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

description:
Library name: Sample 18
Chr8_isogenic_system_mRNA.xlsx


title: 1184, Macaca fascicularis, Spleen,Spleen

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: itox001184

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 count mapped to human

molecule: total RNA

organism: Macaca fascicularis

source_name: Spleen,Spleen

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: Spleen,Spleen

tag: batch


title: 1172, Macaca fascicularis, SpinalCord,SpinalCord

description: Library name: itox001172

source_name: SpinalCord,SpinalCord

value: SpinalCord,SpinalCord


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

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 16
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

organism: Homo sapiens

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.

tag: cell line

value: lung epithelial cell

tag: genotype

value: 8p loss


title: 3p WT cell, ribosome profiling, biological replicate 3

description:
Library name: Sample 15
Chr3_isogenic_Riboseq.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
Library strategy: Ribo-Seq

value: 3p WT


title: 3p loss cell, ribosome profiling, biological replicate 3

description:
Library name: Sample 12
Chr3_isogenic_Riboseq.xlsx

value: 3p loss


title: 1191, Macaca fascicularis, Stomach,Stomach

description: Library name: itox001191

source_name: Stomach,Stomach

value: Stomach,Stomach


title: 3p WT cell, ribosome profiling, biological replicate 2

description:
Library name: Sample 14
Chr3_isogenic_Riboseq.xlsx


title: 1192, Macaca fascicularis, Stomach,Stomach

description: Library name: itox001192


title: IRF1-Untretaed

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

description: Library name: Sample 2

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

molecule: genomic DNA

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

tag: cell type

value: Pancreatic Cancer

value: Pa01C (KRASG12D)

tag: treatment

value: No

tag: chip antibody

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


title: 3p loss cell, ribosome profiling, biological replicate 2

description:
Library name: Sample 11
Chr3_isogenic_Riboseq.xlsx


title: 1193, Macaca fascicularis, Stomach,Stomach

description: Library name: itox001193


title: 1194, Macaca fascicularis, Stomach,Stomach

description: Library name: itox001194


title: 1185, Macaca fascicularis, Spleen,Spleen

description: Library name: itox001185


title: HiC_HG03464

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Sample8

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: 1196, Macaca fascicularis, Stomach,Stomach

description: Library name: itox001196


title: HiC_HG02601

description: Library name: Sample7

source_name: HG02601 lymphoblastoid cell line

value: HG02601 lymphoblastoid cell line


title: 1197, Macaca fascicularis, Stomach,Stomach

description: Library name: itox001197


title: HiC_HG01241

description: Library name: Sample6

source_name: HG01241 lymphoblastoid cell line

value: HG01241 lymphoblastoid cell line


title: HiC_NA18983

description: Library name: Sample5

source_name: GM18983 lymphoblastoid cell line

value: GM18983 lymphoblastoid cell line


title: 1195, Macaca fascicularis, Stomach,Stomach

description: Library name: itox001195


title: Input-Untretaed

description: Library name: Sample 1


title: 10X_LinkedReads_HG03464

description: Library name: Sample4


title: 1198, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001198

source_name: Striatum,Striatum

value: Striatum,Striatum


title: 10X_LinkedReads_HG02601

description: Library name: Sample3


title: 1201, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001201


title: 1200, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001200


title: 1427, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001427

organism: Mus musculus

source_name: Esophagus (mid),Esophagus (mid)

value: Esophagus (mid),Esophagus (mid)


title: 1199, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001199


title: 10X_LinkedReads_NA18983

description: Library name: Sample1


title: 1202, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001202


title: 1205, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001205


title: 1428, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001428


title: 10X_LinkedReads_HG01241

description: Library name: Sample2


title: 1203, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001203


title: 1204, Macaca fascicularis, Striatum,Striatum

description: Library name: itox001204


title: 1430, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001430


title: 985, Macaca fascicularis, MammaryGland,MammaryGland

description: Library name: itox000985

source_name: MammaryGland,MammaryGland

value: MammaryGland,MammaryGland


title: 1431, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001431


title: 1302, Macaca fascicularis, UrinaryBladder,UrinaryBladder

description: Library name: itox001302

source_name: UrinaryBladder,UrinaryBladder

value: UrinaryBladder,UrinaryBladder


title: 1303, Macaca fascicularis, UrinaryBladder,UrinaryBladder

description: Library name: itox001303


title: 1305, Macaca fascicularis, UrinaryBladder,UrinaryBladder

description: Library name: itox001305


title: 1434, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001434


title: 1433, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001433


title: 1304, Macaca fascicularis, UrinaryBladder,UrinaryBladder

description: Library name: itox001304


title: 1429, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001429


title: 1432, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001432


title: 1435, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001435


title: 986, Macaca fascicularis, MammaryGland,MammaryGland

description: Library name: itox000986


title: 1307, Macaca fascicularis, UrinaryBladder,UrinaryBladder

description: Library name: itox001307


title: 1437, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001437


title: 1438, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001438


title: 1311, Macaca fascicularis, Uterus,Uterus

description: Library name: itox001311

source_name: Uterus,Uterus

value: Uterus,Uterus


title: 1436, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001436


title: 1442, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001442


title: 1441, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001441


title: 1321, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001321

source_name: VenaCava,VenaCava

value: VenaCava,VenaCava


title: 1313, Macaca fascicularis, Uterus,Uterus

description: Library name: itox001313


title: 1440, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001440


title: 1312, Macaca fascicularis, Uterus,Uterus

description: Library name: itox001312


title: 1439, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox001439


title: 1445, Mus musculus, Ileum,Ileum

description: Library name: itox001445

source_name: Ileum,Ileum

value: Ileum,Ileum


title: 1306, Macaca fascicularis, UrinaryBladder,UrinaryBladder

description: Library name: itox001306


title: 1308, Macaca fascicularis, UrinaryBladder,UrinaryBladder

description: Library name: itox001308


title: 1447, Mus musculus, Small intestine-Jejunum,Small intestine-Jejunum

description: Library name: itox001447


title: 1324, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001324


title: 987, Macaca fascicularis, MammaryGland,MammaryGland

description: Library name: itox000987


title: 1446, Mus musculus, Ileum,Ileum

description: Library name: itox001446


title: 1322, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001322


title: 1443, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox001443


title: 1327, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001327


title: 1514, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001514

source_name: Thyroid/parathyroid,Thyroid/parathyroid

value: Thyroid/parathyroid,Thyroid/parathyroid


title: 1513, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001513


title: 1326, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001326


title: 1328, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001328


title: 1516, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001516


title: 1325, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001325


title: 1444, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox001444


title: 1515, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001515


title: 1323, Macaca fascicularis, VenaCava,VenaCava

description: Library name: itox001323


title: 1517, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001517


title: 1332, Macaca fascicularis, WhiteFat,WhiteFat

description: Library name: itox001332

source_name: WhiteFat,WhiteFat

value: WhiteFat,WhiteFat


title: 1518, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001518


title: 1330, Macaca fascicularis, WhiteFat,WhiteFat

description: Library name: itox001330


title: 1520, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001520


title: 1519, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001519


title: 1333, Macaca fascicularis, WhiteFat,WhiteFat

description: Library name: itox001333


title: 1334, Macaca fascicularis, WhiteFat,WhiteFat

description: Library name: itox001334


title: 1528, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001528


title: 1527, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001527


title: 989, Macaca fascicularis, MesentericLymphNode,MesentericLymphNode

description: Library name: itox000989

source_name: MesentericLymphNode,MesentericLymphNode

value: MesentericLymphNode,MesentericLymphNode


title: 1335, Macaca fascicularis, WhiteFat,WhiteFat

description: Library name: itox001335


title: 1525, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001525


title: 988, Macaca fascicularis, MesentericLymphNode,MesentericLymphNode

description: Library name: itox000988


title: 1336, Macaca fascicularis, WhiteFat,WhiteFat

description: Library name: itox001336


title: 1083, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001083

source_name: Pituitary,Pituitary

value: Pituitary,Pituitary


title: 1524, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001524


title: 1075, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001075

source_name: PeripheralNerve,PeripheralNerve

value: PeripheralNerve,PeripheralNerve


title: 1523, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001523


title: 1526, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001526


title: 1076, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001076


title: 1002, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox001002

source_name: MotorCortex,MotorCortex

value: MotorCortex,MotorCortex


title: 1084, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001084


title: 1532, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox001532

source_name: Skin (inguinal),Skin (inguinal)

value: Skin (inguinal),Skin (inguinal)


title: 1331, Macaca fascicularis, WhiteFat,WhiteFat

description: Library name: itox001331


title: 1522, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001522


title: 1521, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001521


title: 1531, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001531


title: 1085, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001085


title: 1530, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001530


title: 1533, Mus musculus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox001533


