title: H358 SAFE clone 1

description: Library name: SAFE-1


title: 203968030120_R07C01_20185946_CNG

status: Public on Jul 29 2026

type: genomic

city: Exeter

first: Joshua

last: Harvey

state: Devon

address: RILD Building, RD&E, Barrack Road

department: Clinical and Biomedical Sciences

country: United Kingdom

institute: University of Exeter

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

label: Cy3 & Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Anterior cingulate

label_protocol: Standard Illumina Protocol

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

tag: tissue

value: Anterior cingulate

tag: regiondescription

tag: plate

tag: centre

value: Newcastle Brain Tissue Resource

tag: Sex

value: female

tag: thal

value: FALSE


title: MM_51

type: SRA

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

country: Spain

institute: CIMA

description: Library name: sample 133

library_source: transcriptomic

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
RNA-seq: differential gene expression analysis was performed using DESeq2 and GSEA analyses were conducted using ClusterProfiler.
Assembly: GRCh38.p13
Supplementary files format and content: RNA-seq: one excel file containing the cpm for all the samples (divided cell lines and human samples).

molecule: total RNA

source_name: bone marrow

growth_protocol: MM cell lines were maintained in RPMI-1640 medium containing L-Glutamine supplemented with 1% of penicillin-treptomycin, 2% HEPES Buffer and 20% of Fetal Bovine Serum.

extract_protocol:
RNA was isolated with the MagMAX mirVana total RNA Isolation kit (applied biosystems)
RNA-seq library was prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina).

treatment_protocol: transduction of lentiviral particles containing the empty vector (scramble) or the vector containing the sgRNAs against IRF2 (IRF2-sg1 and IRF2-sg2).

value: bone marrow

tag: cell line

tag: cell type

value: Myeloma Plasma Cell

tag: genotype

tag: treatment


title: vHipp_csds_Saline8

city: Solna

first: Serena

last: Gasperoni

address: Solnavägen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: Library name: P30210_1028_S102

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: vHipp

extract_protocol:
miRNeasy Micro Kit (Qiagen), 100 ng of total RNA was used for construction of sequencing libraries
Illumina Stranded mRNA Prep

value: vHipp

tag: group

value: csds

value: male

value: WT

value: Saline

tag: ID


title: H358 TKO clone 2

city: New York

first: Sam

middle: E

last: Tischfield

state: NY

address: 1275 York Ave

department: Center for Molecular Oncology

country: USA

institute: Memorial Sloan-Kettering Cancer Center

description: Library name: TKO-2

data_processing:
Pseudo-mapping with Kallisto v0.50.0
Quantification with Sleuth v0.30.0
Assembly: HG19
Supplementary files format and content: TPM  values for transcripts in tab delimited matrix

growth_protocol: H358 cells were cultured in in RPMI media supplemented with 10% FBS and 1X Penicillin-Streptomycin (PS) and incubated in 5% CO2 at 37° C.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Universal Mini kit following manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions.

value: SMARCA4/STK11/KEAP1 TKO


title: 203968030120_R06C01_PD954_CNG

value: Imperial Brain Bank


title: MM_50

description: Library name: sample 132


title: mPFC_ctrl_Ketamine26

description: Library name: P30210_1027_S101

source_name: mPFC

value: mPFC

value: ctrl

value: Ketamine


title: H358 TKO clone 1

description: Library name: TKO-1


title: 203968030120_R03C01_19940144_CNG


title: vHipp_ctrl_Ketamine26

description: Library name: P30210_1026_S100


title: MM_48

description: Library name: sample 130


title: mPFC_ctrl_Saline28

description: Library name: P30210_1025_S99


title: 203960330128_R04C01_PD803_CNG


title: MM_47

description: Library name: sample 129


title: 203968030120_R01C01_C073_CNG


title: vHipp_ctrl_Saline28

description: Library name: P30210_1024_S98


title: H358 DKO clone 3

description: Library name: DKO-3

value: STK11/KEAP1 DKO


title: MM_49

description: Library name: sample 131


title: H358 DKO clone 2

description: Library name: DKO-2


title: Sample 5_5B

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description:
Library name: Sample 5
GC_miRNAs_in_Rhino_CPM.xlsx

data_processing:
Raw FASTQ files were first subjected to quality control and adapter trimming using FASTp, with a minimum Phred quality score of 20, a required minimum read length of 15 nucleotides, and a maximum read length of 35 nucleotides. Filtered reads were then processed using the miRDeep2 Mapper module, discarding reads shorter than 15 nucleotides. miRNA quantification was performed with the miRDeep2 Quantifier tool using miRBase release 22.1 as the reference database. Reads were annotated against equine, bovine, and human precursor and mature miRNAs, allowing up to one mismatch.
Differential expression analysis was conducted using DESeq2 within Galaxy.
Assembly: miRBase release 22.1
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Ceratotherium simum simum

