title: ChIP_H3K4me3_Phf6 Tg_rep2

city: San Antonio

first: Ying

last: Guo

state: Texas

address: 8403 Floyd Curl Dr

institute: UT Health Science Center at San Antonio

data_processing:
Raw data of each sample was quality controlled by fastqc and trimmed by TrimGalore
clean reads were aligned to mouse reference genome using bowtie2
The raw sam files generated by bowtie2 were sorted and reads on mitochondrion or with low Mapping quality (<30) were filtered using samtools
Sambamba was used to remove PCR duplications
Peak calling was performed with MACS2 with options: -g mm -n test -B -q 0.05
Assembly: mm10
Supplementary files format and content: BigWig files were generated using deeptools(bamCoverage --normalizeUsing CPM)
Supplementary files format and content: NarrowPeak files were generated using MACS2

extract_protocol:
The chromotin was cross-link, shearing and immunoprecipitated by indicated antibodies using the True MicroChIP-seq Kit (Diagenode). Then ChIP DNA was purified.
The ChIP libraries were prepared using the MicroPlex Library Preparation Kit (Diagenode) and sequenced with single-end 75 bp on Illumina NextSeq 500 system

treatment_protocol: The cKit+ cells were purified from mouse bone marrow cells using BD FACSAria II

value: cKit+ bone marrow cells

value: Phf6R274X Tg

tag: chip antibody

value: H3K4me3 (Diagenode, C15410003)


title: EPB41L4A-AS1_1_A_LP2

status: Public on Jun 01 2026

type: SRA

city: Ghent

first: Xin

last: Wang

address: Corneel Heymanslaan 10, B

country: Belgium

institute: University Gent

description: Library name: RNA017379

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

organism: Homo sapiens

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).

tag: cell line

tag: cell type

value: embryonic kidney cell

tag: genotype

tag: treatment

tag: batch


title: DO iPSC line 5237, untreated

city: Bar Harbor

first: Madison

last: Armstrong

state: ME

address: 600 Main St

country: USA

institute: The Jackson Laboratory

description: Library name: DO_iPSC_5237_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)

molecule: total RNA

organism: Mus musculus

source_name: DO iPSC 5237

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 5237

value: iPSC

value: untreated

tag: Sex

value: female

tag: do generation

tag: run


title: UPN827 cells, TN394RH2 TrailNet Baseline T1D plasma

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

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

source_name: UPN827 cells stimulated with TN394RH2 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: ChIP_H3K4me3_Phf6 Tg_rep1

library_source: genomic

molecule: genomic DNA

source_name: Bone marrow

tag: strain


title: LINC00240_1_C_LP2

description: Library name: RNA017377


title: DO iPSC line 5234, triphenyl phosphate treated

description: Library name: DO_iPSC_5234_TPHP

source_name: DO iPSC 5234

value: DO iPSC 5234

value: triphenyl phosphate

value: male


title: UPN827 cells, TN392 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN392 TrailNet Baseline T1D plasma


title: LINC00240_1_B_LP2

description: Library name: RNA017376


title: ChIP_H3K4me3_WT_rep1

value: wild type


title: UPN827 cells, TN391 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN391 TrailNet Baseline T1D plasma


title: DO iPSC line 5231, triphenyl phosphate treated

description: Library name: DO_iPSC_5231_TPHP

source_name: DO iPSC 5231

value: DO iPSC 5231


title: ChIP_H3K4me1_Phf6 Tg_rep2

value: H3K4me1 (Diagenode, C15410194)


title: UPN827 cells, TN390 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN390 TrailNet Baseline T1D plasma


title: DO iPSC line 5231, untreated

description: Library name: DO_iPSC_5231_CTRL


title: ChIP_H3K4me1_Phf6 Tg_rep1


title: EBLN3P_1_D_LP2

description: Library name: RNA017374


title: ChIP_H3K4me1_WT_rep2


title: UPN827 cells, TN387 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN387 TrailNet Baseline T1D plasma


title: EBLN3P_1_C_LP2

description: Library name: RNA017373


title: DO iPSC line 4792, untreated

description: Library name: DO_iPSC_4792_CTRL

source_name: DO iPSC 4792

value: DO iPSC 4792


title: ChIP_H3K4me1_WT_rep1

value: cKit+ bone marrow cells


title: EBLN3P_1_B_LP2

description: Library name: RNA017372


title: DO iPSC line 4761, triphenyl phosphate treated

description: Library name: DO_iPSC_4761_TPHP

source_name: DO iPSC 4761

value: DO iPSC 4761


title: UPN827 cells, TN385 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN385 TrailNet Baseline T1D plasma


title: ChIP_H3K27ac_Phf6 Tg_rep2

value: Phf6R274X Tg

value: H3K27ac (Diagenode, C15410196)


title: EBLN3P_1_A_LP2

description: Library name: RNA017371

value: embryonic kidney cell


title: UPN827 cells, TN384 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN384 TrailNet Baseline T1D plasma


title: UPN827 cells, TN396 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN396 TrailNet Baseline T1D plasma


title: DO iPSC line 4761, untreated

description: Library name: DO_iPSC_4761_CTRL

value: iPSC


title: DO iPSC line 5237, triphenyl phosphate treated

description: Library name: DO_iPSC_5237_TPHP

value: DO iPSC 5237


title: JPX_1_D_LP2

description: Library name: RNA017370


title: ChIP_H3K27ac_Phf6 Tg_rep1


title: LINC00240_1_D_LP2

description: Library name: RNA017378


title: UPN827 cells, TN383 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN383 TrailNet Baseline T1D plasma


title: DO iPSC line 4745, triphenyl phosphate treated

description: Library name: DO_iPSC_4745_TPHP

source_name: DO iPSC 4745

value: DO iPSC 4745


title: ChIP_H3K4me3_WT_rep2

value: H3K4me3 (Diagenode, C15410003)


title: JPX_1_C_LP2

description: Library name: RNA017369


title: ChIP_H3K27ac_WT_rep2


title: DO iPSC line 4745, untreated

description: Library name: DO_iPSC_4745_CTRL

value: untreated


title: ChIP_H3K27ac_WT_rep1


title: DO iPSC line 4732, triphenyl phosphate treated

description: Library name: DO_iPSC_4732_TPHP

source_name: DO iPSC 4732

value: DO iPSC 4732

value: female


title: JPX_1_A_LP2

description: Library name: RNA017367


title: RNA-seq_Phf6 Tg_rep3

data_processing:
The fastq files were quality controlled by fastqc and trimmed by Trimmomatic
Clean reads were aligned to the reference genome using STAR
The raw read counts of each gene were calculated using HTSeq
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA from individual mice was isolated with RNeasy Plus Mini Kit (QIAGEN)
The RNA libraries were prepared with the NEB Ultra RNA kit and followed by sequencing with a read length of 2 × 150 bp using the Illumina NextSeq 500

treatment_protocol: The Lineage-cKit+Sca-1+ cells were purified from mouse bone marrow cells using BD FACSAria II

value: Lin-cKit+Sca-1+ bone marrow cells


title: DO iPSC line 4732, untreated

description: Library name: DO_iPSC_4732_CTRL


title: DO iPSC line 4726, triphenyl phosphate treated

description: Library name: DO_iPSC_4726_TPHP

source_name: DO iPSC 4726

value: DO iPSC 4726

value: triphenyl phosphate


title: RNA-seq_Phf6 Tg_rep2


title: UPN827 cells, TN379 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN379 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: CTD-2349P21.9_1_D_LP2

description: Library name: RNA017366


title: DO iPSC line 4726, untreated

description: Library name: DO_iPSC_4726_CTRL


title: UPN827 cells, TN378 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN378 TrailNet Baseline T1D plasma


title: RNA-seq_Phf6 Tg_rep1

source_name: Bone marrow


title: CTD-2349P21.9_1_B_LP2

description: Library name: RNA017364


title: DO iPSC line 4713, triphenyl phosphate treated

description: Library name: DO_iPSC_4713_TPHP

source_name: DO iPSC 4713

value: DO iPSC 4713


title: UPN827 cells, TN377 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN377 TrailNet Baseline T1D plasma


title: RNA-seq_Phf6 KO_rep3

value: Phf6 knock out


title: JPX_1_B_LP2

description: Library name: RNA017368


title: UPN827 cells, TN382 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN382 TrailNet Baseline T1D plasma


title: CTD-2349P21.9_1_A_LP2

description: Library name: RNA017363


title: RNA-seq_Phf6 Tg_rep4

value: Phf6R274X Tg


title: UPN827 cells, TN381 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN381 TrailNet Baseline T1D plasma


title: RNA-seq_Phf6 KO_rep2


title: UPN827 cells, TN376 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN376 TrailNet Baseline T1D plasma


title: UPN827 cells, TN380 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN380 TrailNet Baseline T1D plasma


