title: 833, Canis lupus familiaris, HeartArteryCoronary

description: Library name: itox000833


title: 837, Canis lupus familiaris, HeartAtrialAppendage

status: Public on Mar 25 2026

type: SRA

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

country: USA

institute: Pfizer

description: Library name: itox000837

library_source: transcriptomic

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read counts mapped to human

molecule: total RNA

organism: Canis lupus familiaris

source_name: HeartAtrialAppendage

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

tag: tissue

value: HeartAtrialAppendage

tag: batch


title: 824, Canis lupus familiaris, GutJejunum

description: Library name: itox000824

source_name: GutJejunum

value: GutJejunum


title: 835, Canis lupus familiaris, HeartAtrialAppendage

description: Library name: itox000835


title: 839, Canis lupus familiaris, HeartLeftAtrium

description: Library name: itox000839

source_name: HeartLeftAtrium

value: HeartLeftAtrium


title: 840, Canis lupus familiaris, HeartLeftAtrium

description: Library name: itox000840


title: 828, Canis lupus familiaris, HeartArteryCoronary

description: Library name: itox000828

source_name: HeartArteryCoronary

value: HeartArteryCoronary


title: 842, Canis lupus familiaris, HeartLeftAtrium

description: Library name: itox000842


title: 841, Canis lupus familiaris, HeartLeftAtrium

description: Library name: itox000841


title: 15, Canis lupus familiaris, AdiposeWhiteReproductive

description: Library name: itox000015

source_name: AdiposeWhiteReproductive

value: AdiposeWhiteReproductive


title: 844, Canis lupus familiaris, HeartLeftVentricle

description: Library name: itox000844

source_name: HeartLeftVentricle

value: HeartLeftVentricle


title: 843, Canis lupus familiaris, HeartLeftVentricle

description: Library name: itox000843


title: 14, Canis lupus familiaris, AdiposeWhiteReproductive

description: Library name: itox000014


title: 769, Canis lupus familiaris, GallBladder

description: Library name: itox000769

source_name: GallBladder

value: GallBladder


title: 320, Canis lupus familiaris, BrainCorpusCallosum

description: Library name: itox000320

source_name: BrainCorpusCallosum

value: BrainCorpusCallosum


title: 319, Canis lupus familiaris, BrainCorpusCallosum

description: Library name: itox000319


title: 322, Canis lupus familiaris, BrainFrontalCortex

description: Library name: itox000322

source_name: BrainFrontalCortex

value: BrainFrontalCortex


title: 323, Canis lupus familiaris, BrainFrontalCortex

description: Library name: itox000323


title: 328, Canis lupus familiaris, BrainHippocampus

description: Library name: itox000328

source_name: BrainHippocampus

value: BrainHippocampus


title: 326, Canis lupus familiaris, BrainFrontalCortex

description: Library name: itox000326


title: 327, Canis lupus familiaris, BrainFrontalCortex

description: Library name: itox000327


title: 324, Canis lupus familiaris, BrainFrontalCortex

description: Library name: itox000324


title: 329, Canis lupus familiaris, BrainHippocampus

description: Library name: itox000329


title: 325, Canis lupus familiaris, BrainFrontalCortex

description: Library name: itox000325


title: 331, Canis lupus familiaris, BrainHippocampus

description: Library name: itox000331


title: 335, Canis lupus familiaris, BrainHypothalamus

description: Library name: itox000335

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

source_name: BrainHypothalamus

value: BrainHypothalamus


title: 340, Canis lupus familiaris, BrainION

description: Library name: itox000340

source_name: BrainION

value: BrainION


title: 336, Canis lupus familiaris, BrainHypothalamus

description: Library name: itox000336


title: 334, Canis lupus familiaris, BrainHypothalamus

description: Library name: itox000334


title: 332, Canis lupus familiaris, BrainHippocampus

description: Library name: itox000332


title: 338, Canis lupus familiaris, BrainION

description: Library name: itox000338


title: 333, Canis lupus familiaris, BrainHypothalamus

description: Library name: itox000333


title: 740, Canis lupus familiaris, EyeRetina

description: Library name: itox000740

source_name: EyeRetina

value: EyeRetina


title: 737, Canis lupus familiaris, EyeRetina

description: Library name: itox000737


title: 739, Canis lupus familiaris, EyeRetina

description: Library name: itox000739


title: 736, Canis lupus familiaris, EyeOpticNerve

description: Library name: itox000736

source_name: EyeOpticNerve

value: EyeOpticNerve


title: 321, Canis lupus familiaris, BrainCorpusCallosum

description: Library name: itox000321


title: 330, Canis lupus familiaris, BrainHippocampus

description: Library name: itox000330


title: 55, Canis lupus familiaris, ArteryTibial

description: Library name: itox000055

source_name: ArteryTibial

value: ArteryTibial


title: 742, Canis lupus familiaris, EyeRetina

description: Library name: itox000742


title: 748, Canis lupus familiaris, EyeSclera

description: Library name: itox000748

source_name: EyeSclera

value: EyeSclera


title: 750, Canis lupus familiaris, EyeSclera

description: Library name: itox000750


title: 747, Canis lupus familiaris, EyeSclera

description: Library name: itox000747


title: 751, Canis lupus familiaris, EyeSclera

description: Library name: itox000751


title: 741, Canis lupus familiaris, EyeRetina

description: Library name: itox000741


title: 846, Canis lupus familiaris, HeartLeftVentricle

description: Library name: itox000846


title: 847, Canis lupus familiaris, HeartLeftVentricle

description: Library name: itox000847


title: 848, Canis lupus familiaris, HeartRightAtrium

description: Library name: itox000848

source_name: HeartRightAtrium

value: HeartRightAtrium


title: 849, Canis lupus familiaris, HeartRightAtrium

description: Library name: itox000849


title: 749, Canis lupus familiaris, EyeSclera

description: Library name: itox000749


title: 850, Canis lupus familiaris, HeartRightAtrium

description: Library name: itox000850


title: 852, Canis lupus familiaris, HeartRightAtrium

description: Library name: itox000852


title: 851, Canis lupus familiaris, HeartRightAtrium

description: Library name: itox000851


title: 854, Canis lupus familiaris, HeartRightVentricle

description: Library name: itox000854

source_name: HeartRightVentricle

value: HeartRightVentricle


title: 845, Canis lupus familiaris, HeartLeftVentricle

description: Library name: itox000845


title: 752, Canis lupus familiaris, EyeSclera

description: Library name: itox000752


title: 853, Canis lupus familiaris, HeartRightVentricle

description: Library name: itox000853


title: 855, Canis lupus familiaris, HeartRightVentricle

description: Library name: itox000855


title: 1122, Canis lupus familiaris, SalivaryGlandMandibular,SalivaryGlandMandibular

description: Library name: itox001122


title: 857, Canis lupus familiaris, HeartRightVentricle

description: Library name: itox000857


title: 1123, Canis lupus familiaris, SalivaryGlandMandibular,SalivaryGlandMandibular

description: Library name: itox001123


title: 1314, Canis lupus familiaris, Vagina,Vagina

description: Library name: itox001314

source_name: Vagina,Vagina

value: Vagina,Vagina


title: 968, Canis lupus familiaris, LymphNodeMesenteric,LymphNodeMesenteric

description: Library name: itox000968

source_name: LymphNodeMesenteric,LymphNodeMesenteric

value: LymphNodeMesenteric,LymphNodeMesenteric


title: Patient 2 Region4

type: RNA

city: los angeles

first: yizhou

last: wang

address: 8700 beverly blvd

institute: cedars-sinai medical center

description: Formalin-Fixed Paraffin-Embedded (FFPE) tissues were sectioned at 5 μm thickness, placed onto Xenium slides, and underwent deparaffinization and decrosslinking (CG000580) to expose RNA targets.

hyb_protocol: Gene expression detection involved probe hybridization (CG000749) at 50°C overnight, followed by washing, ligation, and rolling circle amplification (RCA) to amplify the signal.

scan_protocol: The prepared slides were analyzed using the Xenium Analyzer (10X Genomics), running on Instrument Software Version 3.0.2.0 with Analysis Version xenium-3.0.0.15.

data_processing:
For cell segmentation, DAPI-stained nuclei from the DAPI morphology image were segmented to define individual cells. Nuclear boundaries were either expanded or combined with a cell boundary stain, ensuring accurate transcript assignment per cell. Cell segmentation was performed with 10X Xenium onboard cell segmentation.Scanpy v1.9.3 was used for downstream analysis. For quality control all cells with n < 50 total transcripts for region 3 and n < 25 total transcripts for region 4 were filtered out before downstream processing. Count data of the remained cells were log-normalized. Dimensionality reduction was performed with principal component analysis (PCA)
For each sample, count matrices were generated based on the expression of transcriptomics inside each segmented cell along with x and y coordinates.

label: Xenium Human Probe Set

organism: Homo sapiens

source_name: human synoival tissue

label_protocol: A pre-designed panel from Xenium (377 genes on the Human Multi-Tissue and Cancer Panel) and an Add-on custom design panel (50 genes) (Supplementary Table 4) were used.

growth_protocol: Not Applicable

treatment_protocol: Not Applicable

value: human synoival tissue


title: 56, Canis lupus familiaris, ArteryTibial

description: Library name: itox000056


title: 1137, Canis lupus familiaris, SkeletalMuscleGastrocnemius,SkeletalMuscleGastrocnemius

description: Library name: itox001137


title: Patient 1 Region3

extract_protocol: Formalin-Fixed Paraffin-Embedded (FFPE) tissues were sectioned at 5 μm thickness, placed onto Xenium slides, and underwent deparaffinization and decrosslinking (CG000580) to expose RNA targets.


title: 856, Canis lupus familiaris, HeartRightVentricle

description: Library name: itox000856


title: 1139, Canis lupus familiaris, SkeletalMuscleGastrocnemius,SkeletalMuscleGastrocnemius

description: Library name: itox001139


title: 298, Macaca fascicularis, BoneMarrow

description: Library name: itox000298

organism: Macaca fascicularis

source_name: BoneMarrow

value: BoneMarrow


title: 28, Macaca fascicularis, Adrenals

description: Library name: itox000028

source_name: Adrenals

value: Adrenals


title: 27, Macaca fascicularis, Adrenals

description: Library name: itox000027


title: 1138, Canis lupus familiaris, SkeletalMuscleGastrocnemius,SkeletalMuscleGastrocnemius

description: Library name: itox001138


title: 1140, Canis lupus familiaris, SkeletalMuscleGastrocnemius,SkeletalMuscleGastrocnemius

description: Library name: itox001140


title: 300, Macaca fascicularis, BoneMarrow

description: Library name: itox000300


title: 299, Macaca fascicularis, BoneMarrow

description: Library name: itox000299


title: 1050, Canis lupus familiaris, PancreasHead,PancreasHead

description: Library name: itox001050

source_name: PancreasHead,PancreasHead

value: PancreasHead,PancreasHead


title: 31, Macaca fascicularis, Adrenals

description: Library name: itox000031


title: 32, Macaca fascicularis, Amygdala

description: Library name: itox000032

source_name: Amygdala

value: Amygdala


title: 1007, Canis lupus familiaris, NKCells,NKCells

description: Library name: itox001007

source_name: NKCells,NKCells

value: NKCells,NKCells


title: 38, Macaca fascicularis, Amygdala

description: Library name: itox000038


title: 1052, Canis lupus familiaris, PancreasTail,PancreasTail

description: Library name: itox001052

source_name: PancreasTail,PancreasTail

value: PancreasTail,PancreasTail


title: Patient 3 Region1

label: Region 1

tag: tag


title: 39, Macaca fascicularis, Amygdala

description: Library name: itox000039


title: 405, Macaca fascicularis, Cecum

description: Library name: itox000405

source_name: Cecum

value: Cecum


title: 1016, Canis lupus familiaris, NervePeripheralTibial,NervePeripheralTibial

description: Library name: itox001016


title: 1141, Canis lupus familiaris, SkeletalMuscleGastrocnemius,SkeletalMuscleGastrocnemius