title: HaCat cells, blank-2, Day3

city: Xi'an

first: Qiang

last: Miao

state: Shaanx

address: Changle West Road

country: China

institute: Air Force Medical University

description: Library name: Sample 8

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: 1529, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001529


title: 963, Macaca fascicularis, Lungs,Lungs

description: Library name: itox000963

source_name: Lungs,Lungs

value: Lungs,Lungs


title: 1086, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001086


title: 1077, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001077


title: 1534, Mus musculus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox001534


title: 1087, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001087


title: 1088, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001088


title: 1090, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001090


title: 1600, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001600

source_name: Brain - Cortex,Brain - Cortex

value: Brain - Cortex,Brain - Cortex


title: 1602, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001602


title: 1603, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001603


title: 1604, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001604


title: Bone_young-vs-old_3_Feature_barcode

city: Indianapolis

first: Gang

last: Peng

state: IN

address: 635 Barnhill Dr

department: Medical & Molecular Genetics

institute: Indiana University

description: Library name: Chrm_536_pool_3_HTO

library_source: genomic single cell

data_processing:
Raw FASTQ files were processed using Cell Ranger (v9.0.1, 10x Genomics) to align reads to the murine reference genome and extract gene expression features.
Demultiplexing of pooled samples was performed computationally based on the expression levels of antibody-derived tags (hashing).
Downstream analysis was performed in R (v4.3.1) using the Seurat package. Quality control filtering excluded low-quality cells defined as having >20% reads mapping to mitochondrial genes or <200 detected genes.
Data across multiple sequencing runs were integrated using Harmony to adjust for batch effects. Dimensionality reduction (PCA), clustering (SNN modularity optimization), and UMAP visualization were performed, followed by marker-based cell type annotation.
Samples were multiplexed using cell hashing. While the sequencing runs contained multiple hash oligos, only biological samples corresponding to Hash IDs 1 and 3 (5_Male and 5_Female) were analyzed. Biological sample identification for each analyzed cell barcode is mapped in the supplemental cell_metadata.csv and Hash_mapping.xlsx files.
Assembly: GRCm39
Supplementary files format and content: HDF5 (.h5) formatted count matrices (both raw and filtered feature-barcode matrices generated by Cell Ranger containing gene expression and hashing counts)
Supplementary files format and content: CSV (.csv) files containing cell-level metadata (such as sample assignments and clustering information)
Supplementary files format and content: Excel (.xlsx) file detailing the hash tag oligo (HTO) to sample mapping.

source_name: Bone

growth_protocol: 5-month-old male and female C57BL/6 mice from the National Institute on Aging rodent colonies were group-housed and maintained in a specific pathogen-free facility on a 12-h light/dark cycle with ad libitum food and water at a constant temperature of 23°C.

extract_protocol:
Four long bones (femurs and tibiae) were dissected, epiphyses removed, and bone marrow flushed. Bones were scraped to remove periosteum and residual marrow, snap-frozen in liquid nitrogen, and stored at -80°C. Frozen bones were pulverized in liquid nitrogen and nuclei were isolated using a customized Nucleus Preparation Buffer (NPB) supplemented with Ribonucleoside Vanadyl Complex (RVC). Liberated nuclei were Dounce homogenized, filtered, stained with Hoechst 33342, labeled with nuclei-hashing TotalSeq-B antibodies, and isolated via fluorescence-activated nuclear sorting (FACS) on a BD FACSAria Fusion system.
Single-nucleus RNA sequencing (snRNA-seq) libraries were prepared using the 10x Genomics Chromium Single Cell System (GEM-X 3' chip, Chromium X Controller) following 10x Genomics protocols CG000315 or CG000732. Nuclei were partitioned into Gel Bead-in-Emulsions (GEMs) for cell barcoding and cDNA synthesis, followed by cDNA amplification. Libraries were sequenced on an Illumina NovaSeq X Plus platform using paired-end reads (28 bp Read 1, 91 bp Read 2) with dual indexing.

treatment_protocol: After a one-week acclimation period, the mice were fasted for 4 hours immediately prior to bone tissue collection.

value: Bone


title: 1089, Macaca fascicularis, Pituitary,Pituitary

description: Library name: itox001089


title: Bone_young-vs-old_4_Gene_Expression

description: Library name: Chrm_536_pool_4_GEX

library_source: transcriptomic single cell

molecule: nuclear RNA


title: 1605, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001605


title: 1094, Macaca fascicularis, Prostate,Prostate

description: Library name: itox001094

source_name: Prostate,Prostate

value: Prostate,Prostate


title: 1097, Macaca fascicularis, Prostate,Prostate

description: Library name: itox001097


title: 1095, Macaca fascicularis, Prostate,Prostate

description: Library name: itox001095


title: 964, Macaca fascicularis, Lungs,Lungs

description: Library name: itox000964


title: 1609, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001609


title: Bone_young-vs-old_2_Gene_Expression

description: Library name: Chrm_536_pool_2_GEX


title: 1607, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001607


title: Bone_young-vs-old_2_Feature_barcode

description: Library name: Chrm_536_pool_2_HTO


title: 1101, Macaca fascicularis, Retina,Retina

description: Library name: itox001101

source_name: Retina,Retina

value: Retina,Retina


title: Bone_young-vs-old_3_Gene_Expression

description: Library name: Chrm_536_pool_3_GEX


title: 1606, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001606


title: 1601, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001601


title: 1096, Macaca fascicularis, Prostate,Prostate

description: Library name: itox001096


title: Chrm_519_GeneExpression

description: Library name: Chrm_519_GEX


title: 1610, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001610


title: Bone_young-vs-old_4_Feature_barcode

description: Library name: Chrm_536_pool_4_HTO


title: 1102, Macaca fascicularis, Retina,Retina

description: Library name: itox001102


title: Mouse_cerebellum_E18_male_replicate4

city: Toronto

first: Michael

middle: D.

last: Taylor

state: Ontario

address: 555 University Ave

department: DSCB

country: Canada

institute: The Hospital for Sick Children

description:
Library name: Mouse_cerebellum_E18M4
10x Genomics

data_processing:
Cell Ranger software v.3.0.2 default pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebellum

extract_protocol:
Hindbrain structures were dissected from mice, dissociated into single cell suspensions using papain and were run on the 10X Genomics Chromium Controller using the Chromium Next GEM Single Cell 3' Solution V3.1 protocols.
10x Genomics Chromium Next GEM Single Cell 3' Solution V3.1 protocols