source_name: Ovarian Follicule

extract_protocol:
For the GC ampless, total RNA, including miRNA, was isolated using the Qiagen miRNeasy Micro Kit (Qiagen, Germantown, MD) per the manufacturer’s instructions. Briefly, granulosa cells were incubated with Qiazol lysis reagent and vortexed to homogenize the cells. After 5 min, chloroform was added to the sample and centrifuged at 10,000 x g for 15 min to separate RNA and protein. The RNA phase was added to an elution column and eluted in water after multiple washes. For the follicular fluid (FF) samples, FF was centrifuged at 300 x g for 10 min, the supernatant was re-centrifuged at 2000 x g for 10 min, and again at 16,500 x g for 30 min. The final supernatant was passed through a 0.20-μm sterile syringe filter, removing particles larger than 200 nm in diameter. For the EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 C using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 xg for 70 min. The washed pellets were then resuspended in DPBS.  To precipitate EVs,  Exo-spin™ buffer was added to each sample and incubated overnight at 4°C. The precipitated EVs were purified using Exo-spin™ mini columns according to the manufacturer’s instructions. Final 180 µL EV aliquots were stored at −80°C for subsequent characterization and analysis. Total RNA including miRNAs was isolated from EVs using a Norgen Exosomal RNA Isolation kit (Norgen, Canada), according to the manufacturer’s instructions. On-column DNA digestion was performed to remove genomic DNA contaminants.
For GC samples library preparation kit was SMARTer smRNA-Seq Library Preparation Kit (Takara Bio) per manufacturer’s instructions. For FF-EV samples, Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Ovarian Follicule

value: Granulosa Cells

tag: corresponding oocyte_maturation

value: PB


title: H358 DKO clone 1

description: Library name: DKO-1


title: Sample 6_5C

description:
Library name: Sample 6
GC_miRNAs_in_Rhino_CPM.xlsx


title: MM_68

description: Library name: sample 150


title: 203960330128_R03C01_20100745_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource

value: female

value: FALSE


title: Sample 2_1B

description:
Library name: Sample 2
GC_miRNAs_in_Rhino_CPM.xlsx


title: 203960330097_R08C01_PD917_CNG


title: MM_46

description: Library name: sample 128

value: bone marrow

value: Myeloma Plasma Cell


title: vHipp_csds_Ketamine5

description: Library name: P30210_1023_S97

value: vHipp

value: csds

value: male

value: WT


title: 203977090024_R07C01_PD1030_CNG

value: Imperial Brain Bank


title: 203976760067_R06C01_PDC107_CNG


title: Case4 insulinoma tissue

type: RNA

city: Kobe

first: Kenji

last: Sugawara

state: Please Select

address: 7-5-1 Kusunoki-cho, Chuo-ku

country: Japan

institute: Kobe university graduate school of medicine

description: Human insulinoma tissue sample analyzed by Agilent one-color gene expression microarray.

hyb_protocol: Cy3-labeled cRNA was hybridized to an Agilent one-color gene expression microarray according to the manufacturer's protocol.

scan_protocol: Arrays were scanned using an Agilent Technologies G2600D scanner.

data_processing: Raw microarray image data were processed using Agilent Feature Extraction software version 11.5.1.1. Normalized log2 expression values for validated probes were summarized.

source_name: insulinoma tissue

label_protocol: Cy3-labeled cRNA was prepared from total RNA and used for Agilent one-color gene expression microarray analysis according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from surgically resected human insulinoma tissue.

value: pancreatic insulinoma tissue

tag: disease

value: insulinoma

tag: sample type

value: surgically resected tumor tissue


title: 203977090024_R06C01_19950019_CNG


title: MM_45

description: Library name: sample 127


title: mPFC_csds_Saline7

description: Library name: P30210_1022_S96

value: mPFC

value: Saline


title: 203960330097_R07C01_NP13/128_CNG

value: Oxford Brain Bank


title: MM_44

description: Library name: sample 126


title: vHipp_csds_Saline7

description: Library name: P30210_1021_S95


title: Case3 insulinoma tissue


title: 203960330097_R03C01_C048_CNG

value: Anterior cingulate


title: MM_43

description: Library name: sample 125


title: mPFC_ctrl_Ketamine25

description: Library name: P30210_1020_S94

value: ctrl

value: Ketamine


title: 203960330097_R02C01_PDC053_CNG

value: female

value: FALSE


title: MM_42

description: Library name: sample 124

value: bone marrow

value: Myeloma Plasma Cell


title: Case2 insulinoma tissue


title: vHipp_ctrl_Ketamine25

description: Library name: P30210_1019_S93

value: vHipp


title: 1036_non-IMV_BL

city: Houston

first: Deepa

middle: B.

last: Gotur

state: TX

address: 6565 Fannin

department: Medicine

institute: Houston Methodist Hospital

description: Library name: Cytostorm RNA SEQ 36_BL

data_processing:
A comparison of gene expression between the groups of samples was performed using DESeq2. The Wald test was applied to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were classified as differentially expressed genes (DEGs). We performed gGene ontology (GO) analysis was performed using g:Profiler (version e107_eg54_p17_bf42210, database updated 15/09/2022) to visualize the enrichment information of the significant DEGs. Homo sapiens was chosen as a specific organism for analysis. GO molecular function (GO:MF), GO cellular component (GO:CC), and GO biological process (GO:BP) categories were used as Gene Ontology data sources. Pathway analysis used KEGG, Reactome, and WikiPathways databases. Analyses were restricted to annotated genes , and with significance thresholds were set using at g:SCS multiple testing correction method at α=0.05. and 0.05.
Assembly: DEGs were further analyzed using gene set enrichment analysis via ShinyGO. Significant DEGs were imported into the ShinyGO V0.77 tool to perform KEGG pathway analysis and obtain a visual graph of KEGG pathways. When submitting the list of gene targets in the Gene Official Symbol format, the selected matching species were human, and the FDR cutoff was set to 0.05 (p ≤ 0.05).
Supplementary files format and content: TPM_values IMV vs NON-IMV Day0.csv
Supplementary files format and content: TPM_values IMV vs NON-IMV Day4.csv
Supplementary files format and content: TPM_values IMV vs NON-IMV Day8.csv

