title: Patient 121

value: MN

value: SNUH


title: Patient 126

status: Public on Mar 22 2026

type: protein

city: Seoul

first: Jae-ik

last: Oh

address: 101, Daehak-ro, Jongno-gu

department: Translational Medicine

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: High multiplexed PEATM probes, matched pairs of antibodies with unique DNA oligonucleotides, bind to their respective proteins in the plasma samples. Then oligonucleotides that are brought into proximity hybridize and are extedned using a DNA polymerase. The piece of DNA barcode that is created is then amplified by PCR. Unique sample indexes are added to every sample, to allow pooling of the DNA amplicons for all samples.

scan_protocol: The final DNA amplicons are sequenced by NGS using Illumina platform.

data_processing: The relative concentration of each biomarker, based on matched counts (the number of reads for each specific combination of sample and assay), is calculated using the Olink NPX Explore HT software. As we conducted proteome profiling in two separate batches (one from the discovery cohort and one from the validation cohort), we additionally introduced bridge normalization by eight overlapping samples from each batch. The NPX values from these bridge samples were used to calculate correction factors for each plate, and all protein expression data were bridge normalized for comparative analysis.

molecule: protein

organism: Homo sapiens

source_name: plasma

growth_protocol: The subjects were enrolled in the KORNERSTONE project before their first diagnostic kidney biopsy. On the same day as the biopsy, the first blood samples for the biorepository project were collected and sent to the laboratory in the study hospital. Plasma was separated from EDTA tubes and stored in deep-freezers.

tag: batch

tag: cohort

value: discovery

tag: disease group

value: Control

tag: center name

value: AJH

tag: age

tag: Sex

value: M

tag: egfr

tag: proteinuria (upcr g/g)

value: U/A albumin negative

tag: hypertension

value: No

tag: diabetes

tag: immunosuppressant

tag: bridgesample


title: Patient 123

value: Yes


title: Patient 117


title: Patient 124

value: validation


title: Patient 129

value: F


title: Patient 127


title: Patient 118


title: Patient 122


title: Patient 111


title: Patient 114


title: Patient 115


title: Patient 109


title: Patient 107

value: MCD


title: Patient 120


title: Patient 110


title: Patient 112


title: Patient 119


title: Patient 113


title: Patient 116


title: Patient 105


title: Patient 106


title: Patient 104


title: Patient 101


title: Patient 96


title: Patient 98


title: Patient 102


title: Patient 97


title: Patient 103


title: Patient 93


title: Patient 99


title: Patient 108


title: Patient 94


title: Patient 92


title: Patient 78


title: Patient 90


title: Patient 88


title: Patient 91


title: Patient 100


title: Patient 82


title: Patient 86


title: Patient 85


title: Patient 79


title: Patient 72


title: Patient 89


title: Patient 76


title: Patient 80


title: Patient 70


title: Patient 87


title: Patient 77


title: Patient 65


title: Patient 81


title: Patient 95


title: Patient 74


title: Patient 83


title: Patient 71


title: Patient 75


title: Patient 69


title: Patient 66


title: Patient 68


title: Patient 63


title: Patient 84


title: Patient 58

value: IgAN


title: Patient 61


title: Patient 59


title: Patient 56


title: Patient 67


title: Patient 54


title: Patient 62


title: Patient 49


title: Patient 57


title: Patient 64


title: Patient 60


title: Patient 43


title: Patient 53


title: Patient 73


title: Patient 51


title: Patient 44


title: Patient 52


title: Patient 41


title: N3_CD4+_costim_T-TM

status: Public on Mar 23 2026

type: SRA

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 South Orange Ave

department: Medicine

country: USA

institute: Rutgers New Jersey Medical School

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._costim_T.TM_s18

library_source: transcriptomic

data_processing:
Sequence Quality control: FastQC_v0.11.5 (default)
Trim adaptors/low quality reads: Cutadapt
Alignment: STAR
Read counts: HTSeq
Normalization: DEseq2 (RLE method)
Genome_build: hg19
Supplementary_files_format_and_content: CSV matrix of normalized expression counts with genes in rows and samples in columns

molecule: polyA RNA

source_name: Peripheral blood CD4+ T-TM

extract_protocol:
Qiagen RNeasy Micro Kit (Qiagen #74004)
Illumina TruSeq RNA Sample Preparation Kit v2

tag: individual

value: donor N3

tag: treatment

value: costim only

tag: cell type

value: T-TM


title: Patient 42


title: Patient 47


title: Patient 48


title: Patient 35


title: Patient 46


title: Patient 55


title: Patient 50


title: Patient 45


title: Patient 37


title: Patient 34


title: Patient 40


title: Patient 38


title: Patient 39


title: Patient 36


title: Patient 28


title: Patient 29


title: Patient 32


title: Patient 30


title: Patient 31


title: Patient 33


title: Patient 27


title: Patient 26


title: Patient 23


title: Patient 25


title: Patient 15


title: Patient 21


title: Patient 13

value: FSGS


title: Patient 22


title: Patient 14


title: Patient 9


title: Patient 18


title: Patient 16


title: Patient 20


title: Patient 10


title: Patient 12


title: Patient 6


title: Patient 4


title: Patient 11


title: Patient 17


title: Patient 8


title: Patient 2


title: Patient 24


title: Patient 3


title: mouse glomeruli WT 8w

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
Library name: Sample3
10x Genomics

data_processing:
10x library equencing was performed on Illumina HiSeq X. Sequencing data were analyzed using Illumina bcl2fastq software (version 2.20.0) and converted to FASTQ format files. Subsequently, alignment was performed using the cellranger count function of Cell Ranger Single Cell software (version 9.0.0, 10x Genomics) with using STAR aligner 2.7.2a. The GRCm38 mouse reference genome, mm10 r102  was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic kidney glomeruli

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

tag: tissue

value: Mouse embryonic kidney glomeruli


title: mouse glomeruli AS 8w

description:
Library name: Sample4
10x Genomics


title: Patient 7

value: SNUH


title: Patient 1

value: discovery


title: CuNZ_1, Macrophage, H3ac (ChIP)

city: Cheonan-si

first: Amal

middle: George

last: Kurian

state: Chungcheongnam-do

address: Pharmacy Bldg, Dankook University

department: Department of Nanobiomedical Science and Tissue regeneration Engineering

institute: Institute of Tissue Regeneration Engineering

description: Library name: CuNZ_1, ChIP

library_source: genomic

data_processing:
ChIP-seq reads were filtered out of low quality reads and adapter sequences using fastp with default options.
Multi-mapped and duplicates reads were removed using samtools-1.17 and ENCODE blacklist regions were removed from the bam files.
Peaks were calling using callpeak command of MACS2 v2.2.8 from the bam files.
CPM-normalized bigWig files were generated using bamCoverage from deepTools (v3.5.6) with a bin size of 10 bp. Normalization was performed using counts per million mapped reads (CPM) to account for differences in sequencing depth across samples
Assembly: GRCm39
Supplementary files format and content: narrowPeak
Supplementary files format and content: BigWig

molecule: genomic DNA

growth_protocol: RAW264.7 was seeded and grown on tcp for proliferation

extract_protocol:
Cells were subsequently lysed with ice-cold Lysis Buffers iL1 and iL2, and chromatin was sheared in ice-cold Shearing Buffer iS1 supplemented with a protease inhibitor cocktail using a Bioruptor Plus (Diagenode, USA) to yield fragments of 150–350 bp.
ChIP-seq libraries were prepared using the NEBNext® UltraTM DNA Library Prep Kit for Illumina following manufacturer's protocols. The chipped DNA was ligated with adaptors. After purification, PCR reaction was done with adaptor-ligated DNA and index primer for multiplexing sequencing. Library was purified by using magnetic beads to remove all reaction components. The size of library was assessed by Agilent 2100 bioanalyzer.

treatment_protocol: Briefly, 1 × 106 cells were seeded in 12-well plates and treated with CuNZ@Gel extracts for 48 h. Cells were crosslinked with 1% formaldehyde in PBS for 10 min at room temperature, and the reaction was quenched with 125 mM glycine. Cells were subsequently lysed with ice-cold Lysis Buffers iL1 and iL2, and chromatin was sheared in ice-cold Shearing Buffer iS1 supplemented with a protease inhibitor cocktail using a Bioruptor Plus (Diagenode, USA) to yield fragments of 150–350 bp. ChIP was performed using an anti-acetylated H3 antibody (Sigma, 06-599) in a reaction mix at 4°C overnight with gentle rocking. Input DNA was prepared in parallel, omitting the immunoprecipitation step. Following quality control, all samples meeting the criteria were subjected to library preparation, which was performed by E-Biogen Inc. (South Korea).

tag: cell line

value: macrophages

tag: chip antibody


title: Patient 19

tag: batch

tag: cohort


title: mouse glomeruli WT 5w

description:
Library name: Sample1
10x Genomics


title: CuNZ21, Macrophage, (Input)

description: Library name: CuNZ_2, INPUT


title: mouse glomeruli AS 5w

description:
Library name: Sample2
10x Genomics


title: Patient 5

tag: disease group

tag: center name


title: Gel_1, Macrophage, (Input)

description: Library name: Gel_1, INPUT

value: Gel


title: CuNZ_2, Macrophage, H3ac (ChIP)

description: Library name: CuNZ_2, ChIP


title: Gel_1, Macrophage, H3ac (ChIP)

description: Library name: Gel_1, ChIP


title: CuNZ_1, Macrophage, (Input)

description: Library name: CuNZ_1, INPUT


title: shSEPP5

city: Shanghai

first: Jiazheng

last: Jiao

state: Shanghai

address: 319 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description: Library name: shSEPP5

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the Cell Ranger v7.1.0 pipeline with default and recommended parameters. FASTQ files generated from Illumina sequencing were aligned to the mouse reference genome (GRCm38) using the STAR aligner. Gene-barcode matrices were generated for each individual sample by counting unique molecular identifiers (UMIs) and filtering non-cell-associated barcodes. The resulting gene-barcode matrices were imported into the Seurat (v4.1.1) R package for quality control and downstream single-cell RNA sequencing analysis. All functions were run with default parameters unless otherwise specified. Low-quality cells were filtered based on three standard quality control metrics: (1) number of detected transcripts (UMIs), (2) number of detected genes, and (3) percentage of reads mapping to mitochondrial genes. Cells with values outside the mean plus or minus two standard deviations were excluded. The percentage of mitochondrial gene expression was calculated using the PercentageFeatureSet function in Seurat. Data were normalized using the NormalizeData function, and highly variable genes were identified while accounting for the relationship between gene variability and average expression. Datasets from different samples were integrated using the FindIntegrationAnchors and IntegrateData functions in Seurat. Principal component analysis (PCA) was performed on the scaled data, and the top 30 principal components were used for downstream analysis. Cell clusters were visualized using t-distributed stochastic neighbor embedding (t-SNE).
Assembly: GRCm38
Supplementary files format and content: Processed data files consist of 10x Genomics gene expression matrices including matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz files for each sample.

source_name: liver tumor

extract_protocol:
Tissues were transported in In sterile culture dish with 10 ml 1x Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to remove the residual tissue storage solution, then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no.25200-072) and 10 ug/mL lDNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues. XX tissues were dissociated at 37℃ with a shaking speed of 50 r.p.m for about 40 min. We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57) . Dissociated cells were washed with 1x DPBS containing 0.4% FBS. Cells were stained with 0.4% AO/PI to check the viability on Countstar Rigel S2 (Countstar,Shanghai ).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 3’end (that is, the 5’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10x beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on Xplus (Illumina) using 2x150 chemistry.