title: DO iPSC line 4713, untreated

description: Library name: DO_iPSC_4713_CTRL


title: NT_B_LP1

description: Library name: RNA017362

value: NT


title: DO iPSC line 4693, triphenyl phosphate treated

description: Library name: DO_iPSC_4693_TPHP

source_name: DO iPSC 4693

value: DO iPSC 4693

value: male


title: RNA-seq_Phf6 KO_rep1


title: FTX_1_B_LP2

description: Library name: RNA017388

value: embryonic kidney cell


title: UPN827 cells, TN375 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN375 TrailNet Baseline T1D plasma


title: FTX_1_A_LP2

description: Library name: RNA017387


title: DO iPSC line 5277, untreated

description: Library name: DO_iPSC_5277_CTRL

source_name: DO iPSC 5277

value: DO iPSC 5277

value: iPSC


title: RNA-seq_WT_rep4

value: wild type


title: DO iPSC line 4693, untreated

description: Library name: DO_iPSC_4693_CTRL

value: untreated


title: NT_A_LP1

description: Library name: RNA017361


title: Mock_B_LP1

description: Library name: RNA017360

value: Mock


title: DO iPSC line 4665, triphenyl phosphate treated

description: Library name: DO_iPSC_4665_TPHP

source_name: DO iPSC 4665

value: DO iPSC 4665

value: female


title: DO iPSC line 5258, triphenyl phosphate treated

description: Library name: DO_iPSC_5258_TPHP

source_name: DO iPSC 5258

value: DO iPSC 5258

value: triphenyl phosphate


title: RNA-seq_WT_rep3

value: Lin-cKit+Sca-1+ bone marrow cells


title: UPN827 cells, TN373 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN373 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: LINC00467_1_B_LP2

description: Library name: RNA017384


title: CTD-2349P21.9_1_C_LP2

description: Library name: RNA017365


title: RNA-seq_WT_rep2


title: DO iPSC line 4665, untreated

description: Library name: DO_iPSC_4665_CTRL


title: Mock_A_LP1

description: Library name: RNA017359


title: PoolCTL_B_LP1

description: Library name: RNA017358

value: PoolCTL


title: DO iPSC line 4656, triphenyl phosphate treated

description: Library name: DO_iPSC_4656_TPHP

source_name: DO iPSC 4656

value: DO iPSC 4656


title: UPN827 cells, TN372RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN372RH2 TrailNet Baseline T1D plasma


title: DO iPSC line 5243, triphenyl phosphate treated

description: Library name: DO_iPSC_5243_TPHP

source_name: DO iPSC 5243

value: DO iPSC 5243


title: UPN827 cells, TN371 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN371 TrailNet Baseline T1D plasma


title: RNA-seq_WT_rep1

source_name: Bone marrow


title: UPN827 cells, TN374 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN374 TrailNet Baseline T1D plasma


title: PoolCTL_A_LP1

description: Library name: RNA017357


title: Osgsk3 Osfca_3

city: nanjing

first: jiaqi

last: zhang

country: China

institute: nanjing agricultural university

description: Library name: Sample 9

data_processing:
The enriched libraries were quantified and sequenced on a DNBSEQ-T7 platform (MGI) using the PE150 sequencing mode to generate paired-end reads. The clean reads were aligned with reference sequences of rice in IRGSP-1.0 (http://rapdb.dna.affrc.go.jp/download/irgsp1.html). Differentially expressed genes (DEGs) were defined by absolute log2(Fold Change) > 1 and P value < 0.05.
Assembly: IRGSP-1.0 (http://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary files format and content: csv file includes reads counts for each Sample

organism: Oryza sativa

source_name: young panicles

growth_protocol: ZH11, Osfca, and Osgsk3 Osfca plants grown in the field at the Nanjing Baima Teaching and Research Base.

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent (Thermo Scientific, cat. #15596026) following the manufacturer's recommended protocol.
For library preparation, the total RNA was used as input for RNA sequencing library preparation utilizing the KCTM mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan, China), according to the manufacturer's instructions.

treatment_protocol: The young panicles were directly sampled for transcriptome analysis without any treatment.

tag: tissue

value: young panicles


title: UPN827 cells, TN370 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN370 TrailNet Baseline T1D plasma


title: DO iPSC line 4656, untreated

description: Library name: DO_iPSC_4656_CTRL

value: male


title: GAL4_B_LP1

description: Library name: RNA017356

value: embryonic kidney cell


title: Osgsk3 Osfca_2

description: Library name: Sample 8


title: DO iPSC line 4652, triphenyl phosphate treated

description: Library name: DO_iPSC_4652_TPHP

source_name: DO iPSC 4652

value: DO iPSC 4652

value: iPSC


title: GAL4_A_LP1

description: Library name: RNA017355


title: DO iPSC line 4652, untreated

description: Library name: DO_iPSC_4652_CTRL

value: untreated


title: UPN827 cells, TN393RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN393RH2 TrailNet Baseline T1D plasma


title: UPN827 cells, TN369 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN369 TrailNet Baseline T1D plasma


title: Osgsk3 Osfca_1

description: Library name: Sample 7


title: NEAT1_B_LP1

description: Library name: RNA017354


title: DO iPSC line 4617, triphenyl phosphate treated

description: Library name: DO_iPSC_4617_TPHP

source_name: DO iPSC 4617

value: DO iPSC 4617


title: UPN827 cells, TN368 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN368 TrailNet Baseline T1D plasma


title: Osfca_3

description: Library name: Sample 6


title: NEAT1_A_LP1

description: Library name: RNA017353


title: DO iPSC line 5234, untreated

description: Library name: DO_iPSC_5234_CTRL

source_name: DO iPSC 5234

value: DO iPSC 5234


title: UPN827 cells, TN367 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN367 TrailNet Baseline T1D plasma


title: Osfca_2

description: Library name: Sample 5


title: DO iPSC line 4617, untreated

description: Library name: DO_iPSC_4617_CTRL


title: DPH1_B_LP1

description: Library name: RNA017352


title: UPN827 cells, TN366 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN366 TrailNet Baseline T1D plasma


title: DO iPSC line 4580, triphenyl phosphate treated

description: Library name: DO_iPSC_4580_TPHP

source_name: DO iPSC 4580

value: DO iPSC 4580

value: female


title: Osfca_1

description: Library name: Sample 4


title: UPN827 cells, TN365 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN365 TrailNet Baseline T1D plasma


title: DPH1_A_LP1

description: Library name: RNA017351


title: ZH11_3

description: Library name: Sample 3


title: RP11-1055B8.9_A_LP4

description: Library name: RNA017507


title: DO iPSC line 4580, untreated

description: Library name: DO_iPSC_4580_CTRL


title: LINC00240_1_A_LP2

description: Library name: RNA017375


title: RP11-196G18.24_C_LP4

description: Library name: RNA017505


title: KO_L2C_RNA-seq_r3

city: Shanghai

first: Xinyu

address: Siping Road 1239

institute: Tongji University

description:
Library name: Sample25
KO L2C RNA-seq replicate3

data_processing:
RNA-seq: For raw paired-end RNA-seq reads, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. HISAT2 was used to align the clean sequence data to the mouse reference genome (mm10). StringTie was used to quantify gene expression from the aligned sequences for each gene, and htseq-count was used to count reads number for each gene. The mouse gene annotation file was obtained from the mouse GENCODE release (GRCm38.99).
Assembly: mm10
Supplementary files format and content: gene fpkm file

source_name: late 2-cell

growth_protocol: Specific pathogen-free (SPF) mice were housed in the animal facility at Tongji University,Shanghai, China, and they were fed a standard diet. The temperature and light were strictly controlled (24 °C; 12 h light and 12 h dark). Smarca4flox/flox mice are from previous study(Qi et al. 2021). All animal experiments were performed in accordance with the University of Health Guide for the Care and Use of Laboratory Animals and were approved by the Biological Research Ethics Committee of Tongji University. To get MII oocytes for ICSI, B6D2F1 or Smarca4flox/flox Gdf9 Cre C57BL/6 female mice (8–12-weeks old) were superovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later.

extract_protocol:
20-30 blastomere per replicate were isolated and washed before they were placed into 1.4 μL of lysis buffer (10 mM Tris-HCl, pH 8.5, 5 mM MgCl2, 0.6% NP-40) for individual reactions. Then, 1.8 μL of MNase master mix (MNase buffer, 0.125 U/μL MNase (NEB, M0247S), 2 mM DTT, and 5% PEG 6000) was added into each tube, and the reaction was incubated at 25 °C for 10 min for chromatin fragmentation. The reaction was stopped by the addition of 0.4 μL of 100 mM EDTA, and then 0.4 μL of 2% Triton X-100 was added to the reaction to release the fragmented chromatin. Then, 0.2 μL of 20 mg/mL protease (Qiagen) was added, and the reaction was incubated at 50 °C for 90 min for protein digestion followed by incubation at 75 °C for 30 min for protease inactivation. The sequencing libraries were prepared using the KAPA Hyper Prep kit for the Illumina platform (Roche, kk8504) following the manufacturer’s instructions. After standard procedures including end repair and A-tailing, adapter ligation, post-ligation cleanup, and library amplification, the resulting products were subjected to a second round of PCR amplification with the same provided primers to generate sufficient DNA materials for highthroughput sequencing.
For mouse embryos, the sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase(Kapa Biosystems, KK8483) and KAPA HyperPrep Kit for the Illumina platform (Roche, kk8504) following manufacturer’s protocol. Paired-end sequencing with 150-bp read length was performed on the HiSeq X Ten (Illumina) platform.

