title: Retina-RPE male 6.0 months biol rep 3

city: Los Angeles

first: Matteo

last: Pellegrini

address: 610 Charles Young Drive East

institute: University of California, Los Angeles

description:
Library name: BC12
Male retina-RPE collected from a 6.0-month-old fish. Biological replicate 3.

library_source: transcriptomic

data_processing:
Base calling, demultiplexing, and FASTQ file generation were performed by GENEWIZ/Azenta.
Raw sequencing reads were analyzed using the MKMC software package.
K-mer counting was performed directly from FASTQ files to generate multi-sample k-mer count matrices.
K-mer count matrices were normalized prior to downstream analyses.
Principal component analysis, UMAP dimensionality reduction, and differential abundance analyses were performed using MKMC as described in the accompanying manuscript.
Assembly: Not applicable (alignment-free k-mer analysis)
Supplementary files format and content: Tab-delimited text files containing normalized k-mer abundance matrices generated by MKMC and used for downstream analyses.
Supplementary files format and content: Tab-delimited text files containing normalized k-mer abundance matrices generated by MKMC and gene-level count matrices used for downstream analyses.

molecule: total RNA

organism: Nothobranchius furzeri

source_name: retina-RPE

growth_protocol: Nothobranchius furzeri animals were raised as described in the accompanying manuscript. All animals used in this study were male fish derived from a mutant line that had been backcrossed for multiple generations onto the GRZ strain. Retina-retinal pigment epithelium (retina-RPE) tissue was collected from fish at 1.5, 3.0, 4.5, and 6.0 months of age.

extract_protocol:
Adult male fish were euthanized using an ice-water slurry. Retina-retinal pigment epithelium (retina-RPE) tissue was dissected by removing the cornea, lens, iris, sclera, and choroid while keeping the retinal pigment epithelium attached to the retina. Samples were washed in ice-cold 1× PBS, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted using the QIAGEN RNeasy Plus Micro Kit (QIAGEN, Cat. No. 74034) according to the manufacturer's instructions and eluted in a final volume of 13 μL.
RNA sequencing libraries were prepared and sequenced by GENEWIZ/Azenta (South Plainfield, NJ, USA) using the Illumina Nextera XT DNA Library Preparation Kit (FC-131-1024). Libraries were sequenced on one lane of an Illumina NovaSeq S4. Base calling, demultiplexing, and FASTQ file generation were performed by GENEWIZ/Azenta.

treatment_protocol: No experimental treatment was applied. Samples were collected from untreated animals at four different ages.

value: retina-RPE

tag: Sex

value: male

tag: age

value: 6.0 months

tag: genotype

value: GRZ backcross mutant line


title: Viral IgG PhIP-Seq for participant 34, timepoint w0, replicate 1

status: Public on Jul 11 2026

type: SRA

city: Boston

first: Stephen

last: Elledge

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description: Library name: Sample_1_56

library_source: other

data_processing:
Seuqencing reads were aligned to library reference files by bowtie.
Read counts were obtained using samtools.
Read counts from multiple samples were merged to generate the read count files.
Assembly: custom peptidome library
Supplementary files format and content: IDs ranging from 1 to 128287 (but 115,753 unique reference sequences reported) vir3_metadata_geo.csv, read counts

molecule: other

organism: Homo sapiens

source_name: blood

extract_protocol:
Phage display libraries were mixed with human sera to allow antibodies from sera to bind to displayed peptides. These complexes were then immunoprecipitated using Dynabeads coated either with protein A/G (for IgG) or strepavidin conjugated to biotinylated anti-IgA antibody (for IgA). Phage were then lysed and the contained DNA coding for the displayed peptides were amplified and barcoded by PCR, pooled, gel extracted, and prepared for Illumina sequencing.
Peptide libraries tiling across the proteins from viruses that infect humans (VirScan) and the human proteome were packaged in T7 bacteriophage and expanded as described in Xu et al (DOI:10.1126/science.aaa0698) and Larman et al (DOI: 10.1038/nbt.1856).

tag: tissue

value: blood

tag: phip isotype

value: IgG

tag: participant id

tag: time point

tag: replicate

tag: run id

value: IgG Vir YL1

tag: outcome

value: birth

tag: series


title: Viral IgG PhIP-Seq for participant 34, timepoint Pre, replicate 1

description: Library name: Sample_1_55

value: Pre


title: Retina-RPE male 6.0 months biol rep 1

description:
Library name: BC10
Male retina-RPE collected from a 6.0-month-old fish. Biological replicate 1.


title: Viral IgG PhIP-Seq for participant 34, timepoint w4, replicate 1

description: Library name: Sample_1_57


title: Retina-RPE male 4.5 months biol rep 3

description:
Library name: Resub-BC14
Male retina-RPE collected from a 4.5-month-old fish. Biological replicate 3.

value: 4.5 months


title: Viral IgG PhIP-Seq for participant 33, timepoint w20, replicate 1

description: Library name: Sample_1_52


title: Retina-RPE male 3.0 months biol rep 3

description:
Library name: BC6
Male retina-RPE collected from a 3.0-month-old fish. Biological replicate 3.

value: 3.0 months


title: Viral IgG PhIP-Seq for participant 33, timepoint w12, replicate 1

description: Library name: Sample_1_50


title: Viral IgG PhIP-Seq for participant 16, timepoint w0, replicate 1

description: Library name: Sample_1_51

value: loss


title: Retina-RPE male 3.0 months biol rep 2

description:
Library name: BC5
Male retina-RPE collected from a 3.0-month-old fish. Biological replicate 2.


title: Viral IgG PhIP-Seq for participant 33, timepoint w4, replicate 1

description: Library name: Sample_1_49


title: Retina-RPE male 3.0 months biol rep 1

description:
Library name: BC4
Male retina-RPE collected from a 3.0-month-old fish. Biological replicate 1.


title: Viral IgG PhIP-Seq for participant 33, timepoint w0, replicate 1

description: Library name: Sample_1_48


title: Retina-RPE male 1.5 months biol rep 3

description:
Library name: BC3
Male retina-RPE collected from a 1.5-month-old fish. Biological replicate 3.

value: 1.5 months


title: Viral IgG PhIP-Seq for participant 32, timepoint w36, replicate 1

description: Library name: Sample_1_46


title: Viral IgG PhIP-Seq for participant 13, timepoint w8, replicate 1

description: Library name: Sample_1_123


title: Viral IgG PhIP-Seq bead control S59, run IgG Vir YL1

description: Library name: Sample_1_109

value: beads


title: Viral IgG PhIP-Seq for participant 12, timepoint w8, replicate 1

description: Library name: Sample_1_107


title: Viral IgG PhIP-Seq for participant 6, timepoint w0, replicate 1

description: Library name: Sample_1_110


title: Viral IgG PhIP-Seq for participant 12, timepoint w0, replicate 1

description: Library name: Sample_1_105


title: Viral IgG PhIP-Seq for participant 32, timepoint w20, replicate 1

description: Library name: Sample_1_44


title: Viral IgG PhIP-Seq for participant 8, timepoint w4, replicate 1

description: Library name: Sample_1_102


title: cbfs_input_Control

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

country: Taiwan

institute: NTU, IPB

description: Library name: cbfs_input_Control

library_source: genomic

data_processing:
The Novoseq PE150 was used for high-throughput sequencing of the ChIP-seq libraries. The raw sequence data were processed using the GAPipeline Illumina sequence data analysis pipeline.
Assembly: Bowtie2 was then employed to map the reads to the Arabidopsis genome (TAIR10). The mapped reads were retained for further analysis.
Supplementary files format and content: The alignments were first converted to Wiggle (WIG) files using deepTools. The data were then imported into the Integrated Genome Viewer (IGV) (Thorvaldsdottir et al., 2013) for visualization. The H3Ac peaks were analyzed by MACS2 (Zhang et al., 2008).

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: aerial parts

growth_protocol: Arabidopsis (Arabidopsis thaliana) plants were germinated on MS medium and grown at 22℃ under short day (8 h light /16 h dark cycle) condition for 14 days.

extract_protocol:
Chromatin extracts were prepared from seedlings treated with 1% formaldehyde. The chromatin was sheared to the mean length of 500 bp by sonication, and proteins and DNA fragments were immunoprecipitated using antibodies against anti-GFP (Abcam, catalog no. ab290). The DNA cross-linked to immunoprecipitated proteins was reversed
2 ng of DNA from ChIP was used to ensure enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries. End repair, adaptor ligation, and amplification were carried out using the KAPA DNA Library Prep kit (cat no. E7645) according to the manufacturer's protocol.

treatment_protocol: For the prolonged cold treatment, 14-day-old Arabidopsis plants were transferred to 4℃ and grown under short day condition for 6 weeks. The hag1 mutant (SALK_048427, hag1–5) was a previously reported T-DNA insertion mutant (Kornet and Scheres, 2009; Chen et al., 2017). The CRISPER-Cas9 generated cbf1/2/3 triple mutants (cbf1/2/3-97 and cbf1/2/3-93) were also reported previously (Xie et al., 2021). All mutants used in this study were in the Col-0 background.

value: aerial parts

tag: ecotype

value: col


title: Viral IgG PhIP-Seq for participant 32, timepoint w12, replicate 1

description: Library name: Sample_1_43


title: hag1_input_pC

description: Library name: hag1_input_pC


title: Viral IgG PhIP-Seq for participant 32, timepoint w4, replicate 1

description: Library name: Sample_1_42


title: hag1_input_Control

description: Library name: hag1_input_Control


title: Viral IgG PhIP-Seq for participant 32, timepoint w0, replicate 1

description: Library name: Sample_1_41


title: Viral IgG PhIP-Seq for participant 2, timepoint w4, replicate 1

description: Library name: Sample_1_82


title: WT_input_pC

description: Library name: WT_input_pC


title: Viral IgG PhIP-Seq for participant 2, timepoint w0, replicate 1

description: Library name: Sample_1_81


title: Viral IgG PhIP-Seq for participant 15, timepoint w4, replicate 1

description: Library name: Sample_1_77


title: Viral IgG PhIP-Seq for participant 16, timepoint Pre, replicate 1

description: Library name: Sample_1_40


title: Viral IgG PhIP-Seq for participant 32, timepoint Pre, replicate 1

description: Library name: Sample_1_39


title: WT_input_Control

description: Library name: WT_input_Control


title: cbfs_Ac_pC_2

description: Library name: cbfs_Ac_pC_2


title: Viral IgG PhIP-Seq for participant 11, timepoint w4, replicate 1

description: Library name: Sample_1_70


title: Viral IgG PhIP-Seq for participant 31, timepoint w36, replicate 1

description: Library name: Sample_1_38


title: cbfs_Ac_pC_1

description: Library name: cbfs_Ac_pC_1


title: cbfs_Ac_Control_2

description: Library name: cbfs_Ac_Control_2


title: Viral IgG PhIP-Seq for participant 31, timepoint Post, replicate 1

description: Library name: Sample_1_37

value: Post


title: Viral IgG PhIP-Seq bead control S190, run IgG Vir YL1

description: Library name: Sample_1_63


title: Viral IgG PhIP-Seq for participant 31, timepoint w20, replicate 1

description: Library name: Sample_1_36


title: cbfs_Ac_Control_1

description: Library name: cbfs_Ac_Control_1


title: Viral IgG PhIP-Seq for participant 31, timepoint w12, replicate 1

description: Library name: Sample_1_35


title: hag1_Ac_pC_2

description: Library name: hag1_Ac_pC_2


title: Viral IgG PhIP-Seq for participant 31, timepoint w4, replicate 1

description: Library name: Sample_1_34


title: hag1_Ac_pC_1

description: Library name: hag1_Ac_pC_1


title: Viral IgG PhIP-Seq for participant 31, timepoint w0, replicate 1

description: Library name: Sample_1_33


title: Viral IgG PhIP-Seq for participant 34, timepoint w12, replicate 1

description: Library name: Sample_1_58


title: hag1_Ac_Control_2

description: Library name: hag1_Ac_Control_2


title: hag1_Ac_Control_1

description: Library name: hag1_Ac_Control_1


title: Viral IgG PhIP-Seq for participant 31, timepoint Pre, replicate 1

description: Library name: Sample_1_32


title: Retina-RPE male 6.0 months biol rep 2

description:
Library name: BC11
Male retina-RPE collected from a 6.0-month-old fish. Biological replicate 2.