description: Library name: itox001141


title: 407, Macaca fascicularis, Cecum

description: Library name: itox000407


title: 1017, Canis lupus familiaris, NervePeripheralTibial,NervePeripheralTibial

description: Library name: itox001017


title: 1143, Canis lupus familiaris, SkinInguinal,SkinInguinal

description: Library name: itox001143

source_name: SkinInguinal,SkinInguinal

value: SkinInguinal,SkinInguinal


title: 337, Canis lupus familiaris, BrainHypothalamus

description: Library name: itox000337

source_name: BrainHypothalamus

value: BrainHypothalamus


title: 969, Canis lupus familiaris, LymphNodeMesenteric,LymphNodeMesenteric

description: Library name: itox000969


title: 406, Macaca fascicularis, Cecum

description: Library name: itox000406


title: 1051, Canis lupus familiaris, PancreasTail,PancreasTail

description: Library name: itox001051


title: 1144, Canis lupus familiaris, SkinInguinal,SkinInguinal

description: Library name: itox001144


title: 409, Macaca fascicularis, Cecum

description: Library name: itox000409


title: 408, Macaca fascicularis, Cecum

description: Library name: itox000408


title: 410, Macaca fascicularis, Cecum

description: Library name: itox000410


title: 1145, Canis lupus familiaris, SkinInguinal,SkinInguinal

description: Library name: itox001145


title: 411, Macaca fascicularis, Cecum

description: Library name: itox000411


title: 42, Macaca fascicularis, Aorta

description: Library name: itox000042

source_name: Aorta

value: Aorta


title: 1147, Canis lupus familiaris, SkinInguinal,SkinInguinal

description: Library name: itox001147


title: 412, Macaca fascicularis, CeliacGanglia

description: Library name: itox000412

source_name: CeliacGanglia

value: CeliacGanglia


title: 1149, Canis lupus familiaris, SkinMidBack,SkinMidBack

description: Library name: itox001149

source_name: SkinMidBack,SkinMidBack

value: SkinMidBack,SkinMidBack


title: 414, Macaca fascicularis, CeliacGanglia

description: Library name: itox000414


title: 1152, Canis lupus familiaris, SkinMidBack,SkinMidBack

description: Library name: itox001152


title: 1150, Canis lupus familiaris, SkinMidBack,SkinMidBack

description: Library name: itox001150


title: 970, Canis lupus familiaris, LymphNodeMesenteric,LymphNodeMesenteric

description: Library name: itox000970


title: 1151, Canis lupus familiaris, SkinMidBack,SkinMidBack

description: Library name: itox001151


title: 1163, Canis lupus familiaris, SpinalCordLumbar,SpinalCordLumbar

description: Library name: itox001163

source_name: SpinalCordLumbar,SpinalCordLumbar

value: SpinalCordLumbar,SpinalCordLumbar


title: 1146, Canis lupus familiaris, SkinInguinal,SkinInguinal

description: Library name: itox001146


title: 413, Macaca fascicularis, CeliacGanglia

description: Library name: itox000413


title: 415, Macaca fascicularis, CeliacGanglia

description: Library name: itox000415


title: 1162, Canis lupus familiaris, SpinalCordLumbar,SpinalCordLumbar

description: Library name: itox001162


title: 1153, Canis lupus familiaris, SkinMidBack,SkinMidBack

description: Library name: itox001153


title: 417, Macaca fascicularis, CeliacGanglia

description: Library name: itox000417


title: 1164, Canis lupus familiaris, SpinalCordLumbar,SpinalCordLumbar

description: Library name: itox001164


title: 971, Canis lupus familiaris, LymphNodeMesenteric,LymphNodeMesenteric

description: Library name: itox000971


title: 419, Macaca fascicularis, CeliacGanglia

description: Library name: itox000419


title: 420, Macaca fascicularis, Cerebellum

description: Library name: itox000420

source_name: Cerebellum

value: Cerebellum


title: 418, Macaca fascicularis, CeliacGanglia

description: Library name: itox000418


title: 421, Macaca fascicularis, Cerebellum

description: Library name: itox000421


title: 1166, Canis lupus familiaris, SpinalCordLumbar,SpinalCordLumbar

description: Library name: itox001166


title: 416, Macaca fascicularis, CeliacGanglia

description: Library name: itox000416


title: 972, Canis lupus familiaris, LymphNodeMesenteric,LymphNodeMesenteric

description: Library name: itox000972


title: 43, Macaca fascicularis, Aorta

description: Library name: itox000043


title: 1165, Canis lupus familiaris, SpinalCordLumbar,SpinalCordLumbar

description: Library name: itox001165


title: 423, Macaca fascicularis, Cerebellum

description: Library name: itox000423


title: 425, Macaca fascicularis, Cerebellum

description: Library name: itox000425


title: 426, Macaca fascicularis, Cerebellum

description: Library name: itox000426


title: 424, Macaca fascicularis, Cerebellum

description: Library name: itox000424


title: 1176, Canis lupus familiaris, Spleen,Spleen

description: Library name: itox001176

source_name: Spleen,Spleen

value: Spleen,Spleen


title: 973, Canis lupus familiaris, LymphNodeMesenteric,LymphNodeMesenteric

description: Library name: itox000973

source_name: LymphNodeMesenteric,LymphNodeMesenteric

value: LymphNodeMesenteric,LymphNodeMesenteric


title: 1177, Canis lupus familiaris, Spleen,Spleen

description: Library name: itox001177


title: 472, Macaca fascicularis, Duodenum

description: Library name: itox000472

source_name: Duodenum

value: Duodenum


title: 473, Macaca fascicularis, Duodenum

description: Library name: itox000473


title: 1188, Canis lupus familiaris, StomachFundus,StomachFundus

description: Library name: itox001188

source_name: StomachFundus,StomachFundus

value: StomachFundus,StomachFundus


title: 475, Macaca fascicularis, Duodenum

description: Library name: itox000475


title: 713, Canis lupus familiaris, EyeChoroid

description: Library name: itox000713

source_name: EyeChoroid

value: EyeChoroid


title: 422, Macaca fascicularis, Cerebellum

description: Library name: itox000422


title: 1186, Canis lupus familiaris, StomachFundus,StomachFundus

description: Library name: itox001186


title: 477, Macaca fascicularis, Duodenum

description: Library name: itox000477


title: 474, Macaca fascicularis, Duodenum

description: Library name: itox000474


title: 1187, Canis lupus familiaris, StomachFundus,StomachFundus

description: Library name: itox001187


title: 476, Macaca fascicularis, Duodenum

description: Library name: itox000476


title: 1190, Canis lupus familiaris, StomachFundus,StomachFundus

description: Library name: itox001190


title: 1175, Canis lupus familiaris, Spleen,Spleen

description: Library name: itox001175


title: 478, Macaca fascicularis, Duodenum

description: Library name: itox000478


title: 1189, Canis lupus familiaris, StomachFundus,StomachFundus

description: Library name: itox001189


title: 1174, Canis lupus familiaris, Spleen,Spleen

description: Library name: itox001174


title: 974, Canis lupus familiaris, MammaryGland,MammaryGland

description: Library name: itox000974

source_name: MammaryGland,MammaryGland

value: MammaryGland,MammaryGland


title: 685, Macaca fascicularis, Epididymis

description: Library name: itox000685

source_name: Epididymis

value: Epididymis


title: 1294, Canis lupus familiaris, Ureter,Ureter

description: Library name: itox001294

source_name: Ureter,Ureter

value: Ureter,Ureter


title: 687, Macaca fascicularis, Epididymis

description: Library name: itox000687


title: 1296, Canis lupus familiaris, UrinaryBladder,UrinaryBladder

description: Library name: itox001296

source_name: UrinaryBladder,UrinaryBladder

value: UrinaryBladder,UrinaryBladder


title: 975, Canis lupus familiaris, MammaryGland,MammaryGland

description: Library name: itox000975


title: 1298, Canis lupus familiaris, UrinaryBladder,UrinaryBladder

description: Library name: itox001298


title: 724, Macaca fascicularis, EyeCornea

description: Library name: itox000724

source_name: EyeCornea

value: EyeCornea


title: 723, Macaca fascicularis, EyeCornea

description: Library name: itox000723


title: 686, Macaca fascicularis, Epididymis

description: Library name: itox000686


title: 722, Macaca fascicularis, EyeCornea

description: Library name: itox000722


title: 1300, Canis lupus familiaris, UrinaryBladder,UrinaryBladder

description: Library name: itox001300


title: 726, Macaca fascicularis, EyeCornea

description: Library name: itox000726


title: 339, Canis lupus familiaris, BrainION

description: Library name: itox000339

source_name: BrainION

value: BrainION


title: 688, Macaca fascicularis, Epididymis

description: Library name: itox000688


title: 1309, Canis lupus familiaris, Uterus,Uterus

description: Library name: itox001309

source_name: Uterus,Uterus

value: Uterus,Uterus


title: 725, Macaca fascicularis, EyeCornea

description: Library name: itox000725


title: 797, Macaca fascicularis, Gastrocnemius

description: Library name: itox000797

source_name: Gastrocnemius

value: Gastrocnemius


title: 738, Canis lupus familiaris, EyeRetina

description: Library name: itox000738

source_name: EyeRetina

value: EyeRetina


title: 1310, Canis lupus familiaris, Uterus,Uterus

description: Library name: itox001310


title: 1317, Canis lupus familiaris, VenaCava,VenaCava

description: Library name: itox001317

source_name: VenaCava,VenaCava

value: VenaCava,VenaCava


title: 1297, Canis lupus familiaris, UrinaryBladder,UrinaryBladder

description: Library name: itox001297


title: 918, Macaca fascicularis, KidneyMedulla

description: Library name: itox000918

source_name: KidneyMedulla

value: KidneyMedulla


title: 1316, Canis lupus familiaris, VenaCava,VenaCava

description: Library name: itox001316


title: 798, Macaca fascicularis, Gastrocnemius

description: Library name: itox000798


title: 1299, Canis lupus familiaris, UrinaryBladder,UrinaryBladder

description: Library name: itox001299


title: 799, Macaca fascicularis, Gastrocnemius

description: Library name: itox000799


title: 920, Macaca fascicularis, KidneyMedulla

description: Library name: itox000920


title: 1320, Canis lupus familiaris, VenaCava,VenaCava

description: Library name: itox001320


title: 1319, Canis lupus familiaris, VenaCava,VenaCava

description: Library name: itox001319


title: 922, Macaca fascicularis, KidneyMedulla

description: Library name: itox000922


title: 923, Macaca fascicularis, KidneyMedulla

description: Library name: itox000923


title: 801, Macaca fascicularis, Gastrocnemius

description: Library name: itox000801


title: 921, Macaca fascicularis, KidneyMedulla

description: Library name: itox000921


title: 1337, Canis lupus familiaris, WholeBlood,WholeBlood

description: Library name: itox001337

source_name: WholeBlood,WholeBlood

value: WholeBlood,WholeBlood


title: 919, Macaca fascicularis, KidneyMedulla

description: Library name: itox000919


title: 796, Macaca fascicularis, Gastrocnemius

description: Library name: itox000796


title: 1080, Canis lupus familiaris, Pituitary,Pituitary

description: Library name: itox001080

source_name: Pituitary,Pituitary

value: Pituitary,Pituitary


title: 925, Macaca fascicularis, KidneyMedulla

description: Library name: itox000925


title: 1081, Canis lupus familiaris, Pituitary,Pituitary

description: Library name: itox001081


title: 1338, Canis lupus familiaris, WholeBlood,WholeBlood

description: Library name: itox001338


title: 1078, Canis lupus familiaris, Pituitary,Pituitary

description: Library name: itox001078


title: 924, Macaca fascicularis, KidneyMedulla

description: Library name: itox000924


title: 1339, Canis lupus familiaris, WholeBlood,WholeBlood

description: Library name: itox001339


title: 926, Macaca fascicularis, LeftAtrium

description: Library name: itox000926

source_name: LeftAtrium

value: LeftAtrium


title: 927, Macaca fascicularis, LeftAtrium

description: Library name: itox000927


title: 1082, Canis lupus familiaris, Pituitary,Pituitary

description: Library name: itox001082


title: 1318, Canis lupus familiaris, VenaCava,VenaCava

description: Library name: itox001318


title: 1315, Canis lupus familiaris, Vagina,Vagina

description: Library name: itox001315

source_name: Vagina,Vagina

value: Vagina,Vagina


title: 928, Macaca fascicularis, LeftAtrium

description: Library name: itox000928


title: 1079, Canis lupus familiaris, Pituitary,Pituitary

description: Library name: itox001079


title: 1092, Canis lupus familiaris, Prostate,Prostate

description: Library name: itox001092

source_name: Prostate,Prostate

value: Prostate,Prostate


title: 1091, Canis lupus familiaris, Prostate,Prostate

description: Library name: itox001091


title: 800, Macaca fascicularis, Gastrocnemius

description: Library name: itox000800


title: 1010, Canis lupus familiaris, NervePeripheralSciatic,NervePeripheralSciatic

