title: snRNASeq_PCOS subject5_and_CTRL subject3

description: Library name: Mixed Sample of PCOS5_CTRL3


title: UPN827 cells, TN249 TrailNet Baseline T1D plasma

status: Public on Jun 01 2026

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: UPN827 cells stimulated with TN249 TrailNet Baseline T1D plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: TrailNet Baseline


title: snRNASeq_PCOS subject2_and_CTRL subject2

type: SRA

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: Library name: Mixed Sample of PCOS2_CTRL2

library_source: transcriptomic single cell

data_processing:
FASTQ files are processed with the CogentAP pipeline using appropriate sample WellList.TXT files. Due to two samples with primer A and primer B sex indexes being sequenced on the same pair-end sequencing lane, each pair of FASTQ files will be processed through cogentAP twice, once with the first sample wellList.TXT file and secondly with the second sample WellList.TXT file.
Following trimming, data was aligned to the GRCh19 reference genome and sample count matrices were generated that contain counts for all the single cells analyzed for that sample
Assembly: GRCh19
Supplementary files format and content: CSV files include raw read count values  all the single nuclei profiles for that sample

molecule: nuclear RNA

source_name: subcutaneous abdominal and gluteofemoral fat

extract_protocol:
Frozen adipose tissue (~100mg) was pulverized under liquid nitrogen and homogenized in 2mL of homogenization buffer (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 250mM sucrose, 1µm DDT, 1 x protease inhibitor, 0.2 U/µL SUPERase•In RNase Inhibitor (Thermofisher Scientific) in nuclease-free water) with a glasscol homogenizer. The homogenate was incubated for 30 minutes on ice with the addition of Triton-X100 (0.1% v/v) with regular vortexing. Samples were filtered through a 100µm and 40µm strainer (BD Falcon), centrifuged at 2,700g for 10 min at 4°C, resuspended in homogenization buffer and recentrifuged again at 2,700g for 10 min at 4°C. The pellet was then re-suspended in 1mL nuclei isolation medium (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 1 mM EDTA, 0.2 U/µL Ribolock RNAase inhibitor, 1% BSA in nuclease-free water) and centrifuged at 2,700g for 10 min at 4°C. Following re-suspension in 500µL nuclei isolation medium, sample was filtered 10 x with a 25g syringe prior to being counted. Single-nuclei suspension (40K/mL)  was distributed into eight wells of a 384-well source plate (Takara) and dispensed onto a ICELL8® 350v Chip (Takara) using an ICELL8 MultiSample NanoDispenser (MSND, Takara). Following dispense, the chip nanowells were imaged using the ICELL8 Imaging Station to identify nanowells containing a single nucleus. Only these nanowells were subjected for downstream dispenses. After imaging, the chip was subjected to freeze-thaw to lyse the cells/nuclei, followed by a 3 min incubation at 72oC to denature the RNA.
Selected nuclei were subjected to first-strand cDNA synthesis initiated by oligo dT primer (SMART-Seq ICELL8 CDS), followed by template switching with template switching oligo (SMART-Seq ICELL8 oligonucleotide) for 2nd strand cDNA synthesis, prior to unbiased amplification of full-length cDNA. Synthesized full-length cDNA was tagmented by TDE1 (Illumina Tagment DNA enzyme) and amplified using forward (i5) and reverse (i7) indexing primers. Each single nucleus was indexed by a unique combination of 1 of 72 forward and 1 of 72 reverse indexing primers allowing for downstream identification. Collected cDNA was purified twice using a 1:1 proportion of AMPure XP beads (Beckman, A63880), further amplified according to manufacturer’s instructions and purified again at a 1:1 proportion of AMPure XP beads. The resultant sequencing-ready cDNA library was assessed for concentration by fluorometer (Qubit) and quality by electrophoresis (Agilent Bioanalyzer high sensitivity DNA chips) respectively. Libraries were sequenced with Illumina NovaSeq X Plus.

tag: tissue

tag: batch


title: UPN827 cells, TN247 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN247 TrailNet Baseline T1D plasma


title: Donor_22_Dopa_neuron_Bipolar

city: New York

first: Swadha

last: Singh

state: NY

address: 1470 Madison Ave

department: Psychiatry

institute: Icahn School of medicine, Mount sinai

description: Library name: Donor 22

library_source: genomic

data_processing:
Hi-C data processing began with alignment and interaction calling using the HiC-Pro pipeline (v3.1.0), aligning reads to the human reference genome (hg38/GRCh38) and generating valid cis and trans interaction pairs. Quality metrics—including intra-/inter-chromosomal contact ratios, chimeric and duplicate reads, and ligation quality—were assessed, with further QC using HiCRep, QTLtools, and PCA. Interaction matrices were produced at resolutions from 20 kb to 1 Mb. HiC-Pro output was converted to .hic and then to .cool format, and matrices were normalized using hicNormalize and hicCorrectMatrix (Knight–Ruiz balancing).
Topologically associated domains (TADs) were identified using TopDom from matrices at 10 kb, 50 kb, and 100 kb resolution. Chromatin compartments (A/B) were assigned using CscoreTools on 50 kb matrices, with sign-alignment to ensure positive PC1 values corresponded to active (A) compartments. Chromatin loops were detected using HICCUPS (juicer tools 1.22.01) at 5, 10, and 25 kb resolution, and only loops reproducible across at least two resolutions were retained.
Hi-C matrices and loop calls were filtered, quality-checked, and integrated for downstream comparative analyses between dopaminergic and non-neuronal nuclei.
Normalized matrices, compartment scores, TAD boundaries, and loop annotations were compiled for visualization and statistical analysis of chromatin architecture in schizophrenia, bipolar disorder, and control samples.
Assembly: GRCh38 / hg38 (UCSC).
Supplementary files format and content: Processed data include valid-pairs files (text), normalized Hi-C contact matrices (.cool/.mcool at multiple resolutions), compartment PC1 score tracks (bedGraph or text), TAD annotation files (BED), and chromatin loop calls (BEDPE from HICCUPS). These files represent the finalized chromatin contact maps, structural domains, compartments, and loops for dopaminergic (NeuN+/Nurr1+) and non-neuronal (NeuN−/Nurr1−) nuclei.

molecule: genomic DNA

source_name: Midbrain

growth_protocol: Postmortem human ventral midbrain (substantia nigra, A10 region) tissue was obtained from established brain banks under approved ethical protocols. Donors had no in-vitro growth phase; tissue was dissected immediately postmortem and processed for nuclei isolation (SCZ, BD, and neurotypical controls).

extract_protocol:
For nuclei extraction, tissue was dounced in a sucrose-containing lysis buffer until fully homogenized, then layered onto a sucrose cushion and ultracentrifuged to isolate intact nuclei. The pellet was resuspended in BSA and filtered through a 40 μm strainer. Nuclei were immunolabeled with anti-Nurr1 (Alexa 647) and anti-NeuN (Alexa 488), followed by DAPI. Fluorescence-activated nuclei sorting (FANS) was used to collect ~6,000 dopaminergic (NeuN+/Nurr1+) nuclei and ~50,000 non-neuronal (NeuN−/Nurr1−) nuclei per sample. Sorted nuclei were pelleted and stored at −80 °C until Hi-C library preparation.
Hi-C libraries were generated using the Arima-HiC kit (A510008). Chromatin underwent restriction digestion and proximity ligation following the Arima workflow, followed by purification with SPRIselect beads. DNA was sonicated to ~300–500 bp using a Covaris S220 and size-selected. Biotinylated fragments were enriched using the Arima biotin-pull-down steps. End-repair and adapter ligation were performed with the Swift Accel-NGS 2S Plus DNA library kit, and unique dual indices were added. Libraries were amplified with KAPA Hyper Prep reagents, purified, and sequenced on an Illumina NovaSeq 6000 (150 bp paired-end, ~400M read pairs/library).

treatment_protocol: No experimental treatments were applied. Samples reflect untreated postmortem donor tissue. For Hi-C, nuclei were fixed with 1% formaldehyde for five minutes at room temperature and quenched with 217 mM glycine during nuclei preparation.

value: Midbrain

tag: cell line

value: postmortem brain tissue

tag: cell type

value: Dopa neuron

tag: treatment

value: Bipolar


title: DO iPSC line 2431, untreated

city: Bar Harbor

first: Madison

last: Armstrong

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Library name: DO_iPSC_2431_CTRL

library_source: transcriptomic

data_processing:
Raw RNA-seq reads were combined across lanes for each sample to obtain over 30 million raw reads per sample. Combined RNA-seq reads were processed using the Jackson Laboratory Data Science Nextflow DSL2 Workflows (version 24.10.6, https://github.com/TheJacksonLaboratory/jds-nf-workflows/wiki). Reads were aligned and quantified using EMASE (Expectation Maximization for Allele-Specific Expression)[Munger, S.C., et al., RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics, 2014. 198(1): p. 59–73.]
Raw gbrs expected read counts were compiled into a counts matrix. Raw transcript per million counts were compiled into a tpm matrix.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Count tsv file with counts per gene (rows) for each sample (columns)
Supplementary files format and content: Transcript per million tsv with tpm per gene (rows) for each sample (columns)

organism: Mus musculus

source_name: DO iPSC 2431

growth_protocol: 218 Diversity Outbred iPSC lines were thawed from early passage aliquots, plating ~1 million cells onto gelatinized 60mm tissue culture treated plates with mESC medium +2i/LIF (DMEM supplemented with 15% ES cell grade FBS [Gibco, 16141079], 1X GlutaMAX [100X, Gibco, 35050061], 1X penicillin/streptomycin [100X, Gibco, 15140], 1X nonessential amino acids [100X, Gibco, 11140], 1X sodium pyruvate [100X, Gibco, 11360], 0.1 mM β‐mercaptoethanol [55 mM, Gibco 21985023], and 1,000 U/ml leukemia inhibitory factor [Chemicon ESG1106 or 1107], supplemented with 2i [3 uM CHIR99021, Stemgent 04-0004, GSK3 inhibition and 1 uM PD0325901, Stemgent 04-0006, MEK/ERK inhibition]). Cells were grown to confluency in 5% CO2 at 37°C before passaging for a minimum of three passages before beginning the treament protocol.

extract_protocol:
Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher). Cells were homogenized in MR1 buffer (Macherey-Nagel) by vortexing.  RNA isolation was performed according to the manufacturer’s protocol. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape Assay (Agilent Technologies).
Stranded libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Density plating experiments identified plating with 75,000 cells produced optimal numbers of cells following treatment. Cells were plated on gelatinized 12-well tissue culture treated glass-like bottom plates to reduce chemical precipitation. Following plating with 75,000 cells per well in mESC medium +2i/LIF, cells were allowed to recover from passaging and expand for 24 hours at 5% CO2 at 37°C. After 24 hours of recovery, control sample cell media was replaced with fresh mESC medium +2i/LIF while treated sample cell media was replaced with mESC medium +2i/LIF with added 80μM triphenyl phosphate (TPHP, dissolved in DMSO, Acros Organics 147672500). Cells were treated for 24 hours at 5% CO2 at 37°C. Cells were collected using trypsin (0.05%, Gibco 25300-054) and cell pellets were store at -80°C until RNA extraction.