molecule: polyA RNA

source_name: PBMC

extract_protocol:
RNA extraction from frozen cell pellets, library preparation using poly-A selection for mRNA enrichment, and sequencing on an Illumina platform with paired-end 2×150 bp configuration targeting 20–30 million reads per sample were performed by GENEWIZ. RNA integrity and library quality were assessed by GENEWIZ using Agilent TapeStation, Qubit fluorometric quantification, and qPCR before sequencing. Samples with inadequate RNA integrity or sequencing quality metrics were excluded from downstream analyses.
Standard RNA analysis package

value: PBMC

value: non-IMV

tag: time point

value: BL


title: Case1 insulinoma tissue

value: pancreatic insulinoma tissue


title: 203968030133_R08C01_RI92/1434_CNG

value: male


title: 203960330127_R08C01_P54/13_CNG

value: QSBB


title: MM_41

description: Library name: sample 123


title: mPFC_ctrl_Saline27

description: Library name: P30210_1018_S92

value: mPFC

value: WT


title: 1035_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 35_D8


title: MM_40

description: Library name: sample 122


title: C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep4

city: Ulsan

first: Jun Pyo

last: Jeon

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, Republic of Korea

country: South Korea

institute: Unist

description: Library name: WT4

library_source: genomic

data_processing:
Adapter sequences and low-quality bases were trimmed using Skewer (v.0.2.2).
Pre-alignment was performed using Bowtie2 (v2.5.4). The filtered reads were then aligned to the mouse reference genome (mm10) using Bowtie2.
PCR duplicates were marked and removed using Picard MarkDuplicates (v2.24.0).
Peaks overlapping blacklisted regions (ENCODE mm10 blacklist) were removed using bedtools intersect (v2.30.0).
For visualization and peak analysis, HOMER (v4.11.1) was used. Tag directories were generated using makeTagDirectory for each sample. Biological replicates from the same condition were pooled using HOMER's mergeTagDirectory. The pooled tag directories were used to generate genome browser tracks (UCSC track files, bedgraph)
Assembly: mm10
Supplementary files format and content: bedgraph file compressed in gzip format

source_name: spleen & lymph-node

extract_protocol:
100,000 cells were washed with PBS and lysed using a cold lysis buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Cells were incubated on ice for 5 minutes. Nuclei were pelleted by centrifugation at 500 x g for 10 minutes at 4°C, washed with 1ml cold lysis buffer without digitonin and Tween-20, and resuspended in transposition reaction buffer.
Transposition was carried out in a 50 µL reaction containing 25 µL 2× TD buffer, 2.5 µL Tn5 transposase, 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL nuclease-free water. The reaction was incubated at 37°C for 45 minutes with with tapping every 10 minutes. Directly following transposition, each sample was purified using a DNA clean & ConcentratorTM-5. Following purification, transposed fragments were PCR-amplified using Nextera dual-index primers and NEBNext High-Fidelity Master Mix. PCR products were cleaned using AMPure XP beads.

treatment_protocol: Cells were immediately plated onto anti-CD3 (1 μg ml⁻¹) / anti-CD28 (2 μg ml⁻¹)–coated 24-well plates and cultured for 12 hours in complete RPMI-1640 (10 % FBS) in humidified atmosphere with 5% CO2 at 37℃