value: cerebellum

tag: developmental stage

value: Embryonic day 18.5

tag: Sex

value: male

tag: strain

value: wild type


title: 1611, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001611


title: 965, Macaca fascicularis, Lungs,Lungs

description: Library name: itox000965


title: Chrm_519_HTO

description: Library name: Chrm_519_HTO


title: 1612, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001612


title: Mouse_cerebellum_E18_female_replicate4

description:
Library name: Mouse_cerebellum_E18F4
10x Genomics

value: female


title: Mouse_cerebellum_E18_female_replicate3

description:
Library name: Mouse_cerebellum_E18F3
10x Genomics


title: 1613, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001613


title: Mouse_cerebellum_E16_male_replicate4

description:
Library name: Mouse_cerebellum_E16M4
10x Genomics

value: Embryonic day 16.5


title: 1104, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001104

source_name: RightAtrium,RightAtrium

value: RightAtrium,RightAtrium


title: 1103, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001103


title: 1615, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001615


title: 1105, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001105


title: Mouse_cerebellum_E16_female_replicate4

description:
Library name: Mouse_cerebellum_E16F4
10x Genomics


title: 1614, Mus musculus, Brain-Cortex,Brain-Cortex

description: Library name: itox001614

source_name: Brain-Cortex,Brain-Cortex

value: Brain-Cortex,Brain-Cortex


title: Mouse_cerebellum_E16_female_replicate3

description:
Library name: Mouse_cerebellum_E16F3
10x Genomics


title: Mouse_cerebellum_E14_male_replicate3

description:
Library name: Mouse_cerebellum_E14M3
10x Genomics

value: Embryonic day 14.5


title: Mouse_cerebellum_E16_male_replicate3

description:
Library name: Mouse_cerebellum_E16M3
10x Genomics


title: 1616, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001616


title: Mouse_cerebellum_E18_male_replicate3

description:
Library name: Mouse_cerebellum_E18M3
10x Genomics


title: Mouse_cerebellum_E14_female_replicate4

description:
Library name: Mouse_cerebellum_E14F4
10x Genomics


title: 1617, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001617


title: 1107, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001107


title: Mouse_cerebellum_E13_male_replicate4

description:
Library name: Mouse_cerebellum_E13M4
10x Genomics

value: Embryonic day 13.5


title: Mouse_cerebellum_E14_female_replicate3

description:
Library name: Mouse_cerebellum_E14F3
10x Genomics


title: Mouse_cerebellum_E13_male_replicate3

description:
Library name: Mouse_cerebellum_E13M3
10x Genomics


title: 1108, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001108


title: 1618, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001618

source_name: Brain- Hippocampus,Brain- Hippocampus

value: Brain- Hippocampus,Brain- Hippocampus


title: Mouse_cerebellum_E13_female_replicate3

description:
Library name: Mouse_cerebellum_E13F3
10x Genomics


title: Mouse_cerebellum_E13_female_replicate4

description:
Library name: Mouse_cerebellum_E13F4
10x Genomics


title: 1619, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001619


title: 1106, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001106


title: 1109, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001109


title: Mouse_hindbrain_E12_male_replicate4

description:
Library name: Mouse_hindbrain_E12M4
10x Genomics

source_name: hindbrain

value: hindbrain

value: Embryonic day 12.5


title: 1111, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001111

source_name: RightVentricle,RightVentricle

value: RightVentricle,RightVentricle


title: Mouse_hindbrain_E12_male_replicate3

description:
Library name: Mouse_hindbrain_E12M3
10x Genomics


title: Mouse_hindbrain_E11_male_replicate3

description:
Library name: Mouse_hindbrain_E11M3
10x Genomics

value: Embryonic day 11.5


title: 1110, Macaca fascicularis, RightAtrium,RightAtrium

description: Library name: itox001110


title: 1112, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001112


title: Mouse_hindbrain_E11_male_replicate4

description:
Library name: Mouse_hindbrain_E11M4
10x Genomics


title: Mouse_hindbrain_E11_female_replicate4

description:
Library name: Mouse_hindbrain_E11F4
10x Genomics


title: Mouse_hindbrain_E10_male_replicate4

description:
Library name: Mouse_hindbrain_E10M4
10x Genomics

value: Embryonic day 10.5


title: 1620, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001620


title: Mouse_hindbrain_E11_female_replicate3

description:
Library name: Mouse_hindbrain_E11F3
10x Genomics


title: 1621, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001621


title: 1113, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001113


title: 1687, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001687


title: 1688, Mus musculus, Brain-Spinal cord (cervical),Brain-Spinal cord (cervical)

description: Library name: itox001688


title: Mouse_hindbrain_E12_female_replicate4

description:
Library name: Mouse_hindbrain_E12F4
10x Genomics


title: 1689, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001689

source_name: Brain-Striatum,Brain-Striatum

value: Brain-Striatum,Brain-Striatum


title: Mouse_hindbrain_E10_male_replicate3

description:
Library name: Mouse_hindbrain_E10M3
10x Genomics


title: Mouse_cerebellum_E14_male_replicate4

description:
Library name: Mouse_cerebellum_E14M4
10x Genomics

value: cerebellum


title: Mouse_hindbrain_E12_female_replicate3

description:
Library name: Mouse_hindbrain_E12F3
10x Genomics


title: Mouse_hindbrain_E9_male_replicate3

description:
Library name: Mouse_hindbrain_E9M3
10x Genomics

value: Embryonic day 9.5


title: Mouse_hindbrain_E10_female_replicate3

description:
Library name: Mouse_hindbrain_E10F3
10x Genomics


title: 1690, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001690


title: 1691, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001691


title: 1114, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001114


title: 1115, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001115


title: Mouse_cerebellum_E18_XY_Testes_replicate3

description:
Library name: E18XYM3
10x Genomics

data_processing:
Cell Ranger software v.5.0.1 default pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cerebellar structures were dissected from mice, dissociated into single cell suspensions using papain and were run on the 10X Genomics Chromium Controller using the Chromium Next GEM Single Cell 3' Solution V3.1 protocols.
10x Genomics Chromium Next GEM Single Cell 3' Solution V3.1 protocols

value: Embryonic day 18.5

tag: chromosomes

value: XY

tag: gonads

value: Testes

tag: mouse line

value: Four Core Genotype

value: XY-Sry


title: Mouse_hindbrain_E10_female_replicate4

description:
Library name: Mouse_hindbrain_E10F4
10x Genomics

value: female

value: wild type


title: Mouse_cerebellum_E18_XY_Ovaries_replicate3

description:
Library name: E18XYF3
10x Genomics

value: Ovaries

value: XY-


title: Mouse_cerebellum_E18_XY_Testes_replicate2

description:
Library name: E18XYM2
10x Genomics


title: Mouse_hindbrain_E9_female_replicate3

description:
Library name: Mouse_hindbrain_E9F3
10x Genomics

value: hindbrain


title: 1116, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001116


title: 966, Macaca fascicularis, Lungs,Lungs

description: Library name: itox000966

value: Lungs,Lungs


title: 1692, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001692


title: 1117, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001117

value: RightVentricle,RightVentricle


title: Mouse_cerebellum_E18_XY_Ovaries_replicate2

description:
Library name: E18XYF2
10x Genomics


title: 1694, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001694


title: Mouse_cerebellum_E18_XX_Testes_replicate2

description:
Library name: E18XXM2
10x Genomics

value: XX

value: XXSry


title: Mouse_cerebellum_E18_XX_Ovaries_replicate2

description:
Library name: E18XXF2
10x Genomics


title: 1693, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001693

value: Brain-Striatum,Brain-Striatum


title: Mouse_cerebellum_E18_XX_Ovaries_replicate3

description:
Library name: E18XXF3
10x Genomics

value: cerebellum


title: Mouse_cerebellum_E18_XX_Testes_replicate3

description:
Library name: E18XXM3
10x Genomics


title: 1009, Macaca fascicularis, NaturalKillerCells,NaturalKillerCells

description: Library name: itox001009

source_name: NaturalKillerCells,NaturalKillerCells

value: NaturalKillerCells,NaturalKillerCells


title: Mouse_cerebellum_E16_XY_Testes_replicate3

description:
Library name: E16XYM3
10x Genomics

value: Embryonic day 16.5


title: adjacent normal tissue from patient ca-933

type: genomic

city: Xinxiang

first: Fangfang

last: Shen

address: No. 599 hualan east street

institute: The Third Affiliated Hospital of Xinxiang Medical University

description: adjacent normal fresh-frozen tissues from esophageal squamous cell carcinoma  patient

hyb_protocol: Hybridization of the fragmented DNA to the Illumina Infinium MethylationEPIC BeadChip was performed in an Illumina Hybridization Oven at 48°C for 16–24 hours as described in the Illumina Infinium HD Methylation Assay Guide

scan_protocol: The BeadChips were scanned using the Illumina iScan System with autoloader.

data_processing: Raw IDAT files were imported into GenomeStudio Methylation Module to obtain raw signal intensities and detection p‑values. Data were exported and processed in R (v3.6.1).

label: Cy3 and Cy5

source_name: fresh-frozen tissue

label_protocol: Bisulfite conversion of genomic DNA was performed with the Zymo EZ DNA Methylation Kit following the Illumina Infinium HD Methylation Assay protocol.

extract_protocol: Genomic DNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  DNA was quantified using a NanoDrop-1000 spectrophotometer.

value: fresh-frozen tissue


title: 1026, Macaca fascicularis, OccipitalCortex,OccipitalCortex

description: Library name: itox001026

source_name: OccipitalCortex,OccipitalCortex

value: OccipitalCortex,OccipitalCortex


title: Mouse_cerebellum_E16_XY_Testes_replicate2

description:
Library name: E16XYM2
10x Genomics

value: XY

value: Testes

value: Four Core Genotype


title: 1695, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001695


title: 1118, Macaca fascicularis, RightVentricle,RightVentricle

description: Library name: itox001118


title: 1027, Macaca fascicularis, OccipitalCortex,OccipitalCortex

description: Library name: itox001027


title: esophageal squamous cell carcinoma tumor tissue from patient ca-933

description: fresh-frozen tumor tissue from esophageal squamous cell carcinoma  patient