description: Library name: itox001010


title: 933, Macaca fascicularis, LeftAtrium

description: Library name: itox000933


title: 1030, Canis lupus familiaris, Ovary,Ovary

description: Library name: itox001030

source_name: Ovary,Ovary

value: Ovary,Ovary


title: 935, Macaca fascicularis, LeftVentricle

description: Library name: itox000935

source_name: LeftVentricle

value: LeftVentricle


title: 1032, Canis lupus familiaris, Ovary,Ovary

description: Library name: itox001032


title: 929, Macaca fascicularis, LeftAtrium

description: Library name: itox000929


title: 1093, Canis lupus familiaris, Prostate,Prostate

description: Library name: itox001093


title: 958, Canis lupus familiaris, LungRightCaudalLobe,LungRightCaudalLobe

description: Library name: itox000958

source_name: LungRightCaudalLobe,LungRightCaudalLobe

value: LungRightCaudalLobe,LungRightCaudalLobe


title: 930, Macaca fascicularis, LeftAtrium

description: Library name: itox000930


title: 934, Macaca fascicularis, LeftVentricle

description: Library name: itox000934


title: 1018, Canis lupus familiaris, NervePeripheralTibial,NervePeripheralTibial

description: Library name: itox001018


title: 937, Macaca fascicularis, LeftVentricle

description: Library name: itox000937


title: 1019, Canis lupus familiaris, NervePeripheralTibial,NervePeripheralTibial

description: Library name: itox001019


title: 1039, Canis lupus familiaris, PanTCells,PanTCells

description: Library name: itox001039

source_name: PanTCells,PanTCells

value: PanTCells,PanTCells


title: 936, Macaca fascicularis, LeftVentricle

description: Library name: itox000936


title: 1037, Canis lupus familiaris, Oviduct,Oviduct

description: Library name: itox001037

source_name: Oviduct,Oviduct

value: Oviduct,Oviduct


title: 932, Macaca fascicularis, LeftAtrium

description: Library name: itox000932


title: 1040, Canis lupus familiaris, PanTCells,PanTCells

description: Library name: itox001040


title: 939, Macaca fascicularis, LeftVentricle

description: Library name: itox000939


title: 1038, Canis lupus familiaris, Oviduct,Oviduct

description: Library name: itox001038


title: 940, Macaca fascicularis, LeftVentricle

description: Library name: itox000940


title: 941, Macaca fascicularis, LeftVentricle

description: Library name: itox000941


title: 1041, Canis lupus familiaris, PancreasBody,PancreasBody

description: Library name: itox001041

source_name: PancreasBody,PancreasBody

value: PancreasBody,PancreasBody


title: 959, Canis lupus familiaris, LungRightCaudalLobe,LungRightCaudalLobe

description: Library name: itox000959


title: 881, Macaca fascicularis, Ileum

description: Library name: itox000881

source_name: Ileum

value: Ileum


title: 947, Macaca fascicularis, LiverRt.Medial

description: Library name: itox000947


title: 948, Macaca fascicularis, LiverRt.Medial

description: Library name: itox000948


title: 1042, Canis lupus familiaris, PancreasBody,PancreasBody

description: Library name: itox001042


title: 931, Macaca fascicularis, LeftAtrium

description: Library name: itox000931


title: 1031, Canis lupus familiaris, Ovary,Ovary

description: Library name: itox001031


title: 1043, Canis lupus familiaris, PancreasBody,PancreasBody

description: Library name: itox001043


title: 1046, Canis lupus familiaris, PancreasHead,PancreasHead

description: Library name: itox001046

source_name: PancreasHead,PancreasHead

value: PancreasHead,PancreasHead


title: 885, Macaca fascicularis, Infenorparietal

description: Library name: itox000885

source_name: Infenorparietal

value: Infenorparietal


title: 884, Macaca fascicularis, Infenorparietal

description: Library name: itox000884


title: 883, Macaca fascicularis, Ileum

description: Library name: itox000883


title: 1047, Canis lupus familiaris, PancreasHead,PancreasHead

description: Library name: itox001047


title: 1049, Canis lupus familiaris, PancreasHead,PancreasHead

description: Library name: itox001049


title: 1045, Canis lupus familiaris, PancreasBody,PancreasBody

description: Library name: itox001045


title: 1240, Canis lupus familiaris, Thymus,Thymus

description: Library name: itox001240

source_name: Thymus,Thymus

value: Thymus,Thymus


title: 1048, Canis lupus familiaris, PancreasHead,PancreasHead

description: Library name: itox001048


title: 938, Macaca fascicularis, LeftVentricle

description: Library name: itox000938


title: 949, Macaca fascicularis, LiverRt.Medial

description: Library name: itox000949


title: 888, Macaca fascicularis, Infenorparietal

description: Library name: itox000888


title: 887, Macaca fascicularis, Infenorparietal

description: Library name: itox000887


title: 978, Canis lupus familiaris, MammaryGland,MammaryGland

description: Library name: itox000978

source_name: MammaryGland,MammaryGland

value: MammaryGland,MammaryGland


title: 889, Macaca fascicularis, Infenorparietal

description: Library name: itox000889


title: 979, Canis lupus familiaris, MammaryGland,MammaryGland

description: Library name: itox000979


title: 886, Macaca fascicularis, Infenorparietal

description: Library name: itox000886


title: 1241, Canis lupus familiaris, Thymus,Thymus

description: Library name: itox001241


title: 24, Macaca fascicularis, Adrenals

description: Library name: itox000024

source_name: Adrenals

value: Adrenals


title: 1242, Canis lupus familiaris, Thymus,Thymus

description: Library name: itox001242


title: 30, Macaca fascicularis, Adrenals

description: Library name: itox000030


title: 890, Macaca fascicularis, InferiorParietal

description: Library name: itox000890

source_name: InferiorParietal

value: InferiorParietal


title: 1243, Canis lupus familiaris, Thymus,Thymus

description: Library name: itox001243


title: 29, Macaca fascicularis, Adrenals

description: Library name: itox000029


title: 1244, Canis lupus familiaris, Thymus,Thymus

description: Library name: itox001244


title: 891, Macaca fascicularis, InferiorParietal

description: Library name: itox000891


title: 996, Canis lupus familiaris, Monocytes,Monocytes

description: Library name: itox000996

source_name: Monocytes,Monocytes

value: Monocytes,Monocytes


title: 295, Macaca fascicularis, BoneMarrow

description: Library name: itox000295

source_name: BoneMarrow

value: BoneMarrow


title: 296, Macaca fascicularis, BoneMarrow

description: Library name: itox000296


title: 297, Macaca fascicularis, BoneMarrow

description: Library name: itox000297


title: 1012, Canis lupus familiaris, NervePeripheralSciatic,NervePeripheralSciatic

description: Library name: itox001012


title: 957, Canis lupus familiaris, LungRightCaudalLobe,LungRightCaudalLobe

description: Library name: itox000957


title: 294, Macaca fascicularis, BoneMarrow

description: Library name: itox000294


title: 40, Macaca fascicularis, Aorta

description: Library name: itox000040

source_name: Aorta

value: Aorta


title: 1011, Canis lupus familiaris, NervePeripheralSciatic,NervePeripheralSciatic

description: Library name: itox001011


title: 956, Canis lupus familiaris, LungRightCaudalLobe,LungRightCaudalLobe

description: Library name: itox000956


title: 1021, Canis lupus familiaris, Neutrophils,Neutrophils

description: Library name: itox001021

source_name: Neutrophils,Neutrophils

value: Neutrophils,Neutrophils


title: 1119, Canis lupus familiaris, SalivaryGlandMandibular,SalivaryGlandMandibular

description: Library name: itox001119


title: 882, Macaca fascicularis, Ileum

description: Library name: itox000882


title: 1120, Canis lupus familiaris, SalivaryGlandMandibular,SalivaryGlandMandibular

description: Library name: itox001120


title: 396, Macaca fascicularis, BrownFat

description: Library name: itox000396

source_name: BrownFat

value: BrownFat


title: 400, Macaca fascicularis, BrownFat

description: Library name: itox000400


title: 398, Macaca fascicularis, BrownFat

description: Library name: itox000398


title: 399, Macaca fascicularis, BrownFat

description: Library name: itox000399


title: 397, Macaca fascicularis, BrownFat

description: Library name: itox000397


title: 1261, Canis lupus familiaris, Thyroid,Thyroid

description: Library name: itox001261

source_name: Thyroid,Thyroid

value: Thyroid,Thyroid


title: 1260, Canis lupus familiaris, Thyroid,Thyroid

description: Library name: itox001260


title: 1262, Canis lupus familiaris, Thyroid,Thyroid

description: Library name: itox001262


title: 1263, Canis lupus familiaris, Thyroid,Thyroid

description: Library name: itox001263


title: 1121, Canis lupus familiaris, SalivaryGlandMandibular,SalivaryGlandMandibular

description: Library name: itox001121


title: 1266, Canis lupus familiaris, Tongue,Tongue

description: Library name: itox001266

source_name: Tongue,Tongue

value: Tongue,Tongue


title: 402, Macaca fascicularis, BrownFat

description: Library name: itox000402


title: 1259, Canis lupus familiaris, Thyroid,Thyroid

description: Library name: itox001259


title: 1267, Canis lupus familiaris, Tongue,Tongue

description: Library name: itox001267


title: 1265, Canis lupus familiaris, Tongue,Tongue

description: Library name: itox001265


title: 427, Macaca fascicularis, Cerebellum

description: Library name: itox000427

source_name: Cerebellum

value: Cerebellum


title: 1268, Canis lupus familiaris, Tongue,Tongue

description: Library name: itox001268


title: 403, Macaca fascicularis, BrownFat

description: Library name: itox000403


title: 404, Macaca fascicularis, Cecum

description: Library name: itox000404

source_name: Cecum

value: Cecum


title: 1269, Canis lupus familiaris, Tongue,Tongue

description: Library name: itox001269


title: 430, Macaca fascicularis, CingulateCortex

description: Library name: itox000430

source_name: CingulateCortex

value: CingulateCortex


title: 1006, Canis lupus familiaris, NKCells,NKCells

description: Library name: itox001006

source_name: NKCells,NKCells

value: NKCells,NKCells


title: 401, Macaca fascicularis, BrownFat

description: Library name: itox000401


title: 431, Macaca fascicularis, CingulateCortex

description: Library name: itox000431


title: 41, Macaca fascicularis, Aorta

description: Library name: itox000041


title: 44, Macaca fascicularis, Aorta

description: Library name: itox000044


title: 1013, Canis lupus familiaris, NervePeripheralSciatic,NervePeripheralSciatic