value: DO iPSC 2431

value: iPSC

value: untreated

tag: Sex

value: female

tag: do generation

tag: run


title: DO iPSC line 2427, triphenyl phosphate treated

description: Library name: DO_iPSC_2427_TPHP

source_name: DO iPSC 2427

value: DO iPSC 2427

value: triphenyl phosphate


title: UPN827 cells, TN246 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN246 TrailNet Baseline T1D plasma


title: Donor_21_Dopa_neuron_Control

description: Library name: Donor 21

value: Control


title: snRNASeq_PCOS subject3_and_CTRL subject1

description: Library name: Mixed Sample of PCOS3_CTRL1

value: subcutaneous abdominal and gluteofemoral fat


title: DO iPSC line 2427, untreated

description: Library name: DO_iPSC_2427_CTRL


title: Primary - IFNG - Sample 3 - 2

city: Atlanta

first: Taylor

last: Pio

state: GA

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: Library name: 40

data_processing:
FASTQ files were trimmed using Trimmomatic, aligned to hg19 with STAR, and reads were summarized with featureCounts.
Assembly: GRCh37 (hg19)
Supplementary files format and content: feature_counts and metadata files

source_name: Fetal cortex

growth_protocol: TIC treatment consisted of media with TNF-α (30 ng/mL), IL-1α (3 ng/mL), and C1q (400 ng/mL) added to media directly before media change. Vehicle-treated controls received media supplemented with an equivalent volume of sterile 0.1% BSA in PBS, matching the cytokine solution. IFN-γ treatment consisted of media with IFN-γ (0.06 μg/mL) added to media directly before media change.

extract_protocol:
mRNA was isolated using the RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN 74106) and stored at -80°C.
The library was prepared using Magic prep NGS (Tecan 30186621) according to manufacturer recommendations with 150 ng RNA. The prepared libraries were sent to Admera for sequencing (NovaSeq X Plus 10B) targeting approximately 40 million paired end reads per sample.

treatment_protocol: For bulk RNA-seq of organoids, organoids were placed in 1.7mL tubes, all media was removed, then samples were placed on dry ice and stored at -80°C until RNA isolation. For bulk-RNAseq of 2D primary samples, 500 μL Qiazol (Qiagen 79306) was added to each well, pipetted 10-20 times, then moved to 1.7mL tube and snap frozen on dry ice. Samples were stored at -80°C until RNA isolation.

value: Fetal cortex

value: Sample 3

value: Oligodendrocyte-enriched

value: IFNG


title: Donor_20_Dopa_neuron_Bipolar

description: Library name: Donor 20


title: UPN827 cells, TN245 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN245 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: Primary - IFNG - Sample 3 - 1

description: Library name: 39


title: DO iPSC line 2423, triphenyl phosphate treated

description: Library name: DO_iPSC_2423_TPHP

source_name: DO iPSC 2423

value: DO iPSC 2423


title: Donor_19_Dopa_neuron_Bipolar

description: Library name: Donor 19

value: Midbrain

value: postmortem brain tissue

value: Dopa neuron


title: Primary - TIC - Sample 3 - 2

description: Library name: 38

value: TIC


title: UPN827 cells, TN244RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN244RH2 TrailNet Baseline T1D plasma


title: Donor_18_Dopa_neuron_Control

description: Library name: Donor 18


title: DO iPSC line 2423, untreated

description: Library name: DO_iPSC_2423_CTRL

value: iPSC

value: untreated


title: UPN827 cells, TN243 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN243 TrailNet Baseline T1D plasma


title: Primary - TIC - Sample 3 - 1

description: Library name: 37


title: DO iPSC line 2356, triphenyl phosphate treated

description: Library name: DO_iPSC_2356_TPHP

source_name: DO iPSC 2356

value: DO iPSC 2356

value: female


title: UPN827 cells, TN242 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN242 TrailNet Baseline T1D plasma


title: DO iPSC line 2356, untreated

description: Library name: DO_iPSC_2356_CTRL


title: Donor_17_Non_neuron_Control

description: Library name: Donor 17

value: Non neuron

value: Control


title: Primary - Vehicle - Sample 3 - 2

description: Library name: 36

value: Fetal cortex

value: Vehicle


title: Donor_16_Non_neuron_Control

description: Library name: Donor 16


title: UPN827 cells, TN241 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN241 TrailNet Baseline T1D plasma


title: Primary - Vehicle - Sample 3 - 1

description: Library name: 35

value: Sample 3

value: Oligodendrocyte-enriched


title: DO iPSC line 2351, triphenyl phosphate treated

description: Library name: DO_iPSC_2351_TPHP

source_name: DO iPSC 2351

value: DO iPSC 2351

value: triphenyl phosphate


title: Donor_15_Non_neuron_Bipolar

description: Library name: Donor 15

value: Bipolar


title: Primary - IFNG - Sample 2 - 2

description: Library name: 34

value: Sample 2

value: IFNG


title: DO iPSC line 2351, untreated

description: Library name: DO_iPSC_2351_CTRL


title: UPN827 cells, TN239 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN239 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: Donor_14_Non_neuron_Bipolar

description: Library name: Donor 14

value: Midbrain

value: postmortem brain tissue


title: UPN827 cells, TN240 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN240 TrailNet Baseline T1D plasma


title: Primary - IFNG - Sample 2 - 1

description: Library name: 33


title: Donor_13_Non_neuron_Control

description: Library name: Donor 13


title: DO iPSC line 2324, triphenyl phosphate treated

description: Library name: DO_iPSC_2324_TPHP

source_name: DO iPSC 2324

value: DO iPSC 2324

value: iPSC

value: male


title: Primary - TIC - Sample 2 - 2

description: Library name: 32

value: TIC


title: DO iPSC line 2324, untreated

description: Library name: DO_iPSC_2324_CTRL

value: untreated


title: Donor_12_Non_neuron_Control

description: Library name: Donor 12

value: Non neuron

value: Control


title: UPN827 cells, TN238 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN238 TrailNet Baseline T1D plasma


title: UPN827 cells, TN237 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN237 TrailNet Baseline T1D plasma


title: DO iPSC line 2319, triphenyl phosphate treated

description: Library name: DO_iPSC_2319_TPHP

source_name: DO iPSC 2319

value: DO iPSC 2319


title: Primary - TIC - Sample 2 - 1

description: Library name: 31

value: Fetal cortex

value: Oligodendrocyte-enriched


title: Donor_11_Non_neuron_Bipolar

description: Library name: Donor 11

source_name: Midbrain

value: Bipolar


title: UPN827 cells, TN236 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN236 TrailNet Baseline T1D plasma


title: DO iPSC line 2319, untreated

description: Library name: DO_iPSC_2319_CTRL


title: Primary - Vehicle - Sample 2 - 2

description: Library name: 30

source_name: Fetal cortex

value: Sample 2

value: Vehicle


title: Donor_10_Non_neuron_Bipolar

description: Library name: Donor 10


title: DO iPSC line 1752, triphenyl phosphate treated

description: Library name: DO_iPSC_1752_TPHP

source_name: DO iPSC 1752

value: DO iPSC 1752

value: triphenyl phosphate

value: female


title: Primary - Vehicle - Sample 2 - 1

description: Library name: 29


title: UPN827 cells, TN235 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN235 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN234 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN234 TrailNet Baseline T1D plasma


title: Donor_9_Non_neuron_Bipolar

description: Library name: Donor 9

value: Midbrain

value: postmortem brain tissue


title: DO iPSC line 1752, untreated

description: Library name: DO_iPSC_1752_CTRL

value: iPSC


title: Primary - IFNG - Sample 1 - 2

description: Library name: 28

value: Sample 1

value: IFNG


title: Donor_8_Non_neuron_Control

description: Library name: Donor 8

value: Non neuron

value: Control


title: UPN827 cells, TN233 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN233 TrailNet Baseline T1D plasma


title: Primary - IFNG - Sample 1 - 1

description: Library name: 27

value: Fetal cortex


title: Donor_7_Non_neuron_Bipolar

description: Library name: Donor 7


title: DO iPSC line 1749, triphenyl phosphate treated

description: Library name: DO_iPSC_1749_TPHP

source_name: DO iPSC 1749

value: DO iPSC 1749


title: Primary - TIC - Sample 1 - 1

description: Library name: 26

value: Oligodendrocyte-enriched

value: TIC


title: DO iPSC line 1749, untreated

description: Library name: DO_iPSC_1749_CTRL

value: untreated


title: UPN827 cells, TN232rehyb TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN232rehyb TrailNet Baseline T1D plasma


title: Primary - Vehicle - Sample 1 - 2

description: Library name: 24

value: Vehicle


title: UPN827 cells, TN231 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN231 TrailNet Baseline T1D plasma


title: Donor_5_Non_neuron_Bipolar

description: Library name: Donor 5

value: Bipolar


title: DO iPSC line 1747, untreated

description: Library name: DO_iPSC_1747_CTRL

source_name: DO iPSC 1747

value: DO iPSC 1747

value: male


title: Primary - Vehicle - Sample 1 - 1

description: Library name: 23


title: Donor_4_Non_neuron_Bipolar

description: Library name: Donor 4


title: DO iPSC line 1746, triphenyl phosphate treated

description: Library name: DO_iPSC_1746_TPHP

source_name: DO iPSC 1746

value: DO iPSC 1746

value: triphenyl phosphate


title: UPN827 cells, TN230 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN230 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN229 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN229 TrailNet Baseline T1D plasma


title: hSpO - d200 - Line 3 - 2

description: Library name: 22

source_name: Organoid

value: Organoid

value: Spinal Cord Organoid


title: Donor_3_Non_neuron_Bipolar

description: Library name: Donor 3

value: Midbrain

value: postmortem brain tissue

value: Non neuron


title: DO iPSC line 1746, untreated

description: Library name: DO_iPSC_1746_CTRL

value: iPSC


title: hSpO - d200 - Line 3 - 1

description: Library name: 21


title: hSpO - d200 - Line 2 - 2

description: Library name: 12


title: DO iPSC line 1738, triphenyl phosphate treated

description: Library name: DO_iPSC_1738_TPHP

source_name: DO iPSC 1738

value: DO iPSC 1738

value: female


title: Donor_2_Non_neuron_Control

description: Library name: Donor 2

value: Control


title: UPN827 cells, TN228 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN228 TrailNet Baseline T1D plasma


title: UPN827 cells, TN227 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN227 TrailNet Baseline T1D plasma


title: Donor_1_Non_neuron_Control

description: Library name: Donor 1

source_name: Midbrain


title: UPN827 cells, TN226 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN226 TrailNet Baseline T1D plasma


title: DO iPSC line 1738, untreated

description: Library name: DO_iPSC_1738_CTRL

value: untreated


title: hSpO - d200 - Line 2 - 1

description: Library name: 11


title: UPN827 cells, TN225 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN225 TrailNet Baseline T1D plasma


title: Donor_98_Non_neuron_SCZ

description: Library name: Donor 98

data_processing:
• Adapter trimming using Trimmomatic v0.36
• Alignment to the human genome (GRCh38/hg38) with STAR v2.5.3a
• Gene and transcript quantification using GENCODE v27 annotations
• Quality control using QTLtools (mbv) and sex-marker validation
• Normalization and differential expression modeling using voom/limma-dream
Assembly: GRCh38 / hg38 (GENCODE v27 for gene annotation)
Supplementary files format and content: Processed data include normalized gene-level and transcript-level counts (CPM / log2CPM) and differential expression statistics. Files contain gene identifiers (GENCODE v27), expression values per sample, and model outputs.