value: retina-RPE


title: Viral IgG PhIP-Seq for participant 30, timepoint w36, replicate 1

description: Library name: Sample_1_31


title: WT_K27me3_pC_1

description: Library name: WT_K27me3_pC_1

value: wildtype


title: WT_K27me3_pC_2

description: Library name: WT_K27me3_pC_2


title: Viral IgG PhIP-Seq for participant 30, timepoint Post, replicate 1

description: Library name: Sample_1_30


title: Viral IgG PhIP-Seq for participant 10, timepoint w8, replicate 1

description: Library name: Sample_1_29


title: WT_K27me3_Control_2

description: Library name: WT_K27me3_Control_2


title: Viral IgG PhIP-Seq for participant 33, timepoint w36, replicate 1

description: Library name: Sample_1_54


title: Viral IgG PhIP-Seq for participant 30, timepoint w20, replicate 1

description: Library name: Sample_1_28


title: WT_K27me3_Control_1

description: Library name: WT_K27me3_Control_1


title: Retina-RPE male 4.5 months biol rep 2

description:
Library name: Resub-BC13
Male retina-RPE collected from a 4.5-month-old fish. Biological replicate 2.

value: male


title: WT_K4me3_pC_2

description: Library name: WT_K4me3_pC_2


title: Viral IgG PhIP-Seq for participant 30, timepoint w12, replicate 1

description: Library name: Sample_1_27


title: WT_K4me3_pC_1

description: Library name: WT_K4me3_pC_1


title: Viral IgG PhIP-Seq for participant 30, timepoint w4, replicate 1

description: Library name: Sample_1_26


title: Retina-RPE male 4.5 months biol rep 1

description:
Library name: BC8
Male retina-RPE collected from a 4.5-month-old fish. Biological replicate 1.

value: GRZ backcross mutant line


title: WT_K4me3_Control_2

description: Library name: WT_K4me3_Control_2


title: Viral IgG PhIP-Seq bead control S155, run IgG Vir YL1

description: Library name: Sample_1_24

value: blood


title: WT_K4me3_Control_1

description: Library name: WT_K4me3_Control_1


title: Viral IgG PhIP-Seq for participant 30, timepoint w0, replicate 1

description: Library name: Sample_1_23

value: IgG


title: Viral IgG PhIP-Seq for participant 30, timepoint Pre, replicate 1

description: Library name: Sample_1_22

value: IgG Vir YL1


title: WT_H3_pC_2

description: Library name: WT_H3_pC_2


title: WT_H3_pC_1

description: Library name: WT_H3_pC_1


title: WT_H3_Control_2

description: Library name: WT_H3_Control_2


title: Viral IgG PhIP-Seq bead control S156, run IgG Vir YL1

description: Library name: Sample_1_25


title: Viral IgG PhIP-Seq for participant 29, timepoint Post, replicate 1

description: Library name: Sample_1_20

value: birth


title: WT_H3_Control_1

description: Library name: WT_H3_Control_1


title: WT_Ac_pC_4

description: Library name: WT_Ac_pC_4


title: Viral IgG PhIP-Seq for participant 10, timepoint w4, replicate 1

description: Library name: Sample_1_18


title: WT_Ac_pC_3

description: Library name: WT_Ac_pC_3


title: Viral IgG PhIP-Seq for participant 29, timepoint w12, replicate 1

description: Library name: Sample_1_17


title: Viral IgG PhIP-Seq for participant 29, timepoint w4, replicate 1

description: Library name: Sample_1_16


title: WT_Ac_Control_4

description: Library name: WT_Ac_Control_4


title: Viral IgG PhIP-Seq for participant 29, timepoint w0, replicate 1

description: Library name: Sample_1_15


title: Viral IgG PhIP-Seq for participant 29, timepoint Pre, replicate 1

description: Library name: Sample_1_14

value: Pre


title: WT_Ac_pC_1

description: Library name: WT_Ac_pC_1


title: WT_Ac_Control_3

description: Library name: WT_Ac_Control_3


title: Viral IgG PhIP-Seq for participant 28, timepoint w36, replicate 1

description: Library name: Sample_1_13


title: WT_Ac_Control_2

description: Library name: WT_Ac_Control_2


title: Viral IgG PhIP-Seq for participant 28, timepoint Post, replicate 1

description: Library name: Sample_1_12


title: WT_Ac_Control_1

description: Library name: WT_Ac_Control_1


title: Viral IgG PhIP-Seq for participant 28, timepoint w20, replicate 1

description: Library name: Sample_1_11


title: Viral IgG PhIP-Seq for participant 28, timepoint w12, replicate 1

description: Library name: Sample_1_10


title: Liver, desisobutyryl ciclesonide 3

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

institute: University of Pittsburgh

data_processing:
Cutadapt trimmed reads were aligned to the rat reference genome using HISAT2
Raw read counts for all samples were counted using HTSeq
Assembly: Rattus norvegicus, mRatBN7.2 v107
Supplementary files format and content: text file includes raw counts for each sample ( columns: 1. Ensembl ID and 2. raw counts).

organism: Rattus norvegicus

source_name: postnatal day 6 liver

growth_protocol: pups from postnatal day 1-6 were nursed from mothers with free access to food (Prolab Isopro RMH 3000, LabDiet) and water

extract_protocol:
RNA was isolated from frozen rat lung and liver by digesting tissue in Trizol (Invitrogen) using a Lysing Matrix in a MP Biomedicals FastPrep-25 5G homogenizer followed by a chloroform extraction.
Directional mRNA library preparation (poly A enrichment). 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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: beginning on postnatal day 1, pups were injected subcutaneously in the morning daily for 5 days with various treatments and  total liver and lung tissue harvested on postnatal day 6 and snap frozen 24 hours following final treatment

value: postnatal day 6 liver

tag: strain

value: Sprague Dawley

value: WT

tag: treatment

value: 24 hours desisobutyryl ciclesonide


title: Liver, desisobutyryl ciclesonide 2


title: Viral IgG PhIP-Seq for participant 28, timepoint w0, replicate 1

description: Library name: Sample_1_8


title: Viral IgG PhIP-Seq for participant 10, timepoint w0, replicate 1

description: Library name: Sample_1_7

value: loss


title: Liver, dexamethasone 4

value: 24 hours dexamethasone


title: Liver, dexamethasone 3


title: Liver, dexamethasone 2


title: Viral IgG PhIP-Seq for participant 27, timepoint w36, replicate 1

description: Library name: Sample_1_5


title: Viral IgG PhIP-Seq for participant 27, timepoint Post, replicate 1

description: Library name: Sample_1_4


title: Liver, dexamethasone 1


title: Liver, Vehicle 4

value: 24 hours Vehicle


title: HS02 BMS-986158 D3

city: Orlando

first: Cristina

last: Fernandez-Valle

state: FL

address: 6850 Lake Nona Blvd.

institute: Unviersity of Central Florida College of Medicine

description: Library name: D3

data_processing:
Raw sequencing data was processed using the nf-core/atacseq pipeline (v2.1.2, commit hash: 1a1dbe52ffbd82256c941a032b0e22abbd925b8a) running on Nextflow (v23.10.1).
Quality control was performed using FastQC (v0.11.9) and MultiQC to assess read quality metrics.
Reads were aligned to the GRCh38 human reference genome using BWA-MEM (v0.7.17-r1188). Duplicate reads were marked using Picard MarkDuplicates (v3.0.0).
Peak calling was performed using MACS2 (v2.2.7.1) with broad peak settings for BRD4 ChIP-seq analysis. Signal tracks were generated in bigWig format using deepTools (v3.5.1).
Assembly: GRCh38
Supplementary files format and content: BigWig files containing normalized ChIP-seq signal tracks generated from MACS2 peak calling and deepTools normalization.

growth_protocol: HS02 cells were seeded at 10^6 cells/flask, two t75 CellBIND flasks per condition in Schwann Cell Media with 10x Schwann Cell Growth Supplement (ScienCell) and 10% FBS.

extract_protocol:
Flasks were crosslinked for using 10% formaldehyde for 10 min at room temperature and quenched with 25M glycine for 5 min. Nuclear extracted was performed and DNA was digested with MNase (50units/10^6 cells) followed by sonication (30% amplitude, 6 cycles, 10 sec ON, 30 sec OFF). Immunoprecipitation was performed overnight with rabbit anti-BRD4 antibodies (#BL-149-2H5, Fortis) conjugated to Dynabeads Protein A (ThermoFisher). After elution, DNA was reverse crosslinked, thenRNase and proteinase K treated. DNA was extracted using the ChIP DNA Clean & Concentrator Kit (Zymo) and analyzed using Nanodrop8000 and Tapestation 4150 bioanalyzer (Agilent).
Samples were sent to Novogene for library construction. From the quality analysis report "The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. The library was then sequenced using the Illumina NovaSeq platform (12G raw data per sample; 150bp, paired end reads).

treatment_protocol: Cells were treated the following day. Treatments were given at 5x concentration. 3mL media was removed from the 15mL total volume (per flask) and replaced with the respective treatment. Flasks were gently mixed and then incubated for 4h at 37C, 5% CO2.

tag: cell line

tag: cell type

value: schwann cells

tag: chip antibody

tag: batch

value: D


title: Liver, Vehicle 3


title: HS02 BMS-986158 D2

description: Library name: D2


title: Viral IgG PhIP-Seq for participant 27, timepoint w4, replicate 1

description: Library name: Sample_1_1


title: HS02 BMS-986158 D1

description: Library name: D1


title: Liver, Vehicle 2


title: mother fibro

first: Isabella

last: Lin

address: 615 Charles E Young Dr S

institute: University of California Los Angeles

description:
Library name: Mother_F
Column name in countdata_fibro_all.csv

data_processing:
Samples were demultiplexed after sequencing, and fastq sequencing files were processed using established pipelines in the Arboleda lab. Raw read quality, adaptor content, and duplication rates were assessed with FastQC v0.11.8.
Raw reads were then aligned against the Gencode human genome version hg38 (GR38) version 31 using STAR 2.7.0e (3) with default parameters.
Gene counts from raw reads were generated using featureCounts 1.6.5 (4) from the Subread package. Only reads that uniquely mapped to exons of a gene were counted per gene.
Differential expression analysis was completed using DESeq2 v1.24.0 (5).
Assembly: GRCh38
Supplementary files format and content: csv file with gene counts generated using featureCounts

source_name: fibro

growth_protocol: Human blood was collected and processed immediately to extract RNA. Human dermal fibroblasts were cultured in DMEM + 10% FBS + 1% NEAA

extract_protocol:
Total RNA extraction via RNeasy Plus Mini Kit (Qiagen, 74136)
All samples were then prepared with QIAseq FastSelect −rRNA HMR (Qiagen, 334386) and TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599)

value: fibro

value: Mother

value: wt


title: HS02 DMSO A1

description: Library name: A1

value: DMSO

value: A


title: father fibro 2

description:
Library name: Father_F_2
Column name in countdata_fibro_all.csv

value: Father

value: ASXL1 missense


title: Ctrl MO Veh 3

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

description: Library name: SAMPLE 12

data_processing:
The sequencing data, also known as raw reads or raw data, were subjected to quality control (QC) to determine whether the sequencing data were suitable for subsequent analysis. After QC, the clean reads were aligned to the reference sequences. After alignment, the alignment results were subjected to a second QC to evaluate the alignment quality, including alignment rate and distribution of reads on the reference sequences. After that, gene quantification analysis, various analyses based on gene expression levels (such as principal component analysis, correlation analysis, differential gene screening, etc.) were performed. Differential expressed genes between samples were further analyzed for gene ontology (GO) functional enrichment, pathway enrichment, clustering, protein-protein interaction networks, and transcription factors.
Assembly: After obtaining clean reads, we use HISAT to align clean reads to the reference genome sequence. Reference Genome Version: Danio rerio7955.NCBI.GCF000002035.6 GRCz11.v2201
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Danio rerio