value: late 2-cell

value: Smarca4 KO


title: UPN827 cells, TN388 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN388 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 4577, triphenyl phosphate treated

description: Library name: DO_iPSC_4577_TPHP

source_name: DO iPSC 4577

value: DO iPSC 4577

value: triphenyl phosphate


title: ZH11_2

description: Library name: Sample 2


title: UPN827 cells, TN364 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN364 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: CTD-2017D11.1_1_C_LP1

description: Library name: RNA017349


title: DO iPSC line 4577, untreated

description: Library name: DO_iPSC_4577_CTRL


title: ZH11_1

description: Library name: Sample 1


title: UPN827 cells, TN363 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN363 TrailNet Baseline T1D plasma


title: DO iPSC line 4792, triphenyl phosphate treated

description: Library name: DO_iPSC_4792_TPHP

source_name: DO iPSC 4792

value: DO iPSC 4792


title: CTD-2017D11.1_1_B_LP1

description: Library name: RNA017348


title: DO iPSC line 3446, triphenyl phosphate treated

description: Library name: DO_iPSC_3446_TPHP

source_name: DO iPSC 3446

value: DO iPSC 3446


title: AC093642.3_D_LP1

description: Library name: RNA017346


title: UPN827 cells, TN361 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN361 TrailNet Baseline T1D plasma


title: DO iPSC line 3433, triphenyl phosphate treated

description: Library name: DO_iPSC_3433_TPHP

source_name: DO iPSC 3433

value: DO iPSC 3433

value: male


title: lncRNA profile of whole blood cells - SAMPLE 2-43

first: Chunxia

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: DO iPSC line 3446, untreated

description: Library name: DO_iPSC_3446_CTRL

value: iPSC

value: untreated


title: UPN827 cells, TN362 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN362 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 2-41

institute: 上海交通大学附属儿童医院

value: Non-bacterial sepsis


title: lncRNA profile of whole blood cells - SAMPLE 2-42

institute: 上海交通大学附属儿童医院


title: AC093642.3_C_LP1

description: Library name: RNA017345

value: embryonic kidney cell


title: UPN827 cells, TN360 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN360 TrailNet Baseline T1D plasma


title: DO iPSC line 3433, untreated

description: Library name: DO_iPSC_3433_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 2-40

institute: 上海交通大学附属儿童医院


title: AC093642.3_B_LP1

description: Library name: RNA017344


title: UPN827 cells, TN358 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN358 TrailNet Baseline T1D plasma


title: DO iPSC line 3413, triphenyl phosphate treated

description: Library name: DO_iPSC_3413_TPHP

source_name: DO iPSC 3413

value: DO iPSC 3413


title: lncRNA profile of whole blood cells - SAMPLE 2-39

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN386 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN386 TrailNet Baseline T1D plasma


title: AC093642.3_A_LP1

description: Library name: RNA017343


title: UPN827 cells, TN359 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN359 TrailNet Baseline T1D plasma


title: UPN827 cells, TN357 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN357 TrailNet Baseline T1D plasma


title: CTD-2017D11.1_1_D_LP1

description: Library name: RNA017350


title: DO iPSC line 3413, untreated

description: Library name: DO_iPSC_3413_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 2-38

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN356 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN356 TrailNet Baseline T1D plasma


title: CTC-459F4.3_1_D_LP1

description: Library name: RNA017342


title: CTC-459F4.3_1_C_LP1

description: Library name: RNA017341


title: DO iPSC line 3400, triphenyl phosphate treated

description: Library name: DO_iPSC_3400_TPHP

source_name: DO iPSC 3400

value: DO iPSC 3400


title: DO iPSC line 3400, untreated

description: Library name: DO_iPSC_3400_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 2-37

institute: 上海交通大学附属儿童医院


title: lncRNA profile of whole blood cells - SAMPLE 2-36

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN354 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN354 TrailNet Baseline T1D plasma


title: UPN827 cells, TN355 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN355 TrailNet Baseline T1D plasma


title: DO iPSC line 3397, triphenyl phosphate treated

description: Library name: DO_iPSC_3397_TPHP

source_name: DO iPSC 3397

value: DO iPSC 3397


title: CTC-459F4.3_1_B_LP1

description: Library name: RNA017340


title: CTD-2017D11.1_1_A_LP1

description: Library name: RNA017347


title: lncRNA profile of whole blood cells - SAMPLE 2-35

institute: 上海交通大学附属儿童医院


title: CTC-459F4.3_1_A_LP1

description: Library name: RNA017339


title: DO iPSC line 3397, untreated

description: Library name: DO_iPSC_3397_CTRL


title: AC093627.9_D_LP1

description: Library name: RNA017338


title: lncRNA profile of whole blood cells - SAMPLE 2-34

institute: 上海交通大学附属儿童医院


title: lncRNA profile of whole blood cells - SAMPLE 2-33

institute: 上海交通大学附属儿童医院


title: AC093627.9_C_LP1

description: Library name: RNA017337


title: DO iPSC line 3394, triphenyl phosphate treated

description: Library name: DO_iPSC_3394_TPHP

source_name: DO iPSC 3394

value: DO iPSC 3394


title: UPN827 cells, TN352rehyb TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN352rehyb TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN353 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN353 TrailNet Baseline T1D plasma


title: UPN827 cells, TN351 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN351 TrailNet Baseline T1D plasma


title: DO iPSC line 3394, untreated

description: Library name: DO_iPSC_3394_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 2-32

institute: 上海交通大学附属儿童医院

source_name: whole blood cells


title: AC093627.9_B_LP1

description: Library name: RNA017336


title: DO iPSC line 3379, triphenyl phosphate treated

description: Library name: DO_iPSC_3379_TPHP

source_name: DO iPSC 3379

value: DO iPSC 3379

value: triphenyl phosphate


title: AC093627.9_A_LP1

description: Library name: RNA017335


title: lncRNA profile of whole blood cells - SAMPLE 2-29

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3379, untreated

description: Library name: DO_iPSC_3379_CTRL


title: CTC-444N24.11_1_D_LP1

description: Library name: RNA017334


title: lncRNA profile of whole blood cells - SAMPLE 2-28

institute: 上海交通大学附属儿童医院


title: CTC-444N24.11_1_C_LP1

description: Library name: RNA017333


title: UPN827 cells, TN349 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN349 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 3376, untreated

description: Library name: DO_iPSC_3376_CTRL

source_name: DO iPSC 3376

value: DO iPSC 3376


title: UPN827 cells, TN350 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN350 TrailNet Baseline T1D plasma


title: UPN827 cells, TN346 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN346 TrailNet Baseline T1D plasma


title: UPN827 cells, TN348 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN348 TrailNet Baseline T1D plasma


title: DO iPSC line 3373, triphenyl phosphate treated

description: Library name: DO_iPSC_3373_TPHP

source_name: DO iPSC 3373

value: DO iPSC 3373


title: lncRNA profile of whole blood cells - SAMPLE 2-24

institute: 上海交通大学附属儿童医院


title: CTC-444N24.11_1_A_LP1

description: Library name: RNA017331


title: lncRNA profile of whole blood cells - SAMPLE 2-23

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN344RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN344RH2 TrailNet Baseline T1D plasma


title: UPN827 cells, TN345 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN345 TrailNet Baseline T1D plasma


title: DO iPSC line 3367, triphenyl phosphate treated

description: Library name: DO_iPSC_3367_TPHP

source_name: DO iPSC 3367

value: DO iPSC 3367

value: male


title: UPN827 cells, TN342 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN342 TrailNet Baseline T1D plasma


title: DO iPSC line 3367, untreated

description: Library name: DO_iPSC_3367_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 2-21

institute: 上海交通大学附属儿童医院

value: whole blood cells


title: AC093323.3_B_LP1

description: Library name: RNA017328


title: lncRNA profile of whole blood cells - SAMPLE 2-20

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3363, triphenyl phosphate treated

description: Library name: DO_iPSC_3363_TPHP

source_name: DO iPSC 3363

value: DO iPSC 3363

value: iPSC


title: UPN827 cells, TN341 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN341 TrailNet Baseline T1D plasma


title: AC093323.3_A_LP1

description: Library name: RNA017327


title: PVT1_D_LP4

description: Library name: RNA017486


title: KO_PN3_RNA-seq_r4

description:
Library name: Sample13
KO PN3 RNA-seq replicate4

source_name: PN3 stage zygote

value: PN3 stage zygote

value: Smarca4 KO


title: RNU11_D_LP4

description: Library name: RNA017494

value: embryonic kidney cell


title: DO iPSC line 3352, triphenyl phosphate treated

description: Library name: DO_iPSC_3352_TPHP

source_name: DO iPSC 3352

value: DO iPSC 3352


title: UPN827 cells, TN506 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN506 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 2-18