description: Library name: itox001013


title: 432, Macaca fascicularis, CingulateCortex

description: Library name: itox000432


title: 1015, Canis lupus familiaris, NervePeripheralTibial,NervePeripheralTibial

description: Library name: itox001015


title: 1014, Canis lupus familiaris, NervePeripheralSciatic,NervePeripheralSciatic

description: Library name: itox001014


title: 1053, Canis lupus familiaris, PancreasTail,PancreasTail

description: Library name: itox001053

source_name: PancreasTail,PancreasTail

value: PancreasTail,PancreasTail


title: 1054, Canis lupus familiaris, PancreasTail,PancreasTail

description: Library name: itox001054


title: 1055, Canis lupus familiaris, PancreasTail,PancreasTail

description: Library name: itox001055


title: 437, Macaca fascicularis, CingulateCortex

description: Library name: itox000437


title: 440, Macaca fascicularis, AoEC

description: Library name: itox000440

source_name: AoEC

value: AoEC


title: 439, Macaca fascicularis, AoEC

description: Library name: itox000439


title: 434, Macaca fascicularis, CingulateCortex

description: Library name: itox000434


title: 1065, Canis lupus familiaris, Parathyroid,Parathyroid

description: Library name: itox001065

source_name: Parathyroid,Parathyroid

value: Parathyroid,Parathyroid


title: 441, Macaca fascicularis, LMVEC

description: Library name: itox000441

source_name: LMVEC

value: LMVEC


title: 438, Macaca fascicularis, AoEC

description: Library name: itox000438


title: 977, Canis lupus familiaris, MammaryGland,MammaryGland

description: Library name: itox000977

source_name: MammaryGland,MammaryGland

value: MammaryGland,MammaryGland


title: 45, Macaca fascicularis, Aorta

description: Library name: itox000045


title: 976, Canis lupus familiaris, MammaryGland,MammaryGland

description: Library name: itox000976


title: 443, Macaca fascicularis, LSEC

description: Library name: itox000443

source_name: LSEC

value: LSEC


title: 1064, Canis lupus familiaris, Parathyroid,Parathyroid

description: Library name: itox001064


title: 445, Macaca fascicularis, Colon

description: Library name: itox000445

source_name: Colon

value: Colon


title: 1225, Canis lupus familiaris, TestisTubules,TestisTubules

description: Library name: itox001225

source_name: TestisTubules,TestisTubules

value: TestisTubules,TestisTubules


title: 1069, Canis lupus familiaris, Parathyroid,Parathyroid

description: Library name: itox001069


title: 435, Macaca fascicularis, CingulateCortex

description: Library name: itox000435


title: 1067, Canis lupus familiaris, Parathyroid,Parathyroid

description: Library name: itox001067


title: 1066, Canis lupus familiaris, Parathyroid,Parathyroid

description: Library name: itox001066


title: 1226, Canis lupus familiaris, TestisTubules,TestisTubules

description: Library name: itox001226


title: 1068, Canis lupus familiaris, Parathyroid,Parathyroid

description: Library name: itox001068


title: 433, Macaca fascicularis, CingulateCortex

description: Library name: itox000433


title: 447, Macaca fascicularis, Colon

description: Library name: itox000447


title: 444, Macaca fascicularis, Colon

description: Library name: itox000444


title: 1227, Canis lupus familiaris, TestisTubules,TestisTubules

description: Library name: itox001227


title: 446, Macaca fascicularis, Colon

description: Library name: itox000446


title: 448, Macaca fascicularis, Colon

description: Library name: itox000448


title: 1279, Canis lupus familiaris, Trachea,Trachea

description: Library name: itox001279

source_name: Trachea,Trachea

value: Trachea,Trachea


title: 1278, Canis lupus familiaris, Trachea,Trachea

description: Library name: itox001278


title: 703, Macaca fascicularis, Esophagus

description: Library name: itox000703

source_name: Esophagus

value: Esophagus


title: 449, Macaca fascicularis, Colon

description: Library name: itox000449


title: 442, Macaca fascicularis, LSEC

description: Library name: itox000442


title: 1280, Canis lupus familiaris, Trachea,Trachea

description: Library name: itox001280


title: 704, Macaca fascicularis, Esophagus

description: Library name: itox000704


title: 705, Macaca fascicularis, Esophagus

description: Library name: itox000705


title: 1281, Canis lupus familiaris, Trachea,Trachea

description: Library name: itox001281


title: 1290, Canis lupus familiaris, Ureter,Ureter

description: Library name: itox001290

source_name: Ureter,Ureter

value: Ureter,Ureter


title: 1291, Canis lupus familiaris, Ureter,Ureter

description: Library name: itox001291


title: 706, Macaca fascicularis, Esophagus

description: Library name: itox000706


title: 1292, Canis lupus familiaris, Ureter,Ureter

description: Library name: itox001292


title: 708, Macaca fascicularis, Esophagus

description: Library name: itox000708


title: 707, Macaca fascicularis, Esophagus

description: Library name: itox000707


title: 710, Macaca fascicularis, Esophagus

description: Library name: itox000710


title: 1340, Canis lupus familiaris, WholeBlood,WholeBlood

description: Library name: itox001340

source_name: WholeBlood,WholeBlood

value: WholeBlood,WholeBlood


title: 1293, Canis lupus familiaris, Ureter,Ureter

description: Library name: itox001293


title: 709, Macaca fascicularis, Esophagus

description: Library name: itox000709


title: 893, Macaca fascicularis, Jejunum

description: Library name: itox000893

source_name: Jejunum

value: Jejunum


title: 1342, Canis lupus familiaris, WholeBlood,WholeBlood

description: Library name: itox001342


title: Hyalomma anatolicum whole body transcriptome, PM treatment, biol rep 2

city: Urumqi

first: Ercha

last: Hu

state: Xinjiang

address: East nongda Rd 311，Sayibak district

department: College of Veterinary Medicine

country: China

institute: Xinjiang Agricultural University

description: Library name: PM2

data_processing:
Following sequencing, image files were obtained and converted into raw data in FASTQ format using software provided by the sequencing platform. These raw data, also known as off - machine data, contained a small number of reads with sequencing adapters or low quality. To ensure the quality of subsequent information analysis, raw reads were filtered to obtain clean reads. The data processing steps included using fastp v.0.22.0 to remove sequences with adapters at the 3' end and to discard low - quality reads, which were defined as reads where more than 50% of the bases had a quality score of Qphred ≤ 20. All subsequent analyses were based on high - quality clean data.
Assembly: Not applicable; de novo transcriptome assembly was performed.
Supplementary files format and content: Expression.xlsx；Trinity.fasta

organism: Hyalomma anatolicum

source_name: Ticks as a whole

growth_protocol: To investigate the gene expression profiles of H. anatolicum in response to bacterial challenges, transcriptome and proteome sequencing were conducted in this study. Specifically, female H. anatolicum ticks, collected from the same breeding experiment two weeks post - molting, were first immersed in sterile phosphate - buffered saline (PBS) solution and gently agitated for 15 s to clean their surfaces for three times. After thorough drying on sterile medical gauze, the ticks were positioned under a dissecting microscope with their ventral side exposed upwards. Each tick was then individually injected with either S. aureus suspended in phosphate-buffered saline (500 nL containing 10⁷ CFU) or P. mirabilis suspended in PBS (500 nL containing 10⁷ CFU), and a small amount of sterile petrolatum was picked up with a sterile needle and quickly applied to seal the wound upon needle withdrawal. This was accomplished through a puncture into their fourth coxal segment using a precision microsyringe (Hamilton Bonaduz, LTD, Switzerland). The control group received an equivalent volume of PBS (500 nL, 10 mM) to allow for comparative analysis of responses during bacterial invasion.After injection, each tick was individually positioned in a 5 ml Eppendorf tube for observation. Following a 24 - hour period, those displaying robust vitality and normal mobility were chosen (survival rate > 95% among punctured ticks), and placed into cryovials. For subsequent sequencing sample preparation, each sample comprised a group of ten ticks pooled together, with three biological replicates for each experimental group. The samples were swiftly submerged in liquid nitrogen for freezing and subsequently stored at -80°C for future use.

extract_protocol:
The extraction of total RNA was conducted using Trizol reagent (Invitrogen, California, USA) according to the manufacturer's instructions. The concentration and purity of the total RNA were assessed using a NanoDrop (Thermo Scientific NanoDrop 2000, USA), while the integrity was evaluated using a 2100 Bioanalyzer (Agilent, California, USA) with the RNA 6000 Nano kit. Poly(A) RNA was purified using Poly - T magnetic beads from 5 μg of total RNA, with one round of extraction repeated. The purified mRNA was randomly fragmented using divalent cations through an ionic disruption process. Fragmented mRNA served as the template, with random oligonucleotides acting as primers for cDNA synthesis. The purified double - stranded cDNA underwent end - repair, A - tailing, and ligation of sequencing adapters. cDNA fragments of 400 - 500 bp were selected using AMPure XP beads for PCR amplification. The PCR products were then purified using AMPure XP beads, resulting in the final library. The quality of the library was assessed using an Agilent 2100 Bioanalyzer with the Agilent High Sensitivity DNA Kit. The total concentration of the library was determined using Pico Green, while the effective library concentration was quantified using qPCR. After normalization, the multiple DNA libraries were mixed in equal volumes. The mixed library was then diluted and quantified before being sequenced on an Illumina sequencing platform in PE150 mode.
The purified mRNA was randomly fragmented using divalent cations through an ionic disruption process. Fragmented mRNA served as the template, with random oligonucleotides acting as primers for cDNA synthesis. The purified double - stranded cDNA underwent end - repair, A - tailing, and ligation of sequencing adapters. cDNA fragments of 400 - 500 bp were selected using AMPure XP beads for PCR amplification. The PCR products were then purified using AMPure XP beads, resulting in the final library. The quality of the library was assessed using an Agilent 2100 Bioanalyzer with the Agilent High Sensitivity DNA Kit. The total concentration of the library was determined using Pico Green, while the effective library concentration was quantified using qPCR. After normalization, the multiple DNA libraries were mixed in equal volumes. The mixed library was then diluted and quantified before being sequenced on an Illumina sequencing platform in PE150 mode.