source_name: Whole lysate

growth_protocol: zebrafish were maintained at 28.5°C in a recirculating aquaculture system and maintained under a 14-/10-h light/dark cycle. Heterozygous outcrossed embryos bearing Tg(ins:Flag-NTR)s950 were collected at spawning and maintained in a 28.5°C incubator in egg water-filled petri dishes

extract_protocol:
pool 20-50 zebrafish embryos in a 1.5 ml microfuge tube and remove as much water as possible with a pipette. Immediately add 250 ul of IRizol reagent' to the microfuge tube containing the embryos. TRizol reagent contains phenol and should only be used under a fume hood. Lyse and homogenize the embryos with a pellet pestle (approximately 20 strokes) until the tissue is sufficiently disrupted. When the cells are sufficiently homogenized, add 750 ul TRIzol reagent to equal a total volume of 1 ml. To permit complete dissociation of nucleoprotein complexes, incubate homogenized samples for 5 minutes at room temperature. At this stage, the sample can be flash frozen in liquid nitrogen and stored at -80°C or the protocol can be continued. To continue add 0.2 ml of chloroform and rock the tube for 15 seconds to mix. Incubate the sample for 2 minutes at room temperature and then centrifuge at 12,000 x g for 15 minutes at 4°C. The mixture will separate into a lower red phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. The upper aqueous phase contains the RNA. The top layer should comprise of about 60% of the initial volume of TRIzol (approximately 0.6 ml). Transfer the top aqueous layer into a new microfuge tube using a 1 ml pipette being careful not to transfer any of the interphase layer. To precipitate the RNA add 0.5 ml isopropanol. Allow the sample to sit at room temperature for 10 minutes and then centrifuge the sample at 12,000 x g for 10 minutes at 4°C. RNA will form a gel-like pellet on the bottom of the tube. Without disturbing the pellet, remove the supernatant with a pipette and wash the pellet in 1 ml 75% ethanol. Mix the sample by gentle inversion and centrifuge at 7,500 x g for 5 minutes at 4°C. After centrifugation, remove the ethanol with a pipette and allow sample to dry. Resuspend the pellet by adding 100 ul of RNAse-free water and incubate the sample at 55°C for 10 minutes.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3’ end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

value: Whole lysate

value: All Cells

value: Vehicle, Control MO


title: Ctrl MO Veh 2

description: Library name: SAMPLE 11

treatment_protocol: zebrafish were maintained at 28.5°C in a recirculating aquaculture system and maintained under a 14-/10-h light/dark cycle. Heterozygous outcrossed embryos bearing Tg(ins:Flag-NTR)s950 were collected at spawning and maintained in a 28.5°C incubator in egg water-filled petri dishes


title: Ctrl MO Veh 1

description: Library name: SAMPLE 10


title: father fibro

description:
Library name: Father_F_1
Column name in countdata_fibro_all.csv


title: Lung, desisobutyryl ciclesonide 3

source_name: postnatal day 6 lung

value: postnatal day 6 lung

value: Sprague Dawley

value: WT


title: Ctrl MO MTZ 3

description: Library name: SAMPLE 9

value: Metronidazole, Control MO


title: sister fibro

description:
Library name: Sister_F
Column name in countdata_fibro_all.csv

value: Sister


title: Lung, desisobutyryl ciclesonide 2

value: 24 hours desisobutyryl ciclesonide


title: Ctrl MO MTZ 1

description: Library name: SAMPLE 7


title: Smox MO Veh 3

description: Library name: SAMPLE 6

value: Vehicle, smox MO


title: Ctrl MO MTZ 2

description: Library name: SAMPLE 8


title: Viral IgG PhIP-Seq for participant 98, timepoint w12, replicate 1

description: Library name: Sample_2_225

value: blood

value: IgG

value: IgG Vir YL13

value: birth


title: Smox MO Veh 2

description: Library name: SAMPLE 5


title: proband fibro 2

description:
Library name: Proband_F_2
Column name in countdata_fibro_all.csv

value: fibro

value: Proband


title: proband fibro

description:
Library name: Proband_F_1
Column name in countdata_fibro_all.csv

value: ASXL1 missense


title: Smox MO Veh 1

description: Library name: SAMPLE 4

value: Whole lysate


title: Lung, desisobutyryl ciclesonide 1


title: Viral IgG PhIP-Seq for participant 29, timepoint w36, replicate 1

description: Library name: Sample_1_21

value: IgG Vir YL1


title: Lung, dexamethasone 4

value: 24 hours dexamethasone


title: Smox MO MTZ 3

description: Library name: SAMPLE 3

value: All Cells

value: Metronidazole, smox MO


title: Viral IgG PhIP-Seq for participant 29, timepoint w20, replicate 1

description: Library name: Sample_1_19


title: cbfs_pC_3

description: Library name: cbfs_pC_3

data_processing:
The libraries were sequenced on the Novoseq PE150 platform using a paired-end scheme (2 × 150 bp).
Assembly: Reads were mapped to the TAIR10 Arabidopsis genome using RNASTAR (Dobin et al., 2012) with default settings. Normalized reads were calculated by fraturecounts (Liao et al., 2013) and DEseq2 (Love et al., 2014). The expression level was first normalized between WT, hag1-5 and cbf1/2/3-97, and then normalized between control and prolonged cold treated samples among each background.
Supplementary files format and content: The mapped reads were retained for further analysis. The alignments were first converted to Wiggle (WIG) files using deepTools.

organism: Arabidopsis

extract_protocol:
For genome-wide expression analysis, RNA was isolated from control and prolonged cold treated seedlings of WT, hag1-5 and cbf1/2/3-97 plants using the QIAGEN RNeasy Plant Mini Kit (ID 74904) and treated with RNase-free DNase.
RNA from at least three biological replicates was sequenced separately. Sequencing libraries were built using the KAPA RNA library preparation protocol.

value: aerial parts


title: Smox MO MTZ 2

description: Library name: SAMPLE 2


title: WT_Ac_pC_2

description: Library name: WT_Ac_pC_2

value: wildtype

value: col


title: Smox MO MTZ 1

description: Library name: SAMPLE 1


title: Lung, dexamethasone 3

value: postnatal day 6 lung

value: Sprague Dawley

value: WT


title: Liver, desisobutyryl ciclesonide 4

value: postnatal day 6 liver

value: 24 hours desisobutyryl ciclesonide


title: MIA PaCa-2 cells treated with 10 μM HPC, biological replicate 5

city: Shanghai

first: Jinyuan

last: Lu

state: Select

address: No. 325 Guhe Road, Yangpu District, Shanghai

country: China

institute: Naval Medical University

description:
Library name: H5
MIA PaCa-2 cells treated with 10 μM hydroxyprogesterone caproate at 37 °C with 5% CO2 for 24 h; biological replicate 5. Column name in mRNAexpression_All_Samples.FPKM.txt: H5.

data_processing:
Raw paired-end reads were quality-controlled and adapter sequences were removed using fastp v0.23.2. Low-quality bases at the 3′ and 5′ ends were trimmed. Reads shorter than 50 bp after trimming and reads containing ambiguous N bases were discarded, and high-quality paired-end reads were retained.
Clean reads were aligned to the Homo sapiens GRCh38.p13 reference genome using STAR v2.7.7a with GENCODE release 43 gene annotation.
Gene-level expression was quantified from the aligned reads and normalized as FPKM values.
Differential expression between the HPC-treated and DMSO control groups was analyzed using edgeR with a fold-change cutoff of 2 and an adjusted P-value cutoff of 0.05.
Assembly: GRCh38.p13, GENCODE release 43
Supplementary files format and content: gene-level FPKM expression values for all 10 samples. Rows represent genes and columns represent samples C1–C5 and H1–H5.

source_name: MIA PaCa-2

growth_protocol: MIA PaCa-2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from MIA PaCa-2 cells using TRIzol reagent (B511311-0100, Sangon Biotech, China) according to the manufacturer’s instructions. RNA integrity was assessed using 1.5% agarose gel electrophoresis or a fragment analyzer, and RNA purity was measured using a NanoDrop spectrophotometer. RNA samples were snap-frozen in liquid nitrogen before library preparation.
Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads. The enriched mRNA was fragmented and reverse-transcribed into first-strand cDNA using random primers. Second-strand cDNA was synthesized, followed by end repair, A-tailing, adapter ligation, size selection, PCR amplification, and magnetic-bead purification. Libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina and quantified using Qubit 4.0. The libraries were sequenced on an Illumina NovaSeq 6000 platform using 150-bp paired-end reads.

treatment_protocol: MIA PaCa-2 cells were treated with 10 μM hydroxyprogesterone caproate (HPC), while control cells received an equal volume of DMSO. Cells were incubated for 24 h at 37 °C in a humidified atmosphere containing 5% CO2.

value: MIA PaCa-2

value: pancreatic ductal adenocarcinoma cell

value: 10 μM hydroxyprogesterone caproate (HPC) for 24 h


title: cbfs_pC_2

description: Library name: cbfs_pC_2


title: Lung, dexamethasone 2


title: Viral IgG PhIP-Seq for participant 28, timepoint w4, replicate 1

description: Library name: Sample_1_9

value: blood

value: IgG

value: birth


title: MIA PaCa-2 cells treated with 10 μM HPC, biological replicate 4

description:
Library name: H4
MIA PaCa-2 cells treated with 10 μM hydroxyprogesterone caproate at 37 °C with 5% CO2 for 24 h; biological replicate 4. Column name in mRNAexpression_All_Samples.FPKM.txt: H4.


title: cbfs_pC_1

description: Library name: cbfs_pC_1


title: MIA PaCa-2 cells treated with 10 μM HPC, biological replicate 3

description:
Library name: H3
MIA PaCa-2 cells treated with 10 μM hydroxyprogesterone caproate at 37 °C with 5% CO2 for 24 h; biological replicate 3. Column name in mRNAexpression_All_Samples.FPKM.txt: H3.


title: Lung, dexamethasone 1

value: 24 hours dexamethasone


title: Liver, desisobutyryl ciclesonide 1


title: Viral IgG PhIP-Seq for participant 28, timepoint Pre, replicate 1

description: Library name: Sample_1_6

value: Pre

value: IgG Vir YL1


title: MIA PaCa-2 cells treated with 10 μM HPC, biological replicate 2

description:
Library name: H2
MIA PaCa-2 cells treated with 10 μM hydroxyprogesterone caproate at 37 °C with 5% CO2 for 24 h; biological replicate 2. Column name in mRNAexpression_All_Samples.FPKM.txt: H2.


title: cbfs_Control_3

description: Library name: cbfs_Control_3

value: aerial parts


title: MIA PaCa-2 cells treated with 10 μM HPC, biological replicate 1

description:
Library name: H1
MIA PaCa-2 cells treated with 10 μM hydroxyprogesterone caproate at 37 °C with 5% CO2 for 24 h; biological replicate 1. Column name in mRNAexpression_All_Samples.FPKM.txt: H1.


title: Lung, Vehicle 4

value: 24 hours Vehicle


title: MIA PaCa-2 cells treated with DMSO, biological replicate 5

description:
Library name: C5
MIA PaCa-2 cells treated with an equal volume of DMSO at 37 °C with 5% CO2 for 24 h; biological replicate 5. Column name in mRNAexpression_All_Samples.FPKM.txt: C5.