value: spleen & lymph-node

tag: strain

value: Naive CD8+ T cells

value: anti-CD3 / anti-CD28 12h

tag: batch


title: 203960330127_R01C01_PD060_CNG

tag: tissue

value: Anterior cingulate

tag: regiondescription

value: Imperial Brain Bank


title: 1035_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 35_D4


title: 203960330125_R06C01_C054_CNG

tag: plate

tag: centre

value: FALSE


title: MM_39

description: Library name: sample 121

value: bone marrow


title: mPFC_csds_Ketamine3

description: Library name: P30210_1016_S90

value: csds

tag: Sex

value: Ketamine


title: vHipp_ctrl_Saline27

description: Library name: P30210_1017_S91

value: vHipp

value: ctrl

value: Saline


title: MM_55

description: Library name: sample 137

tag: cell line

value: Myeloma Plasma Cell


title: 1035_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 35_BL

tag: cell type

value: PBMC

value: non-IMV

value: BL


title: MM_38

description: Library name: sample 120

tag: genotype


title: 203960330125_R03C01_PD701_CNG

value: male

tag: thal


title: vHipp_csds_Ketamine3

description: Library name: P30210_1015_S89

tag: group

value: WT

tag: treatment


title: 1034_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 34_D8


title: 203960330125_R02C01_NP16/079_CNG

value: Oxford Brain Bank


title: MM_37

description: Library name: sample 119


title: mPFC_csds_Saline4

description: Library name: P30210_1014_S88

value: mPFC

tag: ID


title: 1034_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 34_D4


title: 203968030148_R07C01_P69/10_CNG

value: Anterior cingulate

value: QSBB

value: TRUE


title: vHipp_csds_Saline4

description: Library name: P30210_1013_S87


title: MM_36

description: Library name: sample 118

value: bone marrow


title: 203968030148_R06C01_PD366_CNG

value: Imperial Brain Bank

value: FALSE


title: 1034_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 34_BL


title: MM_35

description: Library name: sample 117


title: mPFC_ctrl_Ketamine23

description: Library name: P30210_1012_S86

value: Ketamine


title: 203968030148_R05C01_PD988_CNG


title: 1033_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 33_D8


title: MM_34

description: Library name: sample 116


title: 203991410102_R04C01_20080109_CNG

value: Newcastle Brain Tissue Resource


title: vHipp_ctrl_Ketamine23

description: Library name: P30210_1011_S85

value: vHipp

value: ctrl


title: 1033_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 33_D4

value: PBMC


title: H358 SAFE clone 2

description: Library name: SAFE-2


title: 203968030168_R07C01_20110891_CNG


title: 203968030133_R01C01_PD744_CNG


title: MM_33

description: Library name: sample 115

value: Myeloma Plasma Cell


title: mPFC_ctrl_Saline24

description: Library name: P30210_1010_S84

value: Saline


title: 1033_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 33_BL

value: non-IMV

value: BL


title: 203968030168_R06C01_PD792_CNG

value: female


title: vHipp_ctrl_Saline24

description: Library name: P30210_1009_S83

value: male

value: WT


title: MM_32

description: Library name: sample 114


title: 1032_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 32_D8


title: 203968030168_R04C01_PD050_CNG

value: Anterior cingulate


title: MM_31

description: Library name: sample 113


title: 1032_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 32_D4


title: mPFC_csds_Ketamine1

description: Library name: P30210_1008_S82

value: mPFC

value: csds


title: 203968030168_R03C01_PD336_CNG

value: Imperial Brain Bank


title: mPFC_csds_Saline8

description: Library name: P30210_1029_S103


title: vHipp_csds_Ketamine1

description: Library name: P30210_1007_S81


title: MM_30

description: Library name: sample 112

value: bone marrow


title: 1032_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 32_BL


title: 203991460130_R03C01_PDC022_CNG

value: TRUE


title: mPFC_csds_Saline2

description: Library name: P30210_1006_S80


title: MM_29

description: Library name: sample 111


title: 1031_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 31_BL


title: 203991460130_R02C01_20050124_CNG

value: Newcastle Brain Tissue Resource

value: FALSE


title: MM_28

description: Library name: sample 110


title: vHipp_csds_Saline2

description: Library name: P30210_1005_S79

value: vHipp


title: 203991460107_R08C01_20160306_CNG


title: 1030_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 30_D8

value: PBMC


title: MM_27

description: Library name: sample 109

value: Myeloma Plasma Cell


title: mPFC_ctrl_Ketamine21

description: Library name: P30210_1004_S78

value: ctrl

value: Ketamine


title: 203991460107_R07C01_NP17/003_CNG

value: Oxford Brain Bank


title: MM_26

description: Library name: sample 108


title: 1030_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 30_D4

value: non-IMV


title: vHipp_ctrl_Ketamine21

description: Library name: P30210_1003_S77

value: male


title: 1030_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 30_BL

value: BL


title: 203991460107_R02C01_PD794_CNG

value: Anterior cingulate


title: MM_25

description: Library name: sample 107


title: mPFC_ctrl_Saline22

description: Library name: P30210_1002_S76

value: mPFC

value: WT

value: Saline


title: 1029_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 29_D8


title: 203991460107_R01C01_PD876_CNG

value: Imperial Brain Bank


title: MM_24

description: Library name: sample 106

value: bone marrow


title: vHipp_ctrl_Saline22

description: Library name: P30210_1001_S75


title: 1029_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 29_D4


title: 203991460127_R08C01_20020080_CNG

value: Newcastle Brain Tissue Resource


title: MM_23

description: Library name: sample 105


title: 1029_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 29_BL


title: Primary cell, KO + ATP, 12 hours after PHx, rep2

city: Hefei

first: Taofei

last: Zeng

state: Anhui

address: 17 Lujiang Road

country: China

institute: The First Affiliated Hospital of USTC

description: Library name: JZ24087474

data_processing:
For bioinformatic processing, paired-end reads from the ATAC-seq library were trimmed using fastp (v0.23.4) and aligned to the UCSC mouse reference genome (mm10) with Bowtie2 (v2.5.4) under default settings. PCR duplicates, multimapping reads, and mitochondrial reads were removed. High-quality reads were extracted using Samtools (v1.2) with the following flags: “-f 1 -F 4 -F 8 -F 256 -F 2048 -q 30.” Peak calling was performed with macs3(v3.0.0) using the ‘callpeak’ command, with default parameters. For data visualization, ATAC-seq read counts were normalized to bins per million mapped reads (BPM) using deepTools (v3.5.5) with the settings “--binSize 10.” Representative gene signal tracks were visualized using the Integrative Genomics Viewer (IGV) software.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) files include normalized signal tracks

source_name: Liver

growth_protocol: Mice were maintained under pathogen-free conditions with controlled humidity, a 12-hour light/dark cycle, and ad libitum access to food and water.