title: 1028, Macaca fascicularis, OccipitalCortex,OccipitalCortex

description: Library name: itox001028


title: Mouse_cerebellum_E16_XY_Ovaries_replicate3

description:
Library name: E16XYF3
10x Genomics


title: adjacent normal tissue from patient ca-942


title: 1697, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001697


title: Mouse_cerebellum_E16_XY_Ovaries_replicate2

description:
Library name: E16XYF2
10x Genomics


title: 1698, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001698


title: 1029, Macaca fascicularis, OccipitalCortex,OccipitalCortex

description: Library name: itox001029


title: Mouse_cerebellum_E16_XX_Testes_replicate3

description:
Library name: E16XXM3
10x Genomics


title: esophageal squamous cell carcinoma tumor tissue from patient ca-942


title: 1696, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001696


title: 1699, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001699


title: adjacent normal tissue from patient ca-944


title: 1700, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001700


title: Mouse_cerebellum_E16_XX_Testes_replicate2

description:
Library name: E16XXM2
10x Genomics


title: 1034, Macaca fascicularis, Ovary,Ovary

description: Library name: itox001034

source_name: Ovary,Ovary

value: Ovary,Ovary


title: esophageal squamous cell carcinoma tumor tissue from patient ca-944


title: adjacent normal tissue from patient ca-962


title: 1035, Macaca fascicularis, Ovary,Ovary

description: Library name: itox001035


title: 1702, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001702


title: Mouse_cerebellum_E16_XX_Ovaries_replicate3

description:
Library name: E16XXF3
10x Genomics

value: Ovaries


title: Three tumors and surrounding cerebella for postnatal day 60 male mouse

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

description: Library name: Tum_D2

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v7.0.1.
Assembly: mm10 with EGFP
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Tumor and surrounding cerebellum

extract_protocol:
Mouse tumors and cerebellum were digested in 3.2 mg/ml collagenase IV (Worthington Biochemical Corporation, LS004209), 1 mg/ml Deoxyribonuclease I (Worthington Biochemical Corporation, LS002007) and 2 mg/ml soybean trypsin inhibitor (Worthington Biochemical Corporation, LS003587) in DPBS for 10 min at 37 °C while shaking to separate cells. Dissociated single cells were checked for viability using a ViaStain AOPI staining solution (Nexcelcom Biosciences, CS2-0106-5ML) and counted using a Cellometer Auto 2000 Viability Counter (Nexcelcom Biosciences). Any dead cells were removed afterwards using a Miltenyi Biotech Dead Cell Removal kit (130-090-101).
CDNA libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics). For quality control, the libraries were tested using High Sensitivity D5000 ScreenTape and 4200 Tapestation system (Agilent Technologies).

value: Tumor and surrounding cerebellum


title: 1703, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001703


title: 1230, Macaca fascicularis, Testis,Testis

description: Library name: itox001230

source_name: Testis,Testis

value: Testis,Testis


title: 1701, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001701


title: Three tumors and surrounding cerebella for postnatal day 60 female mouse

description: Library name: Tum_D1


title: 1229, Macaca fascicularis, Testis,Testis

description: Library name: itox001229


title: Mouse_cerebellum_E16_XX_Ovaries_replicate2

description:
Library name: E16XXF2
10x Genomics


title: Three cerebella for postnatal day 60 male mouse

description: Library name: Ctrl_D2

source_name: Normal cerebellum

value: Normal cerebellum


title: 1704, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001704


title: adjacent normal tissue from patient ca-973


title: 1231, Macaca fascicularis, Testis,Testis

description: Library name: itox001231


title: 1705, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001705


title: esophageal squamous cell carcinoma tumor tissue from patient ca-973


title: 1232, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001232

source_name: Thalamus,Thalamus

value: Thalamus,Thalamus


title: 1706, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001706


title: Three cerebella for postnatal day 60 female mouse

description: Library name: Ctrl_D1


title: with alpa-ketoglutarate, Day10, rep3

city: Fujisawa

first: Tatsunori

last: Nakagawa

address: 1866 Kameino

country: Japan

institute: Nihon University

description:
Library name: ketoglutarate3
Column name in raw_counts_All_Samples.txt: with_ketoglutarate3

data_processing:
The trimming was performed using CLC Genomic Workbench version 20.0.5 (QIAGEN)(parameters for trimming: automatic read-through adapter trimming, low quality sequence limit = 0.05, ambiguous nucleotides n ≤ 2, minimum length nucleotides = 10). To assess variability among the replicates of each test, PCA was conducted using the CLC Genomic Workbench. Based on read count data, DEGs between cultures without or with alpha-ketoglutarate were identified using whole transcriptome RNA-Seq and the normalization method of the trimmed mean of M values (TMM) using Differential Expression in Two Groups 1.1 in CLC Genomic Workbench.
Assembly: The trimmed reads were aligned to the annotated reference genome of N. zosterae NM25 (NZ_AP026695) based on the reference genome annotated with genes only and a gene track of 2,088-coding sequences (CDSs) in NZ_AP026695 using RNA-Seq Analysis 2.21 in CLC Genomic Workbench, by using normalized reads indicated by TPM.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Samples

organism: Nitrosopumilus zosterae

source_name: cell culture

growth_protocol: The NM25 strain used to start the experiments was grown in a 2 L bottle with a screw cap, containing approximately 0.5 L of HEPES-buffered 1 mM ammonium chloride SCM medium supplemented with 100 µM alpha-ketoglutarate. After the strain was incubated at 30 degree C in the dark without shaking for 11 days, the inoculum (1%) was transferred to two types of fresh media: approximately 4 L of HEPES-buffered 1 mM ammonium chloride SCM medium without the addition of alpha-ketoglutarate or with the addition of alpha-ketoglutarate in the culture medium in a 10 L bottle closed with a screw cap. The strain was incubated at 30 degree C in the dark, with stirring using a stir bar.

extract_protocol:
Three L of the incubated medium was filtrated with the Stericap PLUS Universal Bottle-Top Vacuum Filtration Device (Merck Millipore) from the cultures after 10 days of incubation. Ten mL of RNA Protect Bacteria Reagent was immediately added to the filter to fix the RNA in cells on the filter. After incubation of the filter at room temperature for 10 min, the RNA Protect Bacteria Reagent solution in the Bottle-Top Vacuum Filtration Device was filtrated. The filter was cut from the Filtration Device with a knife, added to a 50 mL plastic tube, and stored at -80 degree C. After mixing cells on the filter using the solvent of the first step in the following kit, the total RNA for RNA-Seq was extracted from the suspension using a NucleoBond RNA/DNA 400 and an AXR 400 column (TaKaRa Bio). After the residual DNA was digested with DNase I (RNase free) (TaKaRa Bio), the RNA was purified with a RNeasy Min Eluent Cleanup Kit (QIAGEN).
RNA-Seq libraries were prepared with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina).

treatment_protocol: Approximately 4 L of HEPES-buffered 1 mM ammonium chloride SCM medium without the addition of alpha-ketoglutarate (final concentration of 1 µM alpha-ketoglutarate before incubation) or with the addition of alpha-ketoglutarate in the culture medium (final concentration of 100 µM alpha-ketoglutarate before incubation) in a 10 L bottle was closed with a screw cap.

value: cell culture

value: alpa-ketoglutarate


title: 1036, Macaca fascicularis, Ovary,Ovary

description: Library name: itox001036


title: KPPC_Control

description:
Library name: Sample 1
10x genomics

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the mouse Ensembl GRCh38.76 primary assembly with STAR aligner version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights
Assembly: mouse Ensembl GRCh38.76 primary assembly
Supplementary files format and content: .tsv, .mtx

source_name: Pancreatic Cancer

growth_protocol: KPC mice were genotyped and confirmed to have the correct transgenes.

extract_protocol:
Tumors from mice pancreas were harvested, washed and digested sing a cocktail fo collagenase, hyaluronidase and DNAse into single cell suspension.Nuclei isolation was performed according to 10X genomics protocol-Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (CGOOO338 CA210181)
standard 10X Genomics  5′ GEX Single-Cell Library

treatment_protocol: 4 mice per group were treated with vehicle or Ulixertinib 100mg/kg daily orally for 14 days and taken down

value: Pancreatic Cancer

value: No


title: 1233, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001233


title: esophageal squamous cell carcinoma tumor tissue from patient ca-962


title: KPPC_RMC-6236

description:
Library name: Sample 2
10x genomics


title: 1707, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001707

value: Brain-Striatum,Brain-Striatum


title: with alpa-ketoglutarate, Day10, rep2

description:
Library name: ketoglutarate2
Column name in raw_counts_All_Samples.txt: with_ketoglutarate2


title: 1708, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001708


title: Ulixertinib_Treated

description:
Library name: Sample 2
10x genomics


title: 1458, Mus musculus, Salivary Gland,Salivary Gland

description: Library name: itox001458

source_name: Salivary Gland,Salivary Gland

value: Salivary Gland,Salivary Gland


title: 1235, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001235


title: Control

description:
Library name: Sample 1
10x genomics


title: 1236, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001236


title: without alpa-ketoglutarate, Day10, rep3

description:
Library name: non-ketoglutarate3
Column name in raw_counts_All_Samples.txt: without_ketoglutarate3

value: without alpa-ketoglutarate


title: ATAC-seq Vehicle replicate 1

city: St Louis

first: Tiandao

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing: QC and analysis on ATAC-seq libraries was performed using AIAP. The generated peaks files for each library were incorporated with bedtools merge and counts on each peak were quantified for all libraries using bedtools coverage.