growth_protocol: Postmortem human ventral midbrain (substantia nigra, A9/A10 region) tissue was obtained from established brain banks participating in the CommonMind Consortium. Donors provided informed consent for brain donation, and all tissue collection followed institutional ethical guidelines and the Declaration of Helsinki.

extract_protocol:
Nuclei were isolated from ventral midbrain tissue using Dounce homogenization in sucrose-based lysis buffer, followed by ultracentrifugation through a sucrose cushion to obtain purified nuclei. Immunotagging was performed using NeuN-Alexa488 and Nurr1-Alexa647 antibodies. Approximately 50,000 NeuN+/Nurr1+ (dopaminergic) and 50,000 NeuN-/Nurr1- nuclei were sorted on a BD FACSAria. RNA was extracted from sorted nuclei in TRIzol LS, followed by chloroform extraction and cleanup using the Zymo RNA Clean & Concentrator kit with extended DNase treatment.
RNA-seq libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara). cDNA synthesis, rRNA depletion, adapter ligation, and PCR amplification were performed following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq-6000 (100 bp paired-end).

treatment_protocol: No experimental treatments were applied. Tissue was collected postmortem and processed directly for nuclei isolation and downstream assays. Medication history (including antipsychotic exposure) was recorded by the brain banks but no treatments were administered as part of this study.

value: SCZ


title: hSpO - d200 - Line 1 - 2

description: Library name: 10


title: DO iPSC line 1735, triphenyl phosphate treated

description: Library name: DO_iPSC_1735_TPHP

source_name: DO iPSC 1735

value: DO iPSC 1735


title: Donor_97_Non_neuron_Control

description: Library name: Donor 97


title: hSpO - d200 - Line 1 - 1

description: Library name: 9


title: DO iPSC line 1735, untreated

description: Library name: DO_iPSC_1735_CTRL


title: Donor_96_Non_neuron_Control

description: Library name: Donor 96


title: UPN827 cells, TN224 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN224 TrailNet Baseline T1D plasma


title: DO iPSC line 1732, triphenyl phosphate treated

description: Library name: DO_iPSC_1732_TPHP

source_name: DO iPSC 1732

value: DO iPSC 1732


title: UPN827 cells, TN223 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN223 TrailNet Baseline T1D plasma


title: Donor_95_Non_neuron_SCZ

description: Library name: Donor 95


title: hSpO - d150 - Line 3 - 2

description: Library name: 20


title: DO iPSC line 1732, untreated

description: Library name: DO_iPSC_1732_CTRL


title: UPN827 cells, TN222 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN222 TrailNet Baseline T1D plasma


title: hSpO - d150 - Line 3 - 1

description: Library name: 19


title: E15.5, control cerebellum, replicate 1

first: Alexandra

middle: L.

last: Joyner

state: New York

address: 430 E 67th St

department: Developmental Biology Program

institute: Sloan Kettering Institute

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v6.1.0)
Assembly: Customized genome (mm10 and tdTomato sequence)
Supplementary files format and content: Tab-separated value files and matrix files.

source_name: tdT+ sorted cells from cerebellum

extract_protocol:
Animals were dissected in ice cold Hank’s balanced salt solution (HBSS) (Gibco) and were pooled together for downstream steps. Two replicate experiments were performed. On ice, cerebella were detached from the rest of the brain using forceps and dissociated in Accutase (Innovative Cell Technologies) at 37°C for 7-10 minutes. Following dissociation, accutase was washed out using neural stem cell (NSC) media (Neurobasal, supplemented with N2, B27 and non-essential amino acids, Gibco). Samples were triturated by pipetting up and down using a P1000, filtered through a 35um cell strainer (Falcon)and then centrifuged at 500g at 4°C for 5 minutes. Cells were washed again in NSC media and were finally filtered into polypropylene round bottom tubes (Falcon) prior to sorting for tdT+ cells. tdT+ cells were sorted into polypropylene round bottom tubes, spun down at 500g at 4°C for 5 minutes and resuspended in NSC media prior to single cell library preparation.
Single cell libraries were prepared using 10X Genomics’ Chromium Next GEM Single Cell 3’ Reagent Kits, v3.1 according to manufacturer’s instructions. Prior to loading the 10X Genomics chip, the limited sample preparation protocol was used. Cell viability was quantified using 0.2% (w/v) Trypan Blue on a hemocytometer, and 10,000 viable cells were targeted per pooled sample.

value: tdT+ sorted cells from cerebellum

tag: genotype

value: Ptf1aCre/+; R26LSL-tdT/+


title: Donor_94_Dopa_neuron_Control

description: Library name: Donor 94

value: Dopa neuron


title: DO iPSC line 1729, triphenyl phosphate treated

description: Library name: DO_iPSC_1729_TPHP

source_name: DO iPSC 1729

value: DO iPSC 1729

value: triphenyl phosphate


title: UPN827 cells, TN221 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN221 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: hSpO - d150 - Line 2 - 2

description: Library name: 8

value: Organoid

value: Spinal Cord Organoid


title: Donor_93_Non_neuron_Control

description: Library name: Donor 93

value: Midbrain

value: postmortem brain tissue

value: Non neuron


title: UPN827 cells, TN220 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN220 TrailNet Baseline T1D plasma


title: hSpO - d150 - Line 2 - 1

description: Library name: 7


title: Donor_92_Non_neuron_SCZ

description: Library name: Donor 92


title: DO iPSC line 1725, triphenyl phosphate treated

description: Library name: DO_iPSC_1725_TPHP

source_name: DO iPSC 1725

value: DO iPSC 1725

value: iPSC

value: female


title: DO iPSC line 1729, untreated

description: Library name: DO_iPSC_1729_CTRL

value: untreated


title: Donor_6_Non_neuron_Control

description: Library name: Donor 6

value: Control


title: DO iPSC line 1747, triphenyl phosphate treated

description: Library name: DO_iPSC_1747_TPHP

source_name: DO iPSC 1747

value: DO iPSC 1747

value: male


title: hSpO - d150 - Line 1 - 2

description: Library name: 6

source_name: Organoid


title: Donor_91_Dopa_neuron_Control

description: Library name: Donor 91

value: Dopa neuron


title: UPN827 cells, TN219 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN219 TrailNet Baseline T1D plasma


title: DO iPSC line 1725, untreated

description: Library name: DO_iPSC_1725_CTRL


title: hSpO - d150 - Line 1 - 1

description: Library name: 5


title: Donor_90_Non_neuron_Control

description: Library name: Donor 90


title: UPN827 cells, TN218 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN218 TrailNet Baseline T1D plasma


title: UPN827 cells, TN217 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN217 TrailNet Baseline T1D plasma


title: DO iPSC line 1723, triphenyl phosphate treated

description: Library name: DO_iPSC_1723_TPHP

source_name: DO iPSC 1723

value: DO iPSC 1723


title: DO iPSC line 1723, untreated

description: Library name: DO_iPSC_1723_CTRL


title: hSpO - d120 - Line 3 - 2

description: Library name: 14


title: Donor_89_Non_neuron_BP

description: Library name: Donor 89

source_name: Midbrain

value: BP


title: Donor_88_Dopa_neuron_Control

description: Library name: Donor 88


title: hSpO - d120 - Line 2 - 2

description: Library name: 4


title: UPN827 cells, TN215 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN215 TrailNet Baseline T1D plasma

value: UPN827 cells


title: Donor_87_Dopa_neuron_SCZ

description: Library name: Donor 87

value: SCZ


title: hSpO - d120 - Line 3 - 1

description: Library name: 13

value: Organoid


title: DO iPSC line 1721, triphenyl phosphate treated

description: Library name: DO_iPSC_1721_TPHP

source_name: DO iPSC 1721

value: DO iPSC 1721

value: triphenyl phosphate


title: UPN827 cells, TN216 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN216 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN214 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN214 TrailNet Baseline T1D plasma


title: hSpO - d120 - Line 2 - 1

description: Library name: 3

value: Spinal Cord Organoid


title: DO iPSC line 1721, untreated

description: Library name: DO_iPSC_1721_CTRL


title: Donor_86_Dopa_neuron_Control

description: Library name: Donor 86

value: Midbrain

value: postmortem brain tissue


title: UPN827 cells, TN213 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN213 TrailNet Baseline T1D plasma


title: hSpO - d120 - Line 1 - 2

description: Library name: 2


title: Donor_85_Dopa_neuron_BP

description: Library name: Donor 85


title: DO iPSC line 1713, triphenyl phosphate treated

description: Library name: DO_iPSC_1713_TPHP

source_name: DO iPSC 1713

value: DO iPSC 1713

value: iPSC

value: female


title: hSpO - d120 - Line 1 - 1

description: Library name: 1


title: DO iPSC line 1713, untreated

description: Library name: DO_iPSC_1713_CTRL

value: untreated


title: Donor_84_Non_neuron_SCZ

description: Library name: Donor 84

value: Non neuron


title: UPN827 cells, TN212 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN212 TrailNet Baseline T1D plasma


title: UPN827 cells, TN211 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN211 TrailNet Baseline T1D plasma


title: DO iPSC line 1711, triphenyl phosphate treated

description: Library name: DO_iPSC_1711_TPHP

source_name: DO iPSC 1711

value: DO iPSC 1711


title: UPN827 cells, TN210 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN210 TrailNet Baseline T1D plasma


title: hSpO - d100 - Line 3 - 2

description: Library name: 18


title: Donor_83_Dopa_neuron_Control

description: Library name: Donor 83

value: Dopa neuron

value: Control


title: DO iPSC line 1711, untreated

description: Library name: DO_iPSC_1711_CTRL


title: hSpO - d100 - Line 3 - 1

description: Library name: 17


title: Donor_82_Dopa_neuron_BP

description: Library name: Donor 82

value: BP


title: DO iPSC line 1705, triphenyl phosphate treated

description: Library name: DO_iPSC_1705_TPHP

source_name: DO iPSC 1705

value: DO iPSC 1705


title: UPN827 cells, TN209 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN209 TrailNet Baseline T1D plasma