value: liver tumor


title: shNC2

description: Library name: shNC2


title: RASE

description: Library name: RASE


title: NE-4C cells, Input

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: Library name: NE-4C_input

data_processing:
Raw read data was trimmed using Trim Galore! with default settings.
Data were aligned to the mouse genome (mm10) or human genome (hg38) using Bowtie 2.
Samtools fixmate and markdup were used to remove any PCR duplicates.
Bedtools was used to generate 100-bp windowed bedGraph files. BedGraphs were converted to bigWig format using bedGraphToBigWig.
“True” merged signal tracks were generated for each even–odd ChIRP-seq pair by taking the minimum signal at each base pair of the genome.
Assembly: hg38 for homo sapiens data, mm10 for mus musculus data
Supplementary files format and content: merged "true" bigWig for set of Even and Odd data
Supplementary files format and content: bigWig
Library strategy: ChIRP-seq

growth_protocol: HeLa cells (CCL-2; ATCC) were cultured in DMEM (11965092; Gibco) supplemented with 10% fetal bovine serum (FBS; 26140079; Gibco) and 1% penicillin–streptomycin (15140-122; Gibco). NE-4C cells (CRL-2925; ATCC) were cultured in EMEM (30-2003; ATCC) supplemented with 2 mM L-glutamine (G7513; Sigma-Aldrich), 10% FBS, and 1% penicillin–streptomycin. Both cell lines were propagated at 37 °C in a humidified incubator (Symphony, VWR) with 5% CO2 and were sub-cultured at ~80% confluency.

extract_protocol:
Confluent cells were recovered by treatment with 0.25% trypsin-EDTA (25200072; Gibco) for 5 minutes at room temperature. Trypsin was quenched with an equal volume of culture medium, and cells were dislodged by flushing the flask surface and collected. The suspension was centrifuged at 800 g for 4 minutes, and the medium was aspirated. Cells were washed once with PBS (pH 7.4; 10010031; Gibco), centrifuged at 800 g for 4 minutes, and the PBS was aspirated. Cells were crosslinked for 10 minutes at room temperature using 10 mL freshly prepared 1% glutaraldehyde (G5882, Sigma-Aldrich) per 10 million cells. The crosslinking reaction was quenched with 10% (v/v) 1.25 M glycine (G7126; Sigma-Aldrich) for 5 minutes at room temperature. Crosslinked cells were pelleted by centrifugation at 2,000 g for 5 minutes, and the supernatant was removed. The pellet was washed with chilled PBS and centrifuged at 2,000 g for 5 minutes. PBS was removed, and cells were washed again with 1 mL chilled PBS per 20 million cells. The suspension was centrifuged at 2,000 g for 3 minutes at 4 °C. PBS was removed, and cell pellets were stored at –80 °C. Tissue was placed in 3 mL ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl, and 0.1% Triton X-100), freshly supplemented with 30 μL protease inhibitor cocktail (PIC; P8340; Sigma-Aldrich), 3 μL 100 mM PMSF (P7626; Sigma-Aldrich), 3 μL 1 M DTT(43816; Sigma-Aldrich), and 4.5 μL recombinant RNase inhibitor (RRI; 2313B; Takara Bio). The tissue was homogenized on ice using a Dounce homogenizer (D9063; Sigma-Aldrich), with 15 strokes using loose pestle A followed by 25 strokes with tight pestle B. The homogenate was then filtered through a 40 μm cell strainer (22-363-547; Fisherbrand) and centrifuged at 1,000 g for 10 minutes at 4 °C. The supernatant was removed, and the pellet was resuspended in 500 μL nuclei extraction buffer and 750 μL of 50% iodixanol solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 20 mM Tris-HCl [pH 7.8]). Samples were centrifuged at 10,000 g for 20 minutes at 4 °C, and the supernatant was aspirated. The pellets were incubated with 300 μL of 2% normal goat serum (50062Z; Thermo Fisher Scientific) in DPBS (14190144; Gibco), freshly supplemented with 3 μL PIC, 0.3 μL 100 mM PMSF, 0.3 μL 1 M DTT, and 0.3 μL RRI for 10 minutes on ice. Nuclei were resuspended and incubated with 10 μL of 2ng/μL anti-NeuN antibody conjugated to Alexa Fluor 488 (MAB377X; Sigma-Aldrich) in DPBS (1 μg/mL antibody + 499 μL DPBS) on an end-to-end rotator at 4 °C for 1 hour, followed by FACS sorting.  Following FACS, 800 μL PBS, 200 μL 1.8M Sucrose (S0389; Sigma-Aldrich), 10 μL 1M CaCl2 (21097; Sigma-Aldrich), and 3 μL 1M Mg(Ac)2 (M5661; Sigma-Aldrich) were added to each 200 μL of nuclei suspension. Samples were incubated on ice for 15 minutes. Samples were centrifuged at 1,800 g for 15 minutes at 4 °C, and the supernatant was aspirated.  Pellets were resuspended in 9.6 mL PBS per 10 million nuclei. Then, 0.4 mL of 25% glutaraldehyde was added per 10 million nuclei, and samples were crosslinked at room temperature on an end-to-end rotator for 10 minutes. The reaction was quenched with 10% (v/v) 1.25 M glycine for 5 minutes at room temperature. Crosslinked nuclei were pelleted by centrifugation at 2,000 g for 5 minutes, washed with chilled PBS, and centrifuged again. Nuclei were washed once more with 1 mL chilled PBS per 20 million nuclei and centrifuged at 2,000 g for 3 minutes at 4 °C. Nuclei pellets were stored at –80 °C.
Libraries from human PFC, mouse cortex and Gomafu in HeLa cells were prepared using the Takara DNA Thruplex Kit, while remaining cell line libraries were prepared with the IDT ACCEL-NGS 2S DNA Library Kit, following manufacturer protocols. Library amplification was performed by real-time qPCR (1855200; Bio-Rad) following the corresponding PCR protocol for each kit. Amplification was stopped once fluorescence increased by 1,500 RFU above baseline. Samples were purified using SPRI magnetic beads (B23317; Beckman Coulter) and the fragment size was measured using the Agilent TapeStation. The KAPA Library Quantification Kit (Roche Diagnostics) was used according to the manufacturer’s protocol to measure library concentration. Libraries were pooled such that approximately 50 million raw reads were allocated to each sample and sequenced on a NovaSeq X instrument to generate 150-bp paired-end reads.

treatment_protocol: Mouse study was approved by the Institutional Animal Care and Use Committee at Virginia Tech. C57BL/6J mice were purchased from Jackson Laboratory and housed in standard breeding cages at constant temperature of 22 ± 1°C and a 50% relative humidity with 12 hour light-dark cycles and with access to food, water ad libitum. 80-week-old male mice were sacrificed by cervical dislocation. Mouse brains were rapidly dissected, frozen on dry ice, and stored at -80°C. Human brain samples were obtained via autopsies performed at Basque Institute of Legal Medicine, Bilbao, Spain. The study was conducted in accordance with institutional policies and ethical guidelines for postmortem brain studies78. The Institutional Review Board (IRB) determined that approval was not needed for this study. Samples were obtained via the opting-out policy, no compensation was provided for tissue donation, and samples were documented with reversible anonymization. Retrospective review of hospital and psychiatric records was used to confirm clinical diagnoses and treatment history. Samples were collected from 29 individuals who met DSM-IV criteria for schizophrenia and 29 matched controls, all of Caucasian ancestry. Toxicological screening was performed on blood samples taken at the time of death, and on postmortem brain, when possible, to test for the presence of antipsychotics, ethanol, and other drugs. Toxicological studies were performed at the National Institute of Toxicology, Madrid, Spain, using methods including radioimmunoassay, enzymatic immunoassay, high-performance liquid chromatography (HPLC), and gas chromatography-mass spectrometry (GC-MS). 29 controls were chosen based on negative medical history for neuropsychiatric disorders and drug abuse; having sex, age, postmortem delay (PMD; time between death and autopsy), and freezer storage duration matched to schizophrenia subjects; sudden and unexpected cause of death (motor vehicle accidents); and negative results in the toxicological screening for all drugs aside from ethanol. Frontal Cortex samples were dissected at autopsy (0.5–1 g tissue) on an ice-cold surface and immediately stored at –80 °C. Schizophrenia samples were classified as antipsychotic-treated or antipsychotic-free based on toxicological screening of blood at the time of death. Samples for this study were a subset of 7 control and 7 matching schizophrenia samples.

tag: sample group

value: NE-4C cells, Input


title: Mouse cortex, NeuN+ nuclei, Input

description: Library name: Mouse_NeuN+_input

source_name: Cortex

value: Cortex

value: NeuN+ nuclei

value: Mouse cortex, NeuN+ nuclei, Input


title: shNC

description: Library name: shNC


title: RACT

description: Library name: RACT


title: Gel_2, Macrophage, (Input)

description: Library name: Gel_2, INPUT


title: shNC3

description: Library name: shNC3


title: Mouse cortex, NeuN- nuclei, TERC, Even, rep2

description:
Library name: Mouse_NeuN-_TERC_EVEN_rep2
Mouse_NeuN-_TERC_rep2_UNNORM.merge.bw.gz

value: NeuN- nuclei

value: Mouse cortex, NeuN- nuclei, TERC, Even


title: CAGn_Cas9het3_Spleen_DNA_Tamoxifen

type: genomic

city: Stockholm

first: Maja

last: Jagodic

address: Visionsgatan 18

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, hybridized and imaged

scan_protocol: iScan System

data_processing:
Sesame package in R with additional code from ChatGPT
Average beta value after normalization and signal correction

label: Cy3 and Cy5

source_name: spleen

label_protocol: Infinium HD Methylation

extract_protocol: Approximately 30mg of tissue was used for DNA/RNA extraction with the AllPrep DNA/RNA Mini Kit followed by TissueLyser LT (QIAGEN) homogenization. The DNA was eluted in Elution Buffer and sotred at -20°C until further use.

treatment_protocol: The samples with the prefixes  CAGp_Cas9het_Spleen and CAGn_Cas9het_Spleen were treated with Tamoxifen, and sacrificed 3 weeks after Tamoxifen treatement. All the other samples were treatment naive.

