohort year 1. dog age at collection:3.03190356681116


title: NT034

description: Library name: Sample 28


title: LID_112603_PID_10502

description:
Library name: LID_112603_PID_10502
dog_id:19152507 precision cohort year 1. dog age at collection:7.45128907141228


title: LID_112507_PID_10502

description:
Library name: LID_112507_PID_10502
dog_id:14558932 precision cohort year 1. dog age at collection:11.6674081679215


title: LID_112528_PID_10502

description:
Library name: LID_112528_PID_10502
dog_id:15554968 precision cohort year 1. dog age at collection:1.50513347022587


title: NT033

description: Library name: Sample 27


title: NT025

description: Library name: Sample 23

source_name: Cortical tumor

value: Cortical tumor


title: NT026

description: Library name: Sample 24


title: NT024

description: Library name: Sample 22


title: NT027

description: Library name: Sample 25


title: LID_112433_PID_10501

description:
Library name: LID_112433_PID_10501
dog_id:18715442 precision cohort year 1. dog age at collection:10.2766084873374


title: NT028

description: Library name: Sample 26


title: LID_112520_PID_10502

description:
Library name: LID_112520_PID_10502
dog_id:15569491 precision cohort year 1. dog age at collection:5.16204654346338


title: LID_112321_PID_10501

description:
Library name: LID_112321_PID_10501
dog_id:17882174 precision cohort year 1. dog age at collection:4.58989276751084


title: NT022

description: Library name: Sample 20


title: LID_112592_PID_10502

description:
Library name: LID_112592_PID_10502
dog_id:19163127 precision cohort year 1. dog age at collection:2.36935318275154


title: LID_112473_PID_10502

description:
Library name: LID_112473_PID_10502
dog_id:14091907 precision cohort year 1. dog age at collection:6.9880219028063


title: LID_112524_PID_10502

description:
Library name: LID_112524_PID_10502
dog_id:15594223 precision cohort year 1. dog age at collection:3.39082819986311


title: LID_112383_PID_10501

description:
Library name: LID_112383_PID_10501
dog_id:18687506 precision cohort year 1. dog age at collection:6.18583162217659


title: NT019

description: Library name: Sample 17


title: LID_112512_PID_10502

description:
Library name: LID_112512_PID_10502
dog_id:14492620 precision cohort year 1. dog age at collection:7.23722336299338


title: NT016

description: Library name: Sample 14


title: NT023

description: Library name: Sample 21


title: LID_112463_PID_10501

description:
Library name: LID_112463_PID_10501
dog_id:14043853 precision cohort year 1. dog age at collection:4.22634801125561


title: LID_112394_PID_10501

description:
Library name: LID_112394_PID_10501
dog_id:18802658 precision cohort year 1. dog age at collection:1.21155601186402


title: NT018

description: Library name: Sample 16


title: NT014

description: Library name: Sample 12


title: LID_112548_PID_10502

description:
Library name: LID_112548_PID_10502
dog_id:19037015 precision cohort year 1. dog age at collection:14.9966917636322


title: NT021

description: Library name: Sample 19


title: NT020

description: Library name: Sample 18


title: NT017

description: Library name: Sample 15


title: LID_112590_PID_10502

description:
Library name: LID_112590_PID_10502
dog_id:19213923 precision cohort year 1. dog age at collection:7.10277207392197


title: LID_112326_PID_10501

description:
Library name: LID_112326_PID_10501
dog_id:17905805 precision cohort year 1. dog age at collection:2.83772530230436


title: LID_112567_PID_10502

description:
Library name: LID_112567_PID_10502
dog_id:19112763 precision cohort year 1. dog age at collection:5.27161761350673


title: LID_112431_PID_10501

description:
Library name: LID_112431_PID_10501
dog_id:18726590 precision cohort year 1. dog age at collection:2.27646589094228


title: NT013

description: Library name: Sample 11


title: LID_112562_PID_10502

description:
Library name: LID_112562_PID_10502
dog_id:19017074 precision cohort year 1. dog age at collection:2.99652064795802


title: NT012

description: Library name: Sample 10


title: LID_112599_PID_10502

description:
Library name: LID_112599_PID_10502
dog_id:19189680 precision cohort year 1. dog age at collection:1.29078256901666


title: NT011

description: Library name: Sample 9


title: NT007

description: Library name: Sample 5


title: NT006

description: Library name: Sample 4


title: LID_112522_PID_10502

description:
Library name: LID_112522_PID_10502
dog_id:15554734 precision cohort year 1. dog age at collection:5.67145790554415


title: NT010

description: Library name: Sample 8


title: NT015

description: Library name: Sample 13