value: Ticks as a whole


title: 897, Macaca fascicularis, Jejunum

description: Library name: itox000897


title: 995, Canis lupus familiaris, Monocytes,Monocytes

description: Library name: itox000995

source_name: Monocytes,Monocytes

value: Monocytes,Monocytes


title: 896, Macaca fascicularis, Jejunum

description: Library name: itox000896


title: 898, Macaca fascicularis, Jejunum

description: Library name: itox000898


title: Hyalomma anatolicum whole body transcriptome, PM treatment, biol rep 3

description: Library name: PM3


title: 955, Canis lupus familiaris, LungRightCaudalLobe,LungRightCaudalLobe

description: Library name: itox000955

source_name: LungRightCaudalLobe,LungRightCaudalLobe

value: LungRightCaudalLobe,LungRightCaudalLobe


title: Hyalomma anatolicum whole body transcriptome, PBS treatment, biol rep 3

description: Library name: PBS3


title: 895, Macaca fascicularis, Jejunum

description: Library name: itox000895


title: Hyalomma anatolicum whole body transcriptome, PM treatment, biol rep 1

description: Library name: PM1


title: Hyalomma anatolicum whole body transcriptome, PBS treatment, biol rep 2

description: Library name: PBS2


title: 905, Macaca fascicularis, KidneyCortex

description: Library name: itox000905

source_name: KidneyCortex

value: KidneyCortex


title: 892, Macaca fascicularis, Jejunum

description: Library name: itox000892


title: 904, Macaca fascicularis, KidneyCortex

description: Library name: itox000904


title: Hyalomma anatolicum whole body transcriptome, PBS treatment, biol rep 1

description: Library name: PBS1


title: 906, Macaca fascicularis, KidneyCortex

description: Library name: itox000906


title: 1341, Canis lupus familiaris, WholeBlood,WholeBlood

description: Library name: itox001341


title: Hyalomma anatolicum whole body transcriptome, SA treatment, biol rep 1

description: Library name: SA1


title: adult_opc_ctrl

city: shanghai

first: Wenxiu

last: Dai

address: No. 746, Zhongshan Middle Road, Songjiang District, Shanghai

institute: Shanghai Jiao Tong University

description: Library name: Sample 2

data_processing:
The Raw data obtained from sequencing was filtered using SOAPnuke.
The clean data was aligned to the reference gene set using Bowtie2.
Assembly: GCF_000001895.5 Rnor_6.0
Supplementary files format and content: The txt file contains the FPKM value of each sample gene
Supplementary files format and content: The csv file contains GO information for data processing

organism: Rattus norvegicus

source_name: brain

growth_protocol: OPC grows in OGM culture medium with a humidity of 5% CO2 and a temperature of 37℃.

extract_protocol:
The RNA of adult OPCs was prepared using the Illumina RNA-Seq preparation kit,1 ug of total RNA was used to construct the sequencing library.
Library preparation using the BGI Optimal series dual-module mRNA library construction kit (BGI-Shenzhen, China), RNA-seq libraries were prepared in accordance with the manufacturer's protocol.

treatment_protocol: The OPC was treated with 1uM Abeta for 2 days before sample collection.

value: brain

tag: cell type

value: OPC

tag: genotype

value: WT

tag: treatment

value: DMSO


title: 907, Macaca fascicularis, KidneyCortex

description: Library name: itox000907


title: 909, Macaca fascicularis, KidneyCortex

description: Library name: itox000909


title: 894, Macaca fascicularis, Jejunum

description: Library name: itox000894


title: Hyalomma anatolicum whole body transcriptome, SA treatment, biol rep 2

description: Library name: SA2


title: 908, Macaca fascicularis, KidneyCortex

description: Library name: itox000908


title: 910, Macaca fascicularis, KidneyCortex

description: Library name: itox000910


title: adult_opc_Abeta

description: Library name: Sample 1

value: Aβ


title: 911, Macaca fascicularis, KidneyCortex

description: Library name: itox000911


title: 25, Macaca fascicularis, Adrenals

description: Library name: itox000025

source_name: Adrenals

value: Adrenals


title: 35, Macaca fascicularis, Amygdala

description: Library name: itox000035

source_name: Amygdala

value: Amygdala


title: 36, Macaca fascicularis, Amygdala

description: Library name: itox000036


title: 26, Macaca fascicularis, Adrenals

description: Library name: itox000026


title: 37, Macaca fascicularis, Amygdala

description: Library name: itox000037


title: 450, Macaca fascicularis, Colon

description: Library name: itox000450

value: Colon


title: IDE-KD alpha pancreatic cells, biological rep 4

city: Palencia

first: Sergio

last: Díez-Hermano

state: Palencia

address: C/Felipe II, 10, 2C

country: Spain

institute: University of Valladolid

description: Gene expression data from IDE-KD alphaTC1.9 cells

hyb_protocol: Following fragmentation, 1 ug of cRNA wer hybridized for 16h at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the microarray scanner GenePix4000B

data_processing: The data were analysed with R programming language (v4.4.1), using the default RMA calibration parameters in the oligo package and the default contrast parameters for eBayes in the limma package

label: biotin

organism: Mus musculus

source_name: IDE-KD alphaTC1.9 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: alpha-TC1.9 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with glucose (16 mM), HEPES (15 mM), non-essential amino acids (0.1 mM), 10% FBS, and 100 U/mL penicillin and 100 µg/mL streptomycin

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA (1 µg) was subjected to cDNA microarray analysis

treatment_protocol: Cell were collected by conventional means, No treatment was perfomed.  Four independent RNA replicates were processed and analyzed.

value: Pancreatic mouse tissue

value: Insulin Degrading Enzyme KD


title: Hyalomma anatolicum whole body transcriptome, SA treatment, biol rep 3

description: Library name: SA3


title: 451, Macaca fascicularis, Colon

description: Library name: itox000451


title: IDE-KD alpha pancreatic cells, biological rep 1


title: control alpha pancreatic cells, biological rep 3

description: Gene expression data from control alpha TC1.9 cells

source_name: Control alphaTC1.9 cells

value: Control


title: IDE-KD alpha pancreatic cells, biological rep 2


title: EC, MCD

city: San Antonio

first: Xiaoli

last: Sun

state: TX

address: 7703 Floyd Curl Dr

department: Pharmacology

description:
Library name: EC_MCD
Endothelial cell

data_processing:
All data were aligned to the hg38 or mm10 assembly of the human or mouse genome, and all subsequent data analysis was performed using HOMER, and detailed instructions for analysis can be found at http://homer.salk.edu/homer/ . Mapped data were analyzed with HOMER's "analyzeRepeats.pl" function with options -raw -condenseGenes and -count exons. Differential expression was performed using Homer's getDiffExpression.pl function, which uses DESeq2.
Assembly: mm10 or hg38
Supplementary files format and content: tab-delimited text files include Raw counts and TPM for each sample.

molecule: polyA RNA

source_name: immortalized human aortic endothelial cells

extract_protocol:
Cells were lysed in RNA lysis buffer and total RNA was isolated using PureLink RNA Mini Kit following manufacturer’s instructions (Life Technologies).
RNA quality was assessed by Agilent 4200 TapeStation System. Sequencing libraries were prepared in biological replicates from polyA enriched mRNA. RNA-seq libraries were prepared from poly(A)-enriched mRNA as previously described (PMID:31761566). Libraries were then size selected by beads selection, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and sequenced on a Nextseq 2000 system at the Genome Sequencing Facility of the University of Texas Health Science Center at San Antonio.

tag: cell line

value: Endothelial cell

value: Wildtype

value: MCD


title: 453, Macaca fascicularis, Cornea

description: Library name: itox000453

source_name: Cornea

value: Cornea


title: HSC, MCD

institute: University of Texas Health Science Center at San Antonio

description:
Library name: HSC_MCD
Stellate Cell

source_name: immortalized hepatic stellate cells

value: immortalized hepatic stellate cells

value: Stellate Cell


title: HSC, Ctrl

description:
Library name: HSC_WT
Stellate Cell

value: vehicle


title: 46, Macaca fascicularis, Aorta

description: Library name: itox000046

source_name: Aorta

value: Aorta


title: 452, Macaca fascicularis, Cornea

description: Library name: itox000452


title: control alpha pancreatic cells, biological rep 4


title: control alpha pancreatic cells, biological rep 2


title: EC, Ctrl

description:
Library name: EC_WT
Endothelial cell

value: immortalized human aortic endothelial cells


title: 454, Macaca fascicularis, CorpusCallosum

description: Library name: itox000454

source_name: CorpusCallosum

value: CorpusCallosum


title: HepG2,Ctrl

description:
Library name: HepG2_Ctrl
Hepatocyte

value: Hepatocyte


title: 455, Macaca fascicularis, CorpusCallosum

description: Library name: itox000455


title: HepG2, MCD

description:
Library name: HepG2_MCD
Hepatocyte


title: 456, Macaca fascicularis, CorpusCallosum

description: Library name: itox000456


title: 458, Macaca fascicularis, CorpusCallosum

description: Library name: itox000458


title: PDOX12-P-P snRNA-seq

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

description: Library name: xp026A-83P

library_source: transcriptomic single cell

data_processing:
We used the 10X Cell Ranger platform to generate snRNA-seq and scRNA-seq count matrix.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mouse-xenografted PDO

extract_protocol:
Viable single-cell suspensions of PDOs were prepared and processed using the Chromium X instrument (10x Genomics) with the Chromium Next GEM Single Cell 3ʹ Kit v3.1, 3ʹ CellPlex Kit Set A, and 3ʹ Feature Barcode Kit (10x Genomics), following the manufacturer’s protocols. Four to five samples were multiplexed in each run using CellPlex sample barcodes. Library quality and concentration were evaluated by the TapeStation, and sequencing was performed on the NextSeq 550. Frozen PDOX tumor tissues were processed using the Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics). Isolated nuclei were then fixed and barcoded on the Chromium X using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics) and the Chromium Fixed RNA Kit, Human Transcriptome (10x Genomics), in accordance with the manufacturer’s instructions. Four samples were multiplexed per run using fixed RNA barcodes. Library quality and concentration were evaluated by the TapeStation, and sequencing was performed on the NextSeq 550.
Viable single-cell suspensions of PDOs were prepared and processed using the Chromium X instrument (10x Genomics) with the Chromium Next GEM Single Cell 3ʹ Kit v3.1, 3ʹ CellPlex Kit Set A, and 3ʹ Feature Barcode Kit (10x Genomics), following the manufacturer’s protocols. Four to five samples were multiplexed in each run using CellPlex sample barcodes. Library quality and concentration were evaluated by the TapeStation, and sequencing was performed on the NextSeq 550. Frozen PDOX tumor tissues were processed using the Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics). Isolated nuclei were then fixed and barcoded on the Chromium X using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics) and the Chromium Fixed RNA Kit, Human Transcriptome (10x Genomics), in accordance with the manufacturer’s instructions. Four samples were multiplexed per run using fixed RNA barcodes. Library quality and concentration were evaluated by the TapeStation, and sequencing was performed on the NextSeq 550.

value: Mouse-xenografted PDO


title: PDOX12-A-P snRNA-seq

description: Library name: xp026A-75P


title: 459, Macaca fascicularis, CorpusCallosum

description: Library name: itox000459


title: PDOX12-A-A snRNA-seq

description: Library name: xp026A-75A


title: 460, Macaca fascicularis, CorpusCallosum

description: Library name: itox000460


title: 461, Macaca fascicularis, CorpusCallosum

description: Library name: itox000461


title: PDO17 scRNA-seq

description: Library name: OP037

source_name: Patient-derived organoid

value: Patient-derived organoid


title: PDO14 scRNA-seq

description: Library name: OP031A


title: 457, Macaca fascicularis, CorpusCallosum

description: Library name: itox000457


title: 466, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000466

source_name: DorsalRootGanglia

value: DorsalRootGanglia


title: PDOX12-P snRNA-seq

description: Library name: xp026A-69P


title: PDO16 scRNA-seq

description: Library name: OP038P


title: 465, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000465


title: PDO17H scRNA-seq

description: Library name: OP037H


title: 47, Macaca fascicularis, Aorta

description: Library name: itox000047


title: 463, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000463


title: PDO13 scRNA-seq

description: Library name: OP030


title: 467, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000467


title: PDO10 scRNA-seq

description: Library name: OP022


title: 470, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000470


title: 464, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000464


title: 471, Macaca fascicularis, Duodenum

description: Library name: itox000471

source_name: Duodenum

value: Duodenum


title: PDO12 scRNA-seq

description: Library name: OP026A


title: 758, Macaca fascicularis, FrontalCortex

description: Library name: itox000758

source_name: FrontalCortex

value: FrontalCortex


title: 468, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000468


title: PDO09 scRNA-seq

description: Library name: OP021


title: PDO15 scRNA-seq

description: Library name: OP033A


title: PDO03 scRNA-seq

description: Library name: OP014


title: 469, Macaca fascicularis, DorsalRootGanglia

description: Library name: itox000469


title: 759, Macaca fascicularis, FrontalCortex

description: Library name: itox000759


title: PDO04 scRNA-seq

description: Library name: OP016


title: IDE-KD alpha pancreatic cells, biological rep 3

value: Pancreatic mouse tissue

value: Insulin Degrading Enzyme KD


title: 761, Macaca fascicularis, FrontalCortex

description: Library name: itox000761


title: PDO01 scRNA-seq

description: Library name: OP001


title: 760, Macaca fascicularis, FrontalCortex

description: Library name: itox000760


title: PDO11 scRNA-seq

description: Library name: OP025A


title: 770, Macaca fascicularis, GallBladder

description: Library name: itox000770

source_name: GallBladder

value: GallBladder


title: PDO02 scRNA-seq

description: Library name: OP012


title: PDOX12-A-P scATAC-seq

description: Library name: 20250319sdA-XP026A-75-P

library_source: genomic single cell

data_processing:
The hg19 genome assembly was used for the scATAC-seq analyses. The initial processing of scATAC-seq data to generate barcoded and aligned read bam files was performed using the ATAC-Seq Analysis Toolkit (Bio-Rad). Sequencing data were then processed by converting BAM files into fragment files using Rsamtools (https://bioconductor.org/packages/Rsamtools).
Assembly: hg19
Supplementary files format and content: tsv, fragment count