extract_protocol:
Nuclear extraction from tissues and cell lines was performed using commercial kits (52201-10, Shanghai Biotechnology Corporation, Shanghai, China). Briefly, 30 mg of frozen liver tissue was transferred to a pre-cooled homogenizer, with 1 mL of cold homogenization buffer added. The tissue was gently homogenized, and nuclei were subsequently isolated and purified according to the instructions provided in the Nuclei Isolation Kit.
Approximately 50,000 purified nuclei were used for ATAC-seq library construction, utilizing the ATAC-Seq Library Preparation Kit (Vazyme, TD711-01).Sequencing was conducted on the Illumina platform.

treatment_protocol: Primary hepatocytes were isolated 12 hours post-partial hepatectomy (PHx) following established protocols. After perfusion and digestion, hepatocytes were released, filtered, and subjected to Percoll gradient centrifugation. The cells were resuspended in low-glucose DMEM, plated in collagen-coated plates, and allowed to adhere. After 6 hours, the culture medium was replaced with Williams E medium supplemented with 2 mM glutamine and 1% penicillin-streptomycin. Primary cells were treated with either ATP or PBS for further analysis.

value: Liver

value: Liver Primary cell

value: ATP


title: MM_22

description: Library name: sample 104

value: Myeloma Plasma Cell


title: 203991460127_R07C01_PD171_CNG

value: FALSE


title: 203991460127_R04C01_20030103_CNG

value: female


title: Primary cell, KO + ATP, 12 hours after PHx, rep1

description: Library name: JZ24087473


title: 1028_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 28_D8

value: PBMC


title: MM_21

description: Library name: sample 103


title: 1028_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 28_D4

value: non-IMV


title: 203991460127_R03C01_20163933_CNG

value: male


title: Primary cell, KO + PBS, 12 hours after PHx, rep2

description: Library name: JZ24087472

value: PBS


title: MM_20

description: Library name: sample 102


title: 203991460127_R02C01_P66/11_CNG

value: Anterior cingulate

value: QSBB

value: TRUE


title: Primary cell, KO + PBS, 12 hours after PHx, rep1

description: Library name: JZ24087471


title: 1028_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 28_BL

value: BL


title: MM_19

description: Library name: sample 101


title: Liver tissue, KO-1, 12 hours after PHx

description: Library name: JZ24033576

treatment_protocol: Mice were anesthetized with isoflurane after hair removal and disinfection of the abdominal skin. A midline incision was made to expose the liver, and the left lateral and median lobes were resected. The peritoneum was sutured with absorbable sutures, and the skin was closed with standard sutures. Postoperative care included rewarming with a heating blanket.

value: Partial Hepatectomy


title: 203991460154_R07C01_20110645_CNG


title: MM_18

description: Library name: sample 100

value: bone marrow


title: Liver tissue, KO-2, 12 hours after PHx

description: Library name: JZ24033577


title: 1027_IMV_D4

description: Library name: Cytostorm RNA SEQ 27_D4

value: IMV


title: 1027_IMV_D8

description: Library name: Cytostorm RNA SEQ 27_D8


title: 1027_IMV_BL

description: Library name: Cytostorm RNA SEQ 27_BL


title: MM_17

description: Library name: sample 99


title: 203991460154_R02C01_PDC131_CNG

value: Imperial Brain Bank


title: Liver tissue, WT-2, 12 hours after PHx

description: Library name: JZ24033579

value: Liver

value: WT


title: 203991460154_R06C01_20140523_CNG

value: Newcastle Brain Tissue Resource


title: MM_16

description: Library name: sample 98

value: Myeloma Plasma Cell


title: Liver tissue, WT-1, 12 hours after PHx

description: Library name: JZ24033578


title: 1026_IMV_D4

description: Library name: Cytostorm RNA SEQ 26_D4


title: 203977090026_R01C01_P60/10_CNG


title: MM_15

description: Library name: sample 97


title: Liver single cell nuclear; KO; 0 hour after PHx

description:
Library name: J23080053
10x Genomics

library_source: transcriptomic single cell

data_processing:
Data quality control and gene expression quantification were conducted using 10X Genomics Cell Ranger software (v3.1.0), which processed raw BCL files into FASTQ files, aligned reads to the reference genome, and quantified gene counts. Low-quality barcodes and UMIs were excluded prior to mapping with only reads that uniquely aligned to the transcriptome with at least 50% exon overlap were retained for UMI counting. Sequencing errors in UMI sequences were corrected, and valid barcodes were identified using the EmptyDrops method. This process ultimately yielded cell-by-gene matrices based on UMI counting and cell barcode assignment.
Assembly: GRCm39
Supplementary files format and content: tab-separated values files and matrix file

molecule: nuclear RNA

extract_protocol:
Liver tissues from wild-type (WT) and Ifrd1 knockout  mice were collected. Nuclei were isolated from the cell suspension using a commercially available nuclei isolation kit, following the manufacturer’s protocol.
Barcode-containing gel beads were mixed with cells and enzymes, encapsulated in oil-based droplets to form Gel Beads-In-Emulsions (GEMs), and subsequently collected. Barcode sequences were released upon dissolution, allowing cDNA synthesis and labeling. Amplified cDNA products from all GEMs were pooled for library preparation, with quality assessed via Agilent DNA assay kits and quantification performed on the ABI StepOnePlus Real-Time PCR System. Sequencing was conducted on the NovaSeq 6000 platform using PE150 mode. The library construction is provided by the technical support of Gene Denovo Biotechnology Co., Ltd. (Guangzhou, China).