value: spleen

tag: genotype

value: Tamoxifen


title: Mouse cortex, NeuN- nuclei, Input

description: Library name: Mouse_NeuN-_input

value: Mouse cortex, NeuN- nuclei, Input


title: shSEPP1

description: Library name: shSEPP1


title: Mouse cortex, NeuN+ nuclei, TERC, Even, rep2

description:
Library name: Mouse_NeuN+_TERC_EVEN_rep2
Mouse_NeuN+_TERC_rep2_UNNORM.merge.bw.gz

value: Mouse cortex, NeuN+ nuclei, TERC, Even


title: Mouse cortex, NeuN- nuclei, TERC, Odd, rep1

description:
Library name: Mouse_NeuN-_TERC_ODD_rep1
Mouse_NeuN-_TERC_rep1_UNNORM.merge.bw.gz

value: Mouse cortex, NeuN- nuclei, TERC, Odd


title: CAGp_Cas9het1_Spleen_DNA_Tamoxifen


title: CAGn_Cas9het2_Spleen_DNA_Tamoxifen


title: Gel_2, Macrophage, H3ac (ChIP)

description: Library name: Gel_2, ChIP


title: NE-4C cells, 50K, GOMAFU, Odd, rep2

description:
Library name: NE-4C_50K_GOMAFU_ODD_rep2
NE-4C_50K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: NE-4C cells, 50K, GOMAFU, Odd


title: Het3_Spleen_DNA

value: no


title: CAGp_Cas9het2_Spleen_DNA_Tamoxifen


title: Mouse cortex, NeuN- nuclei, TERC, Even, rep1

description:
Library name: Mouse_NeuN-_TERC_EVEN_rep1
Mouse_NeuN-_TERC_rep1_UNNORM.merge.bw.gz


title: Wt2_Spleen_DNA

value: WT


title: Mouse cortex, NeuN+ nuclei, TERC, Odd, rep2

description:
Library name: Mouse_NeuN+_TERC_ODD_rep2
Mouse_NeuN+_TERC_rep2_UNNORM.merge.bw.gz

value: Mouse cortex, NeuN+ nuclei, TERC, Odd


title: shSEPP6

description: Library name: shSEPP6


title: Mouse cortex, NeuN+ nuclei, TERC, Even, rep1

description:
Library name: Mouse_NeuN+_TERC_EVEN_rep1
Mouse_NeuN+_TERC_rep1_UNNORM.merge.bw.gz


title: NE-4C cells, 50K, GOMAFU, Odd, rep1

description:
Library name: NE-4C_50K_GOMAFU_ODD_rep1
NE-4C_50K_GOMAFU_rep1_UNNORM.merge.bw.gz


title: CAGn_Cas9het1_Spleen_DNA_Tamoxifen


title: Mouse cortex, NeuN- nuclei, TERC, Odd, rep2

description:
Library name: Mouse_NeuN-_TERC_ODD_rep2
Mouse_NeuN-_TERC_rep2_UNNORM.merge.bw.gz


title: Wt3_Spleen_DNA


title: NE-4C cells, 50K, GOMAFU, Even, rep1

description:
Library name: NE-4C_50K_GOMAFU_EVEN_rep1
NE-4C_50K_GOMAFU_rep1_UNNORM.merge.bw.gz

value: NE-4C cells, 50K, GOMAFU, Even


title: G2_mac2-Segment 2

description: Library name: G2_mac2-Segment 2

library_source: other

data_processing:
Nanostring GeoMx Digital Spatial Profiling (DSP) Platform
QC and probeQC were performed using DSP platform.
Probe count extraction and Q3 normalization were performed using DSP platform.
GeoMx Mouse Whole Transcriptome Atlas https://brukerspatialbiology.com/products/geomx-digital-spatial-profiler/geomx-rna-assays/geomx-mouse-whole-transcriptome-atlas/
Assembly: Mouse WTA
Supplementary files format and content: tab-delimited text files include normalization values for each Sample
Library strategy: Spatial Transcriptomics

molecule: other

organism: Rattus norvegicus

source_name: Skin tissue

growth_protocol: Diabetes was induced in 5-week-old male SD rats via STZ injection following standard protocols for experimental use.

extract_protocol:
FFPE tissue sections were mounted on positively charged histology slides. FFPE tissue sections were subjected to in situ hybridization with GeoMX RNA Detection probe (WTA or CTA). Nuclear stain marker and antibodies of target protein were applied to each section. Slides were load on the GeoMX DSP. ROIs were selected and the GeoMX software was used to define each AOI in ROIs as one segment containing positive immonofluorescent signals. Once AOIs were defined, the DSP then exposed AOIs to 365nm light (UV), releasing the indexing oligonucleotides, which were collected with a microcapillary.
The GeoMX libraries for NGS were prepared using GeoMX Library Prep Kit following maufacture's protocols.

treatment_protocol: Full-thickness 8mm skin defects in rats (Sham, Gel, CuNZ@Gel) were splinted/sutured to prevent contraction and treated with hydrogels. Wounds were harvested at day 7 for GeoMx spatial transcriptomic profiling.

value: Skin tissue

value: diabetic skin wound tissue

tag: time

value: Day 7 post-wounding

value: Gel


title: NE-4C cells, 100K, GOMAFU, Odd, rep2

description:
Library name: NE-4C_100K_GOMAFU_ODD_rep2
NE-4C_100K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: NE-4C cells, 100K, GOMAFU, Odd


title: G1_mac2-Segment 2

description: Library name: G1_mac2-Segment 2


title: G1_mac2-Segment 1

description: Library name: G1_mac2-Segment 1


title: het1_Spleen_DNA


title: CuG2-mac2-Segment 2

description: Library name: CuG2-mac2-Segment 2


title: G1_mac1-Segment 1

description: Library name: G1_mac1-Segment 1


title: Mouse cortex, NeuN+ nuclei, TERC, Odd, rep1

description:
Library name: Mouse_NeuN+_TERC_ODD_rep1
Mouse_NeuN+_TERC_rep1_UNNORM.merge.bw.gz

value: Cortex

value: NeuN+ nuclei


title: NE-4C cells, 50K, GOMAFU, Even, rep2

description:
Library name: NE-4C_50K_GOMAFU_EVEN_rep2
NE-4C_50K_GOMAFU_rep2_UNNORM.merge.bw.gz


title: Wt1_Spleen_DNA

value: spleen


title: NE-4C cells, 250K, GOMAFU, Odd, rep2

description:
Library name: NE-4C_250K_GOMAFU_ODD_rep2
NE-4C_250K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: NE-4C cells, 250K, GOMAFU, Odd


title: NE-4C cells, 250K, GOMAFU, Even, rep2

description:
Library name: NE-4C_250K_GOMAFU_EVEN_rep2
NE-4C_250K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: NE-4C cells, 250K, GOMAFU, Even


title: G2_mac2-Segment 1

description: Library name: G2_mac2-Segment 1


title: CuG1-mac2-Segment 2

description: Library name: CuG1-mac2-Segment 2


title: CuG1-mac2-Segment 1

description: Library name: CuG1-mac2-Segment 1


title: Chicken control liver 2

city: Gainesville

first: Lekshmi

middle: K

last: Edison

state: FL

address: 1945 SW 16th Ave

institute: University of Florida

description:
Library name: Sample2
raw data processed with Gallus gallus  bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ  as reference

data_processing:
CLC Genomics workbench v.25.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC-genomics bench work
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: GCF_016700215.2
Supplementary files format and content: fataq.gz file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Gallus gallus

source_name: Liver

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit (Invitrogen™). The samples further processed for rRNA depletion to enrich host  mRNA using using RiboMinus Eukaryote Kit v2 (Invitrogen) and the enriched mRNA fraction was concentrated using the RiboMinus Concentration Module (Invitrogen). All steps were carried out according to the manufacturer’s instructions. Quality and concentration of RNA samples in each step was measured using NanoDrop™ 2000/2000c Spectrophotometer (Thermo Scientific™).
Library preparation was done using TruSeq® Stranded mRNA library kit (Illumina Inc., San Diego, CA, USA) as per manufacturer’s recommendations

treatment_protocol: Liver tissues were collected from hens at an SLD-affected farm. Samples were immediately stabilized in RNAlater™and stored at −80 °C until RNA extraction

value: Liver

value: Invivo samples


title: NE-4C cells, 100K, GOMAFU, Even, rep2

description:
Library name: NE-4C_100K_GOMAFU_EVEN_rep2
NE-4C_100K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: NE-4C cells, 100K, GOMAFU, Even


title: G2_mac1-Segment 1

description: Library name: G2_mac1-Segment 1


title: CAGp_Cas9het3_Spleen_DNA_Tamoxifen

value: Tamoxifen


title: NE-4C cells, 100K, GOMAFU, Odd, rep1

description:
Library name: NE-4C_100K_GOMAFU_ODD_rep1
NE-4C_100K_GOMAFU_rep1_UNNORM.merge.bw.gz


title: G2_mac1-Segment 2

description: Library name: G2_mac1-Segment 2


title: NE-4C cells, 250K, GOMAFU, Odd, rep1

description:
Library name: NE-4C_250K_GOMAFU_ODD_rep1
NE-4C_250K_GOMAFU_rep1_UNNORM.merge.bw.gz


title: CuG2-mac2-Segment 1

description: Library name: CuG2-mac2-Segment 1


title: Chicken infected liver with campylobacter hepaticus 1

description:
Library name: Sample4
raw data processed with Gallus gallus  bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ  as reference

value: WT


title: Chicken infected liver with campylobacter hepaticus 2

description:
Library name: Sample5
raw data processed with Gallus gallus  bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ  as reference


title: CuG1-mac1-Segment 1

description: Library name: CuG1-mac1-Segment 1


title: G1_mac1-Segment 2

description: Library name: G1_mac1-Segment 2


title: CuG2-mac1-Segment 1

description: Library name: CuG2-mac1-Segment 1


title: Chicken infected liver with campylobacter hepaticus 3

description:
Library name: Sample6
raw data processed with Gallus gallus  bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ  as reference


title: Chicken control liver 3

description:
Library name: Sample3
raw data processed with Gallus gallus  bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ  as reference


title: Sample_58

city: LILLE

first: JULIE

last: KERR-CONTE

address: PLACE DE VERDUN

department: University of Lille-Faculty of Medicine

country: France

institute: INSERM U1190

data_processing:
Raw sequencing reads in FASTQ format were initially processed using custom in-house Perl scripts. Adapter sequences, reads containing poly-N stretches, and low-quality reads were filtered out to generate high-quality clean reads. Quality metrics, including Q20, Q30, and GC content, were calculated for the filtered dataset. All subsequent analyses were performed using these high-quality clean reads. The reference genome and annotation files were downloaded from the appropriate database. Genome indexing and alignment of paired-end clean reads were performed using HISAT2 (v2.0.5), a splice-aware aligner that improves mapping accuracy by incorporating known splice junction information. Read counts per gene were obtained using featureCounts (v1.5.0-p3).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample : ProcessData/Gene_counts_samples.txt
Supplementary files format and content: xlsx files include samples and groups for different figures :MetaData/RNAseqsamples.xlsx

source_name: Pancreatic tissue

extract_protocol:
Total RNA was extracted using column-based purification with RNeasy mini kit (Qiagen). One sample of total RNA was shipped to Novogene Europe. RNA quantitation, integrity and purity was evaluated with Agilent 5400 fragment analyzer, before using for the construction of sequencing libraries. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection
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 . The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount

value: Pancreatic tissue

value: Islets

tag: group

value: Normoglycemic

value: post culture


title: NE-4C cells, 250K, GOMAFU, Even, rep1

description:
Library name: NE-4C_250K_GOMAFU_EVEN_rep1
NE-4C_250K_GOMAFU_rep1_UNNORM.merge.bw.gz


title: NE-4C cells, 100K, GOMAFU, Even, rep1

description:
Library name: NE-4C_100K_GOMAFU_EVEN_rep1
NE-4C_100K_GOMAFU_rep1_UNNORM.merge.bw.gz


title: CuG1-mac1-Segment 2

description: Library name: CuG1-mac1-Segment 2

value: Skin tissue

value: diabetic skin wound tissue

value: Day 7 post-wounding


title: CuG2-mac1-Segment 2

description: Library name: CuG2-mac1-Segment 2


title: C2_mac2-Segment 1

description: Library name: C2_mac2-Segment 1

value: Sham


title: Chicken control liver 1

description:
Library name: Sample1
raw data processed with Gallus gallus  bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ  as reference


title: C2_mac1-Segment 2

description: Library name: C2_mac1-Segment 2


title: Sample_56


title: C2_mac2-Segment 2

description: Library name: C2_mac2-Segment 2


title: Sample_55

value: Normoglycemic / NKX6.1-high expression


title: het2_Spleen_DNA

value: spleen

value: no


title: C1_mac1-Segment 2

description: Library name: C1_mac1-Segment 2


title: C2_mac1-Segment 1

description: Library name: C2_mac1-Segment 1


title: Sample_57

value: NKX6.1-low expression


title: NE-4C cells, 500K, GOMAFU, Even, rep2

description:
Library name: NE-4C_500K_GOMAFU_EVEN_rep2
NE-4C_500K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: NE-4C cells, 500K, GOMAFU, Even