value: Equal volume of DMSO vehicle control for 24 h


title: Viral IgG PhIP-Seq for participant 27, timepoint w20, replicate 1

description: Library name: Sample_1_3


title: cbfs_Control_2

description: Library name: cbfs_Control_2


title: MIA PaCa-2 cells treated with DMSO, biological replicate 4

description:
Library name: C4
MIA PaCa-2 cells treated with an equal volume of DMSO at 37 °C with 5% CO2 for 24 h; biological replicate 4. Column name in mRNAexpression_All_Samples.FPKM.txt: C4.


title: Lung, Vehicle 3

value: postnatal day 6 lung


title: IL33KO_CIAKI_3

city: Nanjing

first: Mengqing

last: Ma

state: Jiangsu

address: 68 Changle Road

institute: Nanjing First Hospital, Nanjing Medical University

description:
Library name: Sample 12
Kidney tissue from an Il33 knockout mouse subjected to the CIAKI protocol for bulk RNA-seq.

data_processing:
Raw sequencing reads were subjected to quality control using FastQC.
Adapter sequences and low-quality reads were removed using Cutadapt to generate clean reads.
Clean paired-end reads were aligned to the Mus musculus reference genome using HISAT2.
Aligned reads were assembled and quantified using StringTie to generate gene- and transcript-level read counts and FPKM values.
Differential expression analysis was performed using DESeq2 or edgeR, and P values were adjusted using the Benjamini-Hochberg method.
Assembly: Mus musculus reference genome, Ensembl release 112
Supplementary files format and content: Tab-delimited text files containing gene-level FPKM expression values for all samples in each batch. Rows represent genes and columns represent individual RNA-seq samples.

molecule: polyA RNA

organism: Mus musculus

source_name: kidney

growth_protocol: Male WT C57BL/6, Padi4 knockout, and Il33 knockout mice aged 8 weeks were maintained under standard laboratory conditions before CIAKI induction. Kidney tissues were collected 24 h after iodixanol administration for RNA extraction.

extract_protocol:
Total RNA was extracted from mouse kidney tissues using TRIzol reagent according to the manufacturer's protocol. RNA quantity and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer 2100. RNA samples passing quality control were used for library preparation.
Polyadenylated mRNA was enriched from total RNA using oligo(dT) magnetic beads and fragmented. First-strand cDNA was synthesized by reverse transcription, followed by second-strand cDNA synthesis. After end repair, A-tailing, adaptor ligation, size selection, and PCR amplification, strand-specific RNA-seq libraries were generated and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: A murine contrast-induced acute kidney injury (CIAKI) model was established. Mice underwent unilateral nephrectomy and were allowed to recover for 3 weeks. Before contrast administration, mice were deprived of water for 24 h and received intraperitoneal furosemide 20 min before tail-vein injection of iodixanol. Kidney tissues were harvested 24 h after iodixanol injection.

value: kidney

value: Il33 knockout

value: contrast-induced acute kidney injury

value: batch 2


title: Viral IgG PhIP-Seq for participant 27, timepoint w12, replicate 1

description: Library name: Sample_1_2


title: cbfs_Control_1

description: Library name: cbfs_Control_1


title: MIA PaCa-2 cells treated with DMSO, biological replicate 3

description:
Library name: C3
MIA PaCa-2 cells treated with an equal volume of DMSO at 37 °C with 5% CO2 for 24 h; biological replicate 3. Column name in mRNAexpression_All_Samples.FPKM.txt: C3.

value: MIA PaCa-2


title: IL33KO_CIAKI_2

description:
Library name: Sample 11
Kidney tissue from an Il33 knockout mouse subjected to the CIAKI protocol for bulk RNA-seq.


title: hag1_pC_3

description: Library name: hag1_pC_3


title: IL33KO_CIAKI_1

description:
Library name: Sample 10
Kidney tissue from an Il33 knockout mouse subjected to the CIAKI protocol for bulk RNA-seq.


title: MIA PaCa-2 cells treated with DMSO, biological replicate 2

description:
Library name: C2
MIA PaCa-2 cells treated with an equal volume of DMSO at 37 °C with 5% CO2 for 24 h; biological replicate 2. Column name in mRNAexpression_All_Samples.FPKM.txt: C2.

value: pancreatic ductal adenocarcinoma cell


title: Lung, Vehicle 1

value: Sprague Dawley

value: WT


title: hag1_pC_2

description: Library name: hag1_pC_2


title: MIA PaCa-2 cells treated with DMSO, biological replicate 1

description:
Library name: C1
MIA PaCa-2 cells treated with an equal volume of DMSO at 37 °C with 5% CO2 for 24 h; biological replicate 1. Column name in mRNAexpression_All_Samples.FPKM.txt: C1.


title: WT_CIAKI_IL33KO_set_3

description:
Library name: Sample 9
Kidney tissue from a wild-type mouse subjected to the CIAKI protocol for bulk RNA-seq

value: wild type


title: wt_batch2_SN_rep2

city: Guangzhou

first: Ying

middle: liang

last: Sheng

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

description: Library name: Sample20

data_processing:
RNA-seq raw reads were trimmed using Trim_galore (v0.6.7) and aligned to the mouse genome (mm10 and Gencode gene annotation vM25) using STAR (v2.7.0d)61 and RSEM (v1.3.3)62; The DESeq2 package63 was used for differential expression analysis. Differentially expressed genes were defined by a p-value < 0.05 and an absolute fold-change > 2. GO analysis was performed according to the clusterProfiler64 (v4.8.3).
Raw reads underwent quality control using FastQC (v0.11.9). Subsequently, Trim_galore (v0.6.7) was employed to trim low-quality base and adapter sequences. These processed reads were then aligned to the mouse (mm10) reference genome using Bowtie265 (v2.2.5). To filter out reads with low mapping quality, SAMtools66 (v1.14) was applied with the parameters ‘-F 1804 -f 2 -q 20’. Concurrently, potential PCR duplicates were eliminated using Sambamba67 (v0.7.1). The resulting Bigwig files were generated by DeepTools68 (v3.5.1) using the parameter ‘-normalizeUsing RPKM --extendReads 200 -bs 1’.
Assembly: mm10
Supplementary files format and content: Tab
Supplementary files format and content: bw

source_name: oocyte

extract_protocol:
As previously described by Crosetto et al. (2015), RNA was extracted from lysed cells and precipitated overnight. RNA was then reverse-transcribed into cDNA using Thermo Fisher's SuperScript II Reverse Transcriptase (Cat No. 18064014). Label the oocytes with N3-Kethoxal, then extract the labeled genomic DNA using the BeyoMag™ Genomic DNA Small Sample Extraction Kit (Beyotime D0088S).
cDNA amplification was performed using KAPA HiFi HotStart DNA Polymerase, followed by library construction with the Vazyme TD503 kit.
KAS-seq was conducted following the published protocol60. Label the oocytes with N3-Kethoxal, then extract the labeled genomic DNA using the BeyoMag™ Genomic DNA Small Sample Extraction Kit (Beyotime D0088S). After labeling, fragment the DNA using Tn5 transposase (Vazyme TD501) under incubation conditions of 37 °C and 500 rpm for 30 min. Biotinylate the DNA using DBCO-PEG4-biotin (DMSO solution, Sigma 760,749). Next, purify the biotinylated DNA with the DNA Clean & Concentrator-5 kit (Zymo, D4013), retaining 5 μL of the labeled DNA as input, while the remaining 50 μL of DNA is used for enrichment. Wash 5 μL of Dynabeads™ MyOne™ Streptavidin C1 (Thermo 65,001) three times with 1 × binding and wash buffer. Then, resuspend the pre-washed beads in 2 × binding and wash buffer. Mix the beads with the 50 μL fragmented DNA obtained from the previous step and rotate gently at room temperature for 15 min. After incubation, place the mixture on a magnetic rack to remove the supernatant and wash the beads five times with 1 × binding and wash buffer. Elute the biotinylated fragments at 98 °C for more than 10 min. Perform PCR amplification using KAPA HiFi DNA polymerase; incubate the PCR reaction at 72 °C for 3 min, then at 98 °C for 45 s, followed by 14 cycles of amplification (15 s at 98 °C, 30 s at 60 °C, and 1 min at 72 °C).                                                                                As previously described, ChIP-seq libraries for all samples were prepared using an ultra-low-input native ChIP protocol. Samples were thawed on ice and permeabilized in PBS containing 0.1% Triton-X-100 and 0.1% sodium deoxycholate. Micrococcal nuclease digestion was performed using 200 U of micrococcal nuclease (NEB, M0247S) in a customized digestion buffer. Samples were digested at 21°C for 7.5 min, and the reaction was terminated with 100 mM EDTA. Chromatin samples were pre-cleared with protein A/G beads in complete immunoprecipitation buffer, rotating at 4°C for 2 h, while antibodies were conjugated to beads at 4°C for 3 h. For each immunoprecipitation of oocytes, anti-H3K4me3 or anti-H3K36me3 antibodies were used. Chromatin was added to the antibody-bound beads, and samples were rotated at 4°C overnight. Samples were then subjected to two low-salt washes and one high-salt wash, followed by DNA elution from the beads at 65°C for 1.5 h. DNA was extracted and purified using phenol, chloroform, and isoamyl alcohol. And libraries were constructed using the Vazyme TD607 kit according to the manufacturer's instructions.

value: oocyte


title: hag1_pC_1

description: Library name: hag1_pC_1


title: father fibro 3

description:
Library name: Father_F_3
Column name in countdata_fibro_all.csv

value: fibro

value: Father

value: ASXL1 missense


title: wt_batch2_SN_rep1

description: Library name: Sample19


title: WT_CIAKI_IL33KO_set_2

description:
Library name: Sample 8
Kidney tissue from a wild-type mouse subjected to the CIAKI protocol for bulk RNA-seq


title: hag1_Control_3

description: Library name: hag1_Control_3

value: aerial parts


title: oeSupt6_batch2_SN_rep2

description: Library name: Sample18


title: hag1_Control_2

description: Library name: hag1_Control_2


title: father blood

description:
Library name: Father_B
Column name in countdata_blood_all.csv

value: blood


title: oeSupt6_batch2_SN_rep1

description: Library name: Sample17


title: hag1_Control_1

description: Library name: hag1_Control_1


title: mother blood

description:
Library name: Mother_B
Column name in countdata_blood_all.csv

value: wt


title: oeRnaseh1_wkkd_SN_rep2

description: Library name: Sample16


title: PAD4KO_CIAKI_2

description:
Library name: Sample 5
Kidney tissue from a Padi4 knockout mouse subjected to the CIAKI protocol for bulk RNA-seq.

value: Pad4 knockout

value: batch 1


title: WT_pC_3

description: Library name: WT_pC_3

value: col


title: proband blood

description:
Library name: Proband_B
Column name in countdata_blood_all.csv


title: oeRnaseh1_wkkd_SN_rep1

description: Library name: Sample15


title: PAD4KO_CIAKI_1

description:
Library name: Sample 4
Kidney tissue from a Padi4 knockout mouse subjected to the CIAKI protocol for bulk RNA-seq.

value: kidney

value: contrast-induced acute kidney injury


title: WT_pC_2

description: Library name: WT_pC_2


title: HS05 Fime set I

description:
Library name: I4
HS05_Fime_set_I

data_processing:
Gene and transcript expression quantification results were generated using the nf-core/rnaseq pipeline (v3.12.0, commit hash: 3bec2331cac2b5ff88a1dc71a21fab6529b57a0f), nextflow version  v22.10.6.
Sequenced reads were filtered to remove adapter and low-quality reads.
Quality control was performed using FastQC (v0.11.9) and MultiQC to assess read quality metrics.
Reads were aligned to the GRCh38 (GENCODE v40) human reference genome using STAR aligner (v2.7.9a).
Gene expression quantification was performed using Salmon (v1.10.1).
Assembly: GRCh38 (GENCODE v40 primary assembly)
Supplementary files format and content: Tab-delimited text file containing TPM gene expression values generated by Salmon quantification.