value: KO


title: 1026_IMV_BL

description: Library name: Cytostorm RNA SEQ 26_BL

value: PBMC


title: 203976760069_R08C01_PD763_CNG

value: female

value: FALSE


title: MM_14

description: Library name: sample 96


title: Liver single cell nuclear; WT; 0 hour after PHx

description:
Library name: J23080052
10x Genomics


title: 1025_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 25_D8

value: non-IMV


title: 203976760069_R07C01_P10/02_CNG

value: Anterior cingulate


title: MM_13

description: Library name: sample 95


title: Liver single cell nuclear; KO; 24 hour after PHx

description:
Library name: J23050226
10x Genomics


title: 203976760069_R05C01_20090012_CNG

value: male


title: 1025_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 25_D4


title: MM_12

description: Library name: sample 94


title: 203976760069_R03C01_PD034_CNG


title: 1025_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 25_BL


title: Liver single cell nuclear; WT; 24hour after PHx

description:
Library name: J23050225
10x Genomics


title: MM_11

description: Library name: sample 93


title: Liver single cell nuclear; KO; 12hour after PHx

description:
Library name: J23050224
10x Genomics


title: 1024_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 24_D8


title: 203977090007_R08C01_P33/12_CNG

value: QSBB


title: MM_10

description: Library name: sample 92


title: Liver single cell nuclear; WT; 12hour after PHx

description:
Library name: J23050223
10x Genomics


title: 1024_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 24_D4


title: MM_9

description: Library name: sample 91


title: 203977090007_R07C01_20070009_CNG


title: 1024_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 24_BL

value: BL


title: 203977090007_R03C01_20100082_CNG


title: MM_8

description: Library name: sample 90


title: 203977090008_R08C01_20141164_CNG


title: 1022_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 22_BL


title: MM_7

description: Library name: sample 89


title: 1023_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 23_BL


title: Patient_DKD-12

city: Burjassot

first: José

middle: F.

last: Català-Senent

state: Valencia

address: Dr. Moliner, 50

department: Microbiología y Ecología

institute: Universitat de Valencia

hyb_protocol: The samples were hybridized with the nCounter® Human Metabolic Pathways Panel (XT-CSO-HMP1-12, NanoString) which included 748 genes across 36 annotated pathways.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection.

data_processing: Raw counts from RCC files generated by the NanoString runs

label: Molecular barcode on reporter probe

source_name: Peripheral blood mononuclear cells (PBMCs)

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol

growth_protocol: PBMCs were isolated from peripheral blood (extracted between 8:00 and 9:00 am) using a magnetic beads-based method (MACSprep kits) and later preserved at -80ºC in RNA later until RNA extraction.

extract_protocol: RNA was extracted from PBMCs using Ribospin RNA extraction kits (304-150; GeneAll, Korea). RNA quantity and quality were evaluated with a Nanodrop 2000 spectrophotometer (ThermoFisher) and a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

value: Male

tag: age (years)

tag: subject group


title: MM_6

description: Library name: sample 88

value: bone marrow


title: Patient_DKD-11

value: Peripheral blood mononuclear cells (PBMCs)


