title: 12153, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012153

source_name: Peripheral nerve,Peripheral nerve

value: Peripheral nerve,Peripheral nerve


title: 12172, Sus scrofa, Cerebellum,Cerebellum

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: itox012172

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: Sus scrofa

source_name: Cerebellum,Cerebellum

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: Cerebellum,Cerebellum

tag: batch


title: DSP-1001660035646-A-G10

city: Boston

first: Sharmila

last: Masli

address: 72 E. Concord St Instructional (L)

institute: Boston University

description: Library name: DSP-1001660035646-A-G10

library_source: other

data_processing:
Raw FASTQ files from the instrument were processed using the GeoMX NGS Pipeline using the instrument provided .ini file generated probe count matrices in dcc format
Images were assessed for presence of each cell type based on established markers (CK, SMA, PTPRC, etc.)
Raw counts were loaded with nanostring packages and then normalized, after which differential expression analysis was conducted by DESeq2, followed by Gene Set Enrichment Analysis through clusterProfiler
Supplementary files format and content: .dcc, count matrix files

molecule: other

organism: Mus musculus

source_name: Lacrimal Gland

extract_protocol:
Serial sections of formalin-fixed paraffin-embedded (FFPE) LG tissues harvested from WT (n=3) and TSP-/- (n=4) mice were cut (5 µm thick) and transferred to slides. One set of slides was stained for H&E and another set of slides with consecutive sections were submitted for spatial profiling to the Beth Israel Deaconess Medical Center (BIDMC) Spatial Technologies Unit (STU), MA, USA. The GeoMX Digital Spatial Profiler (DSP) platform was used to generate spatially resolved transcriptomic data, specifically the Whole Transcriptome Atlas (WTA) mouse RNA probe set for Illumina Systems (GMX-RNA-NGS-MsWTA-4) assay. This assay includes RNA probe set for 21,000+ transcripts for mouse protein coding genes plus negative controls designed for Illumina NGS readout with the Seq Code library prep. To visualize tissue structural components and microenvironment, a set of fluorophore-conjugated morphology markers were used. These included Alexa Fluor 532 (green)-conjugated anti-pan-CK (AE1+AE3, Novus, Cat.# NBP2-33200), Alexa Fluor 594 (yellow)-conjugated anti-CD45 (EM-05, Novus, Cat.# NBP1-44763AF594) and Alexa Fluor 647 (red)-conjugated anti-Smooth Muscle Actin (SP171, Abcam, Cat.# ab267537) and nuclear stain SYTO13 (blue). These markers were used to delineate the nuclear, epithelial (acinar and duct), immune and myoepithelial compartments. Immunofluorescence imaging, region of interest (ROI) selection, segmentation into marker-specific areas of interest (AOI) and spatially indexed barcode cleavage and collection were performed on a GeoMx Digital Spatial Profiling instrument (Nanostring). Selected ROIs were exposed to ultraviolet (UV) light to cleave DNA tags in a region-specific manner. The released indexing oligos were then collected using microcapillary aspiration and dispensed into a microplate as per segmentation of each ROI. Four consecutive sections per tissue (total 16 of TSP-1-/- and 12 of WT) were assessed. Approximately, 6-10 ROIs and 11-14 AOIs per tissue sample (total 34 ROIs and 57 AOIs for TSP-1-/- and 21 ROIs and 34 AOIs for WT) were collected.
Library preparation was performed as per manufacturer’s instructions which included PCR amplification to add Illumina adapter sequences and unique dual sample indices. Sequencing was performed to a minimum of 350M PE reads by pooling all 91 uniquely indexed WTA AOIs and sequencing on Illumina NovaSeq 6000 S4 flowcell in a 2x150bp PE, dual index, 8bp i5 and i7 index length configuration.

value: Lacrimal Gland

tag: cell type

value: Multiple


title: DSP-1001660035646-A-G08

description: Library name: DSP-1001660035646-A-G08


title: 2574, Mus musculus, Spleen,Spleen

description: Library name: itox002574

source_name: Spleen,Spleen

value: Spleen,Spleen


title: 1410, Rattus norvegicus, Cecum,Cecum

description: Library name: itox001410

organism: Rattus norvegicus

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 1643, Rattus norvegicus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001643


title: DSP-1001660035646-A-G05

description: Library name: DSP-1001660035646-A-G05


title: 12155, Sus scrofa, Ovary,Ovary

description: Library name: itox012155

source_name: Ovary,Ovary

value: Ovary,Ovary


title: DSP-1001660035646-A-G06

description: Library name: DSP-1001660035646-A-G06


title: 2575, Mus musculus, Spleen,Spleen

description: Library name: itox002575


title: 12175, Sus scrofa, Epididymis,Epididymis

description: Library name: itox012175

source_name: Epididymis,Epididymis

value: Epididymis,Epididymis


title: 2576, Mus musculus, Spleen,Spleen

description: Library name: itox002576


title: 2577, Mus musculus, Ileum,Ileum

description: Library name: itox002577

source_name: Ileum,Ileum

value: Ileum,Ileum


title: 12154, Sus scrofa, Occipital Lobe,Occipital Lobe

description: Library name: itox012154

source_name: Occipital Lobe,Occipital Lobe

value: Occipital Lobe,Occipital Lobe


title: 1411, Rattus norvegicus, Cecum,Cecum

description: Library name: itox001411


title: 1738, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001738

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: DSP-1001660035646-A-G07

description: Library name: DSP-1001660035646-A-G07


title: 1412, Rattus norvegicus, Cecum,Cecum

description: Library name: itox001412


title: 12176, Sus scrofa, Esophagus,Esophagus

description: Library name: itox012176

source_name: Esophagus,Esophagus

value: Esophagus,Esophagus


title: DSP-1001660035646-A-G04

description: Library name: DSP-1001660035646-A-G04


title: 1415, Rattus norvegicus, Colon (mid),Colon (mid)

description: Library name: itox001415

source_name: Colon (mid),Colon (mid)

value: Colon (mid),Colon (mid)


title: 2578, Mus musculus, Ileum,Ileum

description: Library name: itox002578


title: 12199, Sus scrofa, Liver,Liver

description: Library name: itox012199

source_name: Liver,Liver

value: Liver,Liver


title: 1490, Rattus norvegicus, Adrenal Gland,Adrenal Gland

description: Library name: itox001490

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 12177, Sus scrofa, Eye,Eye

description: Library name: itox012177

source_name: Eye,Eye

value: Eye,Eye


title: 1746, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001746


title: 1476, Rattus norvegicus, Tongue,Tongue

description: Library name: itox001476

source_name: Tongue,Tongue

value: Tongue,Tongue


title: DSP-1001660035646-A-G01

description: Library name: DSP-1001660035646-A-G01


title: 1745, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001745


title: DSP-1001660035646-A-G03

description: Library name: DSP-1001660035646-A-G03


title: 12178, Sus scrofa, Eye,Eye

description: Library name: itox012178


title: 12180, Sus scrofa, Frontal Lobe,Frontal Lobe

description: Library name: itox012180

source_name: Frontal Lobe,Frontal Lobe

value: Frontal Lobe,Frontal Lobe


title: 12202, Sus scrofa, Skeletal Muscle,Skeletal Muscle

description: Library name: itox012202

source_name: Skeletal Muscle,Skeletal Muscle

value: Skeletal Muscle,Skeletal Muscle


title: 1747, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001747


title: DSP-1001660035646-A-G02

description: Library name: DSP-1001660035646-A-G02

value: Lacrimal Gland


title: 1755, Mus musculus, Epididymus (head),Epididymus (head)

description: Library name: itox001755

source_name: Epididymus (head),Epididymus (head)

value: Epididymus (head),Epididymus (head)


title: 1557, Rattus norvegicus, Thymus,Thymus

description: Library name: itox001557

source_name: Thymus,Thymus

value: Thymus,Thymus


title: 1753, Mus musculus, Epididymus (tail),Epididymus (tail)

description: Library name: itox001753

source_name: Epididymus (tail),Epididymus (tail)

value: Epididymus (tail),Epididymus (tail)


title: 12181, Sus scrofa, Gallbladder,Gallbladder

description: Library name: itox012181

source_name: Gallbladder,Gallbladder

value: Gallbladder,Gallbladder


title: DSP-1001660035646-A-F11

description: Library name: DSP-1001660035646-A-F11

source_name: Lacrimal Gland

value: Multiple


title: DSP-1001660035646-A-F12

description: Library name: DSP-1001660035646-A-F12


title: 1401, Rattus norvegicus, Heart -Ventricle (left),Heart -Ventricle (left)

description: Library name: itox001401


title: 1756, Mus musculus, Epididymus (tail),Epididymus (tail)

description: Library name: itox001756


title: 1576, Rattus norvegicus, Brain-Cerebellum,Brain-Cerebellum

description: Library name: itox001576

source_name: Brain-Cerebellum,Brain-Cerebellum

value: Brain-Cerebellum,Brain-Cerebellum


title: DSP-1001660035646-A-F10

description: Library name: DSP-1001660035646-A-F10


title: DSP-1001660035646-A-F09

description: Library name: DSP-1001660035646-A-F09


title: 1451, Rattus norvegicus, Stomach (glandular),Stomach (glandular)

description: Library name: itox001451

source_name: Stomach (glandular),Stomach (glandular)

value: Stomach (glandular),Stomach (glandular)


title: 12183, Sus scrofa, Mammary Gland,Mammary Gland

description: Library name: itox012183

source_name: Mammary Gland,Mammary Gland

value: Mammary Gland,Mammary Gland


title: 2459, Rattus norvegicus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox002459


title: 1762, Mus musculus, Oviduct (Fallopian tube),Oviduct (Fallopian tube)

description: Library name: itox001762


title: 12185, Sus scrofa, Prostate Gland,Prostate Gland

description: Library name: itox012185

source_name: Prostate Gland,Prostate Gland

value: Prostate Gland,Prostate Gland


title: DSP-1001660035646-A-F08

description: Library name: DSP-1001660035646-A-F08


title: 2460, Rattus norvegicus, Ureter,Ureter

description: Library name: itox002460

source_name: Ureter,Ureter

value: Ureter,Ureter


title: DSP-1001660035646-A-F07

description: Library name: DSP-1001660035646-A-F07


title: 12184, Sus scrofa, Pituitary Gland,Pituitary Gland

description: Library name: itox012184

source_name: Pituitary Gland,Pituitary Gland

value: Pituitary Gland,Pituitary Gland


title: 1763, Mus musculus, Oviduct (Fallopian tube),Oviduct (Fallopian tube)

description: Library name: itox001763


title: 2589, Rattus norvegicus, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002589

source_name: T Lymphocytes CD8,T Lymphocytes CD8

value: T Lymphocytes CD8,T Lymphocytes CD8


title: 1784, Rattus norvegicus, Uterus,Uterus

description: Library name: itox001784

source_name: Uterus,Uterus

value: Uterus,Uterus


title: 1761, Mus musculus, Epididymus (tail),Epididymus (tail)