growth_protocol: Cells were seeded at 150,000 cells/well in a 6-well CellBIND plate and allowed to attach for ~12h prior to treatment. Cells were grown in Schwann Cell Media with 10x Schwann Cell Growth Supplement (ScienCell) and 10% FBS.

extract_protocol:
Samples were extracted with either the RNeasy Mini Kit (Qiagen) or  Quick RNA Miniprep (Zymo Research) following TRIZOL lysis. All samples were DNase treated and eluted in water.
Library preparation was performed by Novogene. From the quality analysis report "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". Sequencing was conducted using Illumina HiSeq Platform (150bp, paired end reads).

treatment_protocol: Treatments were given at 6x concentration. 500µL media was removed from the 3mL total volume (per well) and replaced with the respective treatment. The plate was gently mixed and then incubated for 36h at 37C, 5% CO2.

value: schwann cells

value: 100nM Fimepinostat

value: I


title: oemCherry_batch2_SN_rep2

description: Library name: Sample14

value: oe-mCherry


title: WT_CIAKI_PAD4KO_set_3

description:
Library name: Sample 3
Kidney tissue from a wild-type mouse subjected to the CIAKI protocol for bulk RNA-seq

value: wild type


title: WT_pC_1

description: Library name: WT_pC_1


title: HS05 Briga set I

description:
Library name: I3
HS05_Briga_set_I

value: 1uM Brigatinib


title: oemCherry_batch2_SN_rep1

description: Library name: Sample13

value: oocyte


title: WT_Control_3

description: Library name: WT_Control_3


title: WT_CIAKI_PAD4KO_set_2

description:
Library name: Sample 2
Kidney tissue from a wild-type mouse subjected to the CIAKI protocol for bulk RNA-seq


title: HS05 DMSO set I 2

description:
Library name: I2
HS05_DMSO_set_I_2


title: oeSupt6_SN_SETD2_rep2

description: Library name: Sample12

data_processing:
RNA-seq raw reads were trimmed using Trim_galore (v0.6.7) and aligned to the mouse genome (mm10 and Gencode gene annotation vM25) using STAR (v2.7.0d)61 and RSEM (v1.3.3)62; The DESeq2 package63 was used for differential expression analysis. Differentially expressed genes were defined by a p-value < 0.05 and an absolute fold-change > 2. GO analysis was performed according to the clusterProfiler64 (v4.8.3).
Raw reads underwent quality control using FastQC (v0.11.9). Subsequently, Trim_galore (v0.6.7) was employed to trim low-quality base and adapter sequences. These processed reads were then aligned to the mouse (mm10) reference genome using Bowtie265 (v2.2.5). To filter out reads with low mapping quality, SAMtools66 (v1.14) was applied with the parameters ‘-F 1804 -f 2 -q 20’. Concurrently, potential PCR duplicates were eliminated using Sambamba67 (v0.7.1). The resulting Bigwig files were generated by DeepTools68 (v3.5.1) using the parameter ‘-normalizeUsing RPKM --extendReads 200 -bs 1’.
Assembly: mm10
Supplementary files format and content: Tab
Supplementary files format and content: bw
Library strategy: CUT&Run


title: WT_CIAKI_PAD4KO_set_1

description:
Library name: Sample 1
Kidney tissue from a wild-type mouse subjected to the CIAKI protocol for bulk RNA-seq


title: WT_Control_2

description: Library name: WT_Control_2


title: HS05 DMSO set I 1

description:
Library name: I1
HS05_DMSO_set_I_1


title: NCH1 chunk M

description:
Library name: TM1
NCH1_chunk_M

source_name: paraspinal schwannoma

value: paraspinal schwannoma


title: WT_Control_1

description: Library name: WT_Control_1


title: RNA-seq of mouse central memory CD8 T cells, replicate 3

city: Beijing

first: Chenlei

last: Xu

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description: Library name: TCM-R3

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Assembly: mm39
Supplementary files format and content: Tab-delimited raw gene-level count matrix generated by featureCounts.

source_name: spleen

extract_protocol:
Tissues were freshly dissected and immediately transferred into RNA lysis buffer. Samples were mechanically homogenized using a tissue homogenizer. Total RNA was isolated using a kit-based extraction workflow according to the manufacturer’s instructions. RNA concentration was measured (e.g., spectrophotometry/fluorometry), and RNA quality was assessed prior to submission for library construction and high-throughput sequencing.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: spleen


title: oeRnaseh1_Supt6_SN_SETD2_rep2

description: Library name: Sample10

value: oe-Rnaseh1 & oe-Supt6


title: 2N+ABA-3

city: Qingdao

first: Junyi

last: Mu

address: No. 72, Binhai Road, Jimo District, Qingdao City

institute: Shandong Unoversity

description: Library name: Mu36

data_processing:
The construction and sequencing of the mRNA library were performed on the DNBSEQ platform at the high-throughput laboratory of Wuhan Huada Gene Technology Service Co., LTD, with a sequencing length of PE150. Sequencing data was filtered using the software SOAPnuke. The quality-controlled clean reads were then aligned to the reference genome (IWGSC RefSeq v1.1) using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) and Bowtie2.
\
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: raw counts, fpkm, tpm, norm_read_count for each Sample

organism: Triticum aestivum

source_name: Root

growth_protocol: These materials were grown in a greenhouse with white light at 400 μmol·m-2·s-1, with a relative humidity of 50%, and a photoperiod of 16 hours of daylight (22°C) and 8 hours of nighttime (16°C). After germinating for 3 days under normal growth conditions, the endosperm was removed, and the seedlings were transferred to wheat nutrient culture medium containing 1.5 mM KCl, 1 mM MgSO4, 0.2 mM KH2PO4, 0.1 mM Fe(III)-EDTA, 1 µM H3BO3, 1µM ZnSO4, 1 µM MnSO4, 0.5 µM CuSO4, 0.05 µM Na2MoO4, 2.5 mM Ca(NO3)2 or CaCl2, pH = 6.0.

extract_protocol:
The roots of wheat were collected and subjected to total RNA extraction using the TriZol RNA extraction kit (TransGen Biotech).
mRNA enrichment from total RNA was performed using Oligo(dT) magnetic beads to isolate polyA-tailed mRNA. The RNA was fragmented, reverse-transcribed with random N6 primers, and converted into double-stranded cDNA. The DNA ends were blunt-ended, 5'-phosphorylated, and A-tailed, followed by ligation to a bubble-shaped adapter with a 3'-T overhang. The ligated products were PCR-amplified, heat-denatured into single strands, and circularized using a bridge primer to generate single-stranded circular DNA libraries. After quality control, qualified libraries were sequenced.

treatment_protocol: For analysis of ABA and nitrogen treated transcriptome, wild-type wheat JW1 at 3 days after germination was removed endosperm and cultured on wheat nutrient culture medium containing 2 mM nitrate for 3 days, and then transferred to a nitrogen-free wheat nutrient culture medium for an additional 2 days. Following this, the wheat seedlings were exposed to wheat nutrient culture medium containing 2 mM KCl or 2 mM KNO3, and/or 5 μM ABA for 3 hours.

value: Root

value: wheat leaf tissue

value: Root cell


title: oeRnaseh1_Supt6_SN_SETD2_rep1

description: Library name: Sample9


title: NCH1 chunk C

description:
Library name: TC1
NCH1_chunk_c


title: RNA-seq of mouse central memory CD8 T cells, replicate 1

description: Library name: TCM-R1


title: SN oocyte_oeRnaseh1_KASseq_rep2

description:
Library name: Sample8
oeRnaseh1_KAS-seq.bw


title: RNA-seq of mouse virtual memory CD8 T cells, replicate 3

description: Library name: TVM-R3


title: 2N+ABA-1

description: Library name: Mu34


title: proband fibro 3

description:
Library name: Proband_F_3
Column name in countdata_fibro_all.csv

value: fibro

value: Proband

value: ASXL1 missense


title: NCH1 chunk A

description:
Library name: TA1
NCH1_chunk_a


title: SN oocyte_oeRnaseh1_KASseq_rep1

description:
Library name: Sample7
oeRnaseh1_KAS-seq.bw


title: RNA-seq of mouse virtual memory CD8 T cells, replicate 2

description: Library name: TVM-R2


title: WT_CIAKI_IL33KO_set_1

description:
Library name: Sample 7
Kidney tissue from a wild-type mouse subjected to the CIAKI protocol for bulk RNA-seq

value: kidney

value: contrast-induced acute kidney injury

value: batch 2


title: PAD4KO_CIAKI_3

description:
Library name: Sample 6
Kidney tissue from a Padi4 knockout mouse subjected to the CIAKI protocol for bulk RNA-seq.

value: Pad4 knockout

value: batch 1


title: 0N+ABA-3

description: Library name: Mu30


title: HS05 Briga + BMS set H

description:
Library name: H5
HS05_Briga_._BMS_set_H

value: schwann cells

value: 1uM Brigatinib + 250nM BMS-986158

value: H


title: SN oocyte_oeSPT6_KASseq_rep2

description:
Library name: Sample6
oeSupt6_KAS-seq.bw

value: oocyte


title: RNA-seq of mouse virtual memory CD8 T cells, replicate 1

description: Library name: TVM-R1

value: spleen


title: 0N+ABA-2

description: Library name: Mu29


title: HS05 BMS set H

description:
Library name: H4
HS05_BMS_set_H


title: SN oocyte_oeSPT6_KASseq_rep1

description:
Library name: Sample5
oeSupt6_KAS-seq.bw


title: Ctrl_hic 2

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

description: Library name: Ctrl_hic

data_processing:
For ATAC-seq:Bowtie2 with ‘-very-sensitive’ option was used to map the high-quality reads to mm10 version of mice genome. The uniquely properly paired mapped reads were extracted for downstream analysis. MACS2 with the ‘-nomodel’ and ‘-extsize 147′ was used to call ATAC peaks. DESeq2 was used to identify significantly differential (FDR <=0.05) ATAC peaks between different conditions.
For cuttag:Cutadapt was used to remove low quality bases and adaptors. Clean reads were mapped to mm10 genome by using bowtie2. MACS2 was used to call cut&tag peaks with default settings. Bam2wig.py script was used to generate bigwig tracks for visualization in IGV5.
For HiC: HiC-Pro was used to perform reads alignment, quality control, and pairing reads. The h5 file was generated by using HiC-Pro. DeepLoops was applied to predict loops.
For RNA-seq: Uniquely mapped reads were retained for gene-level quantification using the htseq-count function from the HTSeq package.
For m3C-seq, raw sequencing reads were first subjected to quality control using FastQC, and adapter trimming was performed with cutadapt (v1.9.1). High-quality reads were then aligned to the mouse reference genome (mm10) using bowtie2 with default parameters. Raw counts and coverage counts were calculated by bedtools (v2.24) software and in-house scripts, then ratio (define as: count/coverage) and fc (defined as: treat-methyl-ratio/Input-methyl-ratio)(Schwartz et al., 2014) were also calculated.
For RIP-seq, after 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality reads were aligned to the reference genome with hisat2 software (v2.0.4). Binding sites on RNAs (peaks) were identified by MACS2 software. Then, HTSeq software (v0.9.1) was used to get the gene level raw count as the expression profiling
Assembly: mm10
Supplementary files format and content: bigwig and normalized coverage signal
Supplementary files format and content: h5 format contain hic information
Supplementary files format and content: txt and counts