institute: 上海交通大学附属儿童医院

source_name: whole blood cells

value: Bacterial sepsis


title: UPN827 cells, TN338 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN338 TrailNet Baseline T1D plasma


title: DO iPSC line 3352, untreated

description: Library name: DO_iPSC_3352_CTRL

value: untreated


title: lncRNA profile of whole blood cells - SAMPLE 2-17

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3346, triphenyl phosphate treated

description: Library name: DO_iPSC_3346_TPHP

source_name: DO iPSC 3346

value: DO iPSC 3346


title: UPN827 cells, TN337 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN337 TrailNet Baseline T1D plasma

value: UPN827 cells


title: CTB-31O20.2_1_A_LP1

description: Library name: RNA017323


title: lncRNA profile of whole blood cells - SAMPLE 2-16

institute: 上海交通大学附属儿童医院

value: Non-bacterial sepsis


title: DO iPSC line 3346, untreated

description: Library name: DO_iPSC_3346_CTRL


title: DO iPSC line 3310, triphenyl phosphate treated

description: Library name: DO_iPSC_3310_TPHP

source_name: DO iPSC 3310

value: DO iPSC 3310

value: triphenyl phosphate


title: UPN827 cells, TN334 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN334 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 3310, untreated

description: Library name: DO_iPSC_3310_CTRL


title: UPN827 cells, TN333 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN333 TrailNet Baseline T1D plasma


title: AC084082.3_B_LP1

description: Library name: RNA017320


title: DO iPSC line 3307, triphenyl phosphate treated

description: Library name: DO_iPSC_3307_TPHP

source_name: DO iPSC 3307

value: DO iPSC 3307


title: lncRNA profile of whole blood cells - SAMPLE 2-12

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN332 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN332 TrailNet Baseline T1D plasma


title: AC084082.3_A_LP1

description: Library name: RNA017319


title: DO iPSC line 3307, untreated

description: Library name: DO_iPSC_3307_CTRL

value: male


title: lncRNA profile of whole blood cells - SAMPLE 2-11

institute: 上海交通大学附属儿童医院

value: whole blood cells


title: CTA-342B11.2_D_LP1

description: Library name: RNA017318


title: UPN827 cells, TN343 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN343 TrailNet Baseline T1D plasma


title: AC093323.3_D_LP1

description: Library name: RNA017330


title: AC093323.3_C_LP1

description: Library name: RNA017329


title: UPN827 cells, TN330 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN330 TrailNet Baseline T1D plasma


title: UPN827 cells, TN339 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN339 TrailNet Baseline T1D plasma


title: CTA-342B11.2_C_LP1

description: Library name: RNA017317


title: lncRNA profile of whole blood cells - SAMPLE 2-19

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3304, untreated

description: Library name: DO_iPSC_3304_CTRL

source_name: DO iPSC 3304

value: DO iPSC 3304


title: CTB-31O20.2_1_C_LP1

description: Library name: RNA017325


title: lncRNA profile of whole blood cells - SAMPLE 2-9

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN329 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN329 TrailNet Baseline T1D plasma


title: CTB-31O20.2_1_B_LP1

description: Library name: RNA017324


title: UPN827 cells, TN336 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN336 TrailNet Baseline T1D plasma


title: CTA-342B11.2_B_LP1

description: Library name: RNA017316


title: DO iPSC line 3302, triphenyl phosphate treated

description: Library name: DO_iPSC_3302_TPHP

source_name: DO iPSC 3302

value: DO iPSC 3302

value: iPSC


title: lncRNA profile of whole blood cells - SAMPLE 2-8

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN328 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN328 TrailNet Baseline T1D plasma


title: UPN827 cells, TN335 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN335 TrailNet Baseline T1D plasma


title: CTA-342B11.2_A_LP1

description: Library name: RNA017315


title: lncRNA profile of whole blood cells - SAMPLE 2-7

institute: 上海交通大学附属儿童医院

source_name: whole blood cells


title: DO iPSC line 3302, untreated

description: Library name: DO_iPSC_3302_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 2-14

institute: 上海交通大学附属儿童医院


title: AC007405.6_D_LP1

description: Library name: RNA017314


title: AC007405.6_C_LP1

description: Library name: RNA017313


title: UPN827 cells, TN326 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN326 TrailNet Baseline T1D plasma


title: DO iPSC line 3298, untreated

description: Library name: DO_iPSC_3298_CTRL

source_name: DO iPSC 3298

value: DO iPSC 3298


title: lncRNA profile of whole blood cells - SAMPLE 2-5

institute: 上海交通大学附属儿童医院


title: AC007405.6_B_LP1

description: Library name: RNA017312

value: embryonic kidney cell


title: UPN827 cells, TN325 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN325 TrailNet Baseline T1D plasma


title: DO iPSC line 3283, triphenyl phosphate treated

description: Library name: DO_iPSC_3283_TPHP

source_name: DO iPSC 3283

value: DO iPSC 3283


title: AC007405.6_A_LP1

description: Library name: RNA017311


title: DO iPSC line 3283, untreated

description: Library name: DO_iPSC_3283_CTRL


title: CRNDE_D_LP1

description: Library name: RNA017310

value: CRNDE


title: DO iPSC line 3274, triphenyl phosphate treated

description: Library name: DO_iPSC_3274_TPHP

source_name: DO iPSC 3274

value: DO iPSC 3274


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

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN322 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN322 TrailNet Baseline T1D plasma


title: UPN827 cells, TN323 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN323 TrailNet Baseline T1D plasma


title: DO iPSC line 3274, untreated

description: Library name: DO_iPSC_3274_CTRL

value: untreated


title: UPN827 cells, TN321 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN321 TrailNet Baseline T1D plasma

value: UPN827 cells


title: lncRNA profile of whole blood cells - SAMPLE 2-1

institute: 上海交通大学附属儿童医院

value: Bacterial sepsis


title: UPN827 cells, TN320 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN320 TrailNet Baseline T1D plasma


title: DO iPSC line 3268, triphenyl phosphate treated

description: Library name: DO_iPSC_3268_TPHP

source_name: DO iPSC 3268

value: DO iPSC 3268


title: CRNDE_A_LP1

description: Library name: RNA017307


title: DO iPSC line 3298, triphenyl phosphate treated

description: Library name: DO_iPSC_3298_TPHP

value: triphenyl phosphate


title: DO iPSC line 3268, untreated

description: Library name: DO_iPSC_3268_CTRL


title: UPN827 cells, TN319 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN319 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: lncRNA profile of whole blood cells - SAMPLE 1-18

institute: 上海交通大学附属儿童医院


title: AC007405.4_D_LP1

description: Library name: RNA017306


title: DO iPSC line 3265, triphenyl phosphate treated

description: Library name: DO_iPSC_3265_TPHP

source_name: DO iPSC 3265

value: DO iPSC 3265


title: UPN827 cells, TN318 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN318 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 1-14

institute: 上海交通大学附属儿童医院

value: Non-bacterial sepsis


title: AC007405.4_C_LP1

description: Library name: RNA017305


title: DO iPSC line 3265, untreated

description: Library name: DO_iPSC_3265_CTRL

value: male


title: lncRNA profile of whole blood cells - SAMPLE 1-13

institute: 上海交通大学附属儿童医院

value: whole blood cells


title: AC007405.4_B_LP1

description: Library name: RNA017304


title: UPN827 cells, TN316 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN316 TrailNet Baseline T1D plasma


title: DO iPSC line 3262, triphenyl phosphate treated

description: Library name: DO_iPSC_3262_TPHP

source_name: DO iPSC 3262

value: DO iPSC 3262


title: lncRNA profile of whole blood cells - SAMPLE 1-12

institute: 上海交通大学附属儿童医院


title: AC007405.4_A_LP1

description: Library name: RNA017303


title: UPN827 cells, TN315 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN315 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 1-11

institute: 上海交通大学附属儿童医院

source_name: whole blood cells


title: Control group,patient5,6month follow-up

city: Kunming

first: Min

last: Zhang

address: No. 295, Xichang Road

institute: The First Affiliated Hospital of Kunming Medical University

description: Library name: Control_05_Baseline

data_processing:
Raw reads were quality controlled and trimmed using fastp (version 0.22.0).
Trimmed reads were aligned to the human reference genome (hg38) using Bismark (with bowtie2).
Methylation calling and differential methylation analysis (DMS/DMR) were performed using DSS (Dispersion Shrinkage for Sequencing), with significance thresholds set at FDR < 0.05 and absolute methylation difference ≥ 3%.
DMS/DMR were annotated to gene regions using ChIPseeker.
Pathway enrichment analysis (KEGG/GO) and protein-protein interaction (PPI) networks were constructed via clusterProfiler, STRING, and Cytoscape. Public transcriptomic data (GSE208194)  were integrated to validate methylation-transcription associations in myocardial remodeling pathways.
Assembly: hg38
Supplementary files format and content: The complete methylation site matrix, generated after Bismark processing and quality control, is stored in TXT format.