value: UPN827 cells


title: hSpO - d100 - Line 2 - 2

description: Library name: 61

source_name: Organoid

value: Organoid


title: Donor_81_Non_neuron_BP

description: Library name: Donor 81


title: hSpO - d100 - Line 2 - 1

description: Library name: 60


title: DO iPSC line 1705, untreated

description: Library name: DO_iPSC_1705_CTRL


title: Donor_80_Dopa_neuron_SCZ

description: Library name: Donor 80

value: SCZ


title: DO iPSC line 1702, triphenyl phosphate treated

description: Library name: DO_iPSC_1702_TPHP

source_name: DO iPSC 1702

value: DO iPSC 1702

value: triphenyl phosphate


title: hSpO - d100 - Line 1 - 2

description: Library name: 59

value: Spinal Cord Organoid


title: Donor_79_Non_neuron_SCZ

description: Library name: Donor 79

value: Midbrain

value: postmortem brain tissue


title: UPN827 cells, TN207 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN207 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN208 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN208 TrailNet Baseline T1D plasma


title: UPN827 cells, TN206RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN206RH2 TrailNet Baseline T1D plasma


title: DO iPSC line 1702, untreated

description: Library name: DO_iPSC_1702_CTRL

value: iPSC

value: female


title: hSpO - d100 - Line 1 - 1

description: Library name: 58


title: Donor_78_Dopa_neuron_Control

description: Library name: Donor 78

source_name: Midbrain


title: DO iPSC line 1696, triphenyl phosphate treated

description: Library name: DO_iPSC_1696_TPHP

source_name: DO iPSC 1696

value: DO iPSC 1696


title: hSpO - d75 - Line 3 - 2

description: Library name: 16


title: UPN827 cells, TN205 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN205 TrailNet Baseline T1D plasma


title: DO iPSC line 1696, untreated

description: Library name: DO_iPSC_1696_CTRL

value: untreated


title: Donor_76_Dopa_neuron_Control

description: Library name: Donor 76

value: Dopa neuron


title: hSpO - d75 - Line 3 - 1

description: Library name: 15


title: UPN827 cells, TN204 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN204 TrailNet Baseline T1D plasma


title: DO iPSC line 1605, triphenyl phosphate treated

description: Library name: DO_iPSC_1605_TPHP

source_name: DO iPSC 1605

value: DO iPSC 1605


title: hSpO - d75 - Line 2 - 2

description: Library name: 57


title: Donor_77_Non_neuron_SCZ

description: Library name: Donor 77

value: Non neuron


title: DO iPSC line 1605, untreated

description: Library name: DO_iPSC_1605_CTRL


title: UPN827 cells, TN201 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN201 TrailNet Baseline T1D plasma


title: hSpO - d75 - Line 2 - 1

description: Library name: 56


title: UPN827 cells, TN202 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN202 TrailNet Baseline T1D plasma


title: Donor_75_Non_neuron_Control

description: Library name: Donor 75

value: Control


title: UPN827 cells, TN203 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN203 TrailNet Baseline T1D plasma

value: UPN827 cells


title: Donor_74_Dopa_neuron_BP

description: Library name: Donor 74

value: BP


title: hSpO - d75 - Line 1 - 2

description: Library name: 55

value: Organoid


title: DO iPSC line 1584, triphenyl phosphate treated

description: Library name: DO_iPSC_1584_TPHP

source_name: DO iPSC 1584

value: DO iPSC 1584


title: Donor_73_Non_neuron_BP

description: Library name: Donor 73


title: DO iPSC line 1584, untreated

description: Library name: DO_iPSC_1584_CTRL


title: hSpO - d75 - Line 1 - 1

description: Library name: 54


title: UPN827 cells, TN200 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN200 TrailNet Baseline T1D plasma


title: Donor_72_Dopa_neuron_BP

description: Library name: Donor 72


title: DO iPSC line 1571, triphenyl phosphate treated

description: Library name: DO_iPSC_1571_TPHP

source_name: DO iPSC 1571

value: DO iPSC 1571

value: triphenyl phosphate

value: male


title: Assembloid - Astrocytes -  TIC - Line 2

description: Library name: Sample 10

data_processing:
Demultiplexing, alignment, barcode and UMI counting, and aggregation were performed using Cell Ranger (cellranger v8.0.1 with default settings), which provided a feature-by-count matrix.
Further analysis was performed using the recommended QC and R package Seurat (v5.0) from the Satija Lab.
Assembly: GRCh37 (hg19)
Supplementary files format and content: RDS files of UMAPs in manuscript and cellranger outputs for each sample

molecule: polyA RNA

source_name: Organoid / assembloid

extract_protocol:
We used a previously established protocol to create single cell dissociation from human organoids and assembloids. Briefly, we mechanically (razor blade) and enzymatically dissociated tissue using papain (Worthington Biochemical LS003126) at 20 U/mL at 37°C for 45 minutes to 1 hour. Organoids and assembloids were dissociated in batches of 2–5 per well in six-well plates. Papain was quenched with ovomucoid solution (Worthington Biochemical LS003086), and samples were triturated using P1000 and P200 pipettes to obtain single-cell suspensions. hSpO and assembloids were dissociated into single cell solution as described above. Dissociated cells were resuspended in ice-cold PBS containing 0.02% BSA, counted using hemocytometer, and loaded onto a GEM-X 3' chip to generate gel beads in emulsion (GEMs).
Libraries were created using 10X Chromium GEM-X Single Cell 3' Reagent kit v4 (CG000731) according to manufacturer instructions.

treatment_protocol: TIC treatment consisted of media with TNF-α (30 ng/mL), IL-1α (3 ng/mL), and C1q (400 ng/mL) added to media directly before media change. Vehicle-treated controls received media supplemented with an equivalent volume of sterile 0.1% BSA in PBS, matching the cytokine solution.

value: Organoid / assembloid

value: Astrocyte

value: Assembloid - TIC


title: DO iPSC line 1571, untreated

description: Library name: DO_iPSC_1571_CTRL

value: iPSC


title: Donor_71_Non_neuron_BP

description: Library name: Donor 71

value: Midbrain

value: postmortem brain tissue


title: Assembloid - Astrocytes -  TIC - Line 1

description: Library name: Sample 9


title: Donor_70_Dopa_neuron_SCZ

description: Library name: Donor 70

value: Dopa neuron

value: SCZ


title: UPN827 cells, TN197 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN197 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN199 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN199 TrailNet Baseline T1D plasma


title: UPN827 cells, TN198 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN198 TrailNet Baseline T1D plasma


title: Assembloid - Astrocytes -  Vehicle - Line 2

description: Library name: Sample 8

value: Assembloid - Vehicle


title: DO iPSC line 1567, triphenyl phosphate treated

description: Library name: DO_iPSC_1567_TPHP

source_name: DO iPSC 1567

value: DO iPSC 1567


title: Donor_68_Dopa_neuron_BP

description: Library name: Donor 68

value: BP


title: UPN827 cells, TN196 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN196 TrailNet Baseline T1D plasma

value: UPN827 cells


title: Assembloid - Astrocytes -  Vehicle - Line 1

description: Library name: Sample 7


title: Donor_67_Dopa_neuron_BP

description: Library name: Donor 67

source_name: Midbrain


title: DO iPSC line 1563, triphenyl phosphate treated

description: Library name: DO_iPSC_1563_TPHP

source_name: DO iPSC 1563

value: DO iPSC 1563


title: Assembloid - Oligodendrocytes -  TIC - Line 2

description: Library name: Sample 6

value: Oligodendrocyte


title: UPN827 cells, TN195 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN195 TrailNet Baseline T1D plasma


title: DO iPSC line 1563, untreated

description: Library name: DO_iPSC_1563_CTRL

value: untreated


title: Donor_65_Dopa_neuron_SCZ

description: Library name: Donor 65


title: UPN827 cells, TN194 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN194 TrailNet Baseline T1D plasma


title: Assembloid - Oligodendrocytes -  TIC - Line 1

description: Library name: Sample 5


title: DO iPSC line 1555, triphenyl phosphate treated

description: Library name: DO_iPSC_1555_TPHP

source_name: DO iPSC 1555

value: DO iPSC 1555

value: triphenyl phosphate

value: male


title: UPN827 cells, TN192 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN192 TrailNet Baseline T1D plasma


title: Donor_64_Non_neuron_SCZ

description: Library name: Donor 64

value: Non neuron


title: DO iPSC line 1555, untreated

description: Library name: DO_iPSC_1555_CTRL

value: iPSC


title: Donor_63_Dopa_neuron_Control

description: Library name: Donor 63

value: Midbrain

value: Control


title: Assembloid - Oligodendrocytes -  Vehicle - Line 1

description: Library name: Sample 3

value: Organoid / assembloid


title: DO iPSC line 1539, triphenyl phosphate treated

description: Library name: DO_iPSC_1539_TPHP

source_name: DO iPSC 1539

value: DO iPSC 1539


title: hSpO - Oligodedrocytes - Line 2

description: Library name: Sample 2

value: hSpO


title: UPN827 cells, TN191 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN191 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: Donor_62_Non_neuron_Control

description: Library name: Donor 62

value: postmortem brain tissue


title: UPN827 cells, TN190 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN190 TrailNet Baseline T1D plasma


title: DO iPSC line 1539, untreated

description: Library name: DO_iPSC_1539_CTRL


title: hSpO - Oligodedrocytes - Line 1

description: Library name: Sample 1


title: DO iPSC line 1531, triphenyl phosphate treated

description: Library name: DO_iPSC_1531_TPHP

source_name: DO iPSC 1531

value: DO iPSC 1531


title: GBC-SD cells, trastuzumab rep3

city: Beijing

first: Huishan

last: Sun

state: Beijing

address: No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing,China

country: China

institute: Peking union medical college hospital

description:
Library name: Sample30
SD5_3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Differential expression analysis of two groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: ensembl_110_homo_sapiens_grch38_primary
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: GBC-SD

growth_protocol: All cells were maintained in RPMI-1640 supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
RNA was extracted using TRNzol Universal total RNA kit (TiANGEN) according to the manufacturer's instructions.
RNA library was prepared using Fast RNA-seq Lib Prep Kit V2 following manufacture's protocals

value: GBC-SD

value: Gallbladder Cancer cell line

value: WT

value: trastuzumab


title: Donor_60_Non_neuron_Control

description: Library name: Donor 60


title: UPN827 cells, TN188 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN188 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN187 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN187 TrailNet Baseline T1D plasma