title: C1_mac1-Segment 1

description: Library name: C1_mac1-Segment 1


title: NE-4C cells, 500K, GOMAFU, Odd, rep2

description:
Library name: NE-4C_500K_GOMAFU_ODD_rep2
NE-4C_500K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: NE-4C cells, 500K, GOMAFU, Odd


title: Sample_53


title: C1_mac2-Segment 1

description: Library name: C1_mac2-Segment 1


title: NE-4C cells, 500K, GOMAFU, Odd, rep1

description:
Library name: NE-4C_500K_GOMAFU_ODD_rep1
NE-4C_500K_GOMAFU_rep1_UNNORM.merge.bw.gz


title: C1_mac2-Segment 2

description: Library name: C1_mac2-Segment 2


title: Sample_52


title: Sample_54

value: Normoglycemic / NKX6.1-low expression


title: SCZ-19, PFC, NeuN+ nuclei, Input

description: Library name: SCZ_19_INPUT

source_name: Prefrontal Cortex

value: Prefrontal Cortex

value: NeuN+ nuclei

value: SCZ-19, PFC, NeuN+ nuclei, Input


title: Raw 264.7, CuNZ@Gel_rep1

description: Library name: Sample 3

data_processing:
Low quality DNA reads and adapter sequences were filtered out using fastp 0.23.1.
Clean reads were aligned to the reference genome sequence using bowtie2 2.3.4.3.
mtDNA sequences and duplicated reads were removed using samtools 1.17 and picard 2.27.5
ENCODE blacklist regions were removed from the bam file, and coordinates were shifted.
peaks in alignment files were identified using MACS2 v2.2.8.
Assembly: GRCm39
Supplementary files format and content: narrowPeak
Supplementary files format and content: TXT file with Gene symbol and Normalised data

growth_protocol: For ATAC sequencing, 1 × 10⁶ cells were seeded per well in 12-well plates and maintained under standard cell culture conditions for attachment.

extract_protocol:
The construction of library was performed using ATAC-Seq Library Prep Kit for Illumina (Active Motif, United States) according to the manufacturer’s instructions
Library purified with SPRI bead (Beckman Coulter, United States) to remove contaminating primer dimers. Library quantity was checked using TapeStation HS D5000 Screen Tape (Agilent Technologies, United States).

treatment_protocol: After cell attachment, the cells were treated with CuNZ@Gel and cultured for 48 hours.

value: macrophages


title: SCZ-23, PFC, NeuN+ nuclei, Input

description: Library name: SCZ_23_INPUT

value: SCZ-23, PFC, NeuN+ nuclei, Input


title: NE-4C cells, 500K, GOMAFU, Even, rep1

description:
Library name: NE-4C_500K_GOMAFU_EVEN_rep1
NE-4C_500K_GOMAFU_rep1_UNNORM.merge.bw.gz


title: SCZ-24, PFC, NeuN+ nuclei, Input

description: Library name: SCZ_24_INPUT

value: SCZ-24, PFC, NeuN+ nuclei, Input


title: ChIP-Seq_IP_SPIN1

city: Chapel Hill

first: Donghai

last: Wang

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

description: Library name: Sample 2

data_processing:
Raw ChIP-seq reads were aligned to the human genome (hg38) using Bowtie2 (version 2.5.3) with default settings. Quality control was performed using FastQC (version 0.12.0), and adapter trimming was done with Trimmomatic (version 0.39). Read coverage was calculated using deepTools (version 3.5.5) and visualized in the IGV software.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Brain

extract_protocol:
or chromatin Immunoprecipitation sequencing analysis (ChIP-Seq), GSC cells were cross-linked with 1% paraformaldehyde for 10 minutes, followed by quenching with glycine for 5 minutes at room temperature. After cell lysis, fixed samples were sonicated to generate DNA fragments ranging from 200 to 600 bp. Immunoprecipitation was performed using a SPIN1 antibody (Proteintech, 12105-1-AP) and Magna ChIP Protein A/G Magnetic Beads (Sigma-Aldrich, 16-663).
1 to 10 ng of immunoprecipitated DNA and the NEBNext Ultra DNA Library Prep Kit for Illumina were used for library preparation, and the samples were subjected to sequencing on the NovaSeq X Plus.

value: Brain

value: Glioblastoma stem cell


title: ChIP-Seq_input

description: Library name: Sample 1


title: Raw 264.7, CuNZ@Gel_rep2

description: Library name: Sample 4


title: Control-23, PFC, NeuN+ nuclei, Input

description: Library name: CNTRL_23_INPUT

value: Control-23, PFC, NeuN+ nuclei, Input


title: Sample_51

value: Pancreatic tissue

value: Islets

value: Type 2 diabetic

value: post culture


title: SCZ-20, PFC, NeuN+ nuclei, Input

description: Library name: SCZ_20_INPUT

value: SCZ-20, PFC, NeuN+ nuclei, Input


title: Control-24, PFC, NeuN+ nuclei, Input

description: Library name: CNTRL_24_INPUT

value: Control-24, PFC, NeuN+ nuclei, Input


title: Sample_50

value: Normoglycemic


title: Raw 264.7, Gel_rep2

description: Library name: Sample 2


title: Raw 264.7, Gel_rep1

description: Library name: Sample 1


title: HFD_HD

city: Chuo-ku

first: Keisuke

last: Sekine

state: Tokyo

address: 5-1-1 Tsukiji

department: Graduate School of Medicine

institute: National Cancer Center Research Institute, Japan

description:
Library name: N36_5143
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences weere aligned to mm10 genome to gene expression count using  Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: list of spatial barcodes, list of gene IDs, gene expression count data.
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: small intestine

extract_protocol:
Tissue were fixed and parafin embedded, and 5um FFPE sections were cut with microtome.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics HD Spatial Gene Expression Reagent Kit with Mouse Transcriptome Probe Kit v2 according to manufacturer's instruction

treatment_protocol: C57BL/6 mice were fed either a stearic acid-rich high-fat diet (HFD) (54.8% kcal fat, Research Diets Inc.)  or a control diet  (10 kcal% fat, D12450H; Research Diets Inc.)  starting at 4 weeks of age. After 2 weeks of HFD feeding, the small intestine of each animal were fixed in Mildform 10N (FUJIFILM Wako Pure Chemical Corporation) and embedded in paraffin.

value: small intestine

value: wild type

value: stearic acid-rich HFD


title: Control-20, PFC, NeuN+ nuclei, Input

description: Library name: CNTRL_20_INPUT

value: Prefrontal Cortex

value: NeuN+ nuclei

value: Control-20, PFC, NeuN+ nuclei, Input


title: SCZ-14, PFC, NeuN+ nuclei, Input

description: Library name: SCZ_14_INPUT

value: SCZ-14, PFC, NeuN+ nuclei, Input


title: SCZ-24, PFC, NeuN+ nuclei, GOMAFU, Odd

description:
Library name: SCZ_24_GOMAFU_ODD
SCZ_24_GOMAFU_UNNORM.merge.bw.gz

value: SCZ-24, PFC, NeuN+ nuclei, GOMAFU, Odd


title: Sample_49


title: SCZ-19, PFC, NeuN+ nuclei, GOMAFU, Odd

description:
Library name: SCZ_19_GOMAFU_ODD
SCZ_19_GOMAFU_UNNORM.merge.bw.gz

value: SCZ-19, PFC, NeuN+ nuclei, GOMAFU, Odd


title: small intestine, HFD_1

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences weere aligned to mm10 genome to gene expression count using  Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: list of spatial barcodes, list of gene IDs, gene expression count data.
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissue were fixed and parafin embedded, and 5um FFPE sections were cut with microtome.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE kit according to manufacturer's instruction

treatment_protocol: Mice were fed stearic acid-rich HFD (54.8% kcal fat, Research Diets Inc.) and  control diet (10 kcal% fat, D12450H; Research Diets Inc.) from the age of 4 weeks. After 2 weeks of HFD feeding, The small intestine of each animal were fixed in Mildform 10N (FUJIFILM Wako Pure Chemical Corporation) and embedded in paraffin.


title: HeLa cells, Input

description: Library name: HeLa_input

source_name: HeLa

value: HeLa

value: HeLa cells, Input


title: Sample_46

value: Pancreatic tissue

value: Islets


title: SCZ-24, PFC, NeuN+ nuclei, GOMAFU, Even

description:
Library name: SCZ_24_GOMAFU_EVEN
SCZ_24_GOMAFU_UNNORM.merge.bw.gz

value: SCZ-24, PFC, NeuN+ nuclei, GOMAFU, Even


title: SCZ-14, PFC, NeuN+ nuclei, GOMAFU, Even

description:
Library name: SCZ_14_GOMAFU_EVEN
SCZ_14_GOMAFU_UNNORM.merge.bw.gz

value: SCZ-14, PFC, NeuN+ nuclei, GOMAFU, Even


title: Control_HD

description:
Library name: N35_5131
FFPE Spatial transcriptome sequencing

value: control dieet


title: EPI2

city: Tucson

first: Sergio Alan

last: Cervantes-Perez

state: Arizona

address: 1140 E South Campus Dr

department: School of Plant Sciences

institute: University of Arizona

data_processing:
FasQC was use to evaluate quality control
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to Phaseoulus vulgaris genome was downloaded from the Phytozome database (Phytozome info: P.vulgaris v2.1; https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1). Mapping was carried out using HiSat2.
Read count extraction and normalization were performed using StringTie
Assembly: Phaseolus vulgaris v2.1
Supplementary files format and content: Normalized counts in csv format

organism: Phaseolus vulgaris

growth_protocol: L88-57 genotype seeds (Phaseolus vulgaris) were germinated in a growth chamber located in the greenhouse facility at the University of Nebraska-Lincoln (UNL). The plants were cultivated under controlled environmental conditions, including low light intensity, a humidity level of 65%, and a temperature of 25 degrees Celsius. For plant growth, a growth medium was prepared by mixing Fafard 3B commercial potting mix and sand at a ratio of 7:3. Before planting, the seeds underwent scarification and were soaked in water overnight.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The plants were grown in normal conditions

tag: hair-like structure

value: EPI (trichomes)


title: Control-24, PFC, NeuN+ nuclei, GOMAFU, Odd, rep2

description:
Library name: CNTRL_24_GOMAFU_ODD_rep2
CNTRL_24_GOMAFU_rep2_UNNORM.merge.bw.gz


title: small intestine, Control_1

description: FFPE Spatial transcriptome sequencing

value: small intestine

value: control diet


title: EPI1


title: BG1

value: BG(hooked hairs)


title: Sample_45

value: Normoglycemic

value: post culture


title: SCZ-14, PFC, NeuN+ nuclei, GOMAFU, Odd

description:
Library name: SCZ_14_GOMAFU_ODD
SCZ_14_GOMAFU_UNNORM.merge.bw.gz

value: Prefrontal Cortex

value: NeuN+ nuclei

value: SCZ-14, PFC, NeuN+ nuclei, GOMAFU, Odd


title: SCZ-23, PFC, NeuN+ nuclei, GOMAFU, Odd

description:
Library name: SCZ_23_GOMAFU_ODD
SCZ_23_GOMAFU_UNNORM.merge.bw.gz

value: SCZ-23, PFC, NeuN+ nuclei, GOMAFU, Odd


title: Sample_42


title: Sample_43


title: Control-24, PFC, NeuN+ nuclei, GOMAFU, Even, rep2

description:
Library name: CNTRL_24_GOMAFU_EVEN_rep2
CNTRL_24_GOMAFU_rep2_UNNORM.merge.bw.gz