description: Library name: itox001761


title: DSP-1001660035646-A-F06

description: Library name: DSP-1001660035646-A-F06


title: 12187, Sus scrofa, Heart,Heart

description: Library name: itox012187

source_name: Heart,Heart

value: Heart,Heart


title: DSP-1001660035646-A-F04

description: Library name: DSP-1001660035646-A-F04


title: 1768, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001768

source_name: Ovary (left),Ovary (left)

value: Ovary (left),Ovary (left)


title: 2599, Rattus norvegicus, Whole Blood,Whole Blood

description: Library name: itox002599

source_name: Whole Blood,Whole Blood

value: Whole Blood,Whole Blood


title: 12189, Sus scrofa, Heart,Heart

description: Library name: itox012189


title: 12237, Sus scrofa, Gallbladder,Gallbladder

description: Library name: itox012237


title: 1715, Mus musculus, Peripheral Nerve (sciatic),Peripheral Nerve (sciatic)

description: Library name: itox001715


title: DSP-1001660035646-A-F05

description: Library name: DSP-1001660035646-A-F05

value: Lacrimal Gland


title: 1789, Rattus norvegicus, Lung (left lobe),Lung (left lobe)

description: Library name: itox001789

source_name: Lung (left lobe),Lung (left lobe)

value: Lung (left lobe),Lung (left lobe)


title: 1771, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001771


title: DSP-1001660035646-A-F03

description: Library name: DSP-1001660035646-A-F03


title: 12188, Sus scrofa, Heart,Heart

description: Library name: itox012188


title: 1785, Rattus norvegicus, Vagina,Vagina

description: Library name: itox001785

source_name: Vagina,Vagina

value: Vagina,Vagina


title: DSP-1001660035646-A-F02

description: Library name: DSP-1001660035646-A-F02


title: 1779, Mus musculus, Testis (tubules\, without capsule),Testis (tubules\, without capsule)

description: Library name: itox001779


title: 12258, Sus scrofa, Skeletal Muscle,Skeletal Muscle

description: Library name: itox012258

source_name: Skeletal Muscle,Skeletal Muscle

value: Skeletal Muscle,Skeletal Muscle


title: 2444, Rattus norvegicus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002444


title: 1716, Mus musculus, Peripheral Nerve (sciatic),Peripheral Nerve (sciatic)

description: Library name: itox001716


title: DSP-1001660035646-A-F01

description: Library name: DSP-1001660035646-A-F01


title: 2443, Rattus norvegicus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox002443

source_name: Brain- Hippocampus,Brain- Hippocampus

value: Brain- Hippocampus,Brain- Hippocampus


title: 12259, Sus scrofa, Optic Nerve,Optic Nerve

description: Library name: itox012259

source_name: Optic Nerve,Optic Nerve

value: Optic Nerve,Optic Nerve


title: 1780, Mus musculus, Testis (tubules\, without capsule),Testis (tubules\, without capsule)

description: Library name: itox001780


title: 1781, Mus musculus, Testis (tubules\, without capsule),Testis (tubules\, without capsule)

description: Library name: itox001781


title: 12261, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012261

source_name: Peripheral nerve,Peripheral nerve

value: Peripheral nerve,Peripheral nerve


title: 1782, Mus musculus, Testis,Testis

description: Library name: itox001782

source_name: Testis,Testis

value: Testis,Testis


title: DSP-1001660035646-A-E12

description: Library name: DSP-1001660035646-A-E12

source_name: Lacrimal Gland

value: Multiple


title: 12260, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012260


title: DSP-1001660035646-A-E10

description: Library name: DSP-1001660035646-A-E10


title: 12262, Sus scrofa, Occipital Lobe,Occipital Lobe

description: Library name: itox012262

source_name: Occipital Lobe,Occipital Lobe

value: Occipital Lobe,Occipital Lobe


title: 2442, Rattus norvegicus, Adrenal Gland,Adrenal Gland

description: Library name: itox002442

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 2440, Rattus norvegicus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox002440


title: 2439, Rattus norvegicus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox002439


title: 1783, Mus musculus, Testis (tubules\, without capsule),Testis (tubules\, without capsule)

description: Library name: itox001783


title: 12263, Sus scrofa, Ovary,Ovary

description: Library name: itox012263

source_name: Ovary,Ovary

value: Ovary,Ovary


title: DSP-1001660035646-A-E11

description: Library name: DSP-1001660035646-A-E11


title: DSP-1001660035646-A-E08

description: Library name: DSP-1001660035646-A-E08


title: DSP-1001660035646-A-E09

description: Library name: DSP-1001660035646-A-E09


title: 2441, Rattus norvegicus, Ureter,Ureter

description: Library name: itox002441

source_name: Ureter,Ureter

value: Ureter,Ureter


title: 2438, Rattus norvegicus, Trachea,Trachea

description: Library name: itox002438

source_name: Trachea,Trachea

value: Trachea,Trachea


title: 1786, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox001786


title: 12264, Sus scrofa, Fallopian tube,Fallopian tube

description: Library name: itox012264

source_name: Fallopian tube,Fallopian tube

value: Fallopian tube,Fallopian tube


title: DSP-1001660035646-A-E07

description: Library name: DSP-1001660035646-A-E07


title: 12265, Sus scrofa, Blood,Blood

description: Library name: itox012265

source_name: Blood,Blood

value: Blood,Blood


title: 1788, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox001788


title: 1787, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox001787


title: DSP-1001660035646-A-E06

description: Library name: DSP-1001660035646-A-E06


title: 2437, Rattus norvegicus, Tongue,Tongue

description: Library name: itox002437

source_name: Tongue,Tongue

value: Tongue,Tongue


title: 2436, Rattus norvegicus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox002436


title: DSP-1001660035646-A-E05

description: Library name: DSP-1001660035646-A-E05

value: Lacrimal Gland


title: 1790, Mus musculus, Trachea,Trachea

description: Library name: itox001790


title: 12268, Sus scrofa, Skin,Skin

description: Library name: itox012268

source_name: Skin,Skin

value: Skin,Skin


title: 2454, Rattus norvegicus, Cervix,Cervix

description: Library name: itox002454

source_name: Cervix,Cervix

value: Cervix,Cervix


title: 1791, Mus musculus, Trachea,Trachea

description: Library name: itox001791


title: DSP-1001660035646-A-E03

description: Library name: DSP-1001660035646-A-E03


title: 2453, Rattus norvegicus, Oviduct (Fallopian tube),Oviduct (Fallopian tube)

description: Library name: itox002453


title: DSP-1001660035646-A-E01

description: Library name: DSP-1001660035646-A-E01


title: 12266, Sus scrofa, Pancreas,Pancreas

description: Library name: itox012266

source_name: Pancreas,Pancreas

value: Pancreas,Pancreas


title: 1717, Mus musculus, Peripheral Nerve (sciatic),Peripheral Nerve (sciatic)

description: Library name: itox001717


title: 1795, Mus musculus, Trachea,Trachea

description: Library name: itox001795


title: 12269, Sus scrofa, Duodenum,Duodenum

description: Library name: itox012269

source_name: Duodenum,Duodenum

value: Duodenum,Duodenum


title: 12267, Sus scrofa, Cerebral cortex,Cerebral cortex

description: Library name: itox012267

source_name: Cerebral cortex,Cerebral cortex

value: Cerebral cortex,Cerebral cortex


title: 2455, Rattus norvegicus, Eye-lens,Eye-lens

description: Library name: itox002455

source_name: Eye-lens,Eye-lens

value: Eye-lens,Eye-lens


title: DSP-1001660035646-A-D12

description: Library name: DSP-1001660035646-A-D12


title: 2456, Rattus norvegicus, Lung (left lobe),Lung (left lobe)

description: Library name: itox002456

source_name: Lung (left lobe),Lung (left lobe)

value: Lung (left lobe),Lung (left lobe)


title: 12271, Sus scrofa, Jejunum,Jejunum

description: Library name: itox012271

source_name: Jejunum,Jejunum

value: Jejunum,Jejunum


title: 1748, Mus musculus, Mammary Gland/Tissue (female only),Mammary Gland/Tissue (female only)

description: Library name: itox001748


title: 1752, Mus musculus, Epididymus (head),Epididymus (head)

description: Library name: itox001752

source_name: Epididymus (head),Epididymus (head)

value: Epididymus (head),Epididymus (head)


title: 12270, Sus scrofa, Ileum,Ileum

description: Library name: itox012270

source_name: Ileum,Ileum

value: Ileum,Ileum


title: DSP-1001660035646-A-E02

description: Library name: DSP-1001660035646-A-E02

source_name: Lacrimal Gland

value: Multiple


title: 12289, Sus scrofa, Thalamus,Thalamus

description: Library name: itox012289

source_name: Thalamus,Thalamus

value: Thalamus,Thalamus


title: 12272, Sus scrofa, Spinal Cord,Spinal Cord

description: Library name: itox012272

source_name: Spinal Cord,Spinal Cord

value: Spinal Cord,Spinal Cord


title: 1796, Mus musculus, Trachea,Trachea

description: Library name: itox001796

source_name: Trachea,Trachea

value: Trachea,Trachea


title: 2461, Rattus norvegicus, B Cells,B Cells

description: Library name: itox002461

source_name: B Cells,B Cells

value: B Cells,B Cells


title: 2458, Rattus norvegicus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox002458


title: 1758, Mus musculus, Epididymus (head),Epididymus (head)

description: Library name: itox001758


title: 2457, Rattus norvegicus, Thymus,Thymus

description: Library name: itox002457

source_name: Thymus,Thymus

value: Thymus,Thymus


title: DSP-1001660035646-A-E04

description: Library name: DSP-1001660035646-A-E04

value: Lacrimal Gland


title: DSP-1001660035646-A-D07

description: Library name: DSP-1001660035646-A-D07


title: 2462, Rattus norvegicus, T Lymphocytes CD4,T Lymphocytes CD4

description: Library name: itox002462

source_name: T Lymphocytes CD4,T Lymphocytes CD4

value: T Lymphocytes CD4,T Lymphocytes CD4


title: 12256, Sus scrofa, Lung,Lung

description: Library name: itox012256

source_name: Lung,Lung

value: Lung,Lung


title: DSP-1001660035646-A-D11

description: Library name: DSP-1001660035646-A-D11


title: DSP-1001660035646-A-D10

description: Library name: DSP-1001660035646-A-D10


title: 1757, Mus musculus, Epididymus (head),Epididymus (head)

description: Library name: itox001757


title: 1834, Rattus norvegicus, Kidney,Kidney

description: Library name: itox001834

source_name: Kidney,Kidney

value: Kidney,Kidney


title: 1775, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001775

source_name: Ovary (left),Ovary (left)

value: Ovary (left),Ovary (left)


title: 12274, Sus scrofa, Stomach,Stomach

description: Library name: itox012274

source_name: Stomach,Stomach

value: Stomach,Stomach


title: 12292, Sus scrofa, Tonsil,Tonsil

description: Library name: itox012292

source_name: Tonsil,Tonsil

value: Tonsil,Tonsil


title: 1759, Mus musculus, Epididymus (head),Epididymus (head)