title: Donor_59_Non_neuron_SCZ

description: Library name: Donor 59

value: SCZ


title: DO iPSC line 1529, triphenyl phosphate treated

description: Library name: DO_iPSC_1529_TPHP

source_name: DO iPSC 1529

value: DO iPSC 1529

value: triphenyl phosphate

value: male


title: GBC-SD cells, trastuzumab rep1

description:
Library name: Sample28
SD5_1


title: Donor_58_Dopa_neuron_Control

description: Library name: Donor 58

value: Midbrain

value: Dopa neuron


title: UPN827 cells, TN186 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN186 TrailNet Baseline T1D plasma


title: DO iPSC line 1529, untreated

description: Library name: DO_iPSC_1529_CTRL

value: iPSC

value: untreated


title: GBC-SD cells, CP724714 rep3

description:
Library name: Sample27
SD4_3


title: DO iPSC line 1567, untreated

description: Library name: DO_iPSC_1567_CTRL

source_name: DO iPSC 1567

value: DO iPSC 1567


title: UPN827 cells, TN185 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN185 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: Donor_57_Non_neuron_Control

description: Library name: Donor 57

source_name: Midbrain

value: postmortem brain tissue

value: Non neuron

value: Control


title: DO iPSC line 1498, triphenyl phosphate treated

description: Library name: DO_iPSC_1498_TPHP

source_name: DO iPSC 1498

value: DO iPSC 1498


title: GBC-SD cells, CP724714 rep2

description:
Library name: Sample26
SD4_2

value: GBC-SD

value: Gallbladder Cancer cell line

value: WT


title: lncRNA profile of whole blood cells - SAMPLE 2-30

city: Shanghai

first: Chunxia

last: Wang

state: Shanghai

address: No.355 Luding Road, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine

department: Department of Critical Care Medicine

institute: 上海交通大学附属儿童医院

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used for hybridization followed by washing

scan_protocol: The results were scanned by Agilent Microarray Scanner (Agilent p/n G2565BA) and data were extracted by Agilent Feature Extraction software.

data_processing:
Based on the first batch result of Arraystar human LncRNA microarray using 16 cases (12 cases with bacteria sepsis vs. 4 cases with non-bacteria sepsis), we firstly revealed the potential key relationship between lncRNAs landscape and pathogen infection (Preliminary data, data not shown). Then, the other batch of Arraystar human LncRNA microarray using 40 cases (24 cases with bacteria sepsis vs. 16 cases with non-bacteria cases) were added. Totally, these two batches included 36 cases with bacterial sepsis and 20 children with non-bacterial sepsis. To remove the batch effects, we merged 2 batches results, and all analyses were conducted with R version 4.0.5 and sva packages.
Use the “limma” package to identify the differentially expressed genes (DEGs) between bacteria sepsis and non-bacteria sepsis. The screening condition were p-value<0.05 and |logFC|≥1. Differentially expressed lncRNAs and mRNAs were screened out by volcano plot.

source_name: whole blood cells

label_protocol: Arraystar Flash RNA Labeling Kit

growth_protocol: Blood samples were collected before received inpatient treatment initiation. Groups: Bacterial sepsis vs. Non-bacterial sepsis

extract_protocol: Arraystar human LncRNA/mRNA microarray was performed on whole blood samples of 36 cases with bacterial sepsis and 20 children with non-bacterial sepsis to analyze differentially expressed LncRNAs. All experimental procedures were performed following Arraystar standard protocol. Briefly, TRIzol reagent were used to prepare RNA samples from whole blood cells, and RNA quantification and quality control (QC) was performed.

treatment_protocol: EDTA-anticoagulated whole blood was collected and stored at -80oC for further microarray analysis

tag: infection group

value: Bacterial sepsis

tag: gender

value: whole blood cells


title: UPN827 cells, TN193 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN193 TrailNet Baseline T1D plasma

value: UPN827 cells


title: Donor_66_Dopa_neuron_BP

description: Library name: Donor 66

value: BP


title: Donor_56_Non_neuron_SCZ

description: Library name: Donor 56

value: Midbrain

value: SCZ


title: GBC-SD cells, CP724714 rep1

description:
Library name: Sample25
SD4_1


title: DO iPSC line 1498, untreated

description: Library name: DO_iPSC_1498_CTRL

value: iPSC

value: male


title: Assembloid - Oligodendrocytes -  Vehicle - Line 2

description: Library name: Sample 4

source_name: Organoid / assembloid

value: Organoid / assembloid

value: Oligodendrocyte

value: Assembloid - Vehicle


title: Donor_55_Non_neuron_SCZ

description: Library name: Donor 55

value: postmortem brain tissue

value: Non neuron


title: UPN827 cells, TN183 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN183 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 1490, triphenyl phosphate treated

description: Library name: DO_iPSC_1490_TPHP

source_name: DO iPSC 1490

value: DO iPSC 1490

value: triphenyl phosphate


title: GBC-SD cells, afatinib rep3

description:
Library name: Sample24
SD3_3

value: GBC-SD

value: Gallbladder Cancer cell line

value: WT

value: afatinib


title: Donor_54_Non_neuron_Control

description: Library name: Donor 54

value: Control


title: DO iPSC line 1490, untreated

description: Library name: DO_iPSC_1490_CTRL

value: untreated


title: GBC-SD cells, afatinib rep2

description:
Library name: Sample23
SD3_2


title: Donor_53_Non_neuron_BP

description: Library name: Donor 53

value: Midbrain

value: BP


title: UPN827 cells, TN182 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN182 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 1486, triphenyl phosphate treated

description: Library name: DO_iPSC_1486_TPHP

source_name: DO iPSC 1486

value: DO iPSC 1486

value: iPSC

value: male


title: GBC-SD cells, afatinib rep1

description:
Library name: Sample22
SD3_1


title: UPN827 cells, TN181RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN181RH2 TrailNet Baseline T1D plasma


title: Donor_52_Non_neuron_Control

description: Library name: Donor 52

value: postmortem brain tissue


title: Donor_61_Dopa_neuron_Control

description: Library name: Donor 61

value: Dopa neuron


title: DO iPSC line 1486, untreated

description: Library name: DO_iPSC_1486_CTRL


title: UPN827 cells, TN180 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN180 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN189 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN189 TrailNet Baseline T1D plasma


title: DO iPSC line 1531, untreated

description: Library name: DO_iPSC_1531_CTRL

source_name: DO iPSC 1531

value: DO iPSC 1531


title: DO iPSC line 3376, triphenyl phosphate treated

description: Library name: DO_iPSC_3376_TPHP

source_name: DO iPSC 3376

value: DO iPSC 3376

value: triphenyl phosphate


title: DO iPSC line 3363, untreated

description: Library name: DO_iPSC_3363_CTRL

source_name: DO iPSC 3363

value: DO iPSC 3363


title: DO iPSC line 3373, untreated

description: Library name: DO_iPSC_3373_CTRL

source_name: DO iPSC 3373

value: DO iPSC 3373


title: CTC-444N24.11_1_B_LP1

city: Ghent

first: Xin

address: Corneel Heymanslaan 10, B

country: Belgium

institute: University Gent

description: Library name: RNA017332

library_source: other

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

molecule: other

growth_protocol: HEK293T-dCas9 cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in the incubator with 5% CO₂.

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .

treatment_protocol: Cells were transfected with a total of 40 ng purified sgRNA per well using Lipofectamine™ CRISPRMAX™ Cas9 Transfection Reagent (Invitrogen, Cat. #CMAX00003).

value: embryonic kidney cell


title: lncRNA profile of whole blood cells - SAMPLE 2-22

institute: 上海交通大学附属儿童医院

value: Non-bacterial sepsis

value: whole blood cells


title: CTB-31O20.2_1_D_LP1

description: Library name: RNA017326


title: lncRNA profile of whole blood cells - SAMPLE 2-27

institute: 上海交通大学附属儿童医院

value: Bacterial sepsis


title: GBC-SD cells, pyrotinib rep3

description:
Library name: Sample21
SD2_3

source_name: GBC-SD

value: GBC-SD

value: Gallbladder Cancer cell line

value: WT

value: pyrotinib


title: Donor_51_Non_neuron_SCZ

description: Library name: Donor 51

source_name: Midbrain

value: Midbrain

value: Non neuron

value: SCZ


title: DO iPSC line 1482, triphenyl phosphate treated

description: Library name: DO_iPSC_1482_TPHP

source_name: DO iPSC 1482

value: DO iPSC 1482

value: iPSC

value: male


title: GBC-SD cells, pyrotinib rep2

description:
Library name: Sample20
SD2_2


title: Donor_50_Dopa_neuron_Control

description: Library name: Donor 50

value: postmortem brain tissue

value: Dopa neuron

value: Control


title: UPN827 cells, TN178 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN178 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: GBC-SD cells, trastuzumab rep2

description:
Library name: Sample29
SD5_2

value: trastuzumab


title: DO iPSC line 1482, untreated

description: Library name: DO_iPSC_1482_CTRL

value: untreated


title: GBC-SD cells, pyrotinib rep1

description:
Library name: Sample19
SD2_1

value: GBC-SD


title: Donor_49_Non_neuron_Control

description: Library name: Donor 49


title: DO iPSC line 1478, triphenyl phosphate treated

description: Library name: DO_iPSC_1478_TPHP

source_name: DO iPSC 1478

value: DO iPSC 1478

value: triphenyl phosphate


title: GBC-SD cells, vehicle rep3

description:
Library name: Sample18
SD1_3

value: Gallbladder Cancer cell line

value: WT

value: Vehicle


title: GBC-SD cells, vehicle rep2

description:
Library name: Sample17
SD1_2


title: DO iPSC line 1478, untreated

description: Library name: DO_iPSC_1478_CTRL


title: Donor_48_Non_neuron_SCZ

description: Library name: Donor 48

value: Midbrain

value: Non neuron

value: SCZ


title: Donor_47_Non_neuron_SCZ

description: Library name: Donor 47


title: UPN827 cells, TN177 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN177 TrailNet Baseline T1D plasma


title: UPN827 cells, TN179 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN179 TrailNet Baseline T1D plasma


title: GBC-SD cells, vehicle rep1

description:
Library name: Sample16
SD1_1


title: UPN827 cells, TN176 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN176 TrailNet Baseline T1D plasma


title: UPN827 cells, TN175 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN175 TrailNet Baseline T1D plasma


title: UPN827 cells, TN174 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN174 TrailNet Baseline T1D plasma


title: UPN827 cells, TN173 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN173 TrailNet Baseline T1D plasma


title: Donor_45_Dopa_neuron_Control

description: Library name: Donor 45


title: DO iPSC line 1470, triphenyl phosphate treated

description: Library name: DO_iPSC_1470_TPHP

source_name: DO iPSC 1470

value: DO iPSC 1470

value: iPSC

value: male


title: SNU1196 cells, trastuzumab rep3

description:
Library name: Sample15
S96_5_3

value: Biliary Tract Cancer Cell Line


title: SNU1196 cells, trastuzumab rep2

description:
Library name: Sample14
S96_5_2


title: Donor_44_Non_neuron_SCZ

description: Library name: Donor 44

value: postmortem brain tissue


title: DO iPSC line 1470, untreated

description: Library name: DO_iPSC_1470_CTRL


title: UPN827 cells, TN172 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN172 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: DO iPSC line 1466, triphenyl phosphate treated