title: AG2

value: AG(trichomes)


title: BG2


title: Control-24, PFC, NeuN+ nuclei, GOMAFU, Odd, rep1

description:
Library name: CNTRL_24_GOMAFU_ODD_rep1
CNTRL_24_GOMAFU_rep1_UNNORM.merge.bw.gz


title: Sample_48


title: Sample_47


title: Control-14, PFC, NeuN+ nuclei, GOMAFU, Odd

description:
Library name: CNTRL_14_GOMAFU_ODD
CNTRL_14_GOMAFU_UNNORM.merge.bw.gz


title: AG1


title: Control-23, PFC, NeuN+ nuclei, GOMAFU, Even

description:
Library name: CNTRL_23_GOMAFU_EVEN
CNTRL_23_GOMAFU_UNNORM.merge.bw.gz


title: SCZ-19, PFC, NeuN+ nuclei, GOMAFU, Even

description:
Library name: SCZ_19_GOMAFU_EVEN
SCZ_19_GOMAFU_UNNORM.merge.bw.gz

value: SCZ-19, PFC, NeuN+ nuclei, GOMAFU, Even


title: Control-14, PFC, NeuN+ nuclei, GOMAFU, Even

description:
Library name: CNTRL_14_GOMAFU_EVEN
CNTRL_14_GOMAFU_UNNORM.merge.bw.gz


title: Sample_41

value: Pancreatic tissue


title: Control-23, PFC, NeuN+ nuclei, GOMAFU, Odd

description:
Library name: CNTRL_23_GOMAFU_ODD
CNTRL_23_GOMAFU_UNNORM.merge.bw.gz


title: Sample_40

value: Islets

value: Type 2 diabetic


title: CTR 4

city: Xian

first: Ziyi

last: Zhou

address: Xijing Hospital, No.127, Changle W. Road, Xincheng District

institute: Xijing Hospital

description: Library name: N_4

data_processing:
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCm39
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: retina

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: retina

value: microglia


title: SCZ-23, PFC, NeuN+ nuclei, GOMAFU, Even

description:
Library name: SCZ_23_GOMAFU_EVEN
SCZ_23_GOMAFU_UNNORM.merge.bw.gz

value: SCZ-23, PFC, NeuN+ nuclei, GOMAFU, Even


title: Sample_44


title: SCZ-24, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: SCZ_24_TERC_ODD
SCZ_24_TERC_UNNORM.merge.bw.gz

value: SCZ-24, PFC, NeuN+ nuclei, TERC, Odd


title: SCZ-23, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: SCZ_23_TERC_ODD
SCZ_23_TERC_UNNORM.merge.bw.gz

value: SCZ-23, PFC, NeuN+ nuclei, TERC, Odd


title: Control-24, PFC, NeuN+ nuclei, GOMAFU, Even, rep1

description:
Library name: CNTRL_24_GOMAFU_EVEN_rep1
CNTRL_24_GOMAFU_rep1_UNNORM.merge.bw.gz


title: Sample_39


title: SCZ-23, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: SCZ_23_TERC_EVEN
SCZ_23_TERC_UNNORM.merge.bw.gz

value: SCZ-23, PFC, NeuN+ nuclei, TERC, Even


title: CTR 3

description: Library name: N_3


title: SCZ-20, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: SCZ_20_TERC_EVEN
SCZ_20_TERC_UNNORM.merge.bw.gz

value: SCZ-20, PFC, NeuN+ nuclei, TERC, Even


title: Sample_37

value: Normoglycemic / NKX6.1-low expression

value: post culture


title: CTR 2

description: Library name: N_2


title: SCZ-19, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: SCZ_19_TERC_ODD
SCZ_19_TERC_UNNORM.merge.bw.gz

value: Prefrontal Cortex

value: NeuN+ nuclei

value: SCZ-19, PFC, NeuN+ nuclei, TERC, Odd


title: Control-14, PFC, NeuN+ nuclei, Input

description: Library name: CNTRL_14_INPUT

value: Control-14, PFC, NeuN+ nuclei, Input


title: Sample_36

value: Normoglycemic


title: Neu+NETS 4

description: Library name: A2_4


title: Control-24, PFC, NeuN+ nuclei, TERC, Even, rep2

description:
Library name: CNTRL_24_TERC_EVEN_rep2
CNTRL_24_TERC_rep2_UNNORM.merge.bw.gz


title: Control-24, PFC, NeuN+ nuclei, TERC, Odd, rep2

description:
Library name: CNTRL_24_TERC_ODD_rep2
CNTRL_24_TERC_rep2_UNNORM.merge.bw.gz


title: SCZ-20, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: SCZ_20_TERC_ODD
SCZ_20_TERC_UNNORM.merge.bw.gz

value: SCZ-20, PFC, NeuN+ nuclei, TERC, Odd


title: Control-24, PFC, NeuN+ nuclei, TERC, Odd, rep1

description:
Library name: CNTRL_24_TERC_ODD_rep1
CNTRL_24_TERC_rep1_UNNORM.merge.bw.gz


title: SCZ-24, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: SCZ_24_TERC_EVEN
SCZ_24_TERC_UNNORM.merge.bw.gz

value: SCZ-24, PFC, NeuN+ nuclei, TERC, Even


title: Neu+NETS 2

description: Library name: A2_2


title: Control-23, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: CNTRL_23_TERC_EVEN
CNTRL_23_TERC_UNNORM.merge.bw.gz


title: Control-23, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: CNTRL_23_TERC_ODD
CNTRL_23_TERC_UNNORM.merge.bw.gz


title: Control-20, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: CNTRL_20_TERC_ODD
CNTRL_20_TERC_UNNORM.merge.bw.gz


title: Sample_34

value: Pancreatic tissue

value: Islets


title: Neu group 4

description: Library name: A1_4

value: retina

value: microglia


title: Control-20, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: CNTRL_20_TERC_EVEN
CNTRL_20_TERC_UNNORM.merge.bw.gz


title: Sample_38


title: SCZ-19, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: SCZ_19_TERC_EVEN
SCZ_19_TERC_UNNORM.merge.bw.gz

value: SCZ-19, PFC, NeuN+ nuclei, TERC, Even


title: Control-14, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: CNTRL_14_TERC_ODD
CNTRL_14_TERC_UNNORM.merge.bw.gz


title: Sample_30

value: NKX6.1-high expression


title: Neu group 2

description: Library name: A1_2


title: SCZ-14, PFC, NeuN+ nuclei, TERC, Odd

description:
Library name: SCZ_14_TERC_ODD
SCZ_14_TERC_UNNORM.merge.bw.gz

value: SCZ-14, PFC, NeuN+ nuclei, TERC, Odd


title: Sample_29


title: HeLa cells, 100K, GOMAFU, Even, rep2

description:
Library name: HeLa_100K_GOMAFU_EVEN_rep2
HeLa_100K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: HeLa

value: HeLa cells, 100K, GOMAFU, Even


title: Neu+NETS 3

description: Library name: A2_3


title: HeLa cells, 100K, GOMAFU, Odd, rep1

description:
Library name: HeLa_100K_GOMAFU_ODD_rep1
HeLa_100K_GOMAFU_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 100K, GOMAFU, Odd


title: Neu group 1

description: Library name: A1_1


title: Sample_32

value: post culture


title: SCZ-14, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: SCZ_14_TERC_EVEN
SCZ_14_TERC_UNNORM.merge.bw.gz

value: Prefrontal Cortex

value: NeuN+ nuclei

value: SCZ-14, PFC, NeuN+ nuclei, TERC, Even


title: Control-14, PFC, NeuN+ nuclei, TERC, Even

description:
Library name: CNTRL_14_TERC_EVEN
CNTRL_14_TERC_UNNORM.merge.bw.gz


title: Neu+NETS 1

description: Library name: A2_1


title: Sample_31

value: Normoglycemic


title: Sample_35

value: Type 2 diabetic


title: HeLa cells, 50K, TERC, Odd, rep1

description:
Library name: HeLa_50K_TERC_ODD_rep1
HeLa_50K_TERC_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 50K, TERC, Odd


title: HeLa cells, 50K, TERC, Odd, rep2

description:
Library name: HeLa_50K_TERC_ODD_rep2
HeLa_50K_TERC_rep2_UNNORM.merge.bw.gz


title: Sample_27

value: Pancreatic tissue


title: Liver immune cell, untreat

city: Beijing

first: Weixuan

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: UT
10x Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver immune cell

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: C57BL/6J mice were treated with low-dose concanavalin A (ConA) (10 mg/kg body weight, intravenous injection) once weekly for three consecutive weeks to establish an immune tolerance model, with age-matched untreated (UT) mice serving as controls. Following the final ConA injection, liver tissues were collected and hepatic immune cells were isolated by Ficoll density gradient centrifugation. CD45⁺ immune cells were then sorted by flow cytometry and subjected to single-cell RNA sequencing.

value: Liver immune cell

value: WT

value: UT


title: CTR 1

description: Library name: N_1

value: retina

value: microglia


title: Liver immune cell, ConA

description:
Library name: ConA
10x Genomics

value: ConA


title: HeLa cells, 50K, TERC, Even, rep1

description:
Library name: HeLa_50K_TERC_EVEN_rep1
HeLa_50K_TERC_rep1_UNNORM.merge.bw.gz

value: HeLa

value: HeLa cells, 50K, TERC, Even


title: Sample_26

value: Islets


title: Sample_28

value: NKX6.1-high expression

value: post culture


title: HeLa cells, 100K, TERC, Even, rep1

description:
Library name: HeLa_100K_TERC_EVEN_rep1
HeLa_100K_TERC_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 100K, TERC, Even


title: Neu group 3

description: Library name: A1_3


title: Sample_24


title: Sample_33


title: HeLa cells, 100K, TERC, Odd, rep1

description:
Library name: HeLa_100K_TERC_ODD_rep1
HeLa_100K_TERC_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 100K, TERC, Odd


title: Control-24, PFC, NeuN+ nuclei, TERC, Even, rep1

description:
Library name: CNTRL_24_TERC_EVEN_rep1
CNTRL_24_TERC_rep1_UNNORM.merge.bw.gz

value: Prefrontal Cortex

value: NeuN+ nuclei


title: HeLa cells, 100K, TERC, Odd, rep2

description:
Library name: HeLa_100K_TERC_ODD_rep2
HeLa_100K_TERC_rep2_UNNORM.merge.bw.gz


title: HeLa cells, 250K, TERC, Odd, rep2

description:
Library name: HeLa_250K_TERC_ODD_rep2
HeLa_250K_TERC_rep2_UNNORM.merge.bw.gz

value: HeLa cells, 250K, TERC, Odd


title: HeLa cells, 100K, GOMAFU, Even, rep1

description:
Library name: HeLa_100K_GOMAFU_EVEN_rep1
HeLa_100K_GOMAFU_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 100K, GOMAFU, Even


title: HeLa cells, 100K, GOMAFU, Odd, rep2

description:
Library name: HeLa_100K_GOMAFU_ODD_rep2
HeLa_100K_GOMAFU_rep2_UNNORM.merge.bw.gz

value: HeLa cells, 100K, GOMAFU, Odd


title: HeLa cells, 250K, TERC, Even, rep1

description:
Library name: HeLa_250K_TERC_EVEN_rep1
HeLa_250K_TERC_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 250K, TERC, Even