description: Library name: itox001759


title: DSP-1001660035646-A-D04

description: Library name: DSP-1001660035646-A-D04


title: 1774, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001774


title: DSP-1001660035646-A-D09

description: Library name: DSP-1001660035646-A-D09


title: 12273, Sus scrofa, Spleen,Spleen

description: Library name: itox012273

source_name: Spleen,Spleen

value: Spleen,Spleen


title: 1767, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001767


title: 1720, Rattus norvegicus, Eye-lens,Eye-lens

description: Library name: itox001720

source_name: Eye-lens,Eye-lens

value: Eye-lens,Eye-lens


title: DSP-1001660035646-A-D08

description: Library name: DSP-1001660035646-A-D08


title: 1764, Mus musculus, Oviduct (Fallopian tube),Oviduct (Fallopian tube)

description: Library name: itox001764


title: 1833, Rattus norvegicus, Kidney,Kidney

description: Library name: itox001833


title: 1845, Rattus norvegicus, Ureter,Ureter

description: Library name: itox001845

source_name: Ureter,Ureter

value: Ureter,Ureter


title: DSP-1001660035646-A-D03

description: Library name: DSP-1001660035646-A-D03


title: 11743, Sus scrofa, Salivary Gland,Salivary Gland

description: Library name: itox011743

source_name: Salivary Gland,Salivary Gland

value: Salivary Gland,Salivary Gland


title: 1723, Rattus norvegicus, Eye-lens,Eye-lens

description: Library name: itox001723


title: 12255, Sus scrofa, Liver,Liver

description: Library name: itox012255

source_name: Liver,Liver

value: Liver,Liver


title: DSP-1001660035646-A-D06

description: Library name: DSP-1001660035646-A-D06

source_name: Lacrimal Gland

value: Multiple


title: 2463, Rattus norvegicus, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002463

source_name: T Lymphocytes CD8,T Lymphocytes CD8

value: T Lymphocytes CD8,T Lymphocytes CD8


title: DSP-1001660035646-A-D05

description: Library name: DSP-1001660035646-A-D05


title: 1843, Rattus norvegicus, Ureter,Ureter

description: Library name: itox001843


title: 11745, Sus scrofa, Heart,Heart

description: Library name: itox011745

source_name: Heart,Heart

value: Heart,Heart


title: 11741, Sus scrofa, Pituitary Gland,Pituitary Gland

description: Library name: itox011741

source_name: Pituitary Gland,Pituitary Gland

value: Pituitary Gland,Pituitary Gland


title: 1725, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001725

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: DSP-1001660035646-A-D02

description: Library name: DSP-1001660035646-A-D02

value: Lacrimal Gland


title: 11742, Sus scrofa, Prostate Gland,Prostate Gland

description: Library name: itox011742

source_name: Prostate Gland,Prostate Gland

value: Prostate Gland,Prostate Gland


title: DSP-1001660035646-A-D01

description: Library name: DSP-1001660035646-A-D01


title: 2587, Rattus norvegicus, B Cells,B Cells

description: Library name: itox002587

source_name: B Cells,B Cells

value: B Cells,B Cells


title: 2464, Mus musculus, B Cells,B Cells

description: Library name: itox002464


title: 1727, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001727


title: 11725, Sus scrofa, Artery,Artery

description: Library name: itox011725

source_name: Artery,Artery

value: Artery,Artery


title: 2588, Rattus norvegicus, T Lymphocytes CD4,T Lymphocytes CD4

description: Library name: itox002588

source_name: T Lymphocytes CD4,T Lymphocytes CD4

value: T Lymphocytes CD4,T Lymphocytes CD4


title: 11750, Sus scrofa, Heart,Heart

description: Library name: itox011750


title: 2465, Mus musculus, T Lymphocytes CD8,T Lymphocytes CD8

description: Library name: itox002465


title: 2596, Rattus norvegicus, Whole Blood,Whole Blood

description: Library name: itox002596

source_name: Whole Blood,Whole Blood

value: Whole Blood,Whole Blood


title: 2473, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002473


title: DSP-1001660035646-A-C12

description: Library name: DSP-1001660035646-A-C12


title: DSP-1001660035646-A-C11

description: Library name: DSP-1001660035646-A-C11


title: 2474, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002474


title: 11728, Sus scrofa, Cerebellum,Cerebellum

description: Library name: itox011728

source_name: Cerebellum,Cerebellum

value: Cerebellum,Cerebellum


title: DSP-1001660035646-A-C10

description: Library name: DSP-1001660035646-A-C10


title: 11727, Sus scrofa, Brainstem,Brainstem

description: Library name: itox011727

source_name: Brainstem,Brainstem

value: Brainstem,Brainstem


title: 11726, Sus scrofa, Bone Marrow,Bone Marrow

description: Library name: itox011726

source_name: Bone Marrow,Bone Marrow

value: Bone Marrow,Bone Marrow


title: 2598, Rattus norvegicus, Whole Blood,Whole Blood

description: Library name: itox002598


title: 2541, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox002541

source_name: Colon (mid),Colon (mid)

value: Colon (mid),Colon (mid)


title: 2600, Rattus norvegicus, Whole Blood,Whole Blood

description: Library name: itox002600


title: DSP-1001660035646-A-C08

description: Library name: DSP-1001660035646-A-C08


title: 11754, Sus scrofa, Cecum,Cecum

description: Library name: itox011754

source_name: Cecum,Cecum

value: Cecum,Cecum


title: DSP-1001660035646-A-C09

description: Library name: DSP-1001660035646-A-C09


title: 2543, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002543


title: 2597, Rattus norvegicus, Whole Blood,Whole Blood

description: Library name: itox002597


title: 1799, Rattus norvegicus, Trechea,Trechea

description: Library name: itox001799

source_name: Trechea,Trechea

value: Trechea,Trechea


title: 2601, Rattus norvegicus, Whole Blood,Whole Blood

description: Library name: itox002601


title: 2544, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002544


title: 2545, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002545


title: 2526, Mus musculus, Thymus,Thymus

description: Library name: itox002526

source_name: Thymus,Thymus

value: Thymus,Thymus


title: DSP-1001660035646-A-C07

description: Library name: DSP-1001660035646-A-C07

source_name: Lacrimal Gland

value: Multiple


title: DSP-1001660035646-A-C04

description: Library name: DSP-1001660035646-A-C04


title: DSP-1001660035646-A-C06

description: Library name: DSP-1001660035646-A-C06


title: 11756, Sus scrofa, Rectum,Rectum

description: Library name: itox011756

source_name: Rectum,Rectum

value: Rectum,Rectum


title: 2423, Rattus norvegicus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox002423

source_name: Brain - Cerebellum,Brain - Cerebellum

value: Brain - Cerebellum,Brain - Cerebellum


title: 11755, Sus scrofa, Colon,Colon

description: Library name: itox011755

source_name: Colon,Colon

value: Colon,Colon


title: 2547, Mus musculus, Ileum,Ileum

description: Library name: itox002547

source_name: Ileum,Ileum

value: Ileum,Ileum


title: 11757, Sus scrofa, Liver,Liver

description: Library name: itox011757

source_name: Liver,Liver

value: Liver,Liver


title: 2527, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox002527

source_name: Skin (inguinal),Skin (inguinal)

value: Skin (inguinal),Skin (inguinal)


title: 2546, Mus musculus, Liver (left lateral lobe),Liver (left lateral lobe)

description: Library name: itox002546


title: 2424, Rattus norvegicus, Brain - Cortex,Brain - Cortex

description: Library name: itox002424

source_name: Brain - Cortex,Brain - Cortex

value: Brain - Cortex,Brain - Cortex


title: 1733, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001733

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: DSP-1001660035646-A-C02

description: Library name: DSP-1001660035646-A-C02

value: Lacrimal Gland


title: DSP-1001660035646-A-C03

description: Library name: DSP-1001660035646-A-C03


title: 11760, Sus scrofa, Skeletal Muscle,Skeletal Muscle

description: Library name: itox011760

source_name: Skeletal Muscle,Skeletal Muscle

value: Skeletal Muscle,Skeletal Muscle


title: 11759, Sus scrofa, Mesenteric Lymph Node,Mesenteric Lymph Node

description: Library name: itox011759


title: DSP-1001660035646-A-C01

description: Library name: DSP-1001660035646-A-C01


title: 2427, Rattus norvegicus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002427


title: DSP-1001660035646-A-C05

description: Library name: DSP-1001660035646-A-C05


title: 11758, Sus scrofa, Lung,Lung

description: Library name: itox011758

source_name: Lung,Lung

value: Lung,Lung


title: 11761, Sus scrofa, Optic Nerve,Optic Nerve

description: Library name: itox011761

source_name: Optic Nerve,Optic Nerve

value: Optic Nerve,Optic Nerve


title: 2426, Rattus norvegicus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox002426

source_name: Brain- Hippocampus,Brain- Hippocampus

value: Brain- Hippocampus,Brain- Hippocampus


title: DSP-1001660035646-A-B12

description: Library name: DSP-1001660035646-A-B12


title: 2528, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox002528


title: 2428, Rattus norvegicus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002428


title: 2425, Rattus norvegicus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox002425


title: 11877, Sus scrofa, Cerebral Cortex,Cerebral Cortex

description: Library name: itox011877

source_name: Cerebral Cortex,Cerebral Cortex

value: Cerebral Cortex,Cerebral Cortex


title: DSP-1001660035646-A-B11

description: Library name: DSP-1001660035646-A-B11


title: 2451, Rattus norvegicus, Uterus (left horn),Uterus (left horn)

description: Library name: itox002451

source_name: Uterus (left horn),Uterus (left horn)

value: Uterus (left horn),Uterus (left horn)


title: 11762, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox011762

source_name: Peripheral nerve,Peripheral nerve

value: Peripheral nerve,Peripheral nerve


title: 2435, Rattus norvegicus, Esophagus (mid),Esophagus (mid)

description: Library name: itox002435

source_name: Esophagus (mid),Esophagus (mid)

value: Esophagus (mid),Esophagus (mid)


title: 2549, Mus musculus, Ileum,Ileum

description: Library name: itox002549


title: 2529, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002529


title: 2550, Mus musculus, Uterus (left horn),Uterus (left horn)

description: Library name: itox002550


title: 2452, Rattus norvegicus, Vagina,Vagina

description: Library name: itox002452

source_name: Vagina,Vagina

value: Vagina,Vagina


title: DSP-1001660035646-A-B10

description: Library name: DSP-1001660035646-A-B10

source_name: Lacrimal Gland

value: Multiple


title: 11878, Sus scrofa, Gallbladder,Gallbladder

description: Library name: itox011878

source_name: Gallbladder,Gallbladder

value: Gallbladder,Gallbladder


title: 2433, Rattus norvegicus, Testis (tubules without capsule),Testis (tubules without capsule)

description: Library name: itox002433


title: 11764, Sus scrofa, Occipital Lobe,Occipital Lobe

description: Library name: itox011764

source_name: Occipital Lobe,Occipital Lobe

value: Occipital Lobe,Occipital Lobe


title: DSP-1001660035646-A-B08

description: Library name: DSP-1001660035646-A-B08


title: 2434, Rattus norvegicus, Eye-lens,Eye-lens

description: Library name: itox002434

source_name: Eye-lens,Eye-lens

value: Eye-lens,Eye-lens


title: 2551, Mus musculus, Uterus (left horn),Uterus (left horn)