description: Library name: DO_iPSC_1466_TPHP

source_name: DO iPSC 1466

value: DO iPSC 1466


title: Donor_42_Dopa_neuron_Control

description: Library name: Donor 42

value: Dopa neuron

value: Control


title: SNU1196 cells, CP724714 rep3

description:
Library name: Sample12
S96_4_3


title: SNU1196 cells, trastuzumab rep1

description:
Library name: Sample13
S96_5_1

value: trastuzumab


title: Donor_43_Non_neuron_SCZ

description: Library name: Donor 43


title: SNU1196 cells, CP724714 rep2

description:
Library name: Sample11
S96_4_2


title: Donor_41_Non_neuron_Control

description: Library name: Donor 41


title: AC084082.3_D_LP1

description: Library name: RNA017322

value: embryonic kidney cell


title: AC084082.3_C_LP1

description: Library name: RNA017321


title: lncRNA profile of whole blood cells - SAMPLE 2-15

institute: 上海交通大学附属儿童医院

source_name: whole blood cells

value: Bacterial sepsis

value: whole blood cells


title: DO iPSC line 1462, triphenyl phosphate treated

description: Library name: DO_iPSC_1462_TPHP

source_name: DO iPSC 1462

value: DO iPSC 1462

value: triphenyl phosphate


title: lncRNA profile of whole blood cells - SAMPLE 2-13

institute: 上海交通大学附属儿童医院


title: Donor_40_Dopa_neuron_BP

description: Library name: Donor 40

value: Midbrain

value: BP


title: SNU1196 cells, CP724714 rep1

description:
Library name: Sample10
S96_4_1

value: WT


title: UPN827 cells, TN170 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN170 TrailNet Baseline T1D plasma


title: UPN827 cells, TN169 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN169 TrailNet Baseline T1D plasma


title: UPN827 cells, TN168 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN168 TrailNet Baseline T1D plasma


title: UPN827 cells, TN171 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN171 TrailNet Baseline T1D plasma


title: UPN827 cells, TN167 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN167 TrailNet Baseline T1D plasma


title: Donor_39_Non_neuron_Control

description: Library name: Donor 39

source_name: Midbrain

value: Non neuron


title: SNU1196 cells, afatinib rep2

description:
Library name: Sample8
S96_3_2

value: Biliary Tract Cancer Cell Line

value: afatinib


title: Donor_38_Dopa_neuron_Control

description: Library name: Donor 38

value: postmortem brain tissue


title: SNU1196 cells, afatinib rep1

description:
Library name: Sample7
S96_3_1


title: UPN827 cells, TN165 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN165 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: DO iPSC line 1458, triphenyl phosphate treated

description: Library name: DO_iPSC_1458_TPHP

source_name: DO iPSC 1458

value: DO iPSC 1458

value: iPSC

value: male


title: DO iPSC line 1458, untreated

description: Library name: DO_iPSC_1458_CTRL

value: untreated


title: DO iPSC line 1456, triphenyl phosphate treated

description: Library name: DO_iPSC_1456_TPHP

source_name: DO iPSC 1456

value: DO iPSC 1456


title: Donor_36_Dopa_neuron_Control

description: Library name: Donor 36

value: Dopa neuron

value: Control


title: DO iPSC line 1456, untreated

description: Library name: DO_iPSC_1456_CTRL


title: Donor_35_Non_neuron_Control

description: Library name: Donor 35


title: SNU1196 cells, pyrotinib rep2

description:
Library name: Sample5
S96_2_2

value: pyrotinib


title: Donor_34_Non_neuron_Control

description: Library name: Donor 34

value: Midbrain


title: DO iPSC line 1454, untreated

description: Library name: DO_iPSC_1454_CTRL

source_name: DO iPSC 1454

value: DO iPSC 1454


title: UPN827 cells, TN164 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN164 TrailNet Baseline T1D plasma


title: UPN827 cells, TN163 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN163 TrailNet Baseline T1D plasma


title: UPN827 cells, TN161RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN161RH2 TrailNet Baseline T1D plasma


title: UPN827 cells, TN166 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN166 TrailNet Baseline T1D plasma


title: UPN827 cells, TN162 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN162 TrailNet Baseline T1D plasma


title: Donor_33_Non_neuron_SCZ

description: Library name: Donor 33

value: SCZ


title: SNU1196 cells, vehicle rep3

description:
Library name: Sample3
S96_1_3

value: WT

value: Vehicle


title: DO iPSC line 1450, triphenyl phosphate treated

description: Library name: DO_iPSC_1450_TPHP

source_name: DO iPSC 1450

value: DO iPSC 1450

value: triphenyl phosphate


title: SNU1196 cells, vehicle rep2

description:
Library name: Sample2
S96_1_2

value: Biliary Tract Cancer Cell Line


title: DO iPSC line 1450, untreated

description: Library name: DO_iPSC_1450_CTRL


title: SNU1196 cells, vehicle rep1

description:
Library name: Sample1
S96_1_1


title: UPN827 cells, TN160 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN160 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: Donor_31_Dopa_neuron_Control

description: Library name: Donor 31

value: postmortem brain tissue


title: UPN827 cells, TN159 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN159 TrailNet Baseline T1D plasma


title: DO iPSC line 1446, triphenyl phosphate treated

description: Library name: DO_iPSC_1446_TPHP

source_name: DO iPSC 1446

value: DO iPSC 1446

value: iPSC

value: male


title: hUCMSCs,H2O2-3

city: 江苏省

first: yajie

last: li

state: China

address: 江苏省徐州市铜山路209号

institute: 徐州医科大学

description:
Library name: Sample6
column name in gene.count.matrix.annotation.csv:S3

data_processing:
Raw sequencing data were filtered to remove adaptor sequences, low-quality reads (Phred score < 20), sequences with high N content, and short sequences using fastp with default parameters, generating high-quality clean reads.
Clean reads were aligned to the reference genome in orientation mode using HISAT2, and alignment metrics (e.g., gene coverage, read distribution across genomic regions/chromosomes) were analyzed.
Mapped reads of each sample were assembled by StringTie, and gene expression levels were quantified as Read Counts using RSEM ; normalized expression values (e.g., FPKM) were calculated for subsequent analysis.
Differential expression analysis was performed using DESeq2 (for samples with biological replicates) or DEGseq. Differentially expressed genes (DEGs) were defined with the threshold: adjusted P-value < 0.05 and log2 fold change> 1.
Functional annotation of DEGs (including GO and KEGG) was conducted using Diamond (https://github.com/bbuchfink/diamond), which assigned genes to biological processes, cellular components, molecular functions (GO), and metabolic pathways (KEGG).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each gene across all samples (control & H2O2-treated hUCMSCs)
Supplementary files format and content: csv files include FPKM values for each gene across all samples

source_name: Umbilical Cord

growth_protocol: Human umbilical cord stem cells (hUCMSCs) were cultured in StemGro Mesenchymal Stem Cell Medium (BasaMedia) supplemented with fetal bovine serum, in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
RNA was harvested from hUCMSCs (control & H2O2-treated groups) using MJZol total RNA extraction kit (Shanghai Majorbio Biomedical Technology Co., Ltd., China). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing (low-input) (Clontech, USA), following the manufacturer’s protocols.

treatment_protocol: Oxidative stress model (designated as hUCMSCs,H2O2) was induced by adding 200 μM H2O2 to hUCMSCs at 2 days post-adhesion.

value: Umbilical Cord

value: Primary hUCMSCs

value: mesenchymal stem cells

value: Hydrogen peroxide (H2O2) treatment


title: Donor_30_Non_neuron_Control

description: Library name: Donor 30

value: Midbrain

value: Non neuron

value: Control


title: DO iPSC line 1446, untreated

description: Library name: DO_iPSC_1446_CTRL

value: untreated


title: DO iPSC line 1442, triphenyl phosphate treated

description: Library name: DO_iPSC_1442_TPHP

source_name: DO iPSC 1442

value: DO iPSC 1442


title: hUCMSCs,H2O2-1

address: 江苏省徐州市铜山路209号

description:
Library name: Sample4
column name in gene.count.matrix.annotation.csv:S1

value: WT


title: UPN827 cells, TN157 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN157 TrailNet Baseline T1D plasma


title: Donor_28_Dopa_neuron_Control

description: Library name: Donor 28

source_name: Midbrain

value: Dopa neuron


title: UPN827 cells, TN156 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN156 TrailNet Baseline T1D plasma

value: UPN827 cells


title: hUCMSCs,Control-3

address: 江苏省徐州市铜山路209号

description:
Library name: Sample3
column name in gene.count.matrix.annotation.csv:D3

value: Control (0 μM H2O2)


title: DO iPSC line 1474, untreated

description: Library name: DO_iPSC_1474_CTRL

source_name: DO iPSC 1474

value: DO iPSC 1474


title: DO iPSC line 1474, triphenyl phosphate treated

description: Library name: DO_iPSC_1474_TPHP

value: triphenyl phosphate


title: Donor_27_Non_neuron_Control

description: Library name: Donor 27

value: postmortem brain tissue


title: DO iPSC line 1442, untreated

description: Library name: DO_iPSC_1442_CTRL

value: iPSC

value: male


title: Donor_46_Non_neuron_SCZ

description: Library name: Donor 46

value: SCZ


title: UPN827 cells, TN155 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN155 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: Donor_26_Dopa_neuron_BP

description: Library name: Donor 26

value: BP


title: DO iPSC line 1438, triphenyl phosphate treated

description: Library name: DO_iPSC_1438_TPHP

source_name: DO iPSC 1438

value: DO iPSC 1438


title: UPN827 cells, TN154 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN154 TrailNet Baseline T1D plasma


title: hUCMSCs,Control-1

address: 江苏省徐州市铜山路209号

description:
Library name: Sample1
column name in gene.count.matrix.annotation.csv:D1

value: Umbilical Cord

value: Primary hUCMSCs

value: mesenchymal stem cells


title: UPN827 cells, TN153 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN153 TrailNet Baseline T1D plasma


title: Donor_25_Non_neuron_BP

description: Library name: Donor 25

value: Midbrain

value: Non neuron


title: Donor_24_Dopa_neuron_Control

description: Library name: Donor 24

value: Dopa neuron

value: Control


title: DO iPSC line 1434, untreated

description: Library name: DO_iPSC_1434_CTRL

source_name: DO iPSC 1434

value: DO iPSC 1434

value: untreated


title: LN229-R, STM2457, rep 3

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

description: Library name: LN229R-STM3

data_processing:
Sequencing reads were trimmed using Trimmomatic (v0.39)
Trimmed sequence reads were mapped to GRCh38 using STAR (v2.7.11a)
Read counts were determined using Salmon (v1.4.0)
Normalized read counts were calculated using DESeq2
Assembly: hg38
Supplementary files format and content: csv files include normalized read counts for each comparison

source_name: LN229, TMZ resistant

growth_protocol: U87 MG and U87-R cells were grown in EMEM with 10% fetal bovine serum and 1% penicillin/streptomycin. LN229 and LN229-R cells were grown in DMEM with 5% fetal bovine serum, 1% penicillin/streptomycin, and 1mM sodium pyruvate. Growth media for U87-R and LN229-R cells was also supplemented with 50uM temozolomide.