title: Sample_23

value: Pancreatic tissue

value: Normoglycemic


title: HeLa cells, 500K, TERC, Even, rep2

description:
Library name: HeLa_500K_TERC_EVEN_rep2
HeLa_500K_TERC_rep2_UNNORM.merge.bw.gz

value: HeLa cells, 500K, TERC, Even


title: Sample_25

value: Normoglycemic / NKX6.1-high expression


title: CITE_Colons3

city: Rochester

first: Virginia

middle: Smith

last: Shapiro

state: MN

address: 200 First St SW

department: Immunology

institute: Mayo Clinic

description: Library name: Sample 18

data_processing:
Data was aligned using CellRanger; cells in which fewer than 200 genes or greater than 8000 were detected, cells with 20% or greater mitochondrial gene counts, and cells in which less than 300 or more than 50,000 molecules detected were filtered out before all analysis. Data were normalized, scaled, and underwent dimensional reduction using the R package Seurat as described by the package creators.
Assembly: mouse mm10
Supplementary files format and content: value and matrix files
Library strategy: CITE-seq

source_name: Colon

extract_protocol:
Immune cells from the SB and colon LP and EP were isolated using the Miltenyi lamina propria dissociation kit (130-097-410) using the manufacturer’s instructions with the following changes: Initial shaking incubations in predigestion solution and RPMI were done for 10 min and repeated until the LP tissue turned pink. Both LP and EP were then suspended in 5 mL of 40% percoll each and underlaid with 2.5 mL of 80% percoll. The interface was harvested and washed twice in PBS. CD45+ immune cells were enriched with a bead-based positive selection kit (StemCell, 18945). KO cells were incubated with TotalSeq-C0301 hashtag (Biolegend, 155861), het cells were incubated with TotalSeq-C0302 hashtag (Biolegend, 155863), and WT cells were incubated with TotalSeq-C-0303 hashtag (Biolegend, 155865). Hashtagging was done for 30min on ice with all hashtagging antibodies at 1:200. Samples were then combined by organ for scRNA sequencing analysis.
Library preperation was done as according to the manufacterers instructions (Illumina Next GEM 5' v2)

value: Colon

value: CD45-enriched cells


title: HeLa cells, 250K, TERC, Even, rep2

description:
Library name: HeLa_250K_TERC_EVEN_rep2
HeLa_250K_TERC_rep2_UNNORM.merge.bw.gz

value: HeLa


title: Sample_21

value: Islets


title: CITE_SB-LP3

description: Library name: Sample 17

source_name: Smalll bowel lamina propria

value: Smalll bowel lamina propria


title: Sample_20

value: Normoglycemic / NKX6.1-low expression

value: post culture


title: GEX_Colons3

description: Library name: Sample 15

data_processing:
Data was aligned using CellRanger; cells in which fewer than 200 genes or greater than 8000 were detected, cells with 20% or greater mitochondrial gene counts, and cells in which less than 300 or more than 50,000 molecules detected were filtered out before all analysis. Data were normalized, scaled, and underwent dimensional reduction using the R package Seurat as described by the package creators.
Assembly: mouse mm10
Supplementary files format and content: value and matrix files


title: HeLa cells, 50K, TERC, Even, rep2

description:
Library name: HeLa_50K_TERC_EVEN_rep2
HeLa_50K_TERC_rep2_UNNORM.merge.bw.gz

value: HeLa cells, 50K, TERC, Even


title: GEX_SB-EP3

description: Library name: Sample 13

source_name: Small bowel epithelium

value: Small bowel epithelium


title: GEX_SB-LP3

description: Library name: Sample 14


title: HeLa cells, 100K, TERC, Even, rep2

description:
Library name: HeLa_100K_TERC_EVEN_rep2
HeLa_100K_TERC_rep2_UNNORM.merge.bw.gz

value: HeLa cells, 100K, TERC, Even


title: Sample_19


title: Sample_22

value: NKX6.1-high expression


title: CITE_SB-EP3

description: Library name: Sample 16


title: GSC23 sh2 rep2

description:
Library name: Sample6
GSC23_sh2_2

data_processing:
Raw FASTQ data were then subjected to quality trimming using Trim Galore. Transcript alignment to the human reference genome (hg38) was carried out with HISAT2. Subsequent processing, including sorting, indexing, and format conversion from SAM files, was achieved with SAMtools. For gene quantification and differential expression analysis, featureCounts and DESeq2 were employed, respectively. Differentially expressed genes (DEGs) were defined by an absolute fold change exceeding 1.5 and an adjusted P-value less than 0.05.
Assembly: hg38
Supplementary files format and content: csv

source_name: GBM tissue

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies, 15596018) following the manufacturer’s standard protocol.
mRNA was isolated from 1 µg of total RNA using mRNA Capture Beads and subsequently fragmented to a size range of 200–500 bp. cDNA synthesis and adaptor ligation were performed using the NEBNext Ultra RNA Library Prep Kit for Illumina. The resulting RNA-Seq libraries were sequenced using 150 bp paired-end reads on a NovaSeq X plus platform.

value: GBM tissue

value: Glioblastoma stem cell


title: HeLa cells, 500K, TERC, Odd, rep2

description:
Library name: HeLa_500K_TERC_ODD_rep2
HeLa_500K_TERC_rep2_UNNORM.merge.bw.gz

value: HeLa cells, 500K, TERC, Odd


title: HeLa cells, 250K, TERC, Odd, rep1

description:
Library name: HeLa_250K_TERC_ODD_rep1
HeLa_250K_TERC_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 250K, TERC, Odd


title: CITE_SB-LP2

description: Library name: Sample 11


title: HeLa cells, In Tube, TERC, Odd

description:
Library name: HeLa_InTube_TERC_ODD
HeLa_InTube_TERC_UNNORM.merge.bw

value: HeLa cells, In Tube, TERC, Odd


title: HeLa cells, 500K, TERC, Even, rep1

description:
Library name: HeLa_500K_TERC_EVEN_rep1
HeLa_500K_TERC_rep1_UNNORM.merge.bw.gz

value: HeLa cells, 500K, TERC, Even


title: HeLa cells, 500K, TERC, Odd, rep1

description:
Library name: HeLa_500K_TERC_ODD_rep1
HeLa_500K_TERC_rep1_UNNORM.merge.bw.gz


title: Sample_17

value: Pancreatic tissue

value: Normoglycemic


title: GSC23 shCONT rep2

description:
Library name: Sample2
GSC23_CONT_2

value: shCONT


title: GSC23 sh1 rep1

description:
Library name: Sample3
GSC23_sh1_1


title: GSC23 shCONT rep1

description:
Library name: Sample1
GSC23_CONT_1


title: GEX_SB-EP2

description: Library name: Sample 7

value: CD45-enriched cells


title: HeLa cells, In Tube, TERC, Even

description:
Library name: HeLa_InTube_TERC_EVEN
HeLa_InTube_TERC_UNNORM.merge.bw

value: HeLa

value: HeLa cells, In Tube, TERC, Even


title: Mouse 20-39, Recurring place cell

city: New York

first: Jingcheng

last: Shi

state: NY

address: 3227 Broadway

department: Neuroscience

institute: Columbia University

description:
Library name: 20-39
Column name in recurring_ds_normcounts.txt: 20-39

data_processing:
STAR alignment to align sequencing date to genome.
HT-Seq for gene count
PyDeSeq2 for differential expression analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited file including normalized count for each sample

molecule: nuclear RNA

source_name: mouse hippocampus

extract_protocol:
Nuclei isolation from Allen Institute
RNA library for RNA-seq were prepared using SMART-Seq® mRNA LP following manufacture's protocol.

value: mouse hippocampus

value: hippocampal pyramidal cell

value: WT

value: Recurring place cell


title: GSC23 sh1 rep2

description:
Library name: Sample4
GSC23_sh1_2


title: GEX_Colons2

description: Library name: Sample 9

value: Colon


title: Sample_18

value: Islets

value: post culture


title: CITE_SB-EP2

description: Library name: Sample 10

value: Small bowel epithelium


title: HeLa cells, 1 million, TERC, Even

description:
Library name: HeLa_1mil_TERC_EVEN
HeLa_1mil_TERC_UNNORM.merge.bw.gz

value: HeLa cells, 1 million, TERC, Even


title: Sample_16

value: NKX6.1-low expression


title: CITE_Colons2

description: Library name: Sample 12


title: Sample_14


title: HeLa cells, 1 million, TERC, Odd

description:
Library name: HeLa_1mil_TERC_ODD
HeLa_1mil_TERC_UNNORM.merge.bw.gz

value: HeLa cells, 1 million, TERC, Odd


title: GSC23 sh2 rep1

description:
Library name: Sample5
GSC23_sh2_1

value: GBM tissue

value: Glioblastoma stem cell


title: Sample_13

value: Pancreatic tissue

value: Normoglycemic / NKX6.1-low expression


title: Mouse 20-30, Recurring place cell

description:
Library name: 20-30
Column name in recurring_ds_normcounts.txt: 20-30


title: CITE_Colons

description: Library name: Sample 6

value: CD45-enriched cells


title: Sample_12


title: Mouse 20-19, Day 0 place cell

description:
Library name: 20-19
Column name in recurring_ds_normcounts.txt: 20-19

value: Day 0 place cell


title: GEX_SB-LP2

description: Library name: Sample 8

value: Smalll bowel lamina propria


title: Mouse 20-28, Recurring place cell

description:
Library name: 20-28
Column name in recurring_ds_normcounts.txt: 20-28

value: mouse hippocampus

value: hippocampal pyramidal cell


title: CITE_SB-EP

description: Library name: Sample 4


title: Sample_15

value: Normoglycemic


title: Sample_11


title: Mouse 20-11, Day 0 place cell

description:
Library name: 20-11
Column name in recurring_ds_normcounts.txt: 20-11

value: WT


title: GEX_Colons

description: Library name: Sample 3

value: Colon


title: PK18_38_2

description:
Library name: 8_PK18_38_2
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were proocessed using Illumina bcl2fastq to generate FASTQ files
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences weere aligned to GRCh38 genome to gene expression count using  Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: list of spatial barcodes, list of gene IDs, gene expression count data.
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Pancreatic cancer tissue

extract_protocol:
Cancer specimen was obtained through surgery. Tissue was inspected and dissected by pathologist. Tissue were fixed and parafin embedded, and 5um FFPE sections were cut with microtome.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE kit according to manufacturer's instruction

value: Pancreatic cancer tissue


title: Sample_10

value: Islets

value: post culture


title: Mouse 20-32, Recurring place cell

description:
Library name: 20-32
Column name in recurring_ds_normcounts.txt: 20-32

value: Recurring place cell


title: GEX_SB-EP

description: Library name: Sample 1

value: Small bowel epithelium


title: Sample_9


title: Mouse 20-7, Day 0 place cell

description:
Library name: 20-7
Column name in recurring_ds_normcounts.txt: 20-7


title: Sample_8


title: Mouse 12-31, silent cell

description:
Library name: 31B
Column name in normCount_all_samples.txt: 31B


title: Mouse 12-27, place cell

description:
Library name: 27B
Column name in normCount_all_samples.txt: 27B


title: Mouse 12-37, place cell

description:
Library name: 37B
Column name in normCount_all_samples.txt: 37B


title: CITE_SB-LP

description: Library name: Sample 5


title: Mouse 12-20, place cell

description:
Library name: 20B
Column name in normCount_all_samples.txt: 20B


title: Mouse 12-21, place cell

description:
Library name: 21B
Column name in normCount_all_samples.txt: 21B


title: Mouse 20-6, Day 0 place cell

description:
Library name: 20-6
Column name in recurring_ds_normcounts.txt: 20-6


title: GEX_SB-LP

description: Library name: Sample 2


title: Mouse 12-10, place cell

description:
Library name: 10B
Column name in normCount_all_samples.txt: 10B


title: PR cre/+ Hdac3 f/f 4

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description:
Library name: PR cre/+ Hdac3 f/f 4
Gene expression data from uterus at decidualization day 3