description: Library name: itox002551


title: 11990, Sus scrofa, Cerebellum,Cerebellum

description: Library name: itox011990

source_name: Cerebellum,Cerebellum

value: Cerebellum,Cerebellum


title: DSP-1001660035646-A-B07

description: Library name: DSP-1001660035646-A-B07


title: DSP-1001660035646-A-B09

description: Library name: DSP-1001660035646-A-B09


title: 2552, Mus musculus, Uterus (left horn),Uterus (left horn)

description: Library name: itox002552


title: DSP-1001660035646-A-B06

description: Library name: DSP-1001660035646-A-B06


title: 2553, Mus musculus, Vagina,Vagina

description: Library name: itox002553


title: 11968, Sus scrofa, Bladder,Bladder

description: Library name: itox011968

source_name: Bladder,Bladder

value: Bladder,Bladder


title: 2554, Mus musculus, Vagina,Vagina

description: Library name: itox002554


title: DSP-1001660035646-A-B05

description: Library name: DSP-1001660035646-A-B05


title: 11969, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox011969

source_name: Small Intestine,Small Intestine

value: Small Intestine,Small Intestine


title: 2555, Mus musculus, Vagina,Vagina

description: Library name: itox002555


title: DSP-1001660035646-A-B04

description: Library name: DSP-1001660035646-A-B04

value: Lacrimal Gland


title: 2432, Rattus norvegicus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox002432


title: 11970, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox011970


title: 2430, Rattus norvegicus, Cecum,Cecum

description: Library name: itox002430

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 11763, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox011763


title: 2556, Mus musculus, Cervix -Pooled,Cervix -Pooled

description: Library name: itox002556

source_name: Cervix -Pooled,Cervix -Pooled

value: Cervix -Pooled,Cervix -Pooled


title: 2557, Mus musculus, Cervix -Pooled,Cervix -Pooled

description: Library name: itox002557


title: 11971, Sus scrofa, Spinal Cord,Spinal Cord

description: Library name: itox011971

source_name: Spinal Cord,Spinal Cord

value: Spinal Cord,Spinal Cord


title: DSP-1001660035646-A-B03

description: Library name: DSP-1001660035646-A-B03


title: 2429, Rattus norvegicus, Stomach (glandular),Stomach (glandular)

description: Library name: itox002429

source_name: Stomach (glandular),Stomach (glandular)

value: Stomach (glandular),Stomach (glandular)


title: 2450, Rattus norvegicus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox002450


title: DSP-1001660035646-A-B02

description: Library name: DSP-1001660035646-A-B02


title: 1724, Rattus norvegicus, Eye-lens,Eye-lens

description: Library name: itox001724


title: 2431, Rattus norvegicus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002431


title: DSP-1001660035646-A-B01

description: Library name: DSP-1001660035646-A-B01


title: 11972, Sus scrofa, Spleen,Spleen

description: Library name: itox011972

source_name: Spleen,Spleen

value: Spleen,Spleen


title: 1736, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001736

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: 11973, Sus scrofa, Stomach,Stomach

description: Library name: itox011973

source_name: Stomach,Stomach

value: Stomach,Stomach


title: DSP-1001660035646-A-A12

description: Library name: DSP-1001660035646-A-A12


title: 2558, Mus musculus, Cervix -Pooled,Cervix -Pooled

description: Library name: itox002558


title: 11909, Sus scrofa, Skin,Skin

description: Library name: itox011909

source_name: Skin,Skin

value: Skin,Skin


title: 2448, Rattus norvegicus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002448


title: DSP-1001660035646-A-A11

description: Library name: DSP-1001660035646-A-A11


title: 11910, Sus scrofa, Duodenum,Duodenum

description: Library name: itox011910

source_name: Duodenum,Duodenum

value: Duodenum,Duodenum


title: 2449, Rattus norvegicus, Ileum,Ileum

description: Library name: itox002449

source_name: Ileum,Ileum

value: Ileum,Ileum


title: 2559, Mus musculus, Peripheral Nerve (sciatic)-Pooled,Peripheral Nerve (sciatic)-Pooled

description: Library name: itox002559


title: DSP-1001660035646-A-A09

description: Library name: DSP-1001660035646-A-A09

source_name: Lacrimal Gland

value: Multiple


title: 11978, Sus scrofa, Tonsil,Tonsil

description: Library name: itox011978

source_name: Tonsil,Tonsil

value: Tonsil,Tonsil


title: 2560, Mus musculus, Peripheral Nerve (sciatic)-Pooled,Peripheral Nerve (sciatic)-Pooled

description: Library name: itox002560


title: DSP-1001660035646-A-A08

description: Library name: DSP-1001660035646-A-A08


title: 2446, Rattus norvegicus, Cecum,Cecum

description: Library name: itox002446


title: 11979, Sus scrofa, Trachea,Trachea

description: Library name: itox011979

source_name: Trachea,Trachea

value: Trachea,Trachea


title: DSP-1001660035646-A-A07

description: Library name: DSP-1001660035646-A-A07


title: 1743, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001743


title: 1744, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001744


title: 2445, Rattus norvegicus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002445


title: 2447, Rattus norvegicus, Colon (mid),Colon (mid)

description: Library name: itox002447

source_name: Colon (mid),Colon (mid)

value: Colon (mid),Colon (mid)


title: Thalamocortical Assembloid, UCLA1, Week 6

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: Sample22_UCLA1_WK6_CX-TH
thalamic and cortical halves separated into 2 processed data files

library_source: transcriptomic single cell

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

molecule: nuclear RNA

organism: Homo sapiens

source_name: Thalamic and Cortical Organoids

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: Thalamic and Cortical Organoids

tag: cell line

value: Neural

tag: genotype

value: Control

tag: treatment

value: lentiviral infection, neural differentiation, fusion


title: 11980, Sus scrofa, Bladder,Bladder

description: Library name: itox011980

source_name: Bladder,Bladder

value: Bladder,Bladder


title: 1751, Mus musculus, Epididymus (head),Epididymus (head)

description: Library name: itox001751

source_name: Epididymus (head),Epididymus (head)

value: Epididymus (head),Epididymus (head)


title: DSP-1001660035646-A-A06

description: Library name: DSP-1001660035646-A-A06

value: Lacrimal Gland


title: DSP-1001660035646-A-A05

description: Library name: DSP-1001660035646-A-A05


title: 11981, Sus scrofa, Uterus,Uterus

description: Library name: itox011981

source_name: Uterus,Uterus

value: Uterus,Uterus


title: Corticocortical Assembloid, UCLA1, Week 6

description:
Library name: Sample21_UCLA1_WK6_CX-CX
both halves of corticocortical assembloids

source_name: Cortical Organoid

value: Cortical Organoid


title: 11982, Sus scrofa, Uterus,Uterus

description: Library name: itox011982


title: DSP-1001660035646-A-A04

description: Library name: DSP-1001660035646-A-A04


title: Thalamocortical Assembloid, Severed Cortex, Pooled, Week 12

description:
Library name: Sample23_Pooled_WK12_CXsev
pooled severed cortex samples from thalamocortical assembloids across cell lines

value: lentiviral infection, neural differentiation, fusion, severance


title: Thalamocortical Assembloid, UCLA1, Week 12

description:
Library name: Sample20_UCLA1_WK12_CX-TH
thalamic and cortical halves separated into 2 processed data files


title: 11983, Sus scrofa, Vagina,Vagina

description: Library name: itox011983

source_name: Vagina,Vagina

value: Vagina,Vagina


title: Corticocortical Assembloid, UCLA1, Week 12

description:
Library name: Sample19_UCLA1_WK12_CX-CX
both halves of corticocortical assembloids


title: 11984, Sus scrofa, Adipose,Adipose

description: Library name: itox011984

source_name: Adipose,Adipose

value: Adipose,Adipose


title: DSP-1001660035646-A-A03

description: Library name: DSP-1001660035646-A-A03


title: 1760, Mus musculus, Epididymus (tail),Epididymus (tail)

description: Library name: itox001760

source_name: Epididymus (tail),Epididymus (tail)

value: Epididymus (tail),Epididymus (tail)


title: 1754, Mus musculus, Epididymus (head),Epididymus (head)

description: Library name: itox001754


title: 1766, Mus musculus, Oviduct (Fallopian tube),Oviduct (Fallopian tube)

description: Library name: itox001766


title: 11986, Sus scrofa, Artery,Artery

description: Library name: itox011986

source_name: Artery,Artery

value: Artery,Artery


title: 1709, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001709

source_name: Brain-Striatum,Brain-Striatum

value: Brain-Striatum,Brain-Striatum


title: Mouse Primary neonatal lung fibroblasts, KO7

first: Mohammad Aslam

last: Saifi

state: MA

address: 60 Fenwood Rd

department: Medicine

institute: Brigham and Women's Hospital

description:
Library name: SK-69M2_B2
PAD2KO lung fibroblasts, sorted

data_processing:
Data processing tool: Sequence reads were processed using fastp for quality control and adapter trimming, and Salmon (v1.3.2) for transcript quantification in quasi-mapping mode.
Mapping: Trimmed sequence reads were mapped to the GRCm39 transcriptome.
Differential expression analysis: DESeq2 (v1.46.0) was used for differential gene expression analysis.
Assembly: GRCm39 (Mouse reference genome assembly)
Supplementary files format and content: Raw sequencing reads are in FASTQ format.
Supplementary files format and content: The processed data is in XLSX format, including FPKM values for each sample

source_name: Lung

extract_protocol:
RNA was isolated from primary lung fibroblasts using Qiagen's RNeasy Mini Plus Kit, and lysates were stored at -80°C until further processing.
RNA-seq libraries were prepared using the SMARTer mRNA-Seq Library Prep Kit, following the manufacturer's protocols. This method was used for preparing RNA libraries for SmartSeq2 protocol.