extract_protocol:
For ATAC-seq, the extracted nuclei were re-suspended fragmented buffer including 1.5 μL transposome (novoprotein N248), and incubated at 37 oC for 30 min. For CUT&Tag, cells were sorted enriched by ConA-magnetic beads, and then incubated overnight with antibody. The next day, beads were washed and incubated with anti-rabbit secondary antibody. Then the beads were washed and incubated with proteinA/G-Tnp transposome in Chitag. Next, cells were resuspended in 100 μL Tagmentation buffer (10 mM MgCl in Chitag Buffer) and incubated at 37 °C for 1 hr. The tagmentation was terminated by adding 1 μL of 10% SDS at 55 °C for 10 min. For HiC, the sorted cells were crosslinked with 1% formaldehyde and lysed in 1 ml lysis buffer. The resulting chromatin was then digested with NUB I (NEB) restriction enzymes at at 37 °C overnight. The DNA ends were blunted and labelled with biotin by Klenow DNA polymerase, followed by ligation using T4 DNA ligase (NEB). After reverse crosslinking, DNA was fragmented by sonication. For RNA-seq, RNA was extracted using the Direct-zol RNA MiniPrep kit (Zymo Research). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.For m3C-seq, RNA samples were subjected to alkaline hydrolysis for fragmentation. RNA fragments were dephosphorylated with antarctic phosphatase (NEB, USA) and then incubated in 1M aniline for cleavage. For RIP-seq, the RNA immunoprecipitation assay was carried out with GenSeq RIP kit (GenSeq Inc.) according to the manufacturer’s instructions. rRNAs were removed by using GenSeq rRNA Removal Kit (GenSeq, Inc.).
For ATAC-seq, the products were purified with tagment DNA extract beads (novoprotein N245), and then amplified by PCR for 14 cycles with NovoNGS index kit for illumine (N239). For CUT&Tag, the DNA fragments added 1 μL spike in (Vazyme) and were extracted by DNA extract beads, then amplified by PCR for 12 cycles with TruePrep index kit for illumine. For HiC, the DNA fragments were then end-repaired and the biotinylated DNA fragments were captured using Dynabeads MyOne Streptavidin C1 beads (Invitrogen, Termo Fisher Scientifc). The DNA on beads was ligated to the Truseq adaptors and amplifed with PCR for library construction. For RNA-seq, Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations.For m3C-seq, RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq Inc.) by following the manufacturer’s instructions.For,RIP-seq, RNA libraries were constructed by using rRNA-depleted RNAs with GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.


title: HS05 Fime set H

description:
Library name: H3
HS05_Fime_set_H

value: 100nM Fimepinostat


title: 0N+ABA-1

description: Library name: Mu28

value: Root


title: oeSPT6_H3K4me3_rep2

description:
Library name: Sample4
oeRnaseh1_Supt6_SN_H3K4me3.bw


title: 2N-3

description: Library name: Mu33

data_processing:
The construction and sequencing of the mRNA library were performed on the DNBSEQ platform at the high-throughput laboratory of Wuhan Huada Gene Technology Service Co., LTD, with a sequencing length of PE150. Sequencing data was filtered using the software SOAPnuke. The quality-controlled clean reads were then aligned to the reference genome (IWGSC RefSeq v1.1) using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) and Bowtie2.
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: raw counts, fpkm, tpm, norm_read_count for each Sample

treatment_protocol: For analysis of ABA and nitrogen treated transcriptome, wild-type wheat JW1 at 3 days after germination was removed endosperm and cultured on wheat nutrient culture medium containing 2 mM nitrate for 3 days, and then transferred to a nitrogen-free wheat nutrient culture medium for an additional 2 days. Following this, the wheat seedlings were exposed to wheat nutrient culture medium containing 2 mM KCl or 2 mM KNO for 3 hours.

value: wheat leaf tissue

value: 2 mM nitrate (2N)


title: Th1-Ctrl_hic

description: Library name: Th1-Ctrl_hic


title: HS05 Briga set H

description:
Library name: H2
HS05_Briga_set_H

value: 1uM Brigatinib


title: oeSPT6_H3K4me3_rep1

description:
Library name: Sample3
oeRnaseh1_Supt6_SN_H3K4me3.bw


title: TFH-m3C_KO_input

description: Library name: TFH-m3C_KO_input


title: 2N-2

description: Library name: Mu32

value: Root cell


title: HS05 Briga + BMS set G

description:
Library name: G5
HS05_Briga_._BMS_set_G

value: G


title: oeSupt6_SN_SETD2_rep1

description: Library name: Sample11


title: oeSPT6_H3K36me3_rep2

description:
Library name: Sample2
oeRnaseh1_Supt6_SN_H3K36me3.bw


title: 2N-1

description: Library name: Mu31


title: TFH-m3C_KO

description: Library name: TFH-m3C_KO


title: HS05 BMS set G

description:
Library name: G4
HS05_BMS_set_G


title: oeSPT6_H3K36me3_rep1

description:
Library name: Sample1
oeRnaseh1_Supt6_SN_H3K36me3.bw


title: TFH-m3C_WT_input

description: Library name: TFH-m3C_WT_input


title: RNA-seq of mouse central memory CD8 T cells, replicate 2

description: Library name: TCM-R2


title: 0N-3

description: Library name: Mu27

value: 0 mM nitrate (0N)


title: HS05 Fime set G

description:
Library name: G3
HS05_Fime_set_G


title: NCH1 chunk F

description:
Library name: TF1
NCH1_chunk_f

value: paraspinal schwannoma


title: rescue_RNAseq_oeRnaseh1_rep2

description: Library name: Sample6

data_processing:
RNA-seq raw reads were trimmed using Trim_galore (v0.6.7) and aligned to the mouse genome (mm10 and Gencode gene annotation vM25) using STAR (v2.7.0d)61 and RSEM (v1.3.3)62; The DESeq2 package63 was used for differential expression analysis. Differentially expressed genes were defined by a p-value < 0.05 and an absolute fold-change > 2. GO analysis was performed according to the clusterProfiler64 (v4.8.3).
Assembly: mm10
Supplementary files format and content: Tab

extract_protocol:
As previously described by Crosetto et al. (2015), RNA was extracted from lysed cells and precipitated overnight. RNA was then reverse-transcribed into cDNA using Thermo Fisher's SuperScript II Reverse Transcriptase (Cat No. 18064014).
cDNA amplification was performed using KAPA HiFi HotStart DNA Polymerase, followed by library construction with the Vazyme TD503 kit.


title: TFH-m3C_WT

description: Library name: TFH-m3C_WT


title: 0N-2

description: Library name: Mu26


title: HS05 Briga set G

description:
Library name: G2
HS05_Briga_set_G


title: rescue_RNAseq_oeRnaseh1_rep1

description: Library name: Sample5


title: 2N+ABA-2

description: Library name: Mu35


title: IgG1 plasma cells-3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: Sample 6

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.3.5.1.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from cells using the miRNeasy Micro kit (QIAGEN N.V.) according to the enclosed instructions.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: IgG1 plasma cell


title: 0N-1

description: Library name: Mu25


title: HS05 DMSO set G

description:
Library name: G1
HS05_DMSO_set_G


title: rescue_RNAseq_oeRnaseh1_oeSupt6_rep2

description: Library name: Sample4


title: IgG1 plasma cells-2

description: Library name: Sample 5


title: HS02 Briga + BMS set F

description:
Library name: F5
HS02_Briga_._BMS_set_F

value: F


title: DEL_MANF_3

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

description: Library name: LIB121940

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN BCLconvert version 4.3.13
Fastq files were combined and aligned with STAR 2.7.11b
Gene counts quantitated with Subread:featureCount 2.0.8 with CPM and TPM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.113
Supplementary files format and content: Gene counts with CPM and TPM in tab-delimitted text format

source_name: TALs

growth_protocol: Kidney organoids were cultured in APEL2 medium containing 1 μg/mL heparin.

extract_protocol:
Kidney organoids were enzymatically dissociated into single-cell suspensions using Accutase cell dissociation reagent (Gibco). Organoids were incubated in Accutase at 37 °C with gentle shaking for 5 minutes. Enzymatic digestion was terminated by adding an equal volume of DMEM/F12 (Gibco) supplemented with 10% fetal bovine serum (Gibco). Following digestion, cell suspensions passed through a 40 μm cell strainer (Alkali Scientific) to remove residual clumps, yielding a single-cell suspension suitable for magnetic bead-based cell sorting. UMOD-positive cells were isolated using a magnetic bead-based immunocapture approach. Biotinylated polyclonal sheep anti-human UMOD antibody (R&D Systems) was incubated with Dynabeads Biotin Binder magnetic beads (Invitrogen). For each preparation, 100 μL of Dynabeads were conjugated with 2 μg of anti-UMOD antibody by incubation at 4 °C for 2 hours with gentle rotation. After washing to remove unbound antibody, the conjugated beads were incubated with the single-cell suspension at 4 °C for 1 hour to allow binding to UMOD-expressing cells. Bead-bound UMOD-positive cells were isolated using a magnetic separation stand. The bead-cell complexes were retained against the magnet, and unbound (UMOD-negative) cells were removed through multiple PBS washes. The enriched UMOD-positive fraction was then collected and processed for downstream RNA extraction using RNeasy Micro Kit (Qiagen).
Takara-Clontech SMARTer Ultra Low RNA

treatment_protocol: For inducible lentiviral vector-mediated MANF overexpression, TRE-MANF-expressing stable hiPSC line-differentiated organoids were cultured in APEL medium supplemented with 1 μg/mL heparin, and 0.5 μg/mL doxycycline administered from day 22 to day 30.

value: TALs

value: UMOD deletion mutation with rtTA-MANF

value: Treatment with doxycycline for MANF expression


title: rescue_RNAseq_oeRnaseh1_oeSupt6_rep1

description: Library name: Sample3


title: DEL_MANF_2

description: Library name: LIB121939


title: HS02 BMS set F

description:
Library name: F4
HS02_BMS_set_F

value: schwann cells


title: rescue_RNAseq_oemCherry_rep2

description: Library name: Sample2

value: oocyte

value: oe-mCherry


title: IgG1 plasma cells-1

description: Library name: Sample 4

value: spleen


title: IgM plasma cells-3

description: Library name: Sample 3

value: IgM plasma cell


title: DEL_MANF_1

description: Library name: LIB121938


title: HS02 Fime set F

description:
Library name: F3
HS02_Fime_set_F

value: 100nM Fimepinostat


title: rescue_RNAseq_oemCherry_rep1

description: Library name: Sample1


title: IgM plasma cells-2

description: Library name: Sample 2


title: HS02 Briga set F

description:
Library name: F2
HS02_Briga_set_F


title: SN oocyte_input

description: Library name: Sample17

data_processing:
Raw reads underwent quality control using FastQC (v0.11.9). Subsequently, Trim_galore (v0.6.7) was employed to trim low-quality base and adapter sequences. These processed reads were then aligned to the mouse (mm10) reference genome using Bowtie265 (v2.2.5). To filter out reads with low mapping quality, SAMtools66 (v1.14) was applied with the parameters ‘-F 1804 -f 2 -q 20’. Concurrently, potential PCR duplicates were eliminated using Sambamba67 (v0.7.1). The resulting Bigwig files were generated by DeepTools68 (v3.5.1) using the parameter ‘-normalizeUsing RPKM --extendReads 200 -bs 1’.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Run