source_name: femoral head

growth_protocol: Following digestion, chondrocytes were harvested and cultured in complete high-glucose Dulbecco’s modified Eagle’s medium (DMEM; Gibco; #31053028) supplemented with 10% fetal bovine serum (FBS; Gibco; #10437), 2 mM L-Glutamine (Gibco; #A2916801), and 1% penicillin/streptomycin.

extract_protocol:
Cells were harvested by TrypLE Express dissociation and centrifuged at 500 RCF for 5 min at 4 ℃. After aspirating the supernatant, cells were washed once with cold PBS. Cell pellets were resuspended in 100 ul ATAC-seq RSB [10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 in water] consisting of 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down and incubating on ice for 3 min. After lysis, 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added and inverted with the lysis reaction. Then, nuclei were pelleted by centrifugation at 800 RCF for 5 min at 4 ℃. Supernatant was removed, and the nuclei were resuspended in 20 µL 2x TD buffer [20 mM Tris pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide]. 50,000 counted nuclei were then transferred to a tube with 2x TD buffer filled up to 25 µL. 25 µL of transposition mix [2.5 µL Transposase (100 nM final) (Illunina, 20034197, 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL water) was added. Transposition reactions were mixed and incubated for 30 min at 37℃ with gentle tapping every 10 min. Reactions were cleaned up with the Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4014).
The ATAC-seq library was amplified for nine cycles on a PCR machine. The PCR reaction was purified with Ampure XP beads (Beckman Coulter, A63880) using double size selection following the manufacturer’s protocol, in which 27.5 µL beads (0.55X sample volume) and 50 µL beads (1.55X sample volume) were used based on 50 µL PCR reaction. The ATAC-seq libraries were quantitated by Qubit assays and sequenced by an Illumina NextSeq platform.

treatment_protocol: Primary chondrocytes were seeded at a density of 50 x 104 cells/well in 12-well plates and treated with vehicle, 5 ng/ml TGFβ1 (R&D Systems; #240-B-010) and 100ng/ml BMP2 (R&D Systems; #355-BM-010) for 24 hours.

value: articular chondrocytes

tag: disease condition

value: Vehicle


title: 1237, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001237


title: ATAC-seq Vehicle replicate 2


title: 1459, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001459


title: without alpa-ketoglutarate, Day10, rep2

description:
Library name: non-ketoglutarate2
Column name in raw_counts_All_Samples.txt: without_ketoglutarate2


title: with alpa-ketoglutarate, Day10, rep1

description:
Library name: ketoglutarate1
Column name in raw_counts_All_Samples.txt: with_ketoglutarate1


title: 1461, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001461


title: without alpa-ketoglutarate, Day10, rep1

description:
Library name: non-ketoglutarate1
Column name in raw_counts_All_Samples.txt: without_ketoglutarate1


title: 1460, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001460


title: ATAC-seq TGFb replicate 2

value: TGFb


title: 1239, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001239


title: 1234, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001234


title: 5.EV.LPS.IFNg.STEMI.24.2

city: Oxford

first: Naveed

last: Akbar

state: England

address: Division of Cardiovascular Medicine, Radcliffe Department of Medicine, HS04

country: United Kingdom

institute: University of Oxford

description: Library name: 5.EV.LPS.IFNg.STEMI.24.2

data_processing:
Quality of raw sequence reads was assessed using FastQC (v0.11.8). Adapter sequences and low-quality bases were trimmed using CLC Genomics Workbench v11.0.1 (Quality limit = 0.05). Trimmed reads were mapped to the Homo sapiens GRCh38 (hg38) reference genome using Salmon v0.99.0 in mapping-based mode with the following parameters: --libType ISR --gcBias --validateMappings. Gene-level counts and normalized TPM/FPKM values were derived from Salmon quantification outputs.
Assembly: Homo sapiens GRCh38 (hg38)

source_name: Peripheral blood mononuclear cells

growth_protocol: Peripheral venous blood was collected from healthy male volunteers in EDTA tubes or from leukapheresis cones obtained from the NHS Blood Bank. PBMCs were isolated by density gradient centrifugation. Peripheral venous blood from MI patients was collected into EDTA tubes and diluted 1:1 with PBS. Monocytes were isolated by negative selection using the EasySep™ Human Monocyte Enrichment Kit (without CD16 depletion) (StemCell Technologies, Grenoble, France) following the manufacturer’s instructions. Enriched monocytes were cultured in complete DMEM (5 mmol/L glucose) supplemented with 10% FBS, 2% penicillin–streptomycin, and 2 mM L-glutamine, under control or M1-proinflammatory conditions (100 ng/mL LPS + 10 ng/mL IFN-γ) for 6 h at 37 °C and 5% CO₂.

extract_protocol:
Following stimulation, cells were washed with PBS, centrifuged, and lysed using the lysis buffer from the miRvana miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Lysates were snap-frozen and stored at −80 °C until RNA extraction.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol, including poly-A selection, RNA fragmentation, first- and second-strand cDNA synthesis, end repair/A-tailing, adapter ligation, and PCR enrichment. Libraries were quantified, pooled in equimolar amounts, and sequenced on Illumina HiSeq 3000/4000 instruments.

treatment_protocol: PBMCs were exposed to plasma extracellular vesicles (EVs) isolated from STEMI or control (NSTEMI) patients for 6 or 18 hours in siolation or followed by M1-type stimulation with 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) and 10 ng/mL recombinant human interferon-γ (IFN-γ; Invitrogen/R&D Systems) for 6 hours at 37 °C and 5% CO₂. Following stimulation, cells were washed with PBS, pelleted, and lysed for RNA extraction. Peripheral blood monocytes from NSTEMI and STMI patients were treated and activated using the same stimulants.

value: Peripheral blood mononuclear cells

value: wild-type


title: ATAC-seq TGFb replicate 1


title: 4.EV.LPS.IFNg.NSTEMI.27.2

description: Library name: 4.EV.LPS.IFNg.NSTEMI.27.2


title: 3.EV.LPS.IFNg.NSTEMI.4.2

description: Library name: 3.EV.LPS.IFNg.NSTEMI.4.2


title: ATAC-seq BMP2 replicate 2


title: 1464, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001464


title: 1246, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001246

source_name: Thymus,Thymus

value: Thymus,Thymus


title: 1238, Macaca fascicularis, Thalamus,Thalamus

description: Library name: itox001238


title: 1245, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001245


title: 1247, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001247


title: 1465, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001465


title: ATAC-seq BMP2 replicate 1


title: 2.EV.LPS.IFNg.NSTEMI.23.2

description: Library name: 2.EV.LPS.IFNg.NSTEMI.23.2


title: 1466, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001466


title: Bulk RNAseq of hepatocyte-like cells treated with vehicle control DMSO for 24 hours, biological replicate 3

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: Library name: HLC_DMSO_Rep3

data_processing:
Partek Genomics Suite (v12.3.1)
read alignment - STAR 2.7.8a aligner
Differentially expressed genes (DEGs) between groups were identified using Deseq2 12.8.0 (R) with statistical significance achieved at p-value (≤ 0.001), fold change (-2,2), and false discovery rate (FDR; ≤ 0.001)
Assembly: hg38 ENSEMBL release 105
Supplementary files format and content: Tab-deliminated list of differentially expressed genes

growth_protocol: Human induced pluripotent stem cells were differentited into Hepatocyte Like cells (HLCs) using the Duncan's Lab diferentiation protocol

extract_protocol:
RNA  was harvested and extracted using Qiagen RNeasy kit.
RNA library preparation (polyA enrichment) and sequencing was performed by BGI

treatment_protocol: Hepatocyte-Like cells (HLCs) treated with DL-1 at EC50 (2ug/ml) for 24 hours vs DMSO vehicle controls

value: iPSC derived hepatocyte

value: wild type

value: DMSO


title: 1248, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001248


title: 1249, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001249


title: 1463, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001463


title: Bulk RNAseq of hepatocyte-like cells treated with vehicle control DMSO for 24 hours, biological replicate 2

description: Library name: HLC_DMSO_Rep2


title: 1.EV.LPS.IFNg.STEMI.19.2

description: Library name: 1.EV.LPS.IFNg.STEMI.19.2


title: 1467, Mus musculus, Tongue,Tongue

description: Library name: itox001467

source_name: Tongue,Tongue

value: Tongue,Tongue


title: Bulk RNAseq of hepatocyte-like cells treated with DL-1 for 24 hours, biological replicate 3

description: Library name: HLC_DL1_Rep3


title: Bulk RNAseq of hepatocyte-like cells treated with vehicle control DMSO for 24 hours, biological replicate 1