value: Lung

value: Primary fibroblasts

value: Batch 2


title: 1714, Mus musculus, Peripheral Nerve (sciatic),Peripheral Nerve (sciatic)

description: Library name: itox001714


title: DSP-1001660035646-A-A02

description: Library name: DSP-1001660035646-A-A02

value: Multiple


title: 1710, Mus musculus, Brain-Striatum,Brain-Striatum

description: Library name: itox001710


title: 11985, Sus scrofa, Adipose,Adipose

description: Library name: itox011985


title: Thalamocortical Assembloid, UCLA2, Week 6

description:
Library name: Sample18_UCLA2_WK6_CX-TH
thalamic and cortical halves separated into 2 processed data files

value: Thalamic and Cortical Organoids

value: Neural

value: Control


title: 1769, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001769

source_name: Ovary (left),Ovary (left)

value: Ovary (left),Ovary (left)


title: Corticocortical Assembloid, UCLA2, Week 6

description:
Library name: Sample17_UCLA2_WK6_CX-CX
both halves of corticocortical assembloids

value: lentiviral infection, neural differentiation, fusion


title: Thalamocortical Assembloid, UCLA2, Week 12

description:
Library name: Sample16_UCLA2_WK12_CX-TH
thalamic and cortical halves separated into 2 processed data files


title: 1719, Mus musculus, Peripheral Nerve (sciatic),Peripheral Nerve (sciatic)

description: Library name: itox001719


title: DSP-1001660035646-A-A01

description: Library name: DSP-1001660035646-A-A01

value: Lacrimal Gland


title: 11991, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox011991

source_name: Corpus Callosum,Corpus Callosum

value: Corpus Callosum,Corpus Callosum


title: Thalamocortical Assembloid, CW20324, Week 6

description:
Library name: Sample14_CW20324_WK6_CX-TH
thalamic and cortical halves separated into 2 processed data files


title: 11988, Sus scrofa, Bone Marrow,Bone Marrow

description: Library name: itox011988

source_name: Bone Marrow,Bone Marrow

value: Bone Marrow,Bone Marrow


title: Corticocortical Assembloid, CW20324, Week 6

description:
Library name: Sample13_CW20324_WK6_CX-CX
both halves of corticocortical assembloids

value: Cortical Organoid


title: Mouse Primary neonatal lung fibroblasts, KO2

description:
Library name: SK-69M2_A9
PAD2KO lung fibroblasts, sorted

value: Batch 1


title: 1811, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001811

source_name: Urinary Bladder,Urinary Bladder

value: Urinary Bladder,Urinary Bladder


title: Mouse Primary neonatal lung fibroblasts, KO6

description:
Library name: SK-69M2_B1
PAD2KO lung fibroblasts, sorted


title: Corticocortical Assembloid, UCLA2, Week 12

description:
Library name: Sample15_UCLA2_WK12_CX-CX
both halves of corticocortical assembloids


title: Mouse Primary neonatal lung fibroblasts, KO3

description:
Library name: SK-69M2_A10
PAD2KO lung fibroblasts, sorted


title: 11987, Sus scrofa, Artery,Artery

description: Library name: itox011987

value: Artery,Artery


title: 1810, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001810


title: 11992, Sus scrofa, Dorsal Root Ganglion,Dorsal Root Ganglion

description: Library name: itox011992


title: 1812, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001812


title: 12061, Sus scrofa, Testis,Testis

description: Library name: itox012061

source_name: Testis,Testis

value: Testis,Testis


title: Corticocortical Assembloid, CW20324, Week 12

description:
Library name: Sample11_CW20324_WK12_CX-CX
both halves of corticocortical assembloids


title: 1813, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001813


title: Mouse Primary neonatal lung fibroblasts, WT6

description:
Library name: SK-69M2_A6
WT Lung fibroblasts, sorted

value: Lung

value: WT


title: Mouse Primary neonatal lung fibroblasts, KO1

description:
Library name: SK-69M2_A8
PAD2KO lung fibroblasts, sorted

value: Primary fibroblasts


title: 12060, Sus scrofa, Temporal Lobe,Temporal Lobe

description: Library name: itox012060

source_name: Temporal Lobe,Temporal Lobe

value: Temporal Lobe,Temporal Lobe


title: Mouse Primary neonatal lung fibroblasts, WT7

description:
Library name: SK-69M2_A7
WT Lung fibroblasts, sorted

value: Batch 2


title: 12042, Sus scrofa, Rectum,Rectum

description: Library name: itox012042

source_name: Rectum,Rectum

value: Rectum,Rectum


title: 1814, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001814


title: 12126, Sus scrofa, Eye,Eye

description: Library name: itox012126

source_name: Eye,Eye

value: Eye,Eye


title: Thalamocortical Assembloid, CW20324, Week 12

description:
Library name: Sample12_CW20324_WK12_CX-TH
thalamic and cortical halves separated into 2 processed data files

source_name: Thalamic and Cortical Organoids

value: Thalamic and Cortical Organoids

value: Neural

value: Control


title: 12043, Sus scrofa, Liver,Liver

description: Library name: itox012043

source_name: Liver,Liver

value: Liver,Liver


title: Corticocortical Assembloid, CW20107, Week 6

description:
Library name: Sample09_CW20107_WK6_CX-CX
both halves of corticocortical assembloids

source_name: Cortical Organoid

value: lentiviral infection, neural differentiation, fusion


title: Corticocortical Assembloid, CW20107, Week 12

description:
Library name: Sample07_CW20107_WK12_CX-CX
both halves of corticocortical assembloids

value: Cortical Organoid


title: 12129, Sus scrofa, Gallbladder,Gallbladder

description: Library name: itox012129

source_name: Gallbladder,Gallbladder

value: Gallbladder,Gallbladder


title: Mouse Primary neonatal lung fibroblasts, WT5

description:
Library name: SK-69M2_A5
WT Lung fibroblasts, sorted


title: Mouse Primary neonatal lung fibroblasts, WT4

description:
Library name: SK-69M2_A4
WT Lung fibroblasts, sorted

value: Batch 1


title: 1818, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001818

value: Urinary Bladder,Urinary Bladder


title: 1817, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001817


title: Thalamocortical Assembloid, CW20107, Week 12

description:
Library name: Sample08_CW20107_WK12_CX-TH
thalamic and cortical halves separated into 2 processed data files


title: Mouse Primary neonatal lung fibroblasts, WT1

description:
Library name: SK-69M2_A1
WT Lung fibroblasts, sorted


title: 1816, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001816


title: Thalamocortical Assembloid, CW20107, Week 6

description:
Library name: Sample10_CW20107_WK6_CX-TH
thalamic and cortical halves separated into 2 processed data files


title: WT-5

city: jinan

first: Shu

middle: hui

last: Kong

state: Huaiyin District

address: 4# Duanxing West Road, Huaiyin District, Jinan, Shandong, 250021

country: China

institute: Shandong Provincial ENT Hospital

description:
Library name: Sample6
WT_5_fpkm

data_processing:
The cluster generation and sequencing were performed on Novaseq 6000 S4 platform ,using NovaSeq 6000 S4 Reagent kit V1.5.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: cochlea

extract_protocol:
The purity of the sample was determined by NanoPhotometer ®（ IMPLEN, CA, USA）；A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （ NR604-01/02） following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: cochlea


title: Thalamocortical Assembloid, Cortex, UCLA6, Week 6

description:
Library name: Sample05_UCLA6_WK6_CX-TH_CX
cortical halves of thalamocortical assembloid


title: 1815, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001815


title: 12044, Sus scrofa, Lung,Lung

description: Library name: itox012044

source_name: Lung,Lung

value: Lung,Lung


title: 12066, Sus scrofa, Trachea,Trachea

description: Library name: itox012066

source_name: Trachea,Trachea

value: Trachea,Trachea


title: Mouse Primary neonatal lung fibroblasts, WT3

description:
Library name: SK-69M2_A3
WT Lung fibroblasts, sorted

value: Lung

value: Primary fibroblasts

value: WT


title: Corticocortical Assembloid, UCLA6, Week 6

description:
Library name: Sample04_UCLA6_WK6_CX-CX
both halves of corticocortical assembloids


title: Thalamocortical Assembloid, Thalamus, UCLA6, Week 6

description:
Library name: Sample06_UCLA6_WK6_CX-TH_TH
thalamic halves of thalamocortical assembloid

source_name: Thalamic Organoid

value: Thalamic Organoid


title: 12065, Sus scrofa, Tonsil,Tonsil

description: Library name: itox012065

source_name: Tonsil,Tonsil

value: Tonsil,Tonsil


title: WT-4

description:
Library name: Sample5
WT_4_fpkm


title: 1819, Mus musculus, Urinary Bladder,Urinary Bladder

description: Library name: itox001819


title: KO-5

description:
Library name: Sample3
KO_5_fpkm

value: NEU4 KO


title: 1820, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001820


title: WT-3

description:
Library name: Sample4
WT_3_fpkm


title: KO-4

description:
Library name: Sample2
KO_4_fpkm


title: 1821, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001821


title: Corticocortical Assembloid, UCLA6, Week 12

description:
Library name: Sample01_UCLA6_WK12_CX-CX
both halves of corticocortical assembloids

value: Neural


title: 1822, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001822


title: 12068, Sus scrofa, Adipose,Adipose

description: Library name: itox012068

source_name: Adipose,Adipose

value: Adipose,Adipose


title: 1823, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001823


title: 12132, Sus scrofa, Pituitary Gland,Pituitary Gland

description: Library name: itox012132

source_name: Pituitary Gland,Pituitary Gland

value: Pituitary Gland,Pituitary Gland


title: 12069, Sus scrofa, Adipose,Adipose

description: Library name: itox012069


title: Thalamocortical Assembloid, Thalamus, UCLA6, Week12

description:
Library name: Sample03_UCLA6_WK12_CX-TH_TH
thalamic halves of thalamocortical assembloid

value: Control

value: lentiviral infection, neural differentiation, fusion


title: 1824, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001824


title: KO-2

description:
Library name: Sample1
KO_2_fpkm


title: Patient_12_dCART_EM

city: Beijing

first: Yipeng

last: Zhang

address: Fuxing Road 22

institute: Chinese PLA gerneral hospital

description: Library name: Sample 10

library_source: genomic

data_processing:
Raw data processed by Cell Ranger mkfastq (v7.1.0). Reads aligned to GRCh38 (GENCODE v32) with STAR. Cells filtered (>500 genes/cell, <20% mitochondrial reads). Normalized via SCTransform (Seurat v5), batch-corrected with Harmony (v0.1.1). Clustering (Leiden, resolution=0.8) and annotation (SingleR v1.10.0). Differential expression by MAST (v1.24.0).
Assembly: GRCh38
Supplementary files format and content: sample_filtered_feature_bc_matrix (including barcodes.tsv, features.tsv and matrix.mtx)
Library strategy: EM-seq

molecule: genomic DNA

source_name: CAR-T

extract_protocol:
CAR-T cells washed with PBS (Mg²+/Ca²+-free), centrifuged (300×g, 5 min), resuspended in PBS at 1×10^6 cells/mL for sequencing.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: CAR-T