molecule: genomic DNA

extract_protocol:
scATAC-seq was performed as previously described16 using the ddSEQ Single-Cell Isolator (Bio-Rad) together with the ddSEQ Single-Cell ATAC-Seq Library Prep Kit (Bio-Rad) according to the manufacturer’s protocol. Library quality and concentration were assessed with the TapeStation (Agilent), and pooled libraries were sequenced on the Illumina NextSeq 550.
scATAC-seq was performed as previously described16 using the ddSEQ Single-Cell Isolator (Bio-Rad) together with the ddSEQ Single-Cell ATAC-Seq Library Prep Kit (Bio-Rad) according to the manufacturer’s protocol. Library quality and concentration were assessed with the TapeStation (Agilent), and pooled libraries were sequenced on the Illumina NextSeq 550.

value: pancreatic cancer cell


title: PDO05 scRNA-seq

description: Library name: OP018


title: 763, Macaca fascicularis, FrontalCortex

description: Library name: itox000763


title: PDO18 RNA-seq

description: Library name: 20230825R-OP039A_S2

data_processing:
To generate the expression count matrix, the raw reads were trimmed using Skewer (v. 0.2.2) to remove adapter sequences. The processed reads were mapped to the hg38 genome and counted using STAR (v2.7.8a).
Assembly: hg38
Supplementary files format and content: tab, raw count

extract_protocol:
Total RNA was extracted from PDOs using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were generated using the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara). Library quality and concentration were assessed with the TapeStation (Agilent), and pooled libraries were sequenced on the Illumina NextSeq 550.


title: 771, Macaca fascicularis, GallBladder

description: Library name: itox000771


title: PDOX12-A-A scATAC-seq

description: Library name: 20250319sdA-XP026A-75-A


title: PDO16 RNA-seq

description: Library name: 20230825R-OP038P_S1


title: 772, Macaca fascicularis, GallBladder

description: Library name: itox000772


title: PDO15 RNA-seq

description: Library name: 20230728R-OP033A_S5


title: 774, Macaca fascicularis, GallBladder

description: Library name: itox000774


title: PDO11 RNA-seq

description: Library name: 20230728R-OP025A_S3


title: PDO09 RNA-seq

description: Library name: 20230728R-OP021_S2


title: PDO12 RNA-seq

description: Library name: 20230728R-OP026A_S4


title: 762, Macaca fascicularis, FrontalCortex

description: Library name: itox000762


title: 777, Macaca fascicularis, GallBladder

description: Library name: itox000777


title: 33, Macaca fascicularis, Amygdala

description: Library name: itox000033

value: Amygdala


title: PDO02 RNA-seq

description: Library name: 20230712R-OP012_S1


title: PDO06 RNA-seq

description: Library name: 20230712R-OP017_S3


title: PDO03 RNA-seq

description: Library name: 20230712R-OP014_S2


title: 775, Macaca fascicularis, GallBladder

description: Library name: itox000775


title: 34, Macaca fascicularis, Amygdala

description: Library name: itox000034


title: 776, Macaca fascicularis, GallBladder

description: Library name: itox000776


title: 746, Macaca fascicularis, EyeRetina

description: Library name: itox000746

source_name: EyeRetina

value: EyeRetina


title: 744, Macaca fascicularis, EyeRetina

description: Library name: itox000744


title: 743, Macaca fascicularis, EyeRetina

description: Library name: itox000743


title: PDO14 RNA-seq

description: Library name: 20230712R-OP031_S5


title: TTseq_HG03464_rep1

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Sample32

data_processing:
10X linked-reads: 10X linked-reads were mapped to the hg38-based reference genome (refdata-GRCh38-2.1.0) provided by 10X Genomics using the Long Ranger pipeline v2.2.2 with the “--precalled” parameter to specify a VCF file containing variant data from the 1000 Genomes Project.
Hi-C: Hi-C reads were mapped to the hg38 human reference genome assembly using bwa mem with the Open2C distiller-nf pipeline. Mapped reads were parsed using pairtools with the walks-policy parameter set to mask and the max_mismatch_bp parameter set to 1. Read pairs were then binned into Hi-C contact matrices. Iterative correction of the matrices and removal of low coverage bins was performed using the "balance" function from cooler.!Sample_data_processing = ATAC-seq: ATAC-seq reads were mapped to the hg38 reference human genome and both haplotypes 1 and 2 of the personal genome using bwa v0.7.17-r1188. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools v1.6. Duplicate reads were filtered out using the Picard v2.27.4 “MarkDuplicates” function. Peak calling was performed using MACS2 v2.2.6.
TT-seq: TT-seq reads were mapped using STAR v2.7.10a with the “--outFilterMultimapNmax” set to 20, the “--alignSJoverhangMin” set to 999, the “--alignSJDBoverhangMin” set to 1, the “--outFilterMismatchNmax” set to 999, the “--outFilterMismatchNoverReadLmax” set to 0.04. Uniquely mapped reads with MAPQ>10 were selected using SAMtools v1.6. Duplicate reads were filtered out using the Picard v2.27.4 “MarkDuplicates” function. Gene counts were obtained using the ”htseq-count” function from HTSeq v0.13.5.
Assembly: hg38
Supplementary files format and content: ATAC-seq: normalized signal tracks in bigWig format; peaks in BED format; peak counts in TXT format. TT-seq: normalized signal tracks in bigWig format; read counts in TXT format. Hi-C: contact matrices in MCOOL format.

source_name: HG03464 lymphoblastoid cell line

growth_protocol: Lymphoblastoid cell lines were cultured in suspension in 80% RPMI-1640 media (Gibco) supplemented with 20% fetal bovine serum, 2 mM L-glutamine, and 1X penicillin/streptomycin.

extract_protocol:
10X linked-reads: Linked-reads data generation was outsourced to NGX Bio. For each sample, 3 million cells were harvested in PBS and the frozen cell pellets were sent to NGX Bio for processing. The resulting high molecular weight DNA was extracted using the MagAttract HMW DNA Extraction Kit (Qiagen). The quality of the DNA was assessed using the TapeStation system (Agilent Technologies).
Hi-C: Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). Cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI (NEB), and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down.
ATAC-seq: Cells were washed in cold PBS and subjected to lysis using a 2x lysis buffer. Subsequently, the cells were centrifuged, and the resulting pellet was treated with 2xTD buffer and 2 uL of transposon mix.
TT-seq: Libraries for TTchem-seq were prepared following a published protocol (Gregersen et al., 2020). Cells were labelled with 2 mM of the uridine analog 4-thiouridine (4sU) for 10 min. Total RNA was isolated and fragmented. The 4sU-biotin labelled RNA was enriched using µMacs Streptavidin Kit (Miltenyi).
10X linked-reads: Libraries were prepared using the 10X Genomics GemCode platform with reagents from 10X Genomics and the KAPA Hyper Prep Kit (Roche).
Hi-C: Hi-C libraries were prepared using a standard end-repair and A-tailing method.
ATAC-seq: PCR amplification was conducted using KAPA HiFi HotStart ReadyMix (Roche). Fragments ranging from 200 to 700 bp were purified utilising AMPure XP beads (Beckman Coulter).
TT-seq: Libraries were prepared using KAPA RNA HyperPrep and KAPA Dual-Indexed Adapter kits (Roche) using dual indexing adapters.

value: HG03464 lymphoblastoid cell line

value: B-Lymphocyte


title: TTseq_HG03464_rep2

description: Library name: Sample33


title: 753, Macaca fascicularis, FallopianTube

description: Library name: itox000753

source_name: FallopianTube

value: FallopianTube


title: 745, Macaca fascicularis, EyeRetina

description: Library name: itox000745


title: 756, Macaca fascicularis, FrontalCortex

description: Library name: itox000756


title: TTseq_HG02601_rep2

description: Library name: Sample31

source_name: HG02601 lymphoblastoid cell line

value: HG02601 lymphoblastoid cell line


title: 773, Macaca fascicularis, GallBladder

description: Library name: itox000773


title: TTseq_HG01241_rep1

description: Library name: Sample28

source_name: HG01241 lymphoblastoid cell line

value: HG01241 lymphoblastoid cell line


title: 754, Macaca fascicularis, FallopianTube

description: Library name: itox000754


title: TTseq_HG02601_rep1

description: Library name: Sample30


title: 757, Macaca fascicularis, FrontalCortex

description: Library name: itox000757


title: TTseq_HG01241_rep2

description: Library name: Sample29


title: TTseq_NA18983_rep2

description: Library name: Sample27

source_name: GM18983 lymphoblastoid cell line

value: GM18983 lymphoblastoid cell line


title: PDO04 RNA-seq

description: Library name: 20230728R-OP015_S1


title: TTseq_NA18983_rep1

description: Library name: Sample26


title: 858, Macaca fascicularis, Hippocampus

description: Library name: itox000858

source_name: Hippocampus

value: Hippocampus


title: TTseq_NA12878_rep1

description: Library name: Sample24

source_name: GM12878 lymphoblastoid cell line

value: GM12878 lymphoblastoid cell line


title: 860, Macaca fascicularis, Hippocampus

description: Library name: itox000860


title: TTseq_NA12878_rep2

description: Library name: Sample25


title: 862, Macaca fascicularis, Hippocampus

description: Library name: itox000862


title: MLNM27

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
RNA (amplified oligo nucleotide probes)
GeoMx_NGS_Pipeline_ 2.0.0

data_processing:
Raw counts corresponding to RNA probes were normalized and analyzed using DESeq2.
The FastQ files generated by the Illumina sequencing were converted
Assembly: GRCh38.p13
Supplementary files format and content: The raw reads count was normalized using: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html. Differential Expression Outputs including mean normalized values in each group, fold change (FC), raw p value and adjusted p value (p value for each probe after adjustment using the Benjamini and Hochberg method for controlling the false discovery rate) between groups were calculated. PCA was used to determine sample clustering. In all HTG-AI data comparisons, a Log2|FC | ≥ 1 and adjusted p value < 0.05 as significant difference between groups was considered.
Library strategy: Targeted transcriptomics