description: Library name: HLC_DMSO_Rep1


title: 5.EV.LPS.IFNg.STEMI.24.1

description: Library name: 5.EV.LPS.IFNg.STEMI.24.1


title: 1250, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001250


title: 3.EV.LPS.IFNg.NSTEMI.4.1

description: Library name: 3.EV.LPS.IFNg.NSTEMI.4.1


title: 1535, Mus musculus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox001535


title: 997, Macaca fascicularis, Monocytes,Monocytes

description: Library name: itox000997

source_name: Monocytes,Monocytes

value: Monocytes,Monocytes


title: 1536, Mus musculus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox001536


title: Bulk RNAseq of hepatocyte-like cells treated with DL-1 for 24 hours, biological replicate 2

description: Library name: HLC_DL1_Rep2


title: 4.EV.LPS.IFNg.NSTEMI.27.1

description: Library name: 4.EV.LPS.IFNg.NSTEMI.27.1


title: 1004, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox001004

source_name: MotorCortex,MotorCortex

value: MotorCortex,MotorCortex


title: 1.EV.LPS.IFNg.STEMI.19.1

description: Library name: 1.EV.LPS.IFNg.STEMI.19.1


title: 1537, Mus musculus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox001537


title: 2.EV.LPS.IFNg.NSTEMI.23.1

description: Library name: 2.EV.LPS.IFNg.NSTEMI.23.1


title: 5.EV.LPS.IFNg.STEMI.23.2

description: Library name: 5.EV.LPS.IFNg.STEMI.23.2


title: Bulk RNAseq of hepatocyte-like cells treated with DL-1 for 24 hours, biological replicate 1

description: Library name: HLC_DL1_Rep1


title: 1468, Mus musculus, Tongue,Tongue

description: Library name: itox001468


title: 1539, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001539


title: Thalamocortical Assembloid, UCLA1, Week 9, CellTag slice, side library

city: Los Angeles

first: Aparna

last: Bhaduri

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

description:
Library name: Sample39_UCLA1_WK9_CX-TH_celltag-slice_sidelibrary
cortical halves of thalamocortical assembloid in slice, CellTag side library

data_processing:
Reads were aligned to the GRCh38 human reference genome using CellRanger v8/9. Cell-by-gene count matrices were generated using the 10X Genomics CellRanger pipelines or Fluent Bio PIPseeker pipeline with default parameters. Single-nuclei data was processed using CellBender (https://github.com/broadinstitute/CellBender), an R package designed to remove background noise from droplet-based single-cell assays. Doublets were predicted and removed from all samples using the DoubletFinder R package (https://github.com/chris-mcginnis-ucsf/DoubletFinder) using default parameters. Nuclei or cells containing a minimum of 500 genes and containing less than 5% mitochondrial gene content were retained for further analysis. Cortical and thalamic cells were segregated bioinformatically using the MapQuery function to compare cells to primary tissue datasets (Nano et al, 2025; Nowakowski et al, 2017) and a pilot organoid batch in which thalamic and cortical halves were dissected prior to sequencing. Relevant samples were demultiplexed using Vireo (https://github.com/single-cell-genetics/vireo). Following normalization and scaling, Principal Component Analysis (PCA) was conducted using the top 2,000 variable genes using the standard Seurat v5 pipeline. Differentially expressed genes and projections of the organoid data onto primary tissue datasets were used to annotate cell type clusters. Uniform Manifold Approximation and Projection (UMAP) was used to visualize clusters in 2D space using the determined dimensions.
Assembly: GRCh38
Supplementary files format and content: Counts Matrix

source_name: Cortical Organoid Slice

extract_protocol:
Organoids were dried by removing all media then flash frozen and stored at -80°C in preparation for single-nuclei RNA-sequencing. Nuclei were extracted from frozen organoids using the 10X Chromium Nuclei Isolation Kit using a 4-minute lysis time. Nuclei were washed twice using the included buffer, counted using a hemacytometer, then resuspended in buffer to achieve a target capture of 10,000 nuclei. During counting, nuclei were also imaged to ensure healthy morphology and lack of debris. For single-cell samples, organoid tissue was dissociated with papain plus DNase (Worthington) and processed via FACS.
Samples were captured using the 10X Genomics Chromium Single Cell 3’ Reagent Kit v3.1 or v4 and 10X Chromium System v3.1 or the PIPseq T2 3’ Single Cell RNA Kit v4.0. All samples were assessed for quality control purposes at both the cDNA and library stages using the Agilent 4200 TapeStation System. Single-nuclei and single-cell libraries were sequenced using the Illumina NovaSeq 6000 or NovaSeq X platform.

treatment_protocol: Severance, CellTag infection, or NRXN1 knockout and non-targeting control in parent lines where indicated

value: Cortical Organoid Slice

value: Neural

value: Control

value: neural differentiation, fusion, slice, CellTag infection


title: Corticocortical Assembloid, UCLA1, Week 9, CellTag slice, side library

description:
Library name: Sample38_UCLA1_WK9_CX-CX_celltag-slice_sidelibrary
both halves of corticocortical assembloids in slice, CellTag side library


title: 1541, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001541

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


title: 3.EV.LPS.IFNg.STEMI.22.2

description: Library name: 3.EV.LPS.IFNg.STEMI.22.2


title: 1020, Macaca fascicularis, Neutrophils,Neutrophils

description: Library name: itox001020

source_name: Neutrophils,Neutrophils

value: Neutrophils,Neutrophils


title: 1540, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001540


title: 950, Macaca fascicularis, LiverRt.Medial,LiverRt.Medial

description: Library name: itox000950


title: Corticocortical Assembloid, UCLA6, Week 9, CellTag slice, side library

description:
Library name: Sample36_UCLA6_WK9_CX-CX_celltag-slice_sidelibrary
both halves of corticocortical assembloids in slice, CellTag side library


title: 1003, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox001003


title: 1542, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001542


title: Thalamocortical Assembloid, UCLA6, Week 9, CellTag slice, side library

description:
Library name: Sample37_UCLA6_WK9_CX-TH_celltag-slice_sidelibrary
cortical halves of thalamocortical assembloid in slice, CellTag side library


title: 951, Macaca fascicularis, LiverRt.Medial,LiverRt.Medial

description: Library name: itox000951


title: Thalamocortical Assembloid, UCLA1, Week 9, CellTag slice

description:
Library name: Sample39_UCLA1_WK9_CX-TH_celltag-slice
cortical halves of thalamocortical assembloid in slice


title: 1543, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001543


title: 960, Macaca fascicularis, Lung,Lung

description: Library name: itox000960

source_name: Lung,Lung

value: Lung,Lung


title: 1.EV.LPS.IFNg.NSTEMI.20.2

description: Library name: 1.EV.LPS.IFNg.NSTEMI.20.2


title: 2.EV.LPS.IFNg.NSTEMI.26.2

description: Library name: 2.EV.LPS.IFNg.NSTEMI.26.2


title: 992, Macaca fascicularis, MesentericLymphNode,MesentericLymphNode

description: Library name: itox000992

source_name: MesentericLymphNode,MesentericLymphNode

value: MesentericLymphNode,MesentericLymphNode


title: 1544, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001544


title: 5.EV.LPS.IFNg.STEMI.23.1

description: Library name: 5.EV.LPS.IFNg.STEMI.23.1


title: 1546, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001546


title: 993, Macaca fascicularis, MesentericLymphNode,MesentericLymphNode

description: Library name: itox000993


title: Corticocortical Assembloid, UCLA1, Week 9, CellTag slice

description:
Library name: Sample38_UCLA1_WK9_CX-CX_celltag-slice
both halves of corticocortical assembloids in slice


title: 1251, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001251


title: 4.EV.LPS.IFNg.STEMI.18.1

description: Library name: 4.EV.LPS.IFNg.STEMI.18.1


title: Thalamocortical Assembloid, KOLF2, clone 2, Week 6, Non-Targeting Control

description:
Library name: Sample35_KOLF2-clone2_WK6_CX-TH_NX1NTC
thalamic and cortical halves separated into 2 processed data files

source_name: Thalamic and Cortical Organoids

value: Thalamic and Cortical Organoids

value: Non-targeting Control Thalamus and Cortex

value: lentiviral infection, neural differentiation, fusion


title: 1545, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001545


title: 1547, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001547


title: 4.EV.LPS.IFNg.NSTEMI.18.2

description: Library name: 4.EV.LPS.IFNg.NSTEMI.18.2

value: Peripheral blood mononuclear cells

value: wild-type


title: Thalamocortical Assembloid, UCLA6, Week 9, CellTag slice

description:
Library name: Sample37_UCLA6_WK9_CX-TH_celltag-slice
cortical halves of thalamocortical assembloid in slice