data_processing:
Raw reads were trimmed with cutadapt v1.18 and Trim Galore! v0.6.4_dev.
Quality control analysis was performed using FastQC v0.11.9.
Trimmed reads were aligned to the GRCm38 genome assembly using STAR v2.7.3a, and feature counting was performed using the command ‘--quantMode GeneCounts’.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for each gene and sample

source_name: Uterus of PR cre/+ Hdac3 f/f adult mouse at decidualization day 3

growth_protocol: Collect uteri from intact adult female mice at decidualization day-3

extract_protocol:
RNA was extracted from the uterine tissues using the RNeasy Mini Kit for total RNA isolation (Qiagen, Valencia, CA, USA).
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT Illumina UDI dual Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNF-474 HS fragment kit (Agilent Technologies, Inc.) using a Fragment Analyzer (Agilent Technologies, Inc.), and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2, 100 bp sequencing kit (Illumina Inc., San Diego, CA, USA) to an average depth of 50M reads per sample. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

value: PR cre/+ Hdac3 f/f


title: FGFR3Y367C/+ condylar's cartilage sample 4

city: Paris

first: Martin

last: Biosse Duplan

address: 24 Boulevard du Montparnasse

institute: Institut Imagine INSERM Université Paris Cité

description: Library name: Sample 16

data_processing:
FASTQ files were mapped to the ENSEMBL Mouse GRCm38/mm10 reference using HISAT2 and counted by featureCounts from the Subread R package. Read count normalizations and groups comparisons were performed by three independent and complementary statistical methods (Deseq2, edgeR, LimmaVoom). Flags were computed from counts normalized to the mean coverage. All normalized counts <20 were considered as background (flag=0) and >=20 as signal (flag=1). P50 lists used for the statistical analysis regroup the genes showing flag=1 for at least half of the compared samples. The results of the three methods were filtered at P <0.05 or P<0.01 and folds 1.2/1.5/2 compared and grouped by Venn diagram. Cluster analysis was performed by hierarchical clustering using the Spearman correlation similarity measure and ward linkage algorithm.
Assembly: FASTQ files were mapped to the ENSEMBL Mouse GRCm38/mm10 reference using HISAT2 and counted by featureCounts from the Subread R package.
Supplementary files format and content: Individual excel file for each sample with read counts

source_name: Condylar cartilage

growth_protocol: Laser-microdissected cartilages were harvested from E16.5 embryos of mice

extract_protocol:
Total RNA extraction was done with RNeasy Micro kit (Qiagen). The concentration and the purity of the total RNA extracted were measured by capillary electrophoresis using a tape Station (Agilent).
The strand-specific RNA-seq libraries were prepared with the Ovation Universal RNA-Seq kit (Tecan). After a preliminary DNase digestion with a thermosensitive DNase (ArcticZymes), total RNA was reverse transcribed, and second strand of cDNA was synthetized. A fragmentation step was performed before Illumina compatible indexed adaptator ligation. The ligation was followed by the strand selection enzymatic reaction to keep the information about the orientation of the transcripts. Insert Dependent Adaptor Cleavage (InDA-C) technology was used to deplete all the cDNA corresponding to ribosomal transcripts before the PCR enrichment. To ensure that no excess of amplification was performed during the final PCR step, the number of PCR cycles applied to each sample was evaluated in a preliminary Q-PCR test using EvaGreen. An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina HiSeq2500 (paired-end reads 130 bases + 130 bases) and ~50 millions paired-end reads per library were produced.

value: Condylar cartilage

value: FGFR3 Y367C/+

value: no treatment


title: Sample_5

value: Pancreatic tissue

value: NKX6.1-high expression


title: Sample_6


title: Mouse 12-9, silent cell

description:
Library name: 9B
Column name in normCount_all_samples.txt: 9B


title: PR cre/+ Hdac3 f/f 2

description:
Library name: PR cre/+ Hdac3 f/f 2
Gene expression data from uterus at decidualization day 3

value: Uterus of PR cre/+ Hdac3 f/f adult mouse at decidualization day 3


title: Sample_7


title: FGFR3Y367C/+ condylar's cartilage sample 1

description: Library name: Sample 13


title: FGFR3Y367C/+ condylar's cartilage sample 3

description: Library name: Sample 15


title: PR cre/+ Hdac3 f/f 3

description:
Library name: PR cre/+ Hdac3 f/f 3
Gene expression data from uterus at decidualization day 3


title: Mouse 12-34, silent cell

description:
Library name: 34B
Column name in normCount_all_samples.txt: 34B

value: mouse hippocampus


title: Sample_4

value: Type 2 diabetic


title: WT condylar cartilage sample 4

description: Library name: Sample 12

value: Wild type


title: PR cre/+ Hdac3 f/f 1

description:
Library name: PR cre/+ Hdac3 f/f 1
Gene expression data from uterus at decidualization day 3


title: Mouse 12-12, silent cell

description:
Library name: 12B
Column name in normCount_all_samples.txt: 12B

value: hippocampal pyramidal cell

value: WT


title: FGFR3Y367C/+ condylar's cartilage sample 2

description: Library name: Sample 14


title: Sample_3


title: Hdac3 f/f 3

description:
Library name: Hdac3 f/f 3
Gene expression data from uterus at decidualization day 3

source_name: Uterus of Hdac3 f/f adult mouse at decidualization day 3

value: Hdac3 f/f


title: Hdac3 f/f 4

description:
Library name: Hdac3 f/f 4
Gene expression data from uterus at decidualization day 3

value: Uterus of Hdac3 f/f adult mouse at decidualization day 3


title: WT condylar cartilage sample 3

description: Library name: Sample 11


title: FGFR3Y367C/+ Meckel's cartilage sample 4

description: Library name: Sample 8

source_name: Meckel's cartilage

value: Meckel's cartilage


title: WT condylar cartilage sample 2

description: Library name: Sample 10


title: Sample_2

source_name: Pancreatic tissue

value: Islets

value: post culture


title: WT condylar cartilage sample 1

description: Library name: Sample 9


title: Hdac3 f/f 2

description:
Library name: Hdac3 f/f 2
Gene expression data from uterus at decidualization day 3


title: FGFR3Y367C/+ Meckel's cartilage sample 3

description: Library name: Sample 7


title: Sample_1

value: Normoglycemic


title: Hdac3 f/f 1

description:
Library name: Hdac3 f/f 1
Gene expression data from uterus at decidualization day 3


title: FGFR3Y367C/+ Meckel's cartilage sample 1

description: Library name: Sample 5


title: FGFR3Y367C/+ Meckel's cartilage sample 2

description: Library name: Sample 6


title: iPSC, 149br.CRX.Cherry, rep2

city: Sydney

first: Carissa

last: Chen

state: NSW

address: 214 Hawkesbury Rd, Westmead

country: Australia

institute: Children's Medical Research Institute

description: Library name: C1

data_processing:
For 10x Visium, counts and spatial locations were obtained by performing the standard 10x Space Ranger (v3.0.1) pipeline
Assembly: GRCh8
Supplementary files format and content: .rda file containing SpatialExperiment object of single organoids segmented per slide
Library strategy: Spatial Transcriptomics

source_name: retinal organoid

extract_protocol:
On collection, organoids were washed with PBS before being cryo-embedded in OCT using liquid nitrogen cooled 2-methylbutane before storage at -80°C. Embedded organoids were sectioned to 10µm using a cryostat, onto transcriptomic slides/chips from the Visium which were then fixed for 10 minutes at -20°C using methanol. Tissue permeabilisation was optimised for 10-week-old organoids on the Visium platform at 1.5 minutes. Slides were then stained with DAPI.
cDNA synthesis, amplification and library prep were all performed with the manufacturer’s instructions.

value: retinal organoid

value: iPSC 149br.CRX.Cherry

value: retinal


title: H7, A81.BRN3b.mCherry, rep2

description: Library name: D1

value: H7 A81.BRN3b.mCherry


title: WT Meckel's cartilage sample 4

description: Library name: Sample 4

value: no treatment


title: Raw 264.7, CuNZ@Gel_rep1

description: Library name: Sample 3

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39(NCBI) whole genome using STAR
Calculation mapped reads using salmon
TMM + CPM calculation using conorm
Differential gene expression analysis and visualization using ExDEGA
Assembly: GRCm39
Supplementary files format and content: TXT file with Gene symbol and Normalised data

growth_protocol: For mRNA sequencing, 1 × 10⁵ cells were seeded per well in 12-well plates and allowed to adhere under standard culture conditions.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: After cell attachment, the cells were treated with CuNZ@Gel and cultured for an additional 48 hours prior to RNA extraction.

value: macrophages


title: organoids, A81, BMS1uM

description:
Library name: Sample 4
10x Genomics

data_processing:
Basecalling is performed by Illumina RTA software in sequencer, further demultiplexing is performed by Illumina bcl2fastq 2.20. Counts were generated using 10x Genomics Cell Ranger.
Assembly: GRCh8
Supplementary files format and content: .h5 files containing raw unfiltered expression matrices as output from cellranger

extract_protocol:
Retinal organoids were dissociated into single cell suspension using the Neurosphere Dissociation Kit (P). Enzymatic digestion was performed as per manufacturer protocol for 10 minutes at 37 ◦C with intermittent agitation, followed by gentle mechanical dissociation, and a further incubation for 5 minutes at 37 ◦C. The cell suspension was further dissociated into single cells by pipetting before the enzymatic reaction was stopped by washing with HBSS. The cell suspension was filtered through MACS SmartStrainer 30μm before being pelleted by centrifugation at 300g for 10 minutes at room temperature.
cDNA library preparation was performed in accordance with the Single-Cell 3’ v3 protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System.


title: Raw 264.7, CuNZ@Gel_rep2

description: Library name: Sample 4


title: WT Meckel's cartilage sample 3

description: Library name: Sample 3


title: Raw 264.7, Gel_rep2

description: Library name: Sample 2


title: WT Meckel's cartilage sample 2

description: Library name: Sample 2


title: Raw 264.7, Gel_rep1

description: Library name: Sample 1


title: 32D cell KO2 RPF rep2

status: Public on Mar 21 2026

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Raw reads were trimmed by Cutadapt with parameters "-e 0.1 -O 5 -n 2". Then, reads with distinct inline barcodes were demultiplexed using in-house scripts, and the 10-mer random sequence was appended to the reads name in bam file for later usage.
Low quality reads were filtered by Trimmomatic with parameter "SLIDINGWINDOW: 4:15".
In Ribo-seq library, reads length in 25-50 bp were retained for subsequent analysis. rRNA reads were removed by aligning reads with rRNA reference sequence on NCBI database by Bowtie2.
Cleaned reads were mapped to Mus musculus genome (Ensembl GRCm39.105) by STAR.
Uniquely mapped reads which with "NH: i:1" flag were retained for further analysis by SAMtools and PCR duplicate reads were removed by in-house script based on sharing identical random sequence. To quantify gene expression and translation abundance, we counted sequenced reads mapping to coding sequence (CDS) region by featureCounts.
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include mRNA count value for each Sample
Library strategy: Ribo-seq

source_name: 32D cells

growth_protocol: Mouse 32D cells were cultured in RPMI1640 Medium supplemented with 10% FBS and mouse (m) IL-3 (10 ng/mL)

extract_protocol:
500 µl lysate was prepared as described. 100 µl lysate was used to prepare total RNA library, meanwhile, ribosome footprinting and subsequent library preparation of ribosome protected RNA fragments (RPFs) was performed with 400 µl lysate. Add 10 U RNase I to 400 µl lysate and incubate for 45 min at room temperature with gentle mixing. Then the nuclease digestion was stopped by adding 1 µl RNase inhibitor. RPFs were purified with MicroSpinS-400 columns (GE Healthcare Life Sciences) followed by size selection, which was conducted using 15% TBE-urea gel. rRNAs were depleted with the NEBNext rRNA depletion kit (New England BioLabs). Following end repair and 3'adaptor ligation, RNAs were reverse transcribed using SuperScript III (Thermo Fisher, USA).
cDNA libraries were prepared as described (Nat Protoc. 2012 Jul 26;7(8):1534-50) and sequenced with Illumina NovaSeq 6000 with strand-specific paired-end 150 bp read length.