source_name: Melanoma lymph node metastasis

extract_protocol:
The tumor areas were marked by referring to the H&E staining of the consecutive slide, with the accordance of a certificated pathologist. The estimated tissue areas were measured using Image J software. Then, the optimal amounts of tissue for each HTG EdgeSeq AI assay were scraped and placed into microfuge tubes. The calculated volume of lysis buffer for each collected sample was added, and the samples were then overlaid with 500 μL of HTG denaturation oil. After centrifugation, the samples were incubated at 95 °C for 15–20 min to denature protein structures and remove paraffin wax from the FFPE tissue sections. Samples were cooled down for 10 min at room temperature (RT), and HTG provided Proteinase K was pipetted into the aqueous (lysis, non-oil) phase of the samples at a volume 1/20th of the total lysis buffer. Finally, the samples were incubated at 50 °C for 3 h, with the aqueous phase being mixed by pipetting every 30 min. Subsequently, 25 μL of the sample lysate was loaded onto the HTG EdgeSeq instrument for probe-capture for 20 h.
Probe-captured FFPE samples for HTG-AI assay were amplified and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buffer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers. The PCR reaction conditions were as follows: (1) 95 °C for 4 min, (2) 95 °C for 15 s, (3) 56 °C for 45 s, (4) 68 °C for 45 s, (5) repeating steps 2–4 for a total of 19 cycles, (6) 68 °C for 10 min, and (7) holding at 4 °C. Following PCR, library cleanup was performed with a mixture of clean up buffer (39% of 5M NaCl, 31.25% of 40% PEG 8000, 29.75% of molecular-grade water) and AMPure XP beads, by combining it with the PCR-amplified sample at 5:2 ratio, respectively. After 5 min of incubation, the samples were placed on the magnetic stand, then washed twice with 80% ethanol, followed by a 5-min air drying period. The elution was performed using 40 μL of 10mM Tris-HCl, pH 8.0.
All libraries were quantitated using the KAPA Library Quant Kit (Illumina Inc., San Diego, CA, USA) and the Universal qPCR Mix Kit (Roche, Basel, Switzerland) in accordance with the manufacturer’s recommendations. Quality checks (QC) for library size were performed on the Agilent Technologies TapeStation 2200 instrument using the High Sensitivity D1000 ScreenTape and High Sensitivity D1000 reagents (Agilent Technologies Inc., Santa Clara, CA, USA). The expected peak size ranged between 150 and 170 base pairs. Samples that did not indicate proper library formation were excluded from sequencing and the library preparation process was repeated.
Quantitated libraries were diluted, normalized, and pooled based on the raw quantity (pM) generated by the HTG EdgeSeq RUO Library calculator software version 2.0.0. Then, libraries were denatured in 0.2 N NaOH for 8 min at RT. NaOH was hydrolyzed with 200mM Tris pH 7.4, and the denatured pool was then diluted down to 4 pM using the Hyb buffer supplied in the NextSeq 550 High Output Kit v2.5 (Illumina Inc., San Diego, CA, USA). To introduce sequencing diversity and a positive sequencing control, 4 pM of 12.5 pM PhiX Control v3 (Illumina Inc., San Diego, CA, USA) was spiked into the diluted and denatured 4 pM sample pool. The final pool consisted of 95% sample libraries and 5% PhiX control by volume. The pooled library was then denatured at 98 °C for 4 min and immediately placed on ice for at least 5 min before loaded onto the Illumina NextSeq 550 instrument, following the Illumina instrument sequencing protocol.
Sequencing on Illumina platforms was conducted according to the HTG instructions, with a read length of 1 × 50 base pairs. The raw sequencing data was transformed into FASTQ files using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0. FASTQ files were analyzed with HTG EdgeSeq Parser software version v5.1.724.4793 to generate raw counts for a total of 2,002 genes. Each sample was profiled for 2,002 genes related to tumor-immune interaction, in addition to 18 control genes.

value: Melanoma lymph node metastasis

tag: tissue id

tag: segment tag

value: LNMM


title: MLNM29


title: MLNM30


title: 861, Macaca fascicularis, Hippocampus

description: Library name: itox000861


title: 863, Macaca fascicularis, Hippocampus

description: Library name: itox000863


title: MLNM21


title: 871, Macaca fascicularis, Hypothalmus

description: Library name: itox000871

source_name: Hypothalmus

value: Hypothalmus


title: 869, Macaca fascicularis, Hypothalamus

description: Library name: itox000869

source_name: Hypothalamus

value: Hypothalamus


title: 864, Macaca fascicularis, Hippocampus

description: Library name: itox000864


title: MLNM28


title: MLNM24


title: MLNM26


title: 865, Macaca fascicularis, Hippocampus

description: Library name: itox000865


title: MLNM22


title: 755, Macaca fascicularis, FallopianTube

description: Library name: itox000755


title: 870, Macaca fascicularis, Hypothalamus

description: Library name: itox000870


title: 859, Macaca fascicularis, Hippocampus

description: Library name: itox000859


title: MLNM19


title: control alpha pancreatic cells, biological rep 1

source_name: Control alphaTC1.9 cells

value: Pancreatic mouse tissue

value: Control


title: 872, Macaca fascicularis, Hypothalmus

description: Library name: itox000872


title: MLNM17


title: MLNM16


title: 873, Macaca fascicularis, Hypothalmus

description: Library name: itox000873


title: MLNM13


title: 875, Macaca fascicularis, Hypothalmus

description: Library name: itox000875


title: 876, Macaca fascicularis, Hypothalmus

description: Library name: itox000876


title: MLNM15


title: MLNM12


title: MLNM10


title: 877, Macaca fascicularis, Ileum

description: Library name: itox000877

source_name: Ileum

value: Ileum


title: 878, Macaca fascicularis, Ileum

description: Library name: itox000878


title: MLNM11


title: 967, Macaca fascicularis, Lungs,Lungs

description: Library name: itox000967

source_name: Lungs,Lungs

value: Lungs,Lungs


title: MLNM9


title: 1124, Macaca fascicularis, SalivaryGland,SalivaryGland

description: Library name: itox001124

source_name: SalivaryGland,SalivaryGland

value: SalivaryGland,SalivaryGland


title: MLNM8

value: Normal LN


title: MLNM7


title: 874, Macaca fascicularis, Hypothalmus

description: Library name: itox000874


title: MLNM5


title: 1126, Macaca fascicularis, SalivaryGland,SalivaryGland

description: Library name: itox001126


title: 1125, Macaca fascicularis, SalivaryGland,SalivaryGland

description: Library name: itox001125


title: 1127, Macaca fascicularis, SalivaryGland,SalivaryGland

description: Library name: itox001127


title: MLNM6


title: MLNM3


title: 879, Macaca fascicularis, Ileum

description: Library name: itox000879


title: MLNM2


title: MLNM4


title: BMDM, Ctrl

description:
Library name: BMDM_WT
Macrophage

source_name: immortalized BMDM

value: immortalized BMDM

value: Macrophage

value: Wildtype

value: vehicle


title: BMDM, MCD

description:
Library name: BMDM_MCD
Macrophage

value: MCD


title: MLNM1


title: 1133, Macaca fascicularis, Septum,Septum

description: Library name: itox001133

source_name: Septum,Septum

value: Septum,Septum


title: 1132, Macaca fascicularis, Septum,Septum

description: Library name: itox001132


title: 880, Macaca fascicularis, Ileum

description: Library name: itox000880


title: HaCat cells, blank-3, Day3

city: Xi'an

first: Qiang

last: Miao

state: Shaanx

address: Changle West Road

institute: Air Force Medical University

description: Library name: Sample 9

data_processing:
Removal of reads containing adapter sequences;
Removal of low-quality reads (including reads with over 10% of bases as "N"; and reads where more than 50% of the bases have a quality score below Q10).
The resulting high-quality data, referred to as CleanData, are provided in FASTQ format.
The raw data in Fastq format was first processed using an in-house Perl script. In this step, clean data was obtained by removing adapter-containing sequences, poly-N sequences, and low-quality sequences from the raw data. Q20, Q30, GC content, and sequence duplication levels were simultaneously calculated. All downstream analyses were based on the high-quality clean data.The clean data was aligned to the reference genome sequence. Based on the reference genome, only sequences that were either perfectly matched or contained a single mismatch were selected for further analysis and annotation. The Hisat2 tool was used for alignment to the reference genome. StringTie employed a reference annotation-based transcript (RABT) assembly approach to identify known transcripts and predict novel transcripts from the Hisat2 alignment results. Gene functions were annotated via sequence alignment against the following databases: Nr (NCBI non-redundant protein sequences), Pfam (Protein family), KOG/COG (Clusters of Orthologous Groups of proteins), Swiss-Prot (A manually annotated and reviewed protein sequence database), KO (KEGG Ortholog database), and GO (Gene Ontology).Gene expression levels were quantified and estimated using Fragments Per Kilobase of transcript per Million mapped fragments (FPKM). !Sample_data_processing = The formula is shown below:
FPKM = {cDNA Fragments \over {Mapped Fragments(Millions) * TranscriptLength(kb)}}
Assembly: Homo_sapiens.GRCh38_release95.genome.fa
Supplementary files format and content: counts, fpkm

source_name: epithelial

extract_protocol:
Extract total RNA using the TRIzo reagent kit
Following sample quality control, library construction was performed primarily through the following steps: (1) Eukaryotic mRNA was enriched using Oligo(dT)-coated magnetic beads.  (2) mRNA was randomly fragmented by adding Fragmentation Buffer.  (3) Using the fragmented mRNA as template, the first and second strands of cDNA were synthesized, followed by cDNA purification.  (4) The purified double-stranded cDNA underwent end repair, A-tailing, and adapter ligation. Fragment size selection was then performed using AMPure XP beads.  (5) Finally, the cDNA library was enriched via PCR amplification.

value: epithelial

value: HaCat

value: epidermal basal layer

value: blank, Day3


title: 1134, Macaca fascicularis, Septum,Septum

description: Library name: itox001134


title: 1130, Macaca fascicularis, Septum,Septum

description: Library name: itox001130


title: 999, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox000999

source_name: MotorCortex,MotorCortex

value: MotorCortex,MotorCortex


title: 1135, Macaca fascicularis, Septum,Septum

description: Library name: itox001135


title: HaCat cells, pdna-3, Day3

description: Library name: Sample 6

value: pdna, Day3


title: 1131, Macaca fascicularis, Septum,Septum

description: Library name: itox001131


title: 1136, Macaca fascicularis, Septum,Septum

description: Library name: itox001136


title: 1128, Macaca fascicularis, SalivaryGland,SalivaryGland

description: Library name: itox001128


title: 998, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox000998


title: HaCat cells, blank-1, Day3

description: Library name: Sample 7


title: HaCat cells, pdna-1, Day3

description: Library name: Sample 4


title: 1129, Macaca fascicularis, Septum,Septum

description: Library name: itox001129


title: 1000, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox001000


title: HaCat cells, Ti-3, Day3

description: Library name: Sample 3

value: Ti, Day3


title: 1008, Macaca fascicularis, NaturalKillerCells,NaturalKillerCells

description: Library name: itox001008

source_name: NaturalKillerCells,NaturalKillerCells

value: NaturalKillerCells,NaturalKillerCells


title: HaCat cells, Ti-2, Day3

description: Library name: Sample 2


title: HaCat cells, Ti-1, Day3

description: Library name: Sample 1


title: HaCat cells, pdna-2, Day3

description: Library name: Sample 5


title: TILs with S4E6Q TCRs

city: Los Angeles

first: Zhiyuan

last: Mao

state: California

address: 675 Charles E. Young Dr. South

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

description:
Library name: S4E6Q_TCR
10X Genomics GEM-X 3’ Gene Expression v4 library

data_processing:
The data processing was conducted using 10X Genomics Cell Ranger-9.0.0, using GRCh38-2024-A as the reference.
Assembly: Human GRCh38-2024-A
Supplementary files format and content: matrix files