title: Patient_12_CART_EM

description: Library name: Sample 9


title: replicate1, 3scRNAseq

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

description:
Library name: 3scRNAseq
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest) [CITE-seq].  The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest) [3' scRNA-seq].  The Pychopper (v2.5.0) software was used to identify, orient and trim long-read sequencing reads with default parameters. The number of reads, read length and quality were analyzed using NanoComp software (v1.33.1) with the parameter of “–raw–store–tsv_stats” and visualized using R package ggplot2 (v3.5.1). Pychopper processed reads were aligned to the reference genome GRCm38 with annotation from ENSEMBL release 101 for mouse and the reference genome GRCh38 using minimap2 (v2.17) with the following parameters: minimap2 -ax splice -uf --secondary=no -C5 --MD. Then, mismatches, insertions, deletions, and non-canonical splice sites in alinged reads were corrected using TranscriptClean (v2.0.3) software. Finally, TranscriptClean-corrected reads were aligned again to the reference mentioned before. Finally, reads were assigned to known genes to generate comprehensive count matrices, enabling the quantification of expression at both the gene and isoform levels for each individual cell [scONT].
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
C57BL/6J mice were purchased from Jiangsu JCYK Bioscience Co. Ltd (Jiangsu, China), housed and bred under SPF condition (Specific Pathogen Free) at the Laboratory Animal Center of West China Second University Hospital, and were allowed access to diet and water ad libitum. All animal experiments were carried out following the protocols approved by the Institutional Animal Care and Use Committee of West China Second University Hospital [(2018) Animal Ethics Approval No. 004]. The bone marrow cells were obtained from the femur and tibia of C57BL/6 mice aged about 8 weeks and filtered via a 70-μm cell strainer (BD Biosciences). After centrifuging (300 g, 5 min, 4℃), the cells were resuspended in 200 mL EasySep Buffer and CD117 MicroBeads (20 μL/one mouse). The whole solution was transferred to a 1.5 mL centrifuge tube and incubated on ice for 20~30 min. A 1 mL sample was added to the MS separation column. The MS separation column was cleared with EasySep Buffer 3 times on the Magnetic Separation Rack, and then the MS separation column was eluted with 5 mL of EasySep Buffer off the Magnetic Separation Rack to obtain Lin- cells. 20 μL cells were taken and counted, and the remaining samples were centrifuged (300 g, 5 min, 4℃). SCM (+) medium was used to resuspend (4 mL/one mouse) and then placed in an incubator (37℃, 5% CO₂) at constant temperature for 12~24 hr.
RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and the concentration was measured using Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). The integrity of RNA was assessed using the Qubit® 1.0 Fluorometer. Single cells were prepared in the Chromium Single Cell Gene Expression Solution using the Chromium Single Cell 5′ Gel Bead, Chip and Library Kits v2 (10x Genomics) as per the manufacturer’s protocol. Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) is a single-cell multi-omics technology that measures RNA and protein expression simultaneously in single cells. We generated a 5’ CITE-seq dataset of mouse bone marrow lineage negative (LIN−) cells, which consists of 388 cells and 8 proteins. The cells were then partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, which was under the action of poly(dT) and enzyme. In GEMs, each pair-end contains read 1 (R1) and read 2 (R2), the former consists of (i) a 16nt 10x Barcode, (ii) a 10nt unique molecular identifier (UMI), and (iii) a 13nt TSO. Libraries were sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China [CITE-seq].  The collected cells were resuspended in PBS containing 1% BSA at the concentration at 1 × 106 cells/mL and prepared for single cell library preparation. Single cells were prepared in the Chromium Single Cell Gene Expression Solution using the Chromium Single Cell 3 Gel Bead, Chip and Library Kits v2 (10× Genomics) as per the manufacturer’s protocol. The cells were then partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing 5 adaptor, and sample index attachment. Libraries were sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China [3' scRNA-seq].  The Pychopper (v2.5.0) software was used to identify, orient and trim long-read sequencing reads with default parameters. The number of reads, read length and quality were analyzed using NanoComp software (v1.33.1) with the parameter of “–raw–store–tsv_stats” and visualized using R package ggplot2 (v3.5.1). Pychopper processed reads were aligned to the reference genome GRCm38 with annotation from ENSEMBL release 101 for mouse and the reference genome GRCh38 using minimap2 (v2.17) with the following parameters: minimap2 -ax splice -uf --secondary=no -C5 --MD. Then, mismatches, insertions, deletions, and non-canonical splice sites in alinged reads were corrected using TranscriptClean (v2.0.3) software. Finally, TranscriptClean-corrected reads were aligned again to the reference mentioned before. Finally, reads were assigned to known genes to generate comprehensive count matrices, enabling the quantification of expression at both the gene and isoform levels for each individual cell [scONT].

value: bone marrow

value: hematopoietic stem and progenitor cells


title: 12067, Sus scrofa, Bladder,Bladder

description: Library name: itox012067

source_name: Bladder,Bladder

value: Bladder,Bladder


title: Patient_09_dCART_EM

description: Library name: Sample 8


title: replicate2, ADT, CITE-seq

description:
Library name: Rep2ADT
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest) [CITE-seq].  The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest) [3' scRNA-seq].  The Pychopper (v2.5.0) software was used to identify, orient and trim long-read sequencing reads with default parameters. The number of reads, read length and quality were analyzed using NanoComp software (v1.33.1) with the parameter of “–raw–store–tsv_stats” and visualized using R package ggplot2 (v3.5.1). Pychopper processed reads were aligned to the reference genome GRCm38 with annotation from ENSEMBL release 101 for mouse and the reference genome GRCh38 using minimap2 (v2.17) with the following parameters: minimap2 -ax splice -uf --secondary=no -C5 --MD. Then, mismatches, insertions, deletions, and non-canonical splice sites in alinged reads were corrected using TranscriptClean (v2.0.3) software. Finally, TranscriptClean-corrected reads were aligned again to the reference mentioned before. Finally, reads were assigned to known genes to generate comprehensive count matrices, enabling the quantification of expression at both the gene and isoform levels for each individual cell [scONT].
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq


title: 12136, Sus scrofa, Heart,Heart

description: Library name: itox012136

source_name: Heart,Heart

value: Heart,Heart


title: Thalamocortical Assembloid, Cortex, UCLA6, Week 12

description:
Library name: Sample02_UCLA6_WK12_CX-TH_CX
cortical halves of thalamocortical assembloids

value: Cortical Organoid


title: 12070, Sus scrofa, Artery,Artery

description: Library name: itox012070

source_name: Artery,Artery

value: Artery,Artery


title: 1826, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001826


title: Patient_07_dCART_EM

description: Library name: Sample 6


title: 1825, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001825


title: replicate1, ADT, CITE-seq

description:
Library name: Rep1ADT
10x Genomics


title: 1827, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001827


title: replicate1, HTO, CITE-seq

description:
Library name: Rep1HTO
10x Genomics


title: 12071, Sus scrofa, Artery,Artery

description: Library name: itox012071


title: 12072, Sus scrofa, Bone Marrow,Bone Marrow

description: Library name: itox012072

source_name: Bone Marrow,Bone Marrow

value: Bone Marrow,Bone Marrow


title: 12139, Sus scrofa, Heart,Heart

description: Library name: itox012139


title: Patient_07_CART_EM

description: Library name: Sample 5


title: replicate2, HTO, CITE-seq

description:
Library name: Rep2HTO
10x Genomics


title: 1721, Mus musculus, Eye-lens,Eye-lens

description: Library name: itox001721

source_name: Eye-lens,Eye-lens

value: Eye-lens,Eye-lens


title: 1828, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001828


title: replicate2, TRANSCRIPTOMIC, CITE-seq

description:
Library name: Rep2RNA
10x Genomics


title: Patient_09_CART_EM

description: Library name: Sample 7


title: 1829, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001829


title: 1830, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001830


title: 12073, Sus scrofa, Brainstem,Brainstem

description: Library name: itox012073

source_name: Brainstem,Brainstem

value: Brainstem,Brainstem


title: Patient_04_dCART_EM

description: Library name: Sample 4


title: FACS-sorted S phase Armc5 knock out mouse embryonic fibroblasts batch 3, P3

city: Montreal

first: Yajie

last: Huang

state: Quebec

address: 900 saint-Denis

country: Canada

institute: CRCHUM

description:
Library name: KO3_S
Column name in All_samples_raw_counts.csv: KO3_S

data_processing:
Alignment files were generated in BAM format and processed through Picard MarkDuplicates to identify and remove duplicate readcounts, thereby ensuring data quality and reducing potential PCR amplification bias. Gene-level quantification was performed using FeatureCounts, which precisely counted unique readcounts mapped to genomic features. Differential expression analysis was conducted using edgeR. Filtering criteria included removing genes with counts per million (CPM) less than 1 in fewer than three samples. Transcript abundance was normalized using the trimmed mean of M-values (TMM) method, and differential expression was assessed using a likelihood ratio test.
Assembly: GRCm39
Supplementary files format and content: A comma-delimited text file documenting raw counts for each sample

source_name: Embryos

growth_protocol: MEFs were cultured in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
After an additional 1.5-hour culture, the cells were stained with 10 µM live dye Vybrant™ DyeCycle™ Violet (Invitrogen, V35003) in the culture medium for an additional 75 minutes at 37 °C. Approximately 1 x 10^6 G1-phase cells and 1 x 10^6 S-phase cells were sorted by fluorescence-activated cell sorting (FACS; BD FACSAria™ III). The total RNA of the sorted cells was extracted with Trizol in phase-lock tubes. The 4sU-labeled RNA was enriched according to a protocol by Biasini et al. with some modifications. Briefly, the total RNA was precipitated with isopropanol. The pellets were washed in 75% ethanol, resuspended in DEPC-treated H2O, and treated with DNase I (Invitrogen™ TURBO DNA-free™ Kit) to eliminate genomic DNA. 4-sU-labeled RNA was biotinylated with EZ-link HPDP-Biotin (Thermo Fisher, 21341) and subsequently purified using phenol: chloroform: isoamyl alcohol (25:24:1, v/v; Invitrogen, 15593031). RNA was precipitated with isopropanol and NaCl, and the pellets were washed twice with 75% ethanol. Biotinylated RNA was captured on streptavidin magnetic beads (New England Biolabs, S1420S), which were washed sequentially with binding (0.5 M NaCl, 20 mM Tris-HCl (pH 7.5), 1 mM EDTA) and ice-cold low-salt washing buffer (0.15 M NaCl, 20 mM Tris-HCl (pH 7.5), 1 mM EDTA). Beads were resuspended in 100 µl water containing freshly prepared 100 mM DTT and incubated at room temperature for 1 minute to elute the biotinylated RNA. The eluted RNA was then purified with Qiagen RNeasy Mini Kit according to the manufacturer’s instructions and finally eluted in nuclease-free water.
The KAPA RNA HyperPrep Kit with RiboErase (HMR) module (Roche Diagnostics) was used for ribodepletion and library preparation for 123 ng 4-sU-labeled RNA. Library distribution was assessed using a 2100 Bioanalyzer (Agilent Technologies), and the libraries were quantified by quantitative PCR (qPCR). Libraries were sequenced as paired-end readcounts (PE100) on a Novaseq 6000 system (Illumina) using an S4 flow cell with 50 million readcounts per library.

treatment_protocol: WT and KO MEF samples were in triplicate. The MEFs (20 x 10^6 cells/sample) synchronized at the G1/S phase were released into the S phase for 1.5 hours and incubated with 500 µM 4-thiouridine (final concentration; Sigma, T4509).

value: Embryos

value: MEF

value: Mouse embryonic fibroblasts

value: Armc5 knock out

value: FACS sorted S phase MEFs


title: replicate1, TRANSCRIPTOMIC, CITE-seq

description:
Library name: Rep1RNA
10x Genomics


title: 12074, Sus scrofa, Vagina,Vagina

description: Library name: itox012074

source_name: Vagina,Vagina

value: Vagina,Vagina


title: Patient_04_CART_EM

description: Library name: Sample 3


title: Patient_03_dCART_EM

description: Library name: Sample 2


title: Patient_03_CART_EM

description: Library name: Sample 1


title: 1831, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001831


title: 12075, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox012075

source_name: Corpus Callosum,Corpus Callosum

value: Corpus Callosum,Corpus Callosum


title: Control10

city: Hangzhou

first: Xiang

last: Qiu

state: Zhejiang

address: No.1 Xueshi Road, Shangcheng District

institute: Zhejiang University

description: Library name: AF2280447

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by thesoftware of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Then we use fastp (v0.20.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.
Differential expression analysis was performed using DESeq2 R package (v1.46.0)
The clusterProfiler R package (v4.14.4) was used to perform the functional pathway enrichment analysis.
The WGCNA R package (v1.73) was employed to analyze the co-expression gene networks and cluster-specific modules.
Machine learning were performed using glmnet (v4.1-8), randomForest (v4.7-1.2), e1071 (v1.7-16) R package.
Assembly: Not applicable.
Supplementary files format and content: CSV file including Reads count for each sample.