extract_protocol:
Cells were lysed in Trizol and RNA was extracted by pehnol/chloroform extraction as per manufacturer instructions, followed by isopropanol precipitation. For U87 MG cell lines, 90ug of total RNA was used for polyA enrichment using the Dynabeads mRNA DIRECT Purification kit (Invitrogen), followed by fractionation using RNA Fragmentation Reagents (Invitrogen).
For U87 MG cell lines, libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina) from 30ng fragmented mRNA. For LN229 cell lines, libraries were prepared using the Watchmaker mRNA Library Prep kit from 1ug of total RNA.

treatment_protocol: Cells were treated 50uM STM2457 for 96 hours (or an equivalent volume of DMSO in controls)

value: LN229, TMZ resistant

value: glioma cultured cells

value: 50uM STM2457, 96 hours


title: DO iPSC line 1466, untreated

description: Library name: DO_iPSC_1466_CTRL

source_name: DO iPSC 1466

value: DO iPSC 1466

value: iPSC

value: male


title: DO iPSC line 1434, triphenyl phosphate treated

description: Library name: DO_iPSC_1434_TPHP

value: triphenyl phosphate


title: LN229-R, STM2457, rep 2

description: Library name: LN229R-STM2


title: UPN827 cells, TN150 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN150 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN502 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN502 TrailNet Baseline T1D plasma


title: UPN827 cells, TN151 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN151 TrailNet Baseline T1D plasma


title: DO iPSC line 1462, untreated

description: Library name: DO_iPSC_1462_CTRL

source_name: DO iPSC 1462

value: DO iPSC 1462


title: Donor_23_Non_neuron_Control

description: Library name: Donor 23

value: postmortem brain tissue


title: DO iPSC line 1430, triphenyl phosphate treated

description: Library name: DO_iPSC_1430_TPHP

source_name: DO iPSC 1430

value: DO iPSC 1430


title: UPN827 cells, TN149 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN149 TrailNet Baseline T1D plasma


title: LN229-R, STM2457, rep 1

description: Library name: LN229R-STM1


title: Donor_22_Non_neuron_BP

description: Library name: Donor 22

value: Midbrain

value: Non neuron

value: BP


title: DO iPSC line 1430, untreated

description: Library name: DO_iPSC_1430_CTRL


title: LN229-R, DMSO, rep 3

description: Library name: LN229R-DMSO3

value: DMSO control


title: Donor_37_Non_neuron_Control

description: Library name: Donor 37

value: Control


title: UPN827 cells, TN148 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN148 TrailNet Baseline T1D plasma


title: Donor_20_Dopa_neuron_Control

description: Library name: Donor 20

source_name: Midbrain

value: Dopa neuron


title: DO iPSC line 1426, untreated

description: Library name: DO_iPSC_1426_CTRL

source_name: DO iPSC 1426

value: DO iPSC 1426

value: untreated


title: LN229-R, DMSO, rep 1

description: Library name: LN229R-DMSO1

value: LN229, TMZ resistant

value: glioma cultured cells


title: UPN827 cells, TN147 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN147 TrailNet Baseline T1D plasma


title: Donor_19_Non_neuron_Control

description: Library name: Donor 19


title: UPN827 cells, TN146 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN146 TrailNet Baseline T1D plasma


title: DO iPSC line 1422, triphenyl phosphate treated

description: Library name: DO_iPSC_1422_TPHP

source_name: DO iPSC 1422

value: DO iPSC 1422

value: iPSC

value: male


title: UPN827 cells, TN145 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN145 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: LN229, STM2457, rep 3

description: Library name: LN229-STM3

value: 50uM STM2457, 96 hours


title: Donor_18_Non_neuron_Control

description: Library name: Donor 18

value: postmortem brain tissue


title: DO iPSC line 1422, untreated

description: Library name: DO_iPSC_1422_CTRL


title: DO iPSC line 1426, triphenyl phosphate treated

description: Library name: DO_iPSC_1426_TPHP

value: triphenyl phosphate


title: UPN827 cells, TN144 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN144 TrailNet Baseline T1D plasma


title: Donor_17_Dopa_neuron_Control

description: Library name: Donor 17

value: Midbrain


title: LN229, STM2457, rep 1

description: Library name: LN229-STM1


title: DO iPSC line 1418, triphenyl phosphate treated

description: Library name: DO_iPSC_1418_TPHP

source_name: DO iPSC 1418

value: DO iPSC 1418


title: Donor_16_Dopa_neuron_Control

description: Library name: Donor 16


title: LN229, DMSO, rep 3

description: Library name: LN229-DMSO3

value: DMSO control


title: DO iPSC line 1415, triphenyl phosphate treated

description: Library name: DO_iPSC_1415_TPHP

source_name: DO iPSC 1415

value: DO iPSC 1415

value: female


title: Donor_15_Dopa_neuron_SCZ

description: Library name: Donor 15

value: Dopa neuron

value: SCZ


title: UPN827 cells, TN143 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN143 TrailNet Baseline T1D plasma


title: UPN827 cells, TN142 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN142 TrailNet Baseline T1D plasma


title: LN229, DMSO, rep 2

description: Library name: LN229-DMSO2


title: UPN827 cells, TN141 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN141 TrailNet Baseline T1D plasma


title: hUCMSCs,H2O2-2

address: 江苏省徐州市铜山路209号

description:
Library name: Sample5
column name in gene.count.matrix.annotation.csv:S2

source_name: Umbilical Cord

value: Umbilical Cord

value: Primary hUCMSCs

value: mesenchymal stem cells

value: WT

value: Hydrogen peroxide (H2O2) treatment


title: Donor_13_Dopa_neuron_SCZ

description: Library name: Donor 13


title: UPN827 cells, TN139 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN139 TrailNet Baseline T1D plasma

value: UPN827 cells


title: Donor_12_Non_neuron_SCZ

description: Library name: Donor 12

value: Non neuron


title: U87-R, STM2457, rep 3

description: Library name: U87R-STM3

source_name: U87 MG, TMZ resistant

value: U87 MG, TMZ resistant

value: glioma cultured cells

value: 50uM STM2457, 96 hours


title: DO iPSC line 1398, triphenyl phosphate treated

description: Library name: DO_iPSC_1398_TPHP

source_name: DO iPSC 1398

value: DO iPSC 1398

value: iPSC

value: triphenyl phosphate


title: DO iPSC line 1398, untreated

description: Library name: DO_iPSC_1398_CTRL

value: untreated


title: Donor_11_Dopa_neuron_Control

description: Library name: Donor 11

value: Midbrain

value: postmortem brain tissue

value: Control


title: U87-R, STM2457, rep 2

description: Library name: U87R-STM2


title: UPN827 cells, TN137 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN137 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 1390, triphenyl phosphate treated

description: Library name: DO_iPSC_1390_TPHP

source_name: DO iPSC 1390

value: DO iPSC 1390

value: female


title: U87-R, STM2457, rep 1

description: Library name: U87R-STM1


title: DO iPSC line 1390, untreated

description: Library name: DO_iPSC_1390_CTRL


title: Donor_10_Non_neuron_Control

description: Library name: Donor 10

source_name: Midbrain


title: UPN827 cells, TN136 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN136 TrailNet Baseline T1D plasma


title: U87-R, DMSO, rep 3

description: Library name: U87R-DMSO3

value: DMSO control


title: Donor_9_Non_neuron_Control

description: Library name: Donor 9


title: U87-R, DMSO, rep 2

description: Library name: U87R-DMSO2


title: UPN827 cells, TN134 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN134 TrailNet Baseline T1D plasma


title: Donor_8_Dopa_neuron_SCZ

description: Library name: Donor 8

value: Dopa neuron

value: SCZ


title: DO iPSC line 1386, untreated

description: Library name: DO_iPSC_1386_CTRL

source_name: DO iPSC 1386

value: DO iPSC 1386


title: Donor_7_Dopa_neuron_SCZ

description: Library name: Donor 7


title: U87-R, DMSO, rep 1

description: Library name: U87R-DMSO1

value: U87 MG, TMZ resistant


title: UPN827 cells, TN133 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN133 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN132 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN132 TrailNet Baseline T1D plasma


title: DO iPSC line 1382, triphenyl phosphate treated

description: Library name: DO_iPSC_1382_TPHP

source_name: DO iPSC 1382

value: DO iPSC 1382


title: U87 MG, STM2457, rep 3

description: Library name: U87-STM3

source_name: U87 MG

value: U87 MG

value: glioma cultured cells

value: 50uM STM2457, 96 hours


title: Donor_6_Non_neuron_SCZ

description: Library name: Donor 6

value: Non neuron


title: DO iPSC line 1382, untreated

description: Library name: DO_iPSC_1382_CTRL

value: iPSC

value: untreated


title: U87 MG, STM2457, rep 2

description: Library name: U87-STM2


title: Donor_5_Non_neuron_SCZ

description: Library name: Donor 5

value: Midbrain

value: postmortem brain tissue


title: Donor_4_Dopa_neuron_Control

description: Library name: Donor 4

value: Control


title: U87 MG, STM2457, rep 1

description: Library name: U87-STM1


title: DO iPSC line 1359, triphenyl phosphate treated

description: Library name: DO_iPSC_1359_TPHP

source_name: DO iPSC 1359

value: DO iPSC 1359

value: triphenyl phosphate

value: female


title: UPN827 cells, TN131 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN131 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN130 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN130 TrailNet Baseline T1D plasma


title: DO iPSC line 1359, untreated

description: Library name: DO_iPSC_1359_CTRL


title: UPN827 cells, TN129 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN129 TrailNet Baseline T1D plasma


title: U87 MG, DMSO, rep 3

description: Library name: U87-DMSO3

value: DMSO control


title: U87 MG, DMSO, rep 2

description: Library name: U87-DMSO2


title: DO iPSC line 1350, triphenyl phosphate treated

description: Library name: DO_iPSC_1350_TPHP

source_name: DO iPSC 1350

value: DO iPSC 1350


title: Donor_2_Dopa_neuron_Control

description: Library name: Donor 2

value: Dopa neuron


title: UPN827 cells, TN128 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN128 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 1350, untreated

description: Library name: DO_iPSC_1350_CTRL


title: U87 MG, DMSO, rep 1

description: Library name: U87-DMSO1

value: U87 MG


title: UPN827 cells, TN127 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN127 TrailNet Baseline T1D plasma


title: Donor_1__Non_neuron_Control

description: Library name: Donor 1


title: DO iPSC line 1338, triphenyl phosphate treated

description: Library name: DO_iPSC_1338_TPHP

source_name: DO iPSC 1338

value: DO iPSC 1338


title: 293FT CMV-Intron NSUN2 cells n=3

city: Nashville

first: John

last: Karijolich

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description: Library name: Sample 6

data_processing:
trim with fastp
align with STAR
quantify with featureCounts
edgeR
Assembly: GRCh38
Supplementary files format and content: txt file for raw counts

growth_protocol: HEK293FT cells were cultured in standard growth media (DMEM, 10% FBS, 1% L-Glutamine, 1% Pen/Strep) for 48 hours and collected at ~85% confluency.