title: 203977090008_R03C01_PD814_CNG

value: Imperial Brain Bank


title: Patient_DKD-9

value: Female


title: 1021_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 21_D8

tag: time point


title: MM_5

description: Library name: sample 87


title: Patient_DKD-8


title: 1021_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 21_D4


title: 203977090005_R06C01_C076_CNG


title: MM_4

description: Library name: sample 86


title: Patient_DKD-7


title: MM_3

description: Library name: sample 85


title: 1020_IMV_D8

description: Library name: Cytostorm RNA SEQ 20_D8

value: IMV


title: 203977090004_R07C01_NP17/021_CNG

value: Oxford Brain Bank


title: 1021_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 21_BL


title: 203977090005_R01C01_RI02/203_CNG


title: Patient_DKD-6


title: MM_1

description: Library name: sample 83

value: Myeloma Plasma Cell


title: Patient_DKD-5


title: 1020_IMV_D4

description: Library name: Cytostorm RNA SEQ 20_D4


title: Patient_DKD-4


title: 1020_IMV_BL

description: Library name: Cytostorm RNA SEQ 20_BL


title: Patient_DKD-3


title: 1019_IMV_D8

description: Library name: Cytostorm RNA SEQ 19_D8


title: SMM_33

description: Library name: sample 81


title: Patient_DKD-2


title: SMM_32

description: Library name: sample 80


title: 1019_IMV_D4

description: Library name: Cytostorm RNA SEQ 19_D4


title: Patient_DKD-1


title: SMM_31

description: Library name: sample 79


title: Patient_T2D-12


title: 203977090025_R03C01_PD311_CNG


title: 203977090025_R02C01_NP17/074_CNG


title: 1018_IMV_D4

description: Library name: Cytostorm RNA SEQ 18_D4


title: Patient_T2D-11


title: SMM_29

description: Library name: sample 77


title: 203977090037_R05C01_C090_CNG


title: 1018_IMV_BL

description: Library name: Cytostorm RNA SEQ 18_BL


title: SMM_28

description: Library name: sample 76


title: 1017_IMV_Ex

description: Library name: Cytostorm RNA SEQ 17_Ex

value: Ex


title: Patient_T2D-9


title: 203977090037_R04C01_20152919_CNG

value: Newcastle Brain Tissue Resource


title: SMM_27

description: Library name: sample 75


title: Patient_T2D-8


title: 1017_IMV_D8

description: Library name: Cytostorm RNA SEQ 17_D8

value: PBMC


title: SMM_26

description: Library name: sample 74


title: 203977090037_R03C01_20185902_CNG

value: FALSE


title: Patient_DKD-10


title: 203977090008_R02C01_20130400_CNG

value: female


title: Patient_T2D-7


title: 1017_IMV_D4

description: Library name: Cytostorm RNA SEQ 17_D4


title: 203977090037_R01C01_P28/11_CNG

value: Anterior cingulate


title: SMM_25

description: Library name: sample 73


title: SMM_24

description: Library name: sample 72


title: 203977000030_R08C01_20185942_CNG

value: male


title: MM_2

description: Library name: sample 84


title: Patient_T2D-6


title: 1017_IMV_BL

description: Library name: Cytostorm RNA SEQ 17_BL


title: 203977090004_R05C01_PD898_CNG


title: Patient_T2D-5


title: 1016_IMV_D8

description: Library name: Cytostorm RNA SEQ 16_D8


title: 203977090004_R04C01_20174952_CNG


title: 203977000030_R04C01_PD976_CNG


title: SMM_34

description: Library name: sample 82


title: SMM_23

description: Library name: sample 71


title: 203977090025_R06C01_20050096_CNG


title: 203977090025_R07C01_20110837_CNG


title: 203977000030_R02C01_PD268_CNG


title: 1016_IMV_D4

description: Library name: Cytostorm RNA SEQ 16_D4


title: 203977000069_R02C01_PDC040_CNG


title: Patient_T2D-4


title: 1016_IMV_BL

description: Library name: Cytostorm RNA SEQ 16_BL


title: 1019_IMV_BL

description: Library name: Cytostorm RNA SEQ 19_BL


title: SMM_22

description: Library name: sample 70


title: 1018_IMV_D8

description: Library name: Cytostorm RNA SEQ 18_D8


title: Patient_T2D-3


title: 203973690061_R07C01_20185903_CNG


title: SMM_21

description: Library name: sample 69


title: 1015_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 15_BL

value: non-IMV


title: Patient_T2D-2


title: SMM_20

description: Library name: sample 68


title: SMM_30

description: Library name: sample 78


title: 1014_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 14_D8


title: Patient_T2D-1


title: 203973690061_R05C01_RI04/042_CNG


title: SMM_19

description: Library name: sample 67


title: 203973690061_R04C01_PDC114_CNG


title: 203977090037_R07C01_PD163_CNG


title: 1014_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 14_D4


title: Healthy_subject12


title: SMM_18

description: Library name: sample 66


title: 203973690061_R03C01_P28/12_CNG

value: QSBB


title: SMM_17

description: Library name: sample 65


title: 1014_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 14_BL

value: BL


title: Patient_T2D-10

value: Male


title: 203973690061_R02C01_20174940_CNG


title: Healthy_subject11

value: Peripheral blood mononuclear cells (PBMCs)


title: 1013_IMV_In

description: Library name: Cytostorm RNA SEQ 13_In

value: In


title: SMM_16

description: Library name: sample 64

value: bone marrow


title: Healthy_subject10


title: 1013_IMV_D8

description: Library name: Cytostorm RNA SEQ 13_D8

value: IMV


title: Healthy_subject9

value: Female


title: SMM_15

description: Library name: sample 63

value: Myeloma Plasma Cell


title: 203973690005_R08C01_NP14/148_CNG

value: Oxford Brain Bank


title: 1013_IMV_D4

description: Library name: Cytostorm RNA SEQ 13_D4


title: Healthy_subject8


title: 1013_IMV_BL

description: Library name: Cytostorm RNA SEQ 13_BL


title: 203973690005_R05C01_NP14/073_CNG


title: SMM_13

description: Library name: sample 61


title: 1012_IMV_D8

description: Library name: Cytostorm RNA SEQ 12_D8


title: SMM_12

description: Library name: sample 60


title: 203973690005_R04C01_NP15/007_CNG


title: Healthy_subject6


title: 1012_IMV_D4

description: Library name: Cytostorm RNA SEQ 12_D4


title: Healthy_subject5


title: SMM_11

description: Library name: sample 59


title: 1012_IMV_BL

description: Library name: Cytostorm RNA SEQ 12_BL


title: Healthy_subject4


title: SMM_10

description: Library name: sample 58


title: 203991450115_R05C01_20163932_CNG

value: Newcastle Brain Tissue Resource


title: SMM_9

description: Library name: sample 57


title: 1011_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 11_D4

value: PBMC


title: Healthy_subject2


title: 203991450115_R01C01_PD944_CNG

value: Imperial Brain Bank

value: FALSE


title: SMM_8

description: Library name: sample 56


title: 1011_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 11_BL


title: 1010_IMV_D8

description: Library name: Cytostorm RNA SEQ 10_D8


title: HACAT cells,treatment,3

city: Harbin

first: Yuan-hong

last: Wang

address: 24 Heping Road

institute: First Hospital of Heilongjiang University of Chinese Medicine

description:
Library name: SIMPLE 6
H3:fpkm

data_processing:
The libraries were circularized using the MGIEasy Universal Library Conversion Kit (App-A). The pooled libraries were serially diluted, quantified, and then sequenced on the BGI DNBSEQ-T7 sequencing platform in PE150 mode.
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use Fastp (0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
Reference genomes and gene model annotation files are directly downloaded from the genomic website. The HISAT2 (v2.1.0) software is used to construct an index of the reference genome, and the paired-end clean reads are subsequently aligned to the reference genome using HISAT2. HISAT2 is chosen as the alignment tool because it can generate a spliced alignment database based on the gene model annotation files, thereby achieving better alignment performance compared to other non-splicing aligners.
HTSeq (v0.9.1) is used to count the reads mapped to each gene, and these counts are taken as
the raw expression level of the genes, referred to as the Read Count. To ensure comparability of
Assembly: gene expression levels across different genes and samples, the expression values are normalized
Supplementary files format and content: using the FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) method.