title: Thalamocortical Assembloid, KOLF2, clone 2, Week 6, NRXN1 Knockout

description:
Library name: Sample34_KOLF2-clone2_WK6_CX-TH_NX1KO
thalamic and cortical halves separated into 2 processed data files

value: NRXN1 Knockout Thalamus, Non-targeting Control Cortex


title: 1548, Mus musculus, Brown Fat (intrascapular),Brown Fat (intrascapular)

description: Library name: itox001548


title: Corticocortical Assembloid, UCLA6, Week 9, CellTag slice

description:
Library name: Sample36_UCLA6_WK9_CX-CX_celltag-slice
both halves of corticocortical assembloids in slice


title: 1253, Macaca fascicularis, ThyroidParathyroid,ThyroidParathyroid

description: Library name: itox001253

source_name: ThyroidParathyroid,ThyroidParathyroid

value: ThyroidParathyroid,ThyroidParathyroid


title: 1252, Macaca fascicularis, Thymus,Thymus

description: Library name: itox001252

value: Thymus,Thymus


title: 1254, Macaca fascicularis, ThyroidParathyroid,ThyroidParathyroid

description: Library name: itox001254


title: 1551, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox001551


title: Thalamocortical Assembloid, KOLF2, clone 2, Week 12, Non-Targeting Control

description:
Library name: Sample33_KOLF2-clone2_WK12_CX-TH_NX1NTC
thalamic and cortical halves separated into 2 processed data files


title: Thalamocortical Assembloid, KOLF2, clone 2, Week 12, NRXN1 Knockout

description:
Library name: Sample32_KOLF2-clone2_WK12_CX-TH_NX1KO
thalamic and cortical halves separated into 2 processed data files


title: 4.EV.NSTEMI.27.2

description: Library name: 4.EV.NSTEMI.27.2

value: EV


title: 953, Macaca fascicularis, Liver,Liver

description: Library name: itox000953

source_name: Liver,Liver

value: Liver,Liver


title: 1.EV.LPS.IFNg.NSTEMI.20.1

description: Library name: 1.EV.LPS.IFNg.NSTEMI.20.1


title: 1554, Mus musculus, Thymus,Thymus

description: Library name: itox001554


title: 2.EV.LPS.IFNg.STEMI.26.1

description: Library name: 2.EV.LPS.IFNg.STEMI.26.1


title: Thalamocortical Assembloid, KOLF2, clone 1, Week 6, NRXN1 Knockout

description:
Library name: Sample30_KOLF2-clone1_WK6_CX-TH_NX1KO
thalamic and cortical halves separated into 2 processed data files


title: 3.EV.NSTEMI.4.2

description: Library name: 3.EV.NSTEMI.4.2


title: 5.EV.STEMI.24.2

description: Library name: 5.EV.STEMI.24.2


title: Thalamocortical Assembloid, KOLF2, clone 1, Week 6, Non-Targeting Control

description:
Library name: Sample31_KOLF2-clone1_WK6_CX-TH_NX1NTC
thalamic and cortical halves separated into 2 processed data files


title: 1255, Macaca fascicularis, ThyroidParathyroid,ThyroidParathyroid

description: Library name: itox001255


title: 1256, Macaca fascicularis, ThyroidParathyroid,ThyroidParathyroid

description: Library name: itox001256


title: 3.EV.LPS.IFNg.NSTEMI.22.1

description: Library name: 3.EV.LPS.IFNg.NSTEMI.22.1


title: 1552, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox001552


title: 1555, Mus musculus, Thymus,Thymus

description: Library name: itox001555


title: 2.EV.NSTEMI.23.2

description: Library name: 2.EV.NSTEMI.23.2


title: Thalamocortical Assembloid, KOLF2, clone 1, Week 12, Non-Targeting Control

description:
Library name: Sample29_KOLF2-clone1_WK12_CX-TH_NX1NTC
thalamic and cortical halves separated into 2 processed data files


title: Thalamocortical Assembloid, KOLF2, clone 1, Week 12, NRXN1 Knockout

description:
Library name: Sample28_KOLF2-clone1_WK12_CX-TH_NX1KO
thalamic and cortical halves separated into 2 processed data files


title: 1.EV.STEMI.19.2

description: Library name: 1.EV.STEMI.19.2


title: 1556, Mus musculus, Thymus,Thymus

description: Library name: itox001556


title: 981, Macaca fascicularis, MammaryGland,MammaryGland

description: Library name: itox000981

source_name: MammaryGland,MammaryGland

value: MammaryGland,MammaryGland


title: 1623, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001623

source_name: Brain- Hippocampus,Brain- Hippocampus

value: Brain- Hippocampus,Brain- Hippocampus


title: Thalamocortical Assembloid, CW20107, Week 6, Non-Targeting Control

description:
Library name: Sample27_CW20107_WK6_CX-TH_NX1NTC
thalamic and cortical halves separated into 2 processed data files

value: Neural


title: 1257, Macaca fascicularis, ThyroidParathyroid,ThyroidParathyroid

description: Library name: itox001257


title: 5.EV.STEMI.24.1

description: Library name: 5.EV.STEMI.24.1


title: 1258, Macaca fascicularis, ThyroidParathyroid,ThyroidParathyroid

description: Library name: itox001258


title: 1622, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001622


title: 4.EV.NSTEMI.27.1

description: Library name: 4.EV.NSTEMI.27.1


title: 3.EV.NSTEMI.4.1

description: Library name: 3.EV.NSTEMI.4.1


title: 982, Macaca fascicularis, MammaryGland,MammaryGland

description: Library name: itox000982


title: 1624, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001624


title: 2.EV.NSTEMI.23.1

description: Library name: 2.EV.NSTEMI.23.1


title: 1625, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001625


title: 1.EV.STEMI.19.1

description: Library name: 1.EV.STEMI.19.1


title: 1264, Macaca fascicularis, Thyroid,Thyroid

description: Library name: itox001264

source_name: Thyroid,Thyroid

value: Thyroid,Thyroid


title: Thalamocortical Assembloid, CW20107, Week 12, NRXN1 Knockout

description:
Library name: Sample24_CW20107_WK12_CX-TH_NX1KO
thalamic and cortical halves separated into 2 processed data files


title: 1270, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001270

value: Tongue,Tongue


title: 1627, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001627


title: 1271, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001271


title: 5.EV.STEMI.23.2

description: Library name: 5.EV.STEMI.23.2


title: 1056, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001056

source_name: Pancreas,Pancreas

value: Pancreas,Pancreas


title: 1626, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001626


title: 1005, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox001005

value: MotorCortex,MotorCortex


title: 1628, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001628


title: 4.EV.NSTEMI.18.2

description: Library name: 4.EV.NSTEMI.18.2


title: RPE p53-/-, parental control, replicate 2

city: Boston

first: Huy

last: Nguyen

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

description: Library name: RPE-WT-EV-2

data_processing:
Kallisto (version 0.48.0) was used to map the raw RNA-seq reads against the GENCODE human reference gene annotation (Release 44) and generate raw transcript abundance estimates.
The tximport Bioconductor R package was used to summarize the transcript abundance estimates to produce gene-level estimated counts.
Assembly: hg38
Supplementary files format and content: tab-delimited file with matrix table of raw gene counts for every gene and every sample

source_name: Eye; Pigmented epithelium; Retina

growth_protocol: RPE p53-/-  parental and SMARCB1 knockout cells were grown in DMEM/F12 containing GlutaMAX (Gibco) and supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich).

extract_protocol:
RNA samples were prepared using RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN). RNA samples were quantified using Qubit 2.0 Fluorometer, and the RNA integrity was checked with 4200 TapeStation.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used following the manufacturer’s recommendations (New England BioLabs). Briefly, mRNAs were initially enriched with Oligo d(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3´ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were clustered on flowcell lanes. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.

value: Eye; Pigmented epithelium; Retina

value: epithelial cell

value: SMARCB1 wildtype


title: RPE p53-/-, parental control, replicate 3

description: Library name: RPE-WT-EV-3


title: 3.EV.STEMI.22.2

description: Library name: 3.EV.STEMI.22.2

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: RPE p53-/-, SMARCB1 knockout, replicate 3

description: Library name: RPE-C10-EV-3

value: SMARCB1 knockout


title: 1057, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001057

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).