extract_protocol:
Label the oocytes with N3-Kethoxal, then extract the labeled genomic DNA using the BeyoMag™ Genomic DNA Small Sample Extraction Kit (Beyotime D0088S).
KAS-seq was conducted following the published protocol60. Label the oocytes with N3-Kethoxal, then extract the labeled genomic DNA using the BeyoMag™ Genomic DNA Small Sample Extraction Kit (Beyotime D0088S). After labeling, fragment the DNA using Tn5 transposase (Vazyme TD501) under incubation conditions of 37 °C and 500 rpm for 30 min. Biotinylate the DNA using DBCO-PEG4-biotin (DMSO solution, Sigma 760,749). Next, purify the biotinylated DNA with the DNA Clean & Concentrator-5 kit (Zymo, D4013), retaining 5 μL of the labeled DNA as input, while the remaining 50 μL of DNA is used for enrichment. Wash 5 μL of Dynabeads™ MyOne™ Streptavidin C1 (Thermo 65,001) three times with 1 × binding and wash buffer. Then, resuspend the pre-washed beads in 2 × binding and wash buffer. Mix the beads with the 50 μL fragmented DNA obtained from the previous step and rotate gently at room temperature for 15 min. After incubation, place the mixture on a magnetic rack to remove the supernatant and wash the beads five times with 1 × binding and wash buffer. Elute the biotinylated fragments at 98 °C for more than 10 min. Perform PCR amplification using KAPA HiFi DNA polymerase; incubate the PCR reaction at 72 °C for 3 min, then at 98 °C for 45 s, followed by 14 cycles of amplification (15 s at 98 °C, 30 s at 60 °C, and 1 min at 72 °C).                                                                                As previously described, ChIP-seq libraries for all samples were prepared using an ultra-low-input native ChIP protocol. Samples were thawed on ice and permeabilized in PBS containing 0.1% Triton-X-100 and 0.1% sodium deoxycholate. Micrococcal nuclease digestion was performed using 200 U of micrococcal nuclease (NEB, M0247S) in a customized digestion buffer. Samples were digested at 21°C for 7.5 min, and the reaction was terminated with 100 mM EDTA. Chromatin samples were pre-cleared with protein A/G beads in complete immunoprecipitation buffer, rotating at 4°C for 2 h, while antibodies were conjugated to beads at 4°C for 3 h. For each immunoprecipitation of oocytes, anti-H3K4me3 or anti-H3K36me3 antibodies were used. Chromatin was added to the antibody-bound beads, and samples were rotated at 4°C overnight. Samples were then subjected to two low-salt washes and one high-salt wash, followed by DNA elution from the beads at 65°C for 1.5 h. DNA was extracted and purified using phenol, chloroform, and isoamyl alcohol. And libraries were constructed using the Vazyme TD607 kit according to the manufacturer's instructions.


title: DEL3

description: Library name: LIB121936

value: No  doxycycline treatment


title: IgM plasma cells-1

description: Library name: Sample 1


title: HS02 DMSO set F

description:
Library name: F1
HS02_DMSO_set_F


title: DEL2

description: Library name: LIB121935


title: SN oocyte_oe-mCherry_SPT6_rep1

description: Library name: Sample16


title: visium_S4

city: Frankfurt am Main

first: Katharina

last: Imkeller

address: Heinrich-Hoffmann-Str. 7

country: Germany

institute: University Hospital Frankfurt

description: Library name: visium_S4

data_processing:
Reads were aligned to the GRCh38-2020-A human genome reference using the Space Ranger 2.0.0 pipeline (10x Genomics), which also generated gene expression counts. CD20 expression was used to annotate immune-rich regions in Loupe Browser (version 6.2, 10x Genomics). Gene expression data from these samples can be obtained from the authors upon request. Following visual inspection of CD20 expression in Loupe Browser, spots falling within CD20-enriched regions were extracted for each sample (roughly 50–100 spots per patient); these regions were designated as immune-rich areas. Regions of high tumor cell density were designated as tumor-rich areas.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix: zipped file containing  barcodes.tsv, features.tsv and  matrix.mtx files to extract the gene counts from the sample.
Supplementary files format and content: TLSannotation_loupe.csv: Comma-delimited csv metadata file containing annotation information about the visium spots used in the analysis. “Tumor only” are spots without MS4A1 counts. The numbers indicate spatially separated areas of MS4A1 expression (immune aggregates).
Library strategy: Spatial transcriptomics

source_name: Brain Metastases (BM)

extract_protocol:
FFPE tissue sections (5 µm thick) were placed onto a Visium Spatial Gene Expression slide and heated at 42°C for 3 hours on a thermocycler using the Visium PCR adaptor. The slides were then processed according to the manufacturer’s protocol for the Visium Spatial Gene Expression for FFPE workflow (CG000160, CG000239, CG000407; 10x Genomics, California, USA).
Briefly, slides were deparaffinized and then stained with hematoxylin and eosin (H&E). Imaging of the stained slides was performed on a PhenoImager HT (Akoya Biosciences, Massachusetts, USA). Coverslips were then removed, and the slides proceeded through decrosslinking, probe hybridization, probe ligation, probe extension, and library preparation. Sequencing was carried out on a NextSeq 1000 (Illumina, California, USA) using a paired-end, dual-indexed protocol (Read 1: 28 cycles; i7 index: 10 cycles; i5 index: 10 cycles; Read 2: 90 cycles).

value: Brain Metastases (BM)

value: TLS

tag: patient


title: DEL1

description: Library name: LIB121934

tag: genotype


title: HS02 Briga + BMS set E

description:
Library name: E5
HS02_Briga_._BMS_set_E

value: 1uM Brigatinib + 250nM BMS-986158

value: E


title: visium_S3

description: Library name: visium_S3

tag: tissue


title: SN oocyte_oe-mCherry_SPT6_rep2

description: Library name: Sample15


title: WT_MANF_3

description: Library name: LIB121932

value: wild-type with rtTA-MANF


title: HS02 BMS set E

description:
Library name: E4
HS02_BMS_set_E


title: SN oocyte_oe-Rnaseh1_SPT6_rep1

description: Library name: Sample14


title: visium_S2

description: Library name: visium_S2

source_name: Glioma(GBM)

value: Glioma(GBM)

value: tumor


title: WT_MANF_2

description: Library name: LIB121931

value: TALs


title: HS02 Fime set E

description:
Library name: E3
HS02_Fime_set_E


title: SN oocyte_oe-Rnaseh1_SPT6_rep2

description: Library name: Sample13


title: HS02 Briga set E

description:
Library name: E2
HS02_Briga_set_E

value: 1uM Brigatinib


title: WT_MANF_1

description: Library name: LIB121930

value: Treatment with doxycycline for MANF expression


title: visium_S1

description: Library name: visium_S1


title: SN oocyte_oe-mCherry_KAS-seq_rep2

description: Library name: Sample10

data_processing:
Raw reads underwent quality control using FastQC (v0.11.9). Subsequently, Trim_galore (v0.6.7) was employed to trim low-quality base and adapter sequences. These processed reads were then aligned to the mouse (mm10) reference genome using Bowtie265 (v2.2.5). To filter out reads with low mapping quality, SAMtools66 (v1.14) was applied with the parameters ‘-F 1804 -f 2 -q 20’. Concurrently, potential PCR duplicates were eliminated using Sambamba67 (v0.7.1). The resulting Bigwig files were generated by DeepTools68 (v3.5.1) using the parameter ‘-normalizeUsing RPKM --extendReads 200 -bs 1’.
Assembly: mm10
Supplementary files format and content: bw


title: IgG1 plasma cells-5

description: Library name: Sample 10

data_processing:
Sequencing was performed on NovaSeq X Plus platform in a 101+101 base paired-end mode.
Illumina RTA4 software was used for base calling.
Generated reads were mapped to the mouse (GRCm38) reference genome using Hisat2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from cells using the miRNeasy Micro kit (QIAGEN N.V.) according to the enclosed instructions.
Sequencing libraries were constructed with the SMART-Seq mRNA HT LP kit (Takara Bio).

value: IgG1 plasma cell


title: WT3

description: Library name: LIB121928


title: HS02 DMSO set E

description:
Library name: E1
HS02_DMSO_set_E

value: schwann cells


title: SN oocyte_oe-mCherry_KAS-seq_rep1

description: Library name: Sample9

value: oocyte

value: oe-mCherry


title: IgG1 plasma cells-4

description: Library name: Sample 9

value: spleen


title: WT2

description: Library name: LIB121927


title: SN oocyte_oe-Rnaseh1_H3K4me3_rep2

description: Library name: Sample8


title: HS05 Briga + BMS set D

description:
Library name: D5
HS05_Briga_._BMS_set_D

value: D


title: IgG1 plasma cells-3

description: Library name: Sample 8


title: WT1

description: Library name: LIB121926

value: No  doxycycline treatment


title: HS05 BMS set D

description:
Library name: D4
HS05_BMS_set_D


title: SN oocyte_oe-Rnaseh1_H3K4me3_rep1

description: Library name: Sample7


title: IgG1 plasma cells-2

description: Library name: Sample 7


title: QGP-1 MEN1 ChIP H3K27Ac rep 2

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

description: Library name: MEN1_2_H3K27

data_processing:
Raw sequencing reads were quality-checked using FastQC and adapter/quality-trimmed using Trim Galore (v0.6.10) in paired-end mode. Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 in local alignment mode. SAM files were converted to BAM format using samtools, sorted and duplicate-marked using sambamba, and filtered to remove unmapped and duplicate reads. Peaks were called using MACS2 with matched input DNA as control: narrow peaks for RelA (q < 0.05), and broad peaks for H3K27ac (q < 0.05, broad-cutoff 0.1). RelA motif analysis was performed on the stringent q < 0.05 RelA peak set using HOMER findMotifsGenome.pl (window size 200 bp, repeat-masked genome). Peaks were annotated using ChIPseeker with hg38 knownGene annotation and a transcription start site window of ±3 kb.
Assembly: Hg38
Supplementary files format and content: Bigwig

growth_protocol: QGP-1 cells were grown in RPMI1640 supplemented with 10% heat-inactivated fetal bovine serum and 1% glutamax.

extract_protocol:
Cells were fixed with 1% formaldehyde and lysed with cell lysis buffer (10mM Tris-HCL pH 8, 10mM NaCl and 0.2% NP-40), folllowed by nuclear lysis buffer (50mM Tris-HCl pH 8, 10mM EDTA and 1% SDS). Chromatin were sonicated using the Misonix Q500 sonicator (QSonica).
Library construction was done using the Novogene DNA Library Prep Kit

treatment_protocol: QGP-1 cells were transfected with pCDH empty vector or pCDH-MEN1 vector to overexpress menin.

value: pancreatic neuroendocrine tumor cell line


title: Lung, Vehicle 2

data_processing:
Cutadapt trimmed reads were aligned to the rat reference genome using HISAT2
Raw read counts for all samples were counted using HTSeq
Assembly: Rattus norvegicus, mRatBN7.2 v107
Supplementary files format and content: text file includes raw counts for each sample ( columns: 1. Ensembl ID and 2. raw counts).