source_name: blood

extract_protocol:
Genomic DNA was extracted from whole blood using the QIAamp DNA Blood Mini Kit. DNA integrity was verified via agarose gel electrophoresis, with only samples showing clear bands retained for analysis.
RRBS libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System. Briefly, genomic DNA was digested with MspI, end-repaired, A-tailed, and ligated to methylated adapters. Bisulfite conversion was performed using the EZ DNA Methylation-Lightning Kit. Libraries were amplified by PCR and size-selected (40-220 bp).

treatment_protocol: Bisulfite conversion and RRBS library preparation

value: blood

value: buffy coat cells

tag: group

value: Control sample

tag: time point

value: 6month follow-up


title: DO iPSC line 3256, triphenyl phosphate treated

description: Library name: DO_iPSC_3256_TPHP

source_name: DO iPSC 3256

value: DO iPSC 3256

value: iPSC


title: lncRNA profile of whole blood cells - SAMPLE 1-10

institute: 上海交通大学附属儿童医院


title: Control group,patient4,6month follow-up

description: Library name: Control_04_Baseline

growth_protocol: Genomic DNA was extracted from whole blood using the QIAamp DNA Blood Mini Kit. DNA integrity was verified via agarose gel electrophoresis, with only samples showing clear bands retained for analysis.


title: UPN827 cells, TN327 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN327 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 2-6

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3262, untreated

description: Library name: DO_iPSC_3262_CTRL

value: untreated


title: UPN827 cells, TN313 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN313 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 3256, untreated

description: Library name: DO_iPSC_3256_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 2-4

institute: 上海交通大学附属儿童医院

value: Bacterial sepsis


title: lncRNA profile of whole blood cells - SAMPLE 1-9

institute: 上海交通大学附属儿童医院


title: Control group,patient3,6month follow-up

description: Library name: Control_03_Baseline


title: UPN827 cells, TN324 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN324 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 2-3

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3253, triphenyl phosphate treated

description: Library name: DO_iPSC_3253_TPHP

source_name: DO iPSC 3253

value: DO iPSC 3253


title: lncRNA profile of whole blood cells - SAMPLE 1-8

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN314 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN314 TrailNet Baseline T1D plasma


title: Control group,patient2,6month follow-up

description: Library name: Control_02_Baseline


title: UPN827 cells, TN312 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN312 TrailNet Baseline T1D plasma


title: DO iPSC line 3253, untreated

description: Library name: DO_iPSC_3253_CTRL


title: lncRNA profile of whole blood cells - SAMPLE 1-7

institute: 上海交通大学附属儿童医院


title: UPN827 cells, TN311RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN311RH2 TrailNet Baseline T1D plasma


title: CRNDE_C_LP1

description: Library name: RNA017309

value: embryonic kidney cell

value: CRNDE


title: Control group,patient1,6month follow-up

description: Library name: Control_01_Baseline


title: lncRNA profile of whole blood cells - SAMPLE 1-6

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3250, triphenyl phosphate treated

description: Library name: DO_iPSC_3250_TPHP

source_name: DO iPSC 3250

value: DO iPSC 3250

value: triphenyl phosphate


title: MBSR group, patient 5, 6month follow-up

description: Library name: MBSR_05_6month

value: Post-MBSR sample


title: UPN827 cells, TN310 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN310 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 3250, untreated

description: Library name: DO_iPSC_3250_CTRL

value: male


title: MBSR group, patient 5, baseline

description: Library name: MBSR_05_Baseline

value: blood

value: Pre-MBSR sample

value: baseline


title: lncRNA profile of whole blood cells - SAMPLE 1-5

institute: 上海交通大学附属儿童医院

value: whole blood cells


title: CRNDE_B_LP1

description: Library name: RNA017308


title: UPN827 cells, TN309 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN309 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 1-4

institute: 上海交通大学附属儿童医院


title: DO iPSC line 3247, triphenyl phosphate treated

description: Library name: DO_iPSC_3247_TPHP

source_name: DO iPSC 3247

value: DO iPSC 3247


title: UPN827 cells, TN308 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN308 TrailNet Baseline T1D plasma


title: MBSR group, patient 4, 6month follow-up

description: Library name: MBSR_04_6month

value: buffy coat cells

value: 6month follow-up


title: DO iPSC line 3247, untreated

description: Library name: DO_iPSC_3247_CTRL

value: iPSC

value: untreated


title: lncRNA profile of whole blood cells - SAMPLE 1-3

institute: 上海交通大学附属儿童医院

value: Bacterial sepsis


title: UPN827 cells, TN307 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN307 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 3244, triphenyl phosphate treated

description: Library name: DO_iPSC_3244_TPHP

source_name: DO iPSC 3244

value: DO iPSC 3244


title: MBSR group, patient 4, baseline

description: Library name: MBSR_04_Baseline


title: UPN827 cells, TN306 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN306 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 1-2

institute: 上海交通大学附属儿童医院

source_name: whole blood cells


title: MBSR group, patient 3, 6month follow-up

description: Library name: MBSR_03_6month

source_name: blood


title: DO iPSC line 3244, untreated

description: Library name: DO_iPSC_3244_CTRL


title: UPN827 cells, TN305 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN305 TrailNet Baseline T1D plasma


title: lncRNA profile of whole blood cells - SAMPLE 1-16

institute: 上海交通大学附属儿童医院


title: lncRNA profile of whole blood cells - SAMPLE 1-1

institute: 上海交通大学附属儿童医院


title: MBSR group, patient 3, baseline

description: Library name: MBSR_03_Baseline


title: DM_RH_3,3 days

city: 昆明

first: 贝贝

last: 邓

address: 云南大学呈贡校区

institute: 云南大学

description: Library name: DM_RH_3

data_processing:
RSEM
Assembly: TAIR10.1
Supplementary files format and content: gene.tpm.matrix.annot.xls files are files in excel format that quantify the expression levels of genes

organism: Arabidopsis

source_name: seedling

growth_protocol: Plants were grown on half-strength MS (½MS) medium with 1.2% (w/v) sucrose.

extract_protocol:
1. Extract total RNA 2. Oligo dT enrichment of mRNA 3. Fragmented mRNA 4. Invert the synthetic cDNA
Illumina TruseqTM RNA sample prep Kit

treatment_protocol: Some of the materials are treated at a high temperature of 37°C

value: seedling


title: MBSR group, patient 2, 6month follow-up

description: Library name: MBSR_02_6month


title: DO iPSC line 2588, triphenyl phosphate treated

description: Library name: DO_iPSC_2588_TPHP

source_name: DO iPSC 2588

value: DO iPSC 2588

value: triphenyl phosphate


title: UPN827 cells, TN304 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN304 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: DO iPSC line 2588, untreated

description: Library name: DO_iPSC_2588_CTRL

value: male


title: DM_RH_2,3 days

description: Library name: DM_RH_2


title: UPN827 cells, TN302 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN302 TrailNet Baseline T1D plasma


title: MBSR group, patient 2, baseline

description: Library name: MBSR_02_Baseline

value: blood


title: DO iPSC line 2574, triphenyl phosphate treated

description: Library name: DO_iPSC_2574_TPHP

source_name: DO iPSC 2574

value: DO iPSC 2574


title: DM_RH_1,3 days

description: Library name: DM_RH_1


title: UPN827 cells, TN301 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN301 TrailNet Baseline T1D plasma


title: MBSR group, patient 1, 6month follow-up

description: Library name: MBSR_01_6month

value: Post-MBSR sample


title: DO iPSC line 2574, untreated

description: Library name: DO_iPSC_2574_CTRL


title: DM_CO_3,control

description: Library name: DM_CO_3


title: MBSR group, patient 1, baseline

description: Library name: MBSR_01_Baseline

value: Pre-MBSR sample

value: baseline


title: UPN827 cells, TN300 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN300 TrailNet Baseline T1D plasma


title: DO iPSC line 2568, triphenyl phosphate treated

description: Library name: DO_iPSC_2568_TPHP

source_name: DO iPSC 2568

value: DO iPSC 2568


title: DM_CO_2,control

description: Library name: DM_CO_2


title: UPN827 cells, TN299 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN299 TrailNet Baseline T1D plasma


title: THP-1-PTX4-OE replicate 3

city: singapore

first: yi

last: chai

department: CSI

country: Singapore

institute: National University of SIngapore

description:
Library name: OE_3
RNA-seq of THP-1 cells overexpressing PTX4

data_processing:
Raw RNA-seq reads were assessed for quality using FastQC v0.11.5
Adaptor sequences, contaminants, and low-quality reads were trimmed
Trimmed reads were aligned to the reference genome using STAR aligner
Gene expression quantification was performed using featureCounts
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text files containing gene expression counts (rows: genes, columns: samples)
Supplementary files format and content: Tab-delimited text files containing normalized expression values (FPKM/TPM)

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. RNA quality and quantity were assessed using NanoDrop and Bioanalyzer.
RNA library construction was performed by Novogene Singapore. Briefly, mRNA was enriched using oligo(dT) beads, fragmented, and reverse transcribed to cDNA. Libraries were prepared following Illumina's protocol with adaptor ligation and PCR amplification.