extract_protocol:
Total RNA was extracted from cell pellets using the Qiagen Rneasy mini kit following the manufacturer's protocol.
The samples were then subjected to mRNA enrichment and cDNA library preparation utilizing the stranded mRNA (polyA-selected) library preparation kit.

treatment_protocol: Cells were transduced with lentivirus to stably express an empty vector (EV) or overexpress NSUN2.

value: Human Embryonic Kidney

value: NSUN2 Overexpression


title: UPN827 cells, TN126 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN126 TrailNet Baseline T1D plasma


title: DO iPSC line 1338, untreated

description: Library name: DO_iPSC_1338_CTRL

value: iPSC


title: GBM_TS_TMZ_3

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description: Library name: GBM_TS_TMZ_3

data_processing:
The quality of the reads was assessed using fastQC (v.0.10.1), and the sequencing adapters were removed using skewer (v.0.2.2).
Filtered reads were mapped to the human reference genome (GRCh38) using STAR (v2.7.10a)
Transcript assembly and quantification for RNA-Seq were performed using featureCounts (v2.0.3)
Read count normalization as TPM is performed with R.
Differentially expressed gene analysis was performed by DESeq2.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files containing TPM values for each sample

source_name: GBM tumorsphere, TMZ treated, replicate 3

growth_protocol: Human tissue samples were obtained from 75 patients with GBM at the Yonsei University Severance Hospital. From these samples, we established GBM TSs. For TS culture, cells were cultured in TS complete media composed of Dulbecco’s modified Eagle’s medium/F12 (Mediatech), 1x B27 (Invitrogen), 20 ng/mL basic fibroblast growth factor, and 20 ng/mL epidermal growth factor (Sigma-Aldrich).

extract_protocol:
RNA was extracted with Rneasy mini plus kit (Qiagen).
The samples of TSs for RNAseq were processed with Aglient SureSelect Human Alll Exon v6 + UTR kit to build sequence libraries under maufacturer's protocols.

treatment_protocol: Sn and TMZ (Sigma-Aldrich, St. Louis, MO, USA) were dissolved in dimethyl sulfoxide (DMSO; Sigma-Aldrich) and treated to the cell cultures for 72 hours before RNA extraction process.

value: Cultured glioblastoma tumorsphere

value: TMZ (temozolomide)


title: 293FT CMV-Intron NSUN2 cells n=2

description: Library name: Sample 5


title: GBM_TS_TMZ_2

description: Library name: GBM_TS_TMZ_2

source_name: GBM tumorsphere, TMZ treated, replicate 2


title: DO iPSC line 1334, triphenyl phosphate treated

description: Library name: DO_iPSC_1334_TPHP

source_name: DO iPSC 1334

value: DO iPSC 1334


title: 293FT CMV-Intron NSUN2 cells n=1

description: Library name: Sample 4


title: GBM_TS_TMZ_1

description: Library name: GBM_TS_TMZ_1

source_name: GBM tumorsphere, TMZ treated, replicate 1


title: UPN827 cells, TN123 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN123 TrailNet Baseline T1D plasma


title: 293FT cells (Control) n=3

description: Library name: Sample 3

value: Empty Vector


title: DO iPSC line 1334, untreated

description: Library name: DO_iPSC_1334_CTRL

value: untreated


title: GBM_TS_SN_3

description: Library name: GBM_TS_SN_3

source_name: GBM tumorsphere, SN treated, replicate 3

value: SN (streptonigrin)


title: DO iPSC line 1326, triphenyl phosphate treated

description: Library name: DO_iPSC_1326_TPHP

source_name: DO iPSC 1326

value: DO iPSC 1326

value: triphenyl phosphate

value: female


title: UPN827 cells, TN121 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN121 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 1326, untreated

description: Library name: DO_iPSC_1326_CTRL


title: 293FT cells (Control) n=1

description: Library name: Sample 1


title: GBM_TS_SN_1

description: Library name: GBM_TS_SN_1

source_name: GBM tumorsphere, SN treated, replicate 1


title: UPN827 cells, TN120RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN120RH2 TrailNet Baseline T1D plasma


title: DO iPSC line 1314, triphenyl phosphate treated

description: Library name: DO_iPSC_1314_TPHP

source_name: DO iPSC 1314

value: DO iPSC 1314


title: MSS CRC tumor organoids + TCA 3

city: Freiburg

first: Rebecca

last: Kesselring

address: Breisacher Straße 115

department: General and Visceral Surgery

country: Germany

institute: Medical Center University Freiburg

description:
Library name: Sample 12
read counts in TCA3.txt

data_processing:
Read QC and trimming: cutadapt 3.7 (with Python 3.6.9) according to FastQC and MultiQC, meaning trimming of adapter sequences and overrepresented sequences in affected line(s) cutadapt -a  -A  --output --paired-output  --error-rate=0.1 --times=1 --overlap=3   --action=trim --minimum-length=20 --pair-filter=any   --quality-cutoff=28
Annotation file: gencode.v45.primary_assembly.annotation.gtf
Raw read counts == output of subread-2.0.6
featureCounts -a 'gencode.v45.primary_assembly.annotation.gtf' -F "GTF" -o -s 0 -Q 0 -t 'exon' -g 'gene_id' --minOverlap  1 --fracOverlap 0 --fracOverlapFeature 0 -p -C --countReadPairs --extraAttributes "gene_biotype"
Assembly: Reference genome: GRCh38.primary_assembly.genome.fa == GRCh38.p14
Supplementary files format and content: tab delimited txt file containing raw counts of the corresponding sample

source_name: primary tumor, MSS colorectal carcinoma

growth_protocol: human tumor organoids of a MSS colorectal carcinoma are cultured in human organoid culture medium

extract_protocol:
RNA was isolated with RNeasy Mini Kit (Qiagen).
bulk RNA sequencing was performed by Azenta, Leipzig according to their in-house SOPs with NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: Human tumor organoids were co-cultured for 24 hours with the primary bile acids (CA, TCA, GCA)

value: primary tumor, MSS colorectal carcinoma

value: tumor organoids

value: tumor cell

value: MSS CRC

value: TCA


title: GBM_TS_Control_3

description: Library name: GBM_TS_Control_3

source_name: GBM tumorsphere, untreated control, replicate 3


title: DO iPSC line 1314, untreated

description: Library name: DO_iPSC_1314_CTRL

value: iPSC


title: MSS CRC tumor organoids + TCA 2

description:
Library name: Sample 11
read counts in TCA2.txt


title: Donor_3_Non_neuron_Control

description: Library name: Donor 3

source_name: Midbrain

value: Midbrain

value: postmortem brain tissue

value: Non neuron

value: Control


title: UPN827 cells, TN119RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN119RH2 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 1310, triphenyl phosphate treated

description: Library name: DO_iPSC_1310_TPHP

source_name: DO iPSC 1310

value: DO iPSC 1310


title: UPN827 cells, TN118 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN118 TrailNet Baseline T1D plasma


title: UPN827 cells, TN125 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN125 TrailNet Baseline T1D plasma


title: GBM_TS_Control_2

description: Library name: GBM_TS_Control_2

source_name: GBM tumorsphere, untreated control, replicate 2

value: Cultured glioblastoma tumorsphere

value: untreated


title: MSS CRC tumor organoids + TCA 1

description:
Library name: Sample 10
read counts in TCA1.txt


title: GBM_TS_Control_1

description: Library name: GBM_TS_Control_1

source_name: GBM tumorsphere, untreated control, replicate 1


title: UPN827 cells, TN124 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN124 TrailNet Baseline T1D plasma


title: MSS CRC tumor organoids + GCA 3

description:
Library name: Sample 9
read counts in GCA3.txt

value: GCA


title: GBM_TS_Combi_3

description: Library name: GBM_TS_Combi_3

source_name: GBM tumorsphere, SN+TMZ treated, replicate 3

value: SN+TMZ


title: DO iPSC line 1310, untreated

description: Library name: DO_iPSC_1310_CTRL

value: female


title: UPN827 cells, TN117 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN117 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN116 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN116 TrailNet Baseline T1D plasma


title: DO iPSC line 1306, triphenyl phosphate treated

description: Library name: DO_iPSC_1306_TPHP

source_name: DO iPSC 1306

value: DO iPSC 1306

value: triphenyl phosphate


title: MSS CRC tumor organoids + GCA 2

description:
Library name: Sample 8
read counts in GCA2.txt

value: primary tumor, MSS colorectal carcinoma

value: tumor organoids

value: tumor cell

value: MSS CRC


title: GBM_TS_Combi_2

description: Library name: GBM_TS_Combi_2

source_name: GBM tumorsphere, SN+TMZ treated, replicate 2


title: 293FT cells (Control) n=2

description: Library name: Sample 2

value: Human Embryonic Kidney

value: Empty Vector


title: GBM_TS_SN_2

description: Library name: GBM_TS_SN_2

source_name: GBM tumorsphere, SN treated, replicate 2

value: SN (streptonigrin)


title: UPN827 cells, TN122 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN122 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN115 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN115 TrailNet Baseline T1D plasma


title: DO iPSC line 1306, untreated

description: Library name: DO_iPSC_1306_CTRL

value: iPSC


title: MSS CRC tumor organoids + GCA 1

description:
Library name: Sample 7
read counts in GCA1.txt

source_name: primary tumor, MSS colorectal carcinoma


title: GBM_TS_Combi_1

description: Library name: GBM_TS_Combi_1

source_name: GBM tumorsphere, SN+TMZ treated, replicate 1

value: Cultured glioblastoma tumorsphere


title: MSS CRC tumor organoids + CA 3

description:
Library name: Sample 6
read counts in CA3.txt

value: CA


title: DO iPSC line 1302, triphenyl phosphate treated

description: Library name: DO_iPSC_1302_TPHP

source_name: DO iPSC 1302

value: DO iPSC 1302