source_name: amniotic fluid

extract_protocol:
Norgen, Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit
IDT, xGenTM Broad-Range RNA Library Prep Kit

value: amniotic fluid

value: amniotic fluid cell-free RNA


title: FACS-sorted S phase wild-type mouse embryonic fibroblasts batch 3, P3

description:
Library name: WT3_S
Column name in All_samples_raw_counts.csv: WT3_S

value: Wild-type


title: 1832, Mus musculus, Kidney (left to include cortex and medulla),Kidney (left to include cortex and medulla)

description: Library name: itox001832


title: 12121, Sus scrofa, Cerebellum,Cerebellum

description: Library name: itox012121

source_name: Cerebellum,Cerebellum

value: Cerebellum,Cerebellum


title: 12190, Sus scrofa, Heart,Heart

description: Library name: itox012190

value: Heart,Heart


title: FACS-sorted G1 phase wild-type mouse embryonic fibroblasts batch 3, P3

description:
Library name: WT3_G1
Column name in All_samples_raw_counts.csv: WT3_G1

value: FACS sorted G1 phase MEFs


title: Control9

description: Library name: AF2280430


title: 12191, Sus scrofa, Heart,Heart

description: Library name: itox012191


title: FACS-sorted G1 phase Armc5 knock out mouse embryonic fibroblasts batch 3, P3

description:
Library name: KO3_G1
Column name in All_samples_raw_counts.csv: KO3_G1


title: FACS-sorted S phase Armc5 knock out mouse embryonic fibroblasts batch 2, P3

description:
Library name: KO2_S
Column name in All_samples_raw_counts.csv: KO2_S


title: 1835, Mus musculus, Ureter,Ureter

description: Library name: itox001835

source_name: Ureter,Ureter

value: Ureter,Ureter


title: FACS-sorted G1 phase Armc5 knock out mouse embryonic fibroblasts batch 2, P3

description:
Library name: KO2_G1
Column name in All_samples_raw_counts.csv: KO2_G1


title: 1837, Mus musculus, Ureter,Ureter

description: Library name: itox001837


title: 12194, Sus scrofa, Kidney,Kidney

description: Library name: itox012194

source_name: Kidney,Kidney

value: Kidney,Kidney


title: 1838, Mus musculus, Trachea,Trachea

description: Library name: itox001838

source_name: Trachea,Trachea

value: Trachea,Trachea


title: 1839, Mus musculus, Ureter,Ureter

description: Library name: itox001839


title: FACS-sorted S phase Armc5 knock out mouse embryonic fibroblasts batch 1, P3

description:
Library name: KO1_S
Column name in All_samples_raw_counts.csv: KO1_S


title: 12193, Sus scrofa, Hippocampus,Hippocampus

description: Library name: itox012193

source_name: Hippocampus,Hippocampus

value: Hippocampus,Hippocampus


title: Control7

description: Library name: AF2280303


title: Control8

description: Library name: AF2280428


title: 12174, Sus scrofa, Dorsal Root Ganglion,Dorsal Root Ganglion

description: Library name: itox012174


title: 1836, Mus musculus, Ureter,Ureter

description: Library name: itox001836


title: FACS-sorted S phase wild-type mouse embryonic fibroblasts batch 2, P3

description:
Library name: WT2_S
Column name in All_samples_raw_counts.csv: WT2_S

value: Embryos


title: Control5

description: Library name: AF2280060


title: Control6

description: Library name: AF2280180


title: 1840, Mus musculus, Ureter,Ureter

description: Library name: itox001840


title: 12173, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox012173


title: 12192, Sus scrofa, Heart,Heart

description: Library name: itox012192


title: Control3

description: Library name: AF2280040


title: 12198, Sus scrofa, Rectum,Rectum

description: Library name: itox012198

source_name: Rectum,Rectum

value: Rectum,Rectum


title: FACS-sorted G1 phase Armc5 knock out mouse embryonic fibroblasts batch 1, P3

description:
Library name: KO1_G1
Column name in All_samples_raw_counts.csv: KO1_G1

value: MEF

value: Mouse embryonic fibroblasts


title: Control4

description: Library name: AF2280059


title: FACS-sorted G1 phase wild-type mouse embryonic fibroblasts batch 2, P3

description:
Library name: WT2_G1
Column name in All_samples_raw_counts.csv: WT2_G1


title: 1722, Mus musculus, Eye-lens,Eye-lens

description: Library name: itox001722

value: Eye-lens,Eye-lens


title: 1841, Mus musculus, Ureter,Ureter

description: Library name: itox001841


title: FACS-sorted S phase wild-type mouse embryonic fibroblasts batch 1, P3

description:
Library name: WT1_S
Column name in All_samples_raw_counts.csv: WT1_S

value: FACS sorted S phase MEFs


title: Control2

description: Library name: AF2180729


title: 12200, Sus scrofa, Lung,Lung

description: Library name: itox012200

source_name: Lung,Lung

value: Lung,Lung


title: 1842, Mus musculus, Ureter,Ureter

description: Library name: itox001842


title: Wild-type mouse embryonic fibroblasts batch 5, P3

description:
Library name: WT5
The processed data file is a spike-in reads normalized bigwig file.

data_processing:
Raw sequencing data were processed using the MUGQIC ChIP-seq pipeline v4.6.0 developed by McGill University and Genome Quebec Innovation Centre. Adapter trimming was performed with Trimmomatic (v0.39), and readcounts were aligned to either the mouse reference genome (GRCm38) or the Drosophila melanogaster BDGP6 genome using BWA MEM v0.7.17 with default parameters. Aligned readcounts were sorted, indexed, and duplicate-marked using Sambamba v0.8.1. Peak quantification and annotation were carried out with HOMER v4.11. Normalized coverage tracks (bigWig files) were generated using bamCoverage (DeepTools) with a bin size of 10 bp and sample-specific scaling factors derived from Drosophila S2 DNA spike-in readcounts. Specifically, the scaling factor of a given sample was the ratio between the lowest total number of uniquely mapped S2 DNA spike-in readcounts per sample among all the samples in a given experiment and the total number of uniquely mapped S2 DNA readcounts in that given sample. These scaling factors were then applied to normalize mouse genome-aligned readcounts.
Assembly: GRCm38
Supplementary files format and content: bigWig

growth_protocol: MEFs were cultured in DMEM supplemented with 10% FBS and antibiotics in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
WT and KO MEF samples were in triplicate. Each sample of the MEFs was cultured in 3 10-cm dishes and was synchronized at the G1/S phase as described above. The cells were released into the S phase for 4 hours. They were rinsed twice with PBS and incubated with 500 µg/ml bTMP in 1 ml PBS in the dark on ice for 20 minutes. The cells were carefully covered with parafilm during the incubation to ensure uniform reagent distribution. The plates with parafilm-covered cells were irradiated at a nominal 12 joules/cm2 according to instrumental readings in a UV crosslinker (UVP, Model CL-1000 Ultraviolet Crosslinker, Upland, CA), whose lamps were replaced by 5 8-W T5 365 nm UVA tubes (Coospider-Repta, Jinyun, China). This UV energy level was pre-tested in a dot blot assay (to be described below) to obtain an optimal level of DNA bTMP labeling for MEFs. After the irradiation, the parafilm was removed. The cells were rinsed twice with ice-cold PBS, scraped into 1 ml PBS supplemented with protease inhibitors and pelleted by centrifugation. The cell pellets were treated with 300 µl of lysis buffer (50 mM Tris-HCl, pH 8.1; 10 mM EDTA; 1% SDS) containing protease inhibitors on ice for 10 minutes. The cell lysates were sonicated using a probe-based sonicator (FB120 with CL-18 probe; ThermoFisher) at 25% amplitude, employing 15-second pulses with 15-second intervals for a total of 3.5 minutes. Proteinase K (60 µg) was added to the sonicated sample and incubated at 55°C for 1 hour. Total bTMP-labelled DNA was extracted from the lysate using an equal volume of phenol:chloroform:isoamyl alcohol, precipitated with 0.3M sodium acetate and two volumes of absolute ethanol. The pellet was washed twice with 70% ethanol and resuspended in 50 µl TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0). Approximately 45 µg bTMP-labeled DNA extracted from MEFs in 600 l of TE buffer was spiked with 5% (i.e., 2.25 µg) of bTMP-labeled naked DNA from the S2 cells. Fifty µl of prewashed magnetic streptavidin beads (Dynabeads MyOne Streptavidin, Invitrogen, Cat. No. 65001) were washed twice with TE buffer and then added to the DNA mix in a 1.5 ml Eppendorf tube, which was rotated at 4°C overnight. The beads were then sequentially washed with the following buffers: TSE I buffer (20 mM Tris HCl pH8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton, 0.1% SDS) followed by a TE buffer rinse, TSE II (20 mM Tris HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton, 0.1% SDS) followed by a TE buffer rinse, and TSE III (10 mM Tris HCl pH 8.1, 1 mM EDTA, 0.25 M LiCl, 1% NP40, 1% Sodium Deoxycholate) followed by a final TE buffer rinse. Each washing step was 5 minutes, with the Eppendorf tube rotating at room temperature. DNA was then eluted from the beads by 50 µl of 10 mM EDTA/95% formamide at 90 °C for 10 minutes. The eluate was collected and supplemented with 350 µl nuclease-free water. DNA was precipitated by the addition of 40 µl 3M sodium acetate, 1 ml anhydrous ethanol, and 20 µg glycogen in 1 l. The sample was incubated at -70°C overnight, then centrifuged to pellet the enriched single-strand bTMP-labelled DNA. The pellet was subsequently washed with 70% ethanol and resuspended in 15 µl low TE buffer (10 mM Tris, 0.1 mM EDTA, pH 8.0).
Input ssDNA quantity was evaluated using a High Sensitivity DNA Kit (150-1500 pg total). Libraries were prepared using xGenTM ssDNA and low-input Library Prep Kit (IDT) with 11-14 PCR cycles for final library amplification. Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) using a High Sensitivity DNA Kit, and libraries were quantified by qPCR. Equimolar libraries were sequenced in paired-end readcounts (PE100) on a Novaseq system (Illumina) at 35 million readcounts per library.

treatment_protocol: For both MEFs in the Armc5 knock-out and wild-type groups, they were synchronized at the G1/S phase by aphidicolin and were then allowed to progress into the S phase for 4 hours before they were harvested and washed with PBS.