treatment_protocol: THP-1 cells were stably transduced with either empty vector (EV) or PTX4 overexpression construct (PTX4-OE). Three biological replicates were prepared for each condition.

value: PTX4 overexpression


title: UPN827 cells, TN317 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN317 TrailNet Baseline T1D plasma


title: DO iPSC line 2568, untreated

description: Library name: DO_iPSC_2568_CTRL

value: iPSC


title: DM_CO_1,control

description: Library name: DM_CO_1


title: UPN827 cells, TN298 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN298 TrailNet Baseline T1D plasma


title: THP-1-PTX4-OE replicate 2

description:
Library name: OE_2
RNA-seq of THP-1 cells overexpressing PTX4


title: DO iPSC line 2564, triphenyl phosphate treated

description: Library name: DO_iPSC_2564_TPHP

source_name: DO iPSC 2564

value: DO iPSC 2564


title: WT_RH_3,3 days

description: Library name: WT_RH_3


title: UPN827 cells, TN297 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN297 TrailNet Baseline T1D plasma


title: THP-1-PTX4-OE replicate 1

description:
Library name: OE_1
RNA-seq of THP-1 cells overexpressing PTX4


title: DO iPSC line 2564, untreated

description: Library name: DO_iPSC_2564_CTRL

value: untreated


title: WT_RH_2,3 days

description: Library name: WT_RH_2


title: UPN827 cells, TN296 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN296 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 2556, triphenyl phosphate treated

description: Library name: DO_iPSC_2556_TPHP

source_name: DO iPSC 2556

value: DO iPSC 2556

value: female


title: WT_RH_1,3 days

description: Library name: WT_RH_1

value: seedling


title: UPN827 cells, TN295 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN295 TrailNet Baseline T1D plasma


title: THP-1-EV replicate 2

description:
Library name: EV_2
RNA-seq of THP-1 cells with empty vector control

value: empty vector


title: THP-1-EV replicate 3

description:
Library name: EV_3
RNA-seq of THP-1 cells with empty vector control


title: DO iPSC line 2556, untreated

description: Library name: DO_iPSC_2556_CTRL


title: WT_CO_3,control

description: Library name: WT_CO_3


title: UPN827 cells, TN293 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN293 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: THP-1-EV replicate 1

description:
Library name: EV_1
RNA-seq of THP-1 cells with empty vector control


title: DO iPSC line 2548, triphenyl phosphate treated

description: Library name: DO_iPSC_2548_TPHP

source_name: DO iPSC 2548

value: DO iPSC 2548

value: triphenyl phosphate


title: UPN827 cells, TN292 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN292 TrailNet Baseline T1D plasma


title: WT_CO_2,control

description: Library name: WT_CO_2

source_name: seedling


title: WT_CO_1,control

description: Library name: WT_CO_1


title: DO iPSC line 2548, untreated

description: Library name: DO_iPSC_2548_CTRL


title: HCT116-OXR oxaliplatin-resistant cells, biological replicate 2

city: Shijiazhuang

first: Tianyang

state: Hebei province

address: Heping West Road No. 215

department: Department of Hepatobiliary Surgery

institute: The Second Hospital of Hebei Medical University

description:
Library name: HCT116OXR_Rep2
Oxaliplatin-resistant HCT116-OXR cells established through 6-month stepwise dose escalation

data_processing:
Raw sequencing reads (FASTQ files) were quality-controlled using FastQC. Reads were aligned to the human reference genome (GRCh38.p13) using STAR aligner (version 2.7.7a) with default parameters. Gene expression quantification was performed using featureCounts or HTSeq to generate raw read counts for each gene.
Differential expression analysis was performed using DESeq2 (version 1.44.0). Genes with |log2 fold change| > 0.5 and false discovery rate (FDR) < 0.05 were considered significantly differentially expressed. The Benjamini-Hochberg method was used for multiple testing correction.
Normalized expression values (TPM or FPKM) were calculated for visualization and downstream analysis.
Gene Ontology (GO) and KEGG pathway enrichment analyses were performed using clusterProfiler (version 4.4.0).
Assembly: GRCh38.p13 (Homo sapiens)
Supplementary files format and content: Tab-delimited text files containing gene expression counts. Each file includes gene identifiers (ENSEMBL gene IDs or gene symbols) in the first column and raw read counts in subsequent columns. Files are named according to sample ID (e.g., HCT116_Rep1_counts.txt).

molecule: polyA RNA

growth_protocol: HCT116 cells were cultured in high-glucose Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2 and routinely subcultured every 72 hours with fresh medium changes.

extract_protocol:
Total RNA was isolated from cultured cells using TRIzol reagent following the manufacturer's instructions. RNA concentration and purity were measured with a NanoDrop 2000 spectrophotometer. RNA integrity was assessed to ensure high-quality samples for sequencing (RIN > 8.0).
RNA-seq libraries were constructed using standard Illumina protocols for poly(A) selected RNA. Briefly, mRNA was purified from total RNA using oligo-dT beads, fragmented, and reverse transcribed to generate first-strand cDNA using random hexamer primers. Second-strand cDNA was synthesized, end-repaired, A-tailed, and ligated with Illumina sequencing adapters. Libraries were PCR amplified, size-selected, and quality-checked before sequencing on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: Oxaliplatin-resistant cell lines (HCT116-OXR) were established through stepwise dose escalation over 6 months. Logarithmic growth phase HCT116 cells were initially exposed to 0.2 μM oxaliplatin for 5-7 days until growth recovery. The oxaliplatin concentration was progressively increased to a final concentration of 20 μM, with cells achieving stable growth at each concentration level before escalation. Resistant cells were maintained in medium containing oxaliplatin to preserve the resistant phenotype. Parental HCT116 cells were cultured in parallel without oxaliplatin treatment.

value: colorectal cancer cell

value: chronic oxaliplatin exposure (6 months dose escalation to 20 μM)


title: UPN827 cells, TN291 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN291 TrailNet Baseline T1D plasma


title: HCT116-OXR oxaliplatin-resistant cells, biological replicate 3

description:
Library name: HCT116OXR_Rep3
Oxaliplatin-resistant HCT116-OXR cells established through 6-month stepwise dose escalation


title: HCT116-OXR oxaliplatin-resistant cells, biological replicate 1

description:
Library name: HCT116OXR_Rep1
Oxaliplatin-resistant HCT116-OXR cells established through 6-month stepwise dose escalation


title: UPN827 cells, TN290 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN290 TrailNet Baseline T1D plasma


title: CPP, Cas9 experiment, Cas9 RNP with AAVS1 gRNA, rep3

city: Bethlehem

first: Joshua

last: Graham

state: PA

address: 124 E Morton st

institute: Lehigh University

description: Library name: CPP_RNP_Cas9_3

data_processing:
fastq files were processed using kallisto with mapping to the Ensembl human reference transcriptome (GRCh38, release 111, cDNA, all transcripts)
Assembly: GRCh38, release 111, cDNA, all transcripts
Supplementary files format and content: .h5a

source_name: Mesenchymal Stem Cell

extract_protocol:
Trizol / Purelink RNA minikit (Thermo Fisher)
Novogene mRNA library preparation (polyA enrichement)

value: Mesenchymal Stem Cell

value: CPP/ Cas9 RNP w/ AAVS1 gRNA


title: DO iPSC line 2544, triphenyl phosphate treated

description: Library name: DO_iPSC_2544_TPHP

source_name: DO iPSC 2544

value: DO iPSC 2544


title: CPP, Cas9 experiment, Cas9 RNP with AAVS1 gRNA, rep2

description: Library name: CPP_RNP_Cas9_2


title: DO iPSC line 2544, untreated

description: Library name: DO_iPSC_2544_CTRL


title: HCT116 parental cells, biological replicate 3

description:
Library name: HCT116_Rep3
Parental HCT116 colorectal cancer cells without oxaliplatin resistance

value: none (parental control)


title: DO iPSC line 2536, triphenyl phosphate treated

description: Library name: DO_iPSC_2536_TPHP

source_name: DO iPSC 2536

value: DO iPSC 2536

value: iPSC


title: CPP, Cas9 experiment, Cas9 RNP with AAVS1 gRNA, rep1

description: Library name: CPP_RNP_Cas9_1


title: HCT116 parental cells, biological replicate 2

description:
Library name: HCT116_Rep2
Parental HCT116 colorectal cancer cells without oxaliplatin resistance


title: UPN827 cells, TN289 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN289 TrailNet Baseline T1D plasma


title: UPN827 cells, TN288 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN288 TrailNet Baseline T1D plasma


title: DO iPSC line 2536, untreated

description: Library name: DO_iPSC_2536_CTRL

value: untreated


title: CPP, Cas9 experiment,  Cas9 mRNA, AAVS1 gRNA, rep3

description: Library name: CPP_mRNA_Cas9_3

value: CPP/ Cas9 mRNA /AAVS1 gRNA


title: HCT116 parental cells, biological replicate 1

description:
Library name: HCT116_Rep1
Parental HCT116 colorectal cancer cells without oxaliplatin resistance