extract_protocol:
RNA was isolated from frozen rat lung and liver by digesting tissue in Trizol (Invitrogen) using a Lysing Matrix in a MP Biomedicals FastPrep-25 5G homogenizer followed by a chloroform extraction.
Directional mRNA library preparation (poly A enrichment). 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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: postnatal day 6 lung

value: Sprague Dawley

value: WT

value: 24 hours Vehicle


title: SN oocyte_oe-mCherry_H3K4me3_rep2

description: Library name: Sample6


title: HS05 Fime set D

description:
Library name: D3
HS05_Fime_set_D

value: 100nM Fimepinostat


title: IgG1 plasma cells-1

description: Library name: Sample 6


title: QGP-1 MEN1 ChIP H3K27Ac rep 1

description: Library name: MEN1_1_H3K27


title: HS05 Briga set D

description:
Library name: D2
HS05_Briga_set_D


title: SN oocyte_oe-mCherry_H3K4me3_rep1

description: Library name: Sample5


title: IgM plasma cells-5

description: Library name: Sample 5

value: IgM plasma cell


title: QGP-1 Empty vector ChIP H3K27Ac rep 2

description: Library name: EV_2_H3K27

value: Empty vector


title: HS05 DMSO set D

description:
Library name: D1
HS05_DMSO_set_D


title: SN oocyte_oe-Rnaseh1_H3K36me3_rep2

description: Library name: Sample4


title: IgM plasma cells-4

description: Library name: Sample 4


title: QGP-1 Empty vector ChIP H3K27Ac rep 1

description: Library name: EV_1_H3K27


title: HS05 Briga + BMS set C

description:
Library name: C5
HS05_Briga_._BMS_set_C

value: 1uM Brigatinib + 250nM BMS-986158

value: C


title: SN oocyte_oe-Rnaseh1_H3K36me3_rep1

description: Library name: Sample3


title: IgM plasma cells-3

description: Library name: Sample 3


title: QGP-1 MEN1 ChIP RelA rep 2

description: Library name: MEN1_2_RelA

value: RelA


title: HS05 BMS set C

description:
Library name: C4
HS05_BMS_set_C

value: schwann cells


title: SN oocyte_oe-mCherry_H3K36me3_rep2

description: Library name: Sample2

value: oocyte


title: IgM plasma cells-2

description: Library name: Sample 2


title: QGP-1 MEN1 ChIP RelA rep 1

description: Library name: MEN1_1_RelA


title: HS02 BMS set B

description:
Library name: B4
HS02_BMS_set_B

value: B


title: IgM plasma cells-1

description: Library name: Sample 1

value: spleen


title: SN oocyte_oe-mCherry_H3K36me3_rep1

description: Library name: Sample1

value: oe-mCherry


title: QGP-1 Empty vector ChIP RelA rep 2

description: Library name: EV2_RELA


title: HS02 Fime set B

description:
Library name: B3
HS02_Fime_set_B


title: SN oocyte_oe-mCherry_EM-seq_rep2

description: Library name: Sample4

data_processing:
The procedures for quality control and filtering of the raw reads were performed as above. The processed reads were then aligned to the mouse (mm10) reference genome using Bismark with the parameters ‘--bowtie2 -N 1 -p 10 -L 20 --non_directional --nucleotide_coverage’. Multiple mapped and duplicated reads were removed. Non-converted reads are filtered out utilizing the parameters ‘filter_non_conversion --threshold 5’.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: EM-seq

extract_protocol:
The extracted DNA was then dissolved in 50 μL of 10 mM Tris-0.1 mM EDTA buffer (pH 8.0). Subsequently, the DNA sample was transferred to a microTUBE (Covaris, 520166) and sheared to 240-290 bp fragments using the Covaris S220 instrument. DNA was sheared twice for 95 sec at duty factor 20%, peak incident power 75, and cycles/burst 1000. Finally, 50 μL of the sheared DNA material was transferred to a PCR tube, and library construction was carried out using the NEBNext® Enzymatic Methyl-seq Kit (NEB, E7120S) according to the manufacturer's guidelines.
Genomic DNA was extracted from 200 oocytes using the Universal Genomic DNA Purification Mini Spin Kit (Beyotime, D0063).


title: DBP-M3

city: Tucson

first: chi

last: zhou

state: AZ

address: 4101 N Campbell Ave, Rm N109, ARC, U of Arizona

department: Animal and Comparative Biomedical Sciences

institute: University of Arizona

description:
Library name: DBP-M3
Fresh frozen spatial transcriptomic sequencing

data_processing:
Raw FASTQ files were processed using 10x Genomics Space Ranger count with the mouse mm10 reference genome. Space Ranger generated filtered feature-barcode matrices, spatial barcode coordinates, scale factors, and tissue images for each Visium sample. Filtered expression matrices and spatial outputs were used for downstream spatial transcriptomic analysis in Seurat.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered feature-barcode gene expression matrix in HDF5 format
Supplementary files format and content: tissue_positions.csv: spatial barcode coordinates specifying tissue-associated Visium spots
Supplementary files format and content: scalefactors_json.json: image scale factors for Visium spatial coordinates
Supplementary files format and content: tissue_hires_image.png: high-resolution tissue image used for spatial visualization
Supplementary files format and content: tissue_lowres_image.png: low-resolution tissue image used for spatial visualization
Supplementary files format and content: aligned_fiducials.jpg: image showing aligned fiducial frame and tissue section
Supplementary files format and content: detected_tissue_image.jpg: image showing detected tissue area and spots
Library strategy: Spatial Transcriptomics

source_name: Placenta

growth_protocol: Adult female CD-1 mice (8 to 10 wk, weight 30±2 g) were orally treated with vehicle (control [CT] group; n=18) or DBP0.1 (n=18) daily for 30day before mating with male CD-1 mice without DBP exposure and throughout pregnancy until GD18.5. Placentas were collected from control and prenatal dibutyl phthalate (DBP)-exposed pregnancies for 10x Genomics Visium spatial transcriptomic analysis.

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Placenta

tag: model

value: Prenatal DBP exposure model

tag: fetal sex

value: Male

value: DBP


title: SN oocyte_oe-mCherry_EM-seq_rep1

description: Library name: Sample3


title: HS02 Briga set B

description:
Library name: B2
HS02_Briga_set_B

data_processing:
Gene and transcript expression quantification results were generated using the nf-core/rnaseq pipeline (v3.12.0, commit hash: 3bec2331cac2b5ff88a1dc71a21fab6529b57a0f), nextflow version  v22.10.6.
Sequenced reads were filtered to remove adapter and low-quality reads.
Quality control was performed using FastQC (v0.11.9) and MultiQC to assess read quality metrics.
Reads were aligned to the GRCh38 (GENCODE v40) human reference genome using STAR aligner (v2.7.9a).
Gene expression quantification was performed using Salmon (v1.10.1).
Assembly: GRCh38 (GENCODE v40 primary assembly)
Supplementary files format and content: Tab-delimited text file containing TPM gene expression values generated by Salmon quantification.

value: 1uM Brigatinib


title: QGP-1 Empty vector ChIP RelA rep 1

description: Library name: EV1_RELA

value: pancreatic neuroendocrine tumor cell line


title: DBP-M2

description:
Library name: DBP-M2
Fresh frozen spatial transcriptomic sequencing


title: HS02 DMSO set B

description:
Library name: B1
HS02_DMSO_set_B


title: DBP-M1

description:
Library name: DBP-M1
Fresh frozen spatial transcriptomic sequencing


title: QGP-1 pCDH MEN1 input rep 1

description: Library name: MEN1_1_INPUT


title: SN oocyte_oe-Rnaseh1_EM-seq_rep2

description: Library name: Sample2


title: QGP-1 pCDH MEN1 input rep 2

description: Library name: MEN1_2_INPUT


title: HS02 Briga + BMS set A

description:
Library name: A5
HS02_Briga_._BMS_set_A

value: A


title: DBP-F3

description:
Library name: DBP-F3
Fresh frozen spatial transcriptomic sequencing

value: Female


title: SN oocyte_oe-Rnaseh1_EM-seq_rep1

description: Library name: Sample1


title: HS02 BMS set A

description:
Library name: A4
HS02_BMS_set_A


title: DBP-F2

description:
Library name: DBP-F2
Fresh frozen spatial transcriptomic sequencing


title: QGP-1 Empty vector input rep 2

description: Library name: EV2_ INPUT

value: Empty vector


title: SN oocyte_oe-mCherry_RNA-seq_rep2

description: Library name: Sample8


title: QGP-1 Empty vector input rep 1

description: Library name: EV1_INPUT


title: HS02 Fime set A

description:
Library name: A3
HS02_Fime_set_A

value: 100nM Fimepinostat


title: T11_z5497

description: Library name: Sample 8

data_processing:
Samples were processed using the nf-core/rnaseq v3.22.2 pipeline with nextflow v25.04.6
Briefly, raw reads were trimmed using Trim Galore! v0.6.10 to remove low-quality bases and adapters. Trimmed reads were aligned to the human reference genome, hg38 with STAR v2.7.11b aligner
Finally, salmon Quant v1.10.3 is utilized for assigning reads.
Assembly: hg38
Supplementary files format and content: Tab delimited file with raw gene counts for every gene and every sample

source_name: pancreatic neuroendocrine tumour

extract_protocol:
RNA extraction was done using the Nucleospin RNA extraction column.
RNA libraries were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (reverse stranded) as per manufacturer's instructions

value: pancreatic neuroendocrine tumour

value: MEN1 mutation


title: DBP-F1

description:
Library name: DBP-F1
Fresh frozen spatial transcriptomic sequencing


title: SN oocyte_oe-Rnaseh1_RNA-seq_rep2

description: Library name: Sample6


title: SN oocyte_oe-mCherry_RNA-seq_rep1

description: Library name: Sample7


title: HS02 Briga set A

description:
Library name: A2
HS02_Briga_set_A

value: schwann cells


title: T10_z11651

description: Library name: Sample 7


title: HS02 DMSO set A

description:
Library name: A1
HS02_DMSO_set_A


title: CT-M3

description:
Library name: CT-M3
Fresh frozen spatial transcriptomic sequencing

value: CT


title: SN oocyte_oe-Rnaseh1_RNA-seq_rep1

description: Library name: Sample5

value: oocyte


title: CT-M2

description:
Library name: CT-M2
Fresh frozen spatial transcriptomic sequencing


title: T7_83791081

description: Library name: Sample 6


title: U251 cells, shNCDN-3

first: Tingrong

last: Ren

address: 131 Dong'an Road, Xuhui District, Shanghai, China

institute: fudan university

description: Library name: sh-NCDN-7

data_processing:
The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent, USA).
Paired-end clean reads were aligned to the hg38 reference genome using HISAT2 (v2.0.5).
Differential expression analysis of the two conditions was performed using the edgeR R package (3.22.5).
rMATS (4.1.0) software was used to analyze the alternative splicing events.
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts and fpkm for each sample
Supplementary files format and content: Excel file includes differentially expressed gene
Supplementary files format and content: Excel file includes raw SE events
Supplementary files format and content: Excel file includes raw RI events
Supplementary files format and content: Excel file includes raw A3SS events
Supplementary files format and content: Excel file includes raw A5SS events
Supplementary files format and content: Excel file includes raw MXE events

source_name: U251 cells

growth_protocol: U251 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum and 100 U/mL of penicillin and 100 μg/mL of streptomycin, and the cells were cultured in a humidified incubator at 37°C in the presence of 5% CO2

extract_protocol:
TRIzol reagent (Invitrogen) was used for total RNA extraction according to the manufacturer’s instructions
RNA-seq library was loaded on an Illumina NovaSeq 6000 instrument for sequencing using a 2×150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: U251 cells were infected with lentivirus encoding control shRNA (shCtrl) or shRNA targeting NCDN (shNCDN). 72h after infection, cells were harvested for RNA extraction

value: U251 cells

value: glioblastoma cell line

value: NCDN knockdown


title: NSN oocyte_oe-mCherry_RNA-seq_rep2

description: Library name: Sample4

value: oe-mCherry


title: CT-M1

description:
Library name: CT-M1
Fresh frozen spatial transcriptomic sequencing

value: Placenta

value: Prenatal DBP exposure model

value: Male


title: U251 cells, shNCDN-2

description: Library name: sh-NCDN-6


title: T5_02000492

description: Library name: Sample 5


title: NSN oocyte_oe-mCherry_RNA-seq_rep1

description: Library name: Sample3


title: T4_z12593

description: Library name: Sample 4


title: CT-F4

description:
Library name: CT-F4
Fresh frozen spatial transcriptomic sequencing


title: U251 cells, shNCDN-1

description: Library name: sh-NCDN-3


title: CT-F3

description:
Library name: CT-F3
Fresh frozen spatial transcriptomic sequencing


title: T3_z9608

description: Library name: Sample 3


title: NSN oocyte_oe-Rnaseh1_RNA-seq_rep2

description: Library name: Sample2


title: U251 cells, shControl-3

description: Library name: sh-NT2

value: WT


title: NSN oocyte_oe-Rnaseh1_RNA-seq_rep1

description: Library name: Sample1


title: T2_z2226

description: Library name: Sample 2


title: U251 cells, shControl-2

description: Library name: sh-NT


title: CT-F2

description:
Library name: CT-F2
Fresh frozen spatial transcriptomic sequencing


title: CT-F1

description:
Library name: CT-F1
Fresh frozen spatial transcriptomic sequencing