treatment_protocol: Cells were incubated with 100 µg /ml cycloheximide (CHX, Sigma) at 37°C for 10 min, washed twice with ice-cold PBS containing 100 µg/ml of CHX and lysed in lysis buffer.

value: 32D cells

value: Mouse bone marrow lymphoblastocytes

value: Nat10 deficiency


title: CD33+cells from pancreatic cancer tissue.

description:
Library name: S2
Single cell RNA sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using  Cell Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz: A sparse matrix in Matrix Market format representing gene expression counts. Rows correspond to genes, columns to cell barcodes, and the entries are UMI counts
Supplementary files format and content: features.tsv.gz:  Metadata for each row (gene) in the matrix.
Supplementary files format and content: barcodes.tsv.gz: Unique cell barcodes corresponding to each column in the matrix.

extract_protocol:
Surgically resected pancreatic cancer tissues from patients were minced into small fragments using a razor blade inin RPMI-1640 medium containing 10% FBS. Each sample was filtered through a 100-μm cell strainer and treated with Tumor & Tissue Dissociation Reagent to generate a single-cell suspension. Human myeloid cells were identified as CD45+ and CD33+. To isolate human myeloid cells from the single-cell suspentions, the cells were stained with the CD45 and CD33 monoclonal antibodies and Fixable Viability Dye. Then, the human myeloid cells were isolated by cell sorting with FACSAria II.
single-cell sequencing libraries were prepared according to the manufacture's instruaction (Chromium single cell protocol 3' Library & Gel Bead kit, 10x Genomics).

value: Pancreatic cancer tissue

value: CD33+ cells


title: p4-p6 twomM MgCl2 rep2 DMS

city: Houston

first: Anthony

last: Mustoe

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: p546_twomM_MgCl2_REP2_mod

data_processing:
Fastq files were aligned and parsed using ShapeMapper2 (v.2.3; https://github.com/Weeks-UNC/shapemapper2)
Parsed mutation files were analyzed using DanceMapper (v1.2; https://github.com/MustoeLab/DanceMapper)
Assembly: sequence files used for alignment are included as supplementary files
Supplementary files format and content: Archives (.tar.gz) include bernouli mixture save files (.bm), normalized N1/3 profiles (profile.txt), and normalized N7 profiles (profile.txtga). A complete description of these files is provided in the DanceMapper and Shapemapper documentation.

organism: Tetrahymena

source_name: in vitro transcript

extract_protocol:
RNA was extracted from cells using TRIzol reagent (Ambion) or RNeasy Mini Kit (Qiagen).
RNA was converted to cDNA using mutational profiling (MaP) reverse transcription. Amplicon libraries were prepared by 2-step PCR. Ribosomal libaries were prepared via Nextera.

treatment_protocol: RNA modified under variable folding conditions with DMS (or ethanol) for 6 minutes at 37 C, quenched with 20% 2-mercaptoethanol, and ethanol precipitated.

value: DMS treated

value: in vitro transcript


title: p4-p6 zeromM MgCl2 rep2 DMS

description: Library name: p546_zeromM_MgCl2_REP2_mod


title: iPSC, 149br.CRX.Cherry, rep1

description: Library name: A1


title: p4-p6 twomM MgCl2 rep1 DMS

description: Library name: p546_twomM_MgCl2_REP1_mod


title: p4-p6 zeromM MgCl2 rep1 DMS

description: Library name: p546_zeromM_MgCl2_REP1_mod


title: H7, A81.BRN3b.mCherry, rep1

description: Library name: B1


title: p4-p6 tenmM MgCl2 rep1 DMS

description: Library name: p546_tenmM_MgCl2_REP1_mod


title: organoids, A81, RA-

description:
Library name: Sample 2
10x Genomics

value: RA-


title: p4-p6 rep1 EtOH

description: Library name: p546_rep1_unmod

value: EtOH control


title: p4-p6 rep2 EtOH

description: Library name: p546_rep2_unmod


title: WT Meckel's cartilage sample 1

description: Library name: Sample 1

value: Meckel's cartilage

value: Wild type


title: 32D cell KO2 RPF rep1


title: organoids, A81, RA10uM

description:
Library name: Sample 1
10x Genomics

value: retinal organoid


title: meRIP Input

description: Library name: Sample 3

data_processing:
Low-quality reads were removed by Trimmomatic software, and rRNA reads were filtered by Bowtie2 software. Clean reads were aligned to the Mus musculus genome (Ensembl GRCm39) using STAR software. The YTHDF1 RIP peaks versus the immunoprecipitation (input) were detected using the MACS software (p value < 10e-5 & fold-enrichment > 3).
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include RIP peak file

source_name: BMDCs

extract_protocol:
BMDCs were dissolved in RIP 1ysis buffer and incubated with magnetic bead-YTHDF1 antibody RIP immunoprecipitation buffer. Then the obtained immunoprecipitation was washed with RIP buffer and purified with proteinase K to get the immunoprecipitation RNAs. RIP lysis product and place without immunoprecipitation were applied as “input”. Co-immunoprecipitated and input RNAs were extracted with Trizol (Invitrogen).
For RIP-sequencing, rRNAs were depleted based on the NEBNext rRNA depletion kit, then was used for library construction with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp.

value: BMDCs

value: Murine cells


title: p4-p6 tenmM MgCl2 rep2 DMS

description: Library name: p546_tenmM_MgCl2_REP2_mod


title: 32D cell KO2 Input rep2


title: healthy control iMGs line 611, baseline, rep 3

city: Amsterdam

first: Dilara

last: Ayyildiz

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute For Neuroscience

description: Library name: 611_OE_mock_3

data_processing:
High-quality reads were aligned to the reference genome GRCh38.p13 using the STAR aligner (version STAR-2.7.10b) with default settings. Aligned reads were counted using featureCounts from the Subread package (version 2.0.2). Counts were assigned to annotated features based on the GENCODE v42, and only reads overlapping exonic regions were included in downstream analyses.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

source_name: human iPSC

extract_protocol:
miRNeasy micro (Qiagen)
DNBSEQ platform at BGI

value: human iPSC

value: microglia

value: healthy control iMGs line 611, baseline


title: healthy control iMGs line 611, baseline, rep 5

description: Library name: 611_OE_mock_5


title: 32D cell KO1 RPF rep1

value: 32D cells


title: healthy control iMGs line 611, baseline, rep 4

description: Library name: 611_OE_mock_4


title: healthy control iMGs line 611, baseline, rep 2

description: Library name: 611_OE_mock_2


title: organoids, A81, RA1uM

description:
Library name: Sample 3
10x Genomics

value: H7 A81.BRN3b.mCherry

value: retinal


title: healthy control iMGs line 611, overexpression, control, rep 4

description: Library name: 611_OE_ctr_4


title: 32D cell WT RPF rep2

value: Mouse bone marrow lymphoblastocytes

value: WT


title: 32D cell KO1 Input rep1

value: Nat10 deficiency


title: healthy control iMGs line 611, overexpression, control, rep 5

description: Library name: 611_OE_ctr_5


title: 32D cell KO2 Input rep1


title: 32D cell KO1 Input rep2


title: 32D cell Input rep2

data_processing:
The hChe-RBPs CLIP-seq datasets were processed in accordance with previous studies, and the eCLIP-seq data processing pipeline was available at “https://github.com/YeoLab/eclip”.
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include NAT10 eCLIP peak file

extract_protocol:
Cells were pelleted, flash frozen in liquid nitrogen and stored at -80°C. The pellet was lysed with lysis buffer (50 mM Tris–HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate and 1× protease inhibitor cocktail, Roche) followed by further RNase I, and Turbo DNase treatment as described. The lysate was incubated with specific 20 µg antibody overnight at 4°C for immunoprecipitation. eCLIP was performed as described previously (Nature methods, 2016, 13(6): 508-14.)
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7335S).

treatment_protocol: Cells were UV-crosslinked at 150 mJ and 254 nm wavelength in 10-cm plates with 3 ml of cold PBS.

tag: acrip antibody


title: healthy control iMGs line 611, overexpression, control, rep 1

description: Library name: 611_OE_ctr_1


title: healthy control iMGs line 611, baseline, rep 1

description: Library name: 611_OE_mock_1


title: 32D cell Input rep1


title: 32D cell WT Input rep2


title: 32D cell KO1 RPF rep2


title: FM232, DEK, replicate 3 (Input)

city: Suzhou

first: Gongjie

last: Wu

address: Renai Road

institute: Xi'an Jiaotong-Liverpool University

description: Library name: FM232-Input-3

data_processing:
Bowtie2 aligner (v2.4.2), MACS2 peak caller (v.2.1.1.20160309)
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig

source_name: Skin

growth_protocol: HeLa S3 and other melanoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, High glucose, Biosharp) supplemented with 10% fetal bovine serum (VivaCell), Penicillin-Streptomycin 100 X solution (Hyclone) in a standard incubator with 5% CO2 at 37°C. Cells were passaged every two to three days by Trypsin-EDTA solution (Sigma-Aldrich) after washing with 1 x PBS. Primary foreskin melanocytes FM232 were cultured in 254CF medium (Gibco) supplemented with human melanocyte growth supplement (HMGS-2, PMA free, Gibco), Penicillin-Streptomycin 100 X solution (Hyclone).

extract_protocol:
Nuclei were sonicated in a Bioruptor to yield chromatin fragments of ~200-500 bp, as confirmed by agarose gel electrophoresis.
ChIP-seq libraries were prepared and sequenced using single-end 50 bp sequencing (SE50) on the BGISEQ-500 platform (BGI, Wuhan, China).

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine, washed in cold PBS and lysed in a high-salt lysis buffer.

value: Skin

value: Primary melanocytes


title: healthy control iMGs line 611, overexpression, mimic, rep 4

description: Library name: 611_OE_mim_4


title: healthy control iMGs line 611, overexpression, mimic, rep 3

description: Library name: 611_OE_mim_3


title: healthy control iMGs line 611, overexpression, mimic, rep 1

description: Library name: 611_OE_mim_1


title: healthy control iMGs line 611, overexpression, control, rep 2

description: Library name: 611_OE_ctr_2


title: healthy control iMGs line 611, overexpression, mimic, rep 5

description: Library name: 611_OE_mim_5


title: 32D cell WT Input rep1


title: healthy control iMGs line 611, overexpression, mimic, rep 2

description: Library name: 611_OE_mim_2


title: 32D cell eCLIP IP rep1

value: NAT10 antibody