title: DO iPSC line 2534, triphenyl phosphate treated

description: Library name: DO_iPSC_2534_TPHP

source_name: DO iPSC 2534

value: DO iPSC 2534


title: CPP, Cas9 experiment, Cas9 mRNA, AAVS1 gRNA, rep2

description: Library name: CPP_mRNA_Cas9_2


title: GS304_BSA_biol rep2

city: CA

first: Weaverly Colleen

last: Lee

address: 327 Campus Drive

department: Biology Department

institute: Stanford University

description: Library name: B15

data_processing:
Basecalls were performed using CASAVA
From Novogene's 'Data Quality Control' methods: "Raw data (raw reads) of fastq 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."
From Novogene's 'Readsmapping to the reference genome' methods: "Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools."
From Novogene's 'Quantification of gene expression level' methods: "featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene."
From Novogene's 'Quantification of gene expression level' methods: "FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels."
Assembly: Homo sapiens hg38
Supplementary files format and content: FPKM values for each gene

source_name: brain

growth_protocol: Patient derived glioblastoma neurospheres were established and maintained in gliomasphere conditions consisting of DMEM/ F12, B27, pencillin-streptomycin, and GlutaMAX supplemented with heparin (5 μg/mL, Sigma), EGF (20 ng/mL, Sigma), and FGF (20 ng/mL, Sigma)

extract_protocol:
After 24h of incubation with the protein ligands, the neurospheres were collected by centrifugation, washed, then extracted using the Qiagen Rneasy Plus Mini Kit (cat. No. 74143) per manufacturer’s instructions.
From Novogene's methods: "Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification."

treatment_protocol: Neurospheres were plated in ultra low adherent 6-well plates at a density of 500,000 cells/ well in 2mL. The following day, 100 ng/ mL of the recombinant protein ligands were added to the growth medium.

value: brain

value: BSA


title: UPN827 cells, TN287 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN287 TrailNet Baseline T1D plasma

value: UPN827 cells


title: DO iPSC line 2534, untreated

description: Library name: DO_iPSC_2534_CTRL

value: female


title: CPP, Cas9 experiment, Cas9 mRNA, AAVS1 gRNA, rep1

description: Library name: CPP_mRNA_Cas9_1


title: UPN827 cells, TN286 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN286 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: GS304_OSM_biol rep2

description: Library name: B14

value: OSM


title: DO iPSC line 2530, triphenyl phosphate treated

description: Library name: DO_iPSC_2530_TPHP

source_name: DO iPSC 2530

value: DO iPSC 2530

value: triphenyl phosphate

value: male


title: UPN827 cells, TN285 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN285 TrailNet Baseline T1D plasma


title: Non-transfected, Cas9 experiment, rep3

description: Library name: NC_Cas9_3

value: Mesenchymal Stem Cell

value: Non-transfected


title: GS304_LIF_biol rep2

description: Library name: B13

value: LIF


title: UPN827 cells, TN284 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN284 TrailNet Baseline T1D plasma


title: UPN827 cells, TN340 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN340 TrailNet Baseline T1D plasma


title: DO iPSC line 2530, untreated

description: Library name: DO_iPSC_2530_CTRL


title: UPN827 cells, TN283 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN283 TrailNet Baseline T1D plasma


title: Non-transfected, Cas9 experiment, rep2

description: Library name: NC_Cas9_2


title: GS304_IL6_biol rep2

description: Library name: B12


title: DO iPSC line 2524, triphenyl phosphate treated

description: Library name: DO_iPSC_2524_TPHP

source_name: DO iPSC 2524

value: DO iPSC 2524


title: Non-transfected, Cas9 experiment, rep1

description: Library name: NC_Cas9_1


title: GS304_BMP4_biol rep2

description: Library name: B11


title: DO iPSC line 2524, untreated

description: Library name: DO_iPSC_2524_CTRL

value: iPSC


title: GS304_BMP3_biol rep2

description: Library name: B10


title: UPN827 cells, TN282 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN282 TrailNet Baseline T1D plasma


title: Etoposide treatment, GFP experiment, rep3

description: Library name: Etoposide_GFP3

value: Etoposide


title: UPN827 cells, TN281 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN281 TrailNet Baseline T1D plasma


title: DO iPSC line 2520, triphenyl phosphate treated

description: Library name: DO_iPSC_2520_TPHP

source_name: DO iPSC 2520

value: DO iPSC 2520


title: Etoposide treatment, GFP experiment, rep2

description: Library name: Etoposide_GFP2

source_name: Mesenchymal Stem Cell


title: UPN827 cells, TN280 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN280 TrailNet Baseline T1D plasma


title: GS304_BMP2_biol rep2

description: Library name: B9


title: DO iPSC line 2520, untreated

description: Library name: DO_iPSC_2520_CTRL

value: untreated


title: Etoposide treatment, GFP experiment, rep1

description: Library name: Etoposide_GFP1


title: GS025_BSA_biol rep2

description: Library name: B7

value: brain


title: UPN827 cells, TN279 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN279 TrailNet Baseline T1D plasma


title: DO iPSC line 2516, triphenyl phosphate treated

description: Library name: DO_iPSC_2516_TPHP

source_name: DO iPSC 2516

value: DO iPSC 2516


title: GS025_OSM_biol rep2

description: Library name: B6


title: Electro, GFP experiment, rep3

description: Library name: Electro_GFP3

value: Electro/ GFP mRNA


title: DO iPSC line 2516, untreated

description: Library name: DO_iPSC_2516_CTRL


title: UPN827 cells, TN277 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN277 TrailNet Baseline T1D plasma

value: UPN827 cells


title: UPN827 cells, TN278 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN278 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: Electro, GFP experiment, rep2

description: Library name: Electro_GFP2


title: GS025_LIF_biol rep2

description: Library name: B5

source_name: brain


title: DO iPSC line 2496, triphenyl phosphate treated

description: Library name: DO_iPSC_2496_TPHP

source_name: DO iPSC 2496

value: DO iPSC 2496

value: female


title: GS025_IL6_biol rep2

description: Library name: B4


title: Electro, GFP experiment, rep1

description: Library name: Electro_GFP1


title: DO iPSC line 2496, untreated

description: Library name: DO_iPSC_2496_CTRL


title: Polymer, GFP experiment, rep3

description: Library name: Polymer_GFP3

value: PEI/ GFP mRNA


title: GS025_BMP4_biol rep2

description: Library name: B3


title: UPN827 cells, TN275 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN275 TrailNet Baseline T1D plasma


title: UPN827 cells, TN276 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN276 TrailNet Baseline T1D plasma


title: DO iPSC line 2491, triphenyl phosphate treated

description: Library name: DO_iPSC_2491_TPHP

source_name: DO iPSC 2491

value: DO iPSC 2491

value: triphenyl phosphate


title: Polymer, GFP experiment, rep2

description: Library name: Polymer_GFP2

value: Mesenchymal Stem Cell


title: GS025_BMP2_biol rep2

description: Library name: B1


title: UPN827 cells, TN274 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN274 TrailNet Baseline T1D plasma


title: DO iPSC line 2491, untreated

description: Library name: DO_iPSC_2491_CTRL


title: Polymer, GFP experiment, rep1

description: Library name: Polymer_GFP1


title: DO iPSC line 2488, triphenyl phosphate treated

description: Library name: DO_iPSC_2488_TPHP

source_name: DO iPSC 2488

value: DO iPSC 2488


title: Lipid, GFP experiment, rep3

description: Library name: Lipid_GFP3

value: Lipofectamine/ GFP mRNA


title: GS304_OSM_biol rep1

description: Library name: A14

value: OSM


title: DO iPSC line 2488, untreated

description: Library name: DO_iPSC_2488_CTRL

value: iPSC


title: UPN827 cells, TN272 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN272 TrailNet Baseline T1D plasma


title: Lipid, GFP experiment, rep2

description: Library name: Lipid_GFP2


title: GS304_BSA_biol rep1

description: Library name: A15

value: BSA


title: GS304_LIF_biol rep1

description: Library name: A13

value: LIF


title: UPN827 cells, TN273 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN273 TrailNet Baseline T1D plasma


title: UPN827 cells, TN271 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN271 TrailNet Baseline T1D plasma


title: DO iPSC line 2483, triphenyl phosphate treated

description: Library name: DO_iPSC_2483_TPHP

source_name: DO iPSC 2483

value: DO iPSC 2483


title: Lipid, GFP experiment, rep1

description: Library name: Lipid_GFP1

source_name: Mesenchymal Stem Cell


title: UPN827 cells, TN270 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN270 TrailNet Baseline T1D plasma


title: GS304_IL6_biol rep1

description: Library name: A12

value: brain


title: DO iPSC line 2483, untreated

description: Library name: DO_iPSC_2483_CTRL

value: untreated


title: CPP, GFP experiment, rep3

description: Library name: CPP_GFP3

value: CPP/ GFP mRNA


title: GS304_BMP4_biol rep1

description: Library name: A11


title: DO iPSC line 2475, triphenyl phosphate treated

description: Library name: DO_iPSC_2475_TPHP

source_name: DO iPSC 2475

value: DO iPSC 2475


title: UPN827 cells, TN269 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN269 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: GS304_BMP3_biol rep1