value: Aphidicolin synchronized and released into S phase


title: 12219, Sus scrofa, Tongue,Tongue

description: Library name: itox012219

source_name: Tongue,Tongue

value: Tongue,Tongue


title: Control1

description: Library name: AF2180109

value: amniotic fluid

value: amniotic fluid cell-free RNA


title: 12201, Sus scrofa, Lymph Node,Lymph Node

description: Library name: itox012201

source_name: Lymph Node,Lymph Node

value: Lymph Node,Lymph Node


title: FACS-sorted G1 phase wild-type mouse embryonic fibroblasts batch 1, P3

description:
Library name: WT1_G1
Column name in All_samples_raw_counts.csv: WT1_G1

value: Wild-type

value: FACS sorted G1 phase MEFs


title: 1844, Mus musculus, Ureter,Ureter

description: Library name: itox001844

value: Ureter,Ureter


title: Wild-type mouse embryonic fibroblasts batch 4, P3

description:
Library name: WT4
The processed data file is a spike-in reads normalized bigwig file.


title: Case10

description: Library name: AF2280245


title: 12203, Sus scrofa, Optic Nerve,Optic Nerve

description: Library name: itox012203

source_name: Optic Nerve,Optic Nerve

value: Optic Nerve,Optic Nerve


title: 1847, Mus musculus, Seminal Vesicles,Seminal Vesicles

description: Library name: itox001847

source_name: Seminal Vesicles,Seminal Vesicles

value: Seminal Vesicles,Seminal Vesicles


title: Case9

description: Library name: AF2180684


title: Case8

description: Library name: AF2180658


title: 1846, Mus musculus, Seminal Vesicles,Seminal Vesicles

description: Library name: itox001846


title: 1848, Mus musculus, Seminal Vesicles,Seminal Vesicles

description: Library name: itox001848


title: Wild-type mouse embryonic fibroblasts batch 2, P3

description:
Library name: WT2
The processed data file is a spike-in reads normalized bigwig file.

value: Embryos


title: Armc5 knock-out mouse embryonic fibroblasts batch 5, P3

description:
Library name: KO5
The processed data file is a spike-in reads normalized bigwig file.

value: Armc5 knock-out


title: 12204, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012204

source_name: Peripheral nerve,Peripheral nerve

value: Peripheral nerve,Peripheral nerve


title: 12205, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012205


title: Armc5 knock-out mouse embryonic fibroblasts batch 2, P3

description:
Library name: KO2
The processed data file is a spike-in reads normalized bigwig file.

value: MEF

value: Mouse embryonic fibroblasts


title: 1849, Mus musculus, Seminal Vesicles,Seminal Vesicles

description: Library name: itox001849


title: 12206, Sus scrofa, Occipital Lobe,Occipital Lobe

description: Library name: itox012206

source_name: Occipital Lobe,Occipital Lobe

value: Occipital Lobe,Occipital Lobe


title: Armc5 knock-out mouse embryonic fibroblasts batch 1, P3

description:
Library name: KO1
The processed data file is a spike-in reads normalized bigwig file.

source_name: Embryos


title: Case5

description: Library name: AF2180359


title: 12207, Sus scrofa, Pancreas,Pancreas

description: Library name: itox012207

source_name: Pancreas,Pancreas

value: Pancreas,Pancreas


title: Case6

description: Library name: AF2180608


title: 12208, Sus scrofa, Cerebral Cortex,Cerebral Cortex

description: Library name: itox012208

source_name: Cerebral Cortex,Cerebral Cortex

value: Cerebral Cortex,Cerebral Cortex


title: 2494, Mus musculus, Uterus (left horn),Uterus (left horn)

description: Library name: itox002494

source_name: Uterus (left horn),Uterus (left horn)

value: Uterus (left horn),Uterus (left horn)


title: Synchronized (S-phase-enriched) mouse embryonic fibroblasts batch 5, P3

description: Library name: Syn5

data_processing:
Raw sequencing reads were processed using the McGill University and Genome Quebec Innovation Centre (MUGQIC) ChIP-seq pipeline. Adapter sequences were trimmed using Trimmomatic (v0.39), and readcounts were aligned to the mouse reference genome (GRCm38) or Drosophila BDGP6 genome using BWA MEM (v0.7.17) with default parameters. Sequence alignment files were processed using Sambamba (v0.8.1) to sort, index, and mark duplicate readcounts. ChIP-seq peak calling was performed using MACS2 (v2.2.7.1) with standard parameters. Peak annotation and motif discovery were conducted using Homer (v4.11). Normalized coverage tracks (bigwig files) were generated using DeepTools bamCoverage (bin size = 10) with sample-specific scaling factors calculated based on S2 DNA spike-in readcounts. Specifically, the scaling factor of a given sample was the ratio between the lowest total number per sample of uniquely mapped S2 DNA spike-in readcounts among all the samples in a given experiment and the total number of uniquely mapped S2 DNA readcounts in that given sample. These factors were used to scale the mouse genome-mapped readcounts by random downsampling.
Assembly: GRCm38
Supplementary files format and content: bigWig

extract_protocol:
Approximately 18 x 106 WT and KO MEFs synchronized at the G1/S phase by aphidicolin were allowed to progress into the S phase for 4 hours before they were harvested and washed with PBS. These S-phase-enriched cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine at room temperature for 10 minutes while being rotated. The cells were pelleted, washed with cold PBS, and resuspended in cell swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, supplemented with protease and phosphatase inhibitors) on ice for 10 minutes to release nuclei. Nuclei were pelleted, resuspended in ChIP sonication buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS) supplemented with protease and phosphatase inhibitors, and sonicated using a probe-based sonicator (FB120 with a CL-18 probe; ThermoFisher) at 25% amplitude with 30-second pulses at 30-second intervals for a total of 3 minutes.
ChIP-seq libraries were prepared using the KAPA Hyperprep Library Kit (Roche Diagnostics). Normalization of the sample quantities was done before final amplification based on the quantification of the ligation products by qPCR. Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) using a High Sensitivity DNA Kit, and libraries were quantified by qPCR. Equimolar libraries were sequenced in paired-end readcounts (PE100) on a Novaseq system (Illumina) at 50 million readcounts per library.


title: Case7

description: Library name: AF2180655

source_name: amniotic fluid

value: amniotic fluid


title: 1850, Mus musculus, Seminal Vesicles,Seminal Vesicles

description: Library name: itox001850


title: 2497, Mus musculus, Vagina,Vagina

description: Library name: itox002497

source_name: Vagina,Vagina

value: Vagina,Vagina


title: 2496, Mus musculus, Vagina,Vagina

description: Library name: itox002496


title: Case4

description: Library name: AF2180317

value: amniotic fluid cell-free RNA


title: Asynchronous mouse embryonic fibroblasts batch 5, P3

description: Library name: Asy5


title: Case3

description: Library name: AF2180236


title: 12209, Sus scrofa, Skin,Skin

description: Library name: itox012209

source_name: Skin,Skin

value: Skin,Skin


title: Synchronized (S-phase-enriched) mouse embryonic fibroblasts batch 4, P3

description: Library name: Syn4


title: Asynchronous mouse embryonic fibroblasts batch 4, P3

description: Library name: Asy4


title: 12211, Sus scrofa, Ileum,Ileum

description: Library name: itox012211

source_name: Ileum,Ileum

value: Ileum,Ileum


title: 12210, Sus scrofa, Duodenum,Duodenum

description: Library name: itox012210

source_name: Duodenum,Duodenum

value: Duodenum,Duodenum


title: human endometrial stromal organoid, co-culture, bio replicate 7

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

description:
Library name: U6
Column name in rawCounts_all.csv: U6

data_processing:
High-quality, trimmed paired-end reads were processed using Partek Flow software. Potential ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) contaminants were removed using Bowtie 2. The cleaned reads were aligned to the mouse reference genome (mm10) using the HISAT 2 aligner. Raw read counts were generated by mapping aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm, and normalization was performed using the Transcripts Per Million (TPM) method.
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each sample

source_name: primary cell derived organoid

extract_protocol:
Arcturus PicoPure RNA Isolation Kit
Total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems), following the manufacturer’s protocol. Library preparation and low-input RNA-seq were conducted on the Illumina NovaSeq 6000 platform by Novogene (Novogene Corporation, Sacramento, CA).

value: primary cell derived organoid

value: co-culture with follicle


title: Synchronized (S-phase-enriched) mouse embryonic fibroblasts batch 3, P3

description: Library name: Syn3

value: Embryos


title: 12212, Sus scrofa, Jejunum,Jejunum

description: Library name: itox012212

source_name: Jejunum,Jejunum

value: Jejunum,Jejunum


title: 1730, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001730

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: Case1

description: Library name: AF2180121


title: 12213, Sus scrofa, Spinal Cord,Spinal Cord

description: Library name: itox012213

source_name: Spinal Cord,Spinal Cord

value: Spinal Cord,Spinal Cord


title: 2500, Mus musculus, Cervix -Pooled,Cervix -Pooled

description: Library name: itox002500

source_name: Cervix -Pooled,Cervix -Pooled

value: Cervix -Pooled,Cervix -Pooled


title: 2501, Mus musculus, Eye-lens -Pooled,Eye-lens -Pooled

description: Library name: itox002501

source_name: Eye-lens -Pooled,Eye-lens -Pooled

value: Eye-lens -Pooled,Eye-lens -Pooled


title: 2498, Mus musculus, Cervix -Pooled,Cervix -Pooled

description: Library name: itox002498


title: Asynchronous mouse embryonic fibroblasts batch 3, P3

description: Library name: Asy3

value: Mouse embryonic fibroblasts


title: 12257, Sus scrofa, Lymph Node,Lymph Node

description: Library name: itox012257

source_name: Lymph Node,Lymph Node

value: Lymph Node,Lymph Node


title: 2504, Mus musculus, Thymus,Thymus

description: Library name: itox002504

source_name: Thymus,Thymus

value: Thymus,Thymus


title: 12277, Sus scrofa, Thymus Gland,Thymus Gland

description: Library name: itox012277

source_name: Thymus Gland,Thymus Gland

value: Thymus Gland,Thymus Gland


title: 2503, Mus musculus, Eye-lens -Pooled,Eye-lens -Pooled

description: Library name: itox002503


title: human endometrial stromal organoid, co-culture, bio replicate 5

description:
Library name: U4
Column name in rawCounts_all.csv: U4


title: 12278, Sus scrofa, Tongue,Tongue

description: Library name: itox012278

source_name: Tongue,Tongue

value: Tongue,Tongue


title: MYC and SMARCD3 overexpression in postnatal day 2 male mouse cerebellum, rep1

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: MYC_mouse_11

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trim Glare (v.0.6.4_dev) and Cutadapt (v.2.6).
Trimmed reads were mapped to mm10 whole genome using Hisat2 (v.2.1.0).
Count matrix was calculated using FeatureCounts (v.1.6.4).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for each sample and gene.

source_name: Tumor

extract_protocol:
RNeasy Plus Mini Kit (Catlog#74134; Qiagen) was used for RNA extraction.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

value: Tumor


title: Case2

description: Library name: AF2180170

value: amniotic fluid

value: amniotic fluid cell-free RNA


title: 2505, Mus musculus, Thymus,Thymus

description: Library name: itox002505