source_name: Tumor infiltrating lymphocytes

extract_protocol:
one million PC3-A2-PAP cells in 100 µL of 1X PBS were injected subcutaneously into the right flank of NSG mice to establish tumor xenografts. Six weeks after tumor engraftment, 5 million TCR-engineered PBMCs were administered intravenously via the tail vein. Five animals were included in each group. Three out of five animals with similar sizes of tumors were sacrificed 10 days post-injection. Tumors were excised, cut into 2-3 mm pieces, and digested with 1 mg/mL Collagenase Type I (Gibco) and 1 mg/mL Dispase (Gibco), supplemented with Rock inhibitor (Tocris Bioscience) and DNase I (Roche, Sigma), at 37°C for one hour. This was followed by a 5-minute treatment with TrypLE (Gibco). The processed cells were then filtered through a 40 µm filter and stained with anti-human CD3 (clone SK7, eBioscience), NGFR (Biolegend), and anti-mouse CD45 (clone 30-F11, eBioscience). Cells identified as DAPI-muCD45-CD3+NGFR+ were single-cell sorted into 1X PBS with 0.04% bovine serum albumin (BSA). Cells from the same group (n = 3) were pooled and subsequently processed by the UCLA Technology Center for Genomics and Bioinformatics (TCGB) core for 10X Genomics GEM-X 3’ Gene Expression v4 library preparation and next-generation sequencing on the Illumina Novaseq X platform.
Library construction was performed following the protocol of Chromium GEM-X Single Cell 3' (polyA) v4 Gene Expression Guide (https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/library-prep/chromium-gem-x-single-cell-3-v4-gene-expression-user-guide)

value: Tumor infiltrating lymphocytes

value: T cells


title: 952, Macaca fascicularis, LiverRt.Medial,LiverRt.Medial

description: Library name: itox000952


title: TILs with S6M TCRs

description:
Library name: S6M_TCR
10X Genomics GEM-X 3’ Gene Expression v4 library


title: 1024, Macaca fascicularis, OccipitalCortex,OccipitalCortex

description: Library name: itox001024

source_name: OccipitalCortex,OccipitalCortex

value: OccipitalCortex,OccipitalCortex


title: TILs with S6Q TCRs

description:
Library name: S6Q_TCR
10X Genomics GEM-X 3’ Gene Expression v4 library


title: 1142, Macaca fascicularis, SkeletalMuscle,SkeletalMuscle

description: Library name: itox001142

source_name: SkeletalMuscle,SkeletalMuscle

value: SkeletalMuscle,SkeletalMuscle


title: 1154, Macaca fascicularis, Skin,Skin

description: Library name: itox001154

source_name: Skin,Skin

value: Skin,Skin


title: 1155, Macaca fascicularis, Skin,Skin

description: Library name: itox001155


title: TILs with 156-WT TCRs

description:
Library name: 156_WT_TCR
10X Genomics GEM-X 3’ Gene Expression v4 library


title: GGGTCAA-capan1-TRIM22-3

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

description: Library name: Sample 6

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: Pancreatic Cancer

growth_protocol: Capan-1 cell was cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic Cancer

value: Capan-1 (KRASG12V)

value: No


title: 1156, Macaca fascicularis, Skin,Skin

description: Library name: itox001156


title: 1025, Macaca fascicularis, OccipitalCortex,OccipitalCortex

description: Library name: itox001025


title: TTTCAGA-capan1-TRIM22-1

description: Library name: Sample 4


title: TILs with F5 TCRs

description:
Library name: F5_TCR
10X Genomics GEM-X 3’ Gene Expression v4 library


title: 1160, Macaca fascicularis, Skin,Skin

description: Library name: itox001160


title: CCAGGCA-capan1-Vector-3

description: Library name: Sample 3


title: 1157, Macaca fascicularis, Skin,Skin

description: Library name: itox001157


title: 1159, Macaca fascicularis, Skin,Skin

description: Library name: itox001159


title: ACCTGAA-capan1-Vector-2

description: Library name: Sample 2


title: 1168, Macaca fascicularis, SpinalCord,SpinalCord

description: Library name: itox001168

source_name: SpinalCord,SpinalCord

value: SpinalCord,SpinalCord


title: 1158, Macaca fascicularis, Skin,Skin

description: Library name: itox001158


title: NF-kBp65-Untretaed

description: Library name: Sample 8

library_source: genomic

data_processing:
Data trimming is performed to remove adapter sequences and low-quality bases from the raw sequencing reads.
Alignment of the trimmed reads to a reference genome is then carried out, mapping the reads to their corresponding genomic locations.
After alignment, reads that map to multiple locations, are of low quality, or represent PCR duplicates (artifacts) are filtered out.
The remaining high-quality reads are used for peak calling, identifying regions of enrichment that represent the binding sites of the protein of interest.
Assembly: CUT&RUN data was aligned to reference genome ( Human g38 )
Supplementary files format and content: bw

growth_protocol: Pa01C cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
CUT&RUN assays were performed to profile chromatin-bound transcription factors in Pa01C pancreatic cancer cells using the CUT&RUN Assay Kit (Cell Signaling Technology, Cat# 86652S), following the manufacturer’s instructions.
Sequencing libraries were prepared using the DNA Library Prep Kit for Illumina Systems (Cell Signaling Technology, Cat# 56795S), including end-repair, adapter ligation, PCR amplification with Multiplex Oligos (Cat# 47538S), and size selection with AMPure XP beads (Beckman Coulter, Cat# A63881).Final libraries were pooled and sequenced using paired-end 75 bp reads on an Illumina NovaSeq X Plus platform.

treatment_protocol: We treated Pa01C with Ulixertinib or MRTX1133 for two weeks

value: Pa01C (KRASG12D)

tag: chip antibody

value: NF-kBp65 (Cell Signaling Tech., Cat.#8242S)


title: TCAAACA-capan1-Vector-1

description: Library name: Sample 1


title: NF-kBp65-Ulixerinib

description: Library name: Sample 9

value: Yes


title: 1161, Macaca fascicularis, SortedNK,SortedNK

description: Library name: itox001161

source_name: SortedNK,SortedNK

value: SortedNK,SortedNK


title: 1169, Macaca fascicularis, SpinalCord,SpinalCord

description: Library name: itox001169


title: IRF9-Ulixertinib

description: Library name: Sample 6

value: IRF-9 (Cell Signaling Tech., Cat.#76684S)


title: 1167, Macaca fascicularis, SpinalCord,SpinalCord

description: Library name: itox001167


title: 1170, Macaca fascicularis, SpinalCord,SpinalCord

description: Library name: itox001170


title: IRF9-Untretaed

description: Library name: Sample 5


title: IRF9-MRTX1133

description: Library name: Sample 7


title: 1171, Macaca fascicularis, SpinalCord,SpinalCord

description: Library name: itox001171


title: IRF1-MRTX1133

description: Library name: Sample 4

value: IRF-1 (Cell Signaling Tech., Cat.# 8478S)


title: 1173, Macaca fascicularis, SpinalCord,SpinalCord

description: Library name: itox001173


title: CAAGCCG-capan1-TRIM22-2

description: Library name: Sample 5


title: IRF1-Ulixertinib

description: Library name: Sample 3


title: 1178, Macaca fascicularis, Spleen,Spleen

description: Library name: itox001178

source_name: Spleen,Spleen

value: Spleen,Spleen


title: 1180, Macaca fascicularis, Spleen,Spleen

description: Library name: itox001180


title: 8p WT cell, mRNA, biological replicate 3

city: West Haven

first: Wenxue

last: Li

state: CT     Connecticut

address: 300 Heffernernan Dr Bldg A42,, Bldg 840, Room ABC 367

institute: Yale University

description:
Library name: Sample 21
Chr8_isogenic_system_mRNA.xlsx

data_processing:
Total mRNA:RNA sequencing from chromosoe 3/chromosome 8 aneuploidy system data was processed using the nf-core/rnaseq pipeline (v3.14.0). The RNAseq were also aligned to the human genome GRCh38. Ribosome Profiling: The analysis of ribosome footprint data was performed using RiboDoc (v0.9.1.1) on Podman (v3.4.4). RPFs ranging from 25 to 45 nucleotides were aligned to the human genome (GRCh38) within the analysis pipeline. For identification and removal of human rRNA contaminants, the SILVA database was utilized.
Assembly: GRCh38
Supplementary files format and content: TPM values:Chr8_isogenic_system_mRNA.xlsx
Supplementary files format and content: TPM values:Chr3_isogenic_system_mRNA.xlsx
Supplementary files format and content: raw counts for each sample:Chr3_isogenic_Riboseq.xlsx

source_name: lung epithelial cell

extract_protocol:
Total mRNA:Cells from the chromosome 3 isogenic aneuploidy system (3p loss/3q gain/WT) were washed three times with PBS, snap-frozen, and then lysed with the QIAShredder columns (#79654, QIAGEN) according to the manufacturer’s instructions. For each cell line, three biological replicates were processed. Total RNA was isolated with the Qiagen RNeasy Mini Kit (#74104, QIAGEN), including the DNA digestion step using the RNAase-Free DNAase set kit (#79254, QIAGEN). Ribosome Profiling:3p loss cells and 3p WT cells were subjected to ribosome profiling. For each cell line, three biological replicates were processed. Cells were cultured under standard conditions until they reached 80% confluency. They were then treated with 10 µg/µL cycloheximide for 5 minutes at 37°C. Following treatment, cells were harvested and lysed. Ribosome-protected fragments (RPFs) were generated and purified using RiboLace Pro (Immagina Biotech; catalog # RL00P-12). The RPFs underwent end repair using the Small RNA Library Prep Kit (NEB; catalog # E7300S) and size selection using the RNA Clean & Concentrator-5 Kit (Zymo; catalog # R1015) to enrich RNA fragments sized smaller than 200 nt.
Total mRNA:PolyA isolation and sequencing library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit (#E7760, NEB). Each set of samples were pooled and sequenced in one lane of HiSeq2500 RR, 100 basepair paired end. For the transcriptome analysis of chromosome 8 isogenic aneuploidy system (8p loss/8p WT), total mRNA samples were prepared as described above with three biological replicates, and the following library preparation was conducted in Yale Center for Genomic Analysis (YCGA). Sequencing was conducted on NovaSeq X Plus platform (Illumina). Ribosome Profiling:RPFs were reverse transcribed and tagged by Small RNA Library Prep Kit (NEB; catalog # E7300S) following the recommended conditions. RPF libraries were then amplified by Phusion High-Fidelity PCR Kit (NEB; E0553L). Further size selection and purification of RPF libraries was conducted using Mag-Bind TotalPure NGS beads (Omega Bio-tek; catalog # M1378-01) at a beads-to-product ratio of 1.3:1. The NGS libraries were quantified using the sparQ Universal Library Quant Kit (Quantabio; catalog # 95210-100) and analyzed using a TapeStation (Agilent) before being sequenced with NovaSeq X Plus (Illumina) in YCGA or NextSeq 1000 system in Quintara Biosciences. The target sequencing depth for the RPF libraries was 200 million reads per library.

value: lung epithelial cell

value: 8p WT


title: 1181, Macaca fascicularis, Spleen,Spleen

description: Library name: itox001181


title: 8p WT cell, mRNA, biological replicate 2

description:
Library name: Sample 20
Chr8_isogenic_system_mRNA.xlsx


title: 1179, Macaca fascicularis, Spleen,Spleen

description: Library name: itox001179


title: 1183, Macaca fascicularis, Spleen,Spleen

description: Library name: itox001183


title: 8p WT cell, mRNA, biological replicate 1

description:
Library name: Sample 19
Chr8_isogenic_system_mRNA.xlsx


title: 1182, Macaca fascicularis, Spleen,Spleen

description: Library name: itox001182


title: 8p loss cell, mRNA, biological replicate 2

description:
Library name: Sample 17
Chr8_isogenic_system_mRNA.xlsx

value: 8p loss