description: Library name: A10


title: CPP, GFP experiment, rep2

description: Library name: CPP_GFP2


title: DO iPSC line 2475, untreated

description: Library name: DO_iPSC_2475_CTRL

value: female


title: UPN827 cells, TN268 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN268 TrailNet Baseline T1D plasma


title: GS304_BMP2_biol rep1

description: Library name: A9


title: DO iPSC line 2472, triphenyl phosphate treated

description: Library name: DO_iPSC_2472_TPHP

source_name: DO iPSC 2472

value: DO iPSC 2472


title: CPP, GFP experiment, rep1

description: Library name: CPP_GFP1


title: UPN827 cells, TN267 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN267 TrailNet Baseline T1D plasma


title: Non-transfected, GFP experiment, rep3

description: Library name: NC_GFP3

value: Non-transfected


title: GS025_BSA_biol rep1

description: Library name: A7

source_name: brain


title: DO iPSC line 2472, untreated

description: Library name: DO_iPSC_2472_CTRL


title: UPN827 cells, TN266 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN266 TrailNet Baseline T1D plasma


title: Non-transfected, GFP experiment, rep2

description: Library name: NC_GFP2

value: Mesenchymal Stem Cell


title: UPN827 cells, TN265 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN265 TrailNet Baseline T1D plasma


title: GS025_OSM_biol rep1

description: Library name: A6


title: DO iPSC line 2467, triphenyl phosphate treated

description: Library name: DO_iPSC_2467_TPHP

source_name: DO iPSC 2467

value: DO iPSC 2467

value: triphenyl phosphate


title: UPN827 cells, TN264 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN264 TrailNet Baseline T1D plasma


title: GS025_LIF_biol rep1

description: Library name: A5


title: Non-transfected, GFP experiment, rep1

description: Library name: NC_GFP1


title: DO iPSC line 2467, untreated

description: Library name: DO_iPSC_2467_CTRL


title: E5

city: Fuzhou

first: tenghong

last: liu

address: Jiaotong Street

institute: Fujian Medical University

description: Library name: Sample 10

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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: tumor

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: tumor

value: BCPAP

value: PTC

value: IL1B overexpression


title: GS025_IL6_biol rep1

description: Library name: A4


title: UPN827 cells, TN263 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN263 TrailNet Baseline T1D plasma


title: E4

description: Library name: Sample 9


title: DO iPSC line 2463, triphenyl phosphate treated

description: Library name: DO_iPSC_2463_TPHP

source_name: DO iPSC 2463

value: DO iPSC 2463

value: iPSC


title: GS025_BMP4_biol rep1

description: Library name: A3

value: brain


title: UPN827 cells, TN262 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN262 TrailNet Baseline T1D plasma


title: DO iPSC line 2463, untreated

description: Library name: DO_iPSC_2463_CTRL

value: untreated


title: E3

description: Library name: Sample 8


title: GS025_BMP3_biol rep1

description: Library name: A2


title: UPN827 cells, TN261 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN261 TrailNet Baseline T1D plasma


title: DO iPSC line 2459, triphenyl phosphate treated

description: Library name: DO_iPSC_2459_TPHP

source_name: DO iPSC 2459

value: DO iPSC 2459

value: male


title: E2

description: Library name: Sample 7


title: GS025_BMP2_biol rep1

description: Library name: A1


title: UPN827 cells, TN260 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN260 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: DO iPSC line 2459, untreated

description: Library name: DO_iPSC_2459_CTRL


title: E1

description: Library name: Sample 6


title: Donor_34_Dopa_neuron_Control

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 34

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.

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

value: postmortem brain tissue

value: Dopa neuron

value: Control


title: DO iPSC line 2455, triphenyl phosphate treated

description: Library name: DO_iPSC_2455_TPHP

source_name: DO iPSC 2455

value: DO iPSC 2455

value: triphenyl phosphate


title: V5

description: Library name: Sample 5

value: tumor

value: BCPAP

value: Vector


title: Donor_33_Dopa_neuron_Control

description: Library name: Donor 33


title: UPN827 cells, TN259 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN259 TrailNet Baseline T1D plasma


title: V4

description: Library name: Sample 4

value: PTC


title: Donor_32_Dopa_neuron_Control

description: Library name: Donor 32


title: UPN827 cells, TN257 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN257 TrailNet Baseline T1D plasma


title: UPN827 cells, TN258 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN258 TrailNet Baseline T1D plasma


title: DO iPSC line 2455, untreated

description: Library name: DO_iPSC_2455_CTRL

value: iPSC


title: DO iPSC line 2451, triphenyl phosphate treated

description: Library name: DO_iPSC_2451_TPHP

source_name: DO iPSC 2451

value: DO iPSC 2451


title: V3

description: Library name: Sample 3

value: untreated


title: Donor_31_Dopa_neuron_Bipolar

description: Library name: Donor 31

value: Bipolar


title: UPN827 cells, TN256 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN256 TrailNet Baseline T1D plasma


title: DO iPSC line 2451, untreated

description: Library name: DO_iPSC_2451_CTRL

value: male


title: V2

description: Library name: Sample 2


title: Donor_30_Dopa_neuron_Bipolar

description: Library name: Donor 30


title: DO iPSC line 2447, triphenyl phosphate treated

description: Library name: DO_iPSC_2447_TPHP

source_name: DO iPSC 2447

value: DO iPSC 2447


title: V1

description: Library name: Sample 1


title: UPN827 cells, TN255 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN255 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: Donor_29_Dopa_neuron_Control

description: Library name: Donor 29

value: Midbrain

value: postmortem brain tissue


title: UPN827 cells, TN254 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN254 TrailNet Baseline T1D plasma


title: DO iPSC line 2447, untreated

description: Library name: DO_iPSC_2447_CTRL


title: scRNASeq_Subject3

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: Library name: Subject3

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

source_name: subcutaneous abdominal and gluteofemoral fat

extract_protocol:
SVF was isolated from ABD and GF-adipose tissue biopsies tissue was digested with collagenase (type 1, 1 mg/ml in HBSS) for 45min at 37ºC with shaking (100 rpm). The mixture was centrifuged at 500g for 5 minutes and floating adipocytes were discarded. Cell pellets were treated with erythrocyte lysis buffer (Invitrogen) for 5 min at room temperature. After discarding the supernatant, cells were repelleted with centrifugation, resupend in PBS/EDTA and the mixture was passed through 100 and 40 micron mesh filters. After centrifugation, the cells were resuspended in PBS/10% FBS/1%EDTA and counted with a Countess II automated cell counter (Thermofisher Scientific). SVF were isolated from 4 women with PCOS. Single cell suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip.
Selected cells 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.


title: DO iPSC line 2443, triphenyl phosphate treated

description: Library name: DO_iPSC_2443_TPHP

source_name: DO iPSC 2443

value: DO iPSC 2443


title: Donor_28_Dopa_neuron_Bipolar

description: Library name: Donor 28

value: Dopa neuron


title: Donor_27_Dopa_neuron_Bipolar

description: Library name: Donor 27


title: scRNASeq_Subject2

description: Library name: Subject2

value: subcutaneous abdominal and gluteofemoral fat


title: UPN827 cells, TN253 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN253 TrailNet Baseline T1D plasma


title: UPN827 cells, TN252 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN252 TrailNet Baseline T1D plasma


title: DO iPSC line 2443, untreated

description: Library name: DO_iPSC_2443_CTRL


title: Donor_26_Dopa_neuron_Control

description: Library name: Donor 26

value: Control


title: scRNASeq_Subject1_and_Subject4

description: Library name: Mixed Sample of Subject1_Subject4


title: DO iPSC line 2439, triphenyl phosphate treated

description: Library name: DO_iPSC_2439_TPHP

source_name: DO iPSC 2439

value: DO iPSC 2439

value: triphenyl phosphate


title: UPN827 cells, TN251 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN251 TrailNet Baseline T1D plasma


title: snRNASeq_PCOS subject1_and_PCOS subject4

description: Library name: Mixed Sample of PCOS1_PCOS4

molecule: nuclear RNA

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.


title: UPN827 cells, TN250 TrailNet Baseline T1D plasma

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

source_name: UPN827 cells stimulated with TN250 TrailNet Baseline T1D plasma


title: Donor_25_Dopa_neuron_Bipolar

description: Library name: Donor 25

source_name: Midbrain


title: DO iPSC line 2439, untreated

description: Library name: DO_iPSC_2439_CTRL


title: snRNASeq_CTRL subject4_and_CTRL subject5

description: Library name: Mixed Sample of CTRL4_CTRL5


title: Donor_24_Dopa_neuron_Bipolar

description: Library name: Donor 24


title: DO iPSC line 2431, triphenyl phosphate treated

description: Library name: DO_iPSC_2431_TPHP

source_name: DO iPSC 2431

value: DO iPSC 2431

value: female


title: Donor_23_Dopa_neuron_control

description: Library name: Donor 23

value: control


title: UPN827 cells, TN248 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN248 TrailNet Baseline T1D plasma