title: Thalamocortical Assembloid, CW20107, Week 12, Non-Targeting Control

description:
Library name: Sample25_CW20107_WK12_CX-TH_NX1NTC
thalamic and cortical halves separated into 2 processed data files

source_name: Cortical Organoid

value: Cortical Organoid

value: Non-targeting Control Thalamus and Cortex

value: lentiviral infection, neural differentiation, fusion


title: 1.EV.NSTEMI.20.2

description: Library name: 1.EV.NSTEMI.20.2

value: wild-type

value: EV


title: RPE p53-/-, parental control, replicate 1

description: Library name: RPE-WT-EV-1


title: 1058, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001058


title: 1060, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001060


title: Thalamocortical Assembloid, CW20107, Week 6, NRXN1 Knockout

description:
Library name: Sample26_CW20107_WK6_CX-TH_NX1KO
thalamic and cortical halves separated into 2 processed data files

value: Thalamic and Cortical Organoids

value: NRXN1 Knockout Thalamus, Non-targeting Control Cortex


title: THP1 cells, Ftxa, tech rep 2

city: Umeå

first: abdelbasset

last: yabrag

address: Tråggränd 41 LGH 1003

department: Molecular biology

country: Sweden

institute: Umeå University

description: Library name: Ftxa_THP1-2

data_processing:
Trimmomatic 0.36
TopHat/2.1.1
Samtools 1.8
HTSeq 0.9.1 stranded mode and exon
DESeq2
Assembly: hg38
Supplementary files format and content: .tsv of gene counts per gene id/name

growth_protocol: THP-1 monocytes (1 × 105 cells in DMEM) were seeded in 24-well plates at 37°C. Following the PMA-induced differentiation into macrophages for 48 hours

extract_protocol:
RNeasy Mini Kit (Qiagen)
Library preparation and sequencing was completed by BMKGene, with a paired-end protocol and read length of 150 nt (PE150), resulting in a total output of 20 million reads per sample.

treatment_protocol: the cells were treated with EVs (at 1 ug/ml) or purified FtxA (at 1 μg/ml) for 4 hours,

value: WT

value: FtxA (1 μg/ml)

tag: time point

value: 4 hr


title: RPE p53-/-, SMARCB1 knockout, replicate 2

description: Library name: RPE-C10-EV-2


title: 1059, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001059

value: Pancreas,Pancreas


title: RPE p53-/-, SMARCB1 knockout, replicate 1

description: Library name: RPE-C10-EV-1


title: 1062, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001062


title: 1631, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001631

value: Brain- Hippocampus,Brain- Hippocampus


title: 1630, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001630


title: 1636, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001636


title: 2.EV.NSTEMI.26.2

description: Library name: 2.EV.NSTEMI.26.2


title: 1632, Mus musculus, Brain-Hippocampus,Brain-Hippocampus

description: Library name: itox001632

source_name: Brain-Hippocampus,Brain-Hippocampus

value: Brain-Hippocampus,Brain-Hippocampus


title: 1061, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001061


title: 4.EV.STEMI.18.1

description: Library name: 4.EV.STEMI.18.1


title: 5.EV.STEMI.23.1

description: Library name: 5.EV.STEMI.23.1


title: THP1 cells, Ftxa, tech rep 1

description: Library name: Ftxa_THP1-1


title: THP1 cells, Fa12, tech rep 2

description: Library name: Fa12_THP1-2

value: EVs 1 ug/μl


title: 3.EV.NSTEMI.22.1

description: Library name: 3.EV.NSTEMI.22.1


title: 1629, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001629


title: 1637, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001637


title: THP1 cells, Fa12, tech rep 1

description: Library name: Fa12_THP1-1


title: 1063, Macaca fascicularis, Pancreas,Pancreas

description: Library name: itox001063


title: 1.EV.NSTEMI.20.1

description: Library name: 1.EV.NSTEMI.20.1


title: 1638, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001638


title: 2.EV.STEMI.26.1

description: Library name: 2.EV.STEMI.26.1


title: 961, Macaca fascicularis, Lung,Lung

description: Library name: itox000961

value: Lung,Lung


title: THP1 cells, Fa1, tech rep 1

description: Library name: Fa1_THP1-1


title: THP1 cells, Fa1, tech rep 2

description: Library name: Fa1_THP1-2


title: 1635, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001635


title: 1070, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001070

source_name: PeripheralNerve,PeripheralNerve

value: PeripheralNerve,PeripheralNerve


title: 1639, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001639


title: 4.LPS.IFNg.0.0.0

description: Library name: 4.LPS.IFNg.0.0.0

value: Peripheral blood mononuclear cells


title: 1640, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001640


title: 5.LPS.IFNg.0.0.0

description: Library name: 5.LPS.IFNg.0.0.0


title: THP1 cells, control, tech rep 1

description: Library name: CT_THP1-1


title: 1071, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001071


title: THP1 cells, control, tech rep 2

description: Library name: CT_THP1-2


title: 2.LPS.IFNg.0.0.0

description: Library name: 2.LPS.IFNg.0.0.0


title: 1641, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001641


title: 1072, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001072


title: 3.LPS.IFNg.0.0.0

description: Library name: 3.LPS.IFNg.0.0.0


title: WZB-D-gal-LPS3

city: Beijing

first: yanlin

last: wang

address: Dongzhimen Hospital

institute: Beijing University of Chinese Medicine

description: Library name: DW-3

data_processing:
Normalized and logarithmic converted expression of mouse genes (FPKM) by using the limma relative log expression normalization method. Then, principal component analyses (PCA) analysis was performed to demonstrate a large degree of differentiation between each group for further analysis. Normalized RNA-seq data was used for a heatmap of gene expression (https://www.omicstudio.cn/home). Furthermore, normalized and logarithmic converted RNA-seq data was used for PCA analysis and others. Software R (version 4.1.2) and the limma R package were used for differential gene expression analysis. The results of differential expression were used as the input for gene set enrichment analysis (GSEA) with the ClusterProfiler package. The gene expression heatmap was generated using the tool in Lianchuan Biological website (https://www.omicstudio.cn/tool). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the clusterProfiler R package. Additionally, the enrichment analysis bubble charts of upregulated and downregulated genes were generated by clusterProfiler.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: CSV file including gene count for each sample.

source_name: liver

growth_protocol: Laboratory animals: 6–8-week-old male C57BL/6 mice purchased from Shanghai Slake Co., Ltd. The use of all mice in this study was approved by the Animal Ethics Committee of the Shanghai Institute of Materia Medica, and all procedures were conducted in accordance with its ethical standards and animal welfare principles. Animal experiments were conducted at the Animal Center of the Shanghai Institute of Materia Medica. The mice were SPF grade. During housing, no more than 5 mice were kept per cage, and the Animal Center provided specialized commercial mouse maintenance feed. Unless otherwise specified, the housing temperature was 22°C. Mice had free access to food and water and were maintained under a 12-hour light-dark cycle (light from 7:00 to 19:00, dark from 19:00 to 7:00).

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Following Illumina's (San Diego, California, USA) experimental protocol, purified total RNA underwent mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3'-end A-addition, adapter ligation, and enrichment to complete sequencing library preparation.

value: liver


title: 1642, Mus musculus, Brain-Hypothalamus,Brain-Hypothalamus

first: Darien

address: 255 Shennecossett Rd

institute: Pfizer

description: Library name: itox001642

source_name: Brain-Hypothalamus,Brain-Hypothalamus

value: Brain-Hypothalamus,Brain-Hypothalamus


title: 962, Macaca fascicularis, Lungs,Lungs

description: Library name: itox000962

source_name: Lungs,Lungs

value: Lungs,Lungs


title: 1.LPS.IFNg.0.0.0

description: Library name: 1.LPS.IFNg.0.0.0

value: wild-type


title: 1405, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001405


title: WZB-D-gal-LPS2

description: Library name: DW-2

treatment_protocol: Laboratory animals: 6–8-week-old male C57BL/6 mice purchased from Shanghai Slake Co., Ltd. The use of all mice in this study was approved by the Animal Ethics Committee of the Shanghai Institute of Materia Medica, and all procedures were conducted in accordance with its ethical standards and animal welfare principles. Animal experiments were conducted at the Animal Center of the Shanghai Institute of Materia Medica. The mice were SPF grade. During housing, no more than 5 mice were kept per cage, and the Animal Center provided specialized commercial mouse maintenance feed. Unless otherwise specified, the housing temperature was 22°C. Mice had free access to food and water and were maintained under a 12-hour light-dark cycle (light from 7:00 to 19:00, dark from 19:00 to 7:00).


title: 1073, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001073


title: 5.Control.0.0.0

description: Library name: 5.Control.0.0.0

value: Control


title: 1074, Macaca fascicularis, PeripheralNerve,PeripheralNerve

description: Library name: itox001074


title: 1406, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001406

source_name: Heart - Atrium,Heart - Atrium

value: Heart - Atrium,Heart - Atrium


title: D-gal-LPS3

description: Library name: D-3


title: WZB-D-gal-LPS1

description: Library name: DW-1


title: 1407, Mus musculus, Cecum,Cecum

description: Library name: itox001407

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 4.Control.0.0.0

description: Library name: 4.Control.0.0.0