source_name: HACAT

extract_protocol:
Extract total RNA using Invitrogen TRIzol reagent. The concentration and purity of total RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific NanoDrop one, Thermo Fisher Scientific, Waltham, MA, USA), while RNA integrity was assessed through either RNA-specific agarose gel electrophoresis or the Agilent Fragment Analyzer 5400 system (Agilent Fragment Analyzer 5400, Agilent Technologies Inc., California, USA).
mRNA enrichment was performed using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., Ipswich, Massachusetts, USA) with Oligo(dT) magnetic beads. The enriched mRNA was then randomly fragmented using divalent cations (ion interruption method) with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs Inc., Ipswich, Massachusetts, USA). Using the fragmented mRNA as a template, double-stranded cDNA was synthesized with random oligonucleotides as primers (for strandspecific library construction, dUTP replaced dTTP in the dNTP mix during second-strand synthesis). The double-stranded cDNA was purified, followed by end repair, A-tailing, and adapter ligation. cDNA fragments of approximately 400 – 500 bp were size-selected using AMPure XP beads (Beckman Coulter, Beverly, CA, USA), PCR-amplified, and the PCR products were purified again with AMPure XP beads to obtain the final library. Library fragment sizes were analyzed using an electrophoresis-based instrument such as the LabChip GX. Total library concentration was measured using Pico green, and the effective concentration of the library was quantified by qPCR.

value: HACAT

value: Immortalized Human Keratinocytes

value: WT

value: palmatine


title: 203991460068_R04C01_20150535_CNG

value: Anterior cingulate

value: male


title: 203991460068_R07C01_PD385_CNG


title: HACAT cells,treatment,2

description:
Library name: SIMPLE 5
H2:fpkm


title: SMM_6

description: Library name: sample 54


title: 203991460069_R08C01_PD172_CNG


title: 1010_IMV_D4

description: Library name: Cytostorm RNA SEQ 10_D4


title: 203973690005_R03C01_20100359_CNG

value: female


title: SMM_5

description: Library name: sample 53


title: HACAT cells,treatment,1

description:
Library name: SIMPLE 4
H1:fpkm


title: 1010_IMV_BL

description: Library name: Cytostorm RNA SEQ 10_BL

value: BL


title: 203991460069_R06C01_19900338_CNG


title: SMM_4

description: Library name: sample 52

value: bone marrow


title: 1009_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 9_D8

value: non-IMV


title: HACAT cells,control,3

description:
Library name: SIMPLE 3
K3:fpkm


title: 203991460069_R02C01_PD093_CNG


title: SMM_3

description: Library name: sample 51


title: 1009_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 9_D4


title: SMM_2

description: Library name: sample 50


title: 203991460069_R01C01_PD904_CNG


title: HACAT cells,control,1

description:
Library name: SIMPLE 1
K1:fpkm


title: 1009_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 9_BL


title: Irf5 KO OC

city: wuhan

first: Huan

last: Zhao

address: 1，University Park Road

institute: Wuhan University

description:
Library name: KO_OC
Gene expression data

data_processing:
Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR v.2.7.2b90. Gene expression counts were calculated using HTSeq v.0.9.1
DESeq2 was used to estimate significance between any two experimental groups

Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone marrow-derived

growth_protocol: BMMs were isolated from wild-type mice and Irf5-deleted mice cultured on plastic substrata for differentiation into osteoclasts with M-CSF and RANKL.

extract_protocol:
Total RNA was isolated from cell lysates with TRIzol reagent  according to the manufacturer's instructions.
The construction of libraries was generated using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.

treatment_protocol: BMMs were cultured with 30 ng/ml M-CSF and 10 ng/ml RANKL, after 1 day, cells becames POCs, after 4 days culture, cells became OCs.

value: Bone marrow-derived

value: Primary cell

value: Primary OC

value: Irf5 knockout

value: M-CSF/RANKL


title: 1008_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 8_D8

value: PBMC


title: SMM_1_DX

description: Library name: sample 48

value: Myeloma Plasma Cell


title: 1008_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 8_D4


title: WT_5

city: Xi’an, Shaanxi

first: Keping

last: Feng

address: No. 157, Xiwu Road

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

description: Library name: WT spleen B-5

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster GenerationSystem using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’sinstructions. After cluster generation, the library preparations were sequenced on an IlluminaNovaseq platform and 150 bp paired-end reads were generated.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: txt files include FPKM values and  raw counts  for each Sample

source_name: splenic B cells

extract_protocol:
RNA was harvested using standard extraction methods, followed by strict quality control of the RNA samples, primarily using the Agilent 2100 Bioanalyzer: precise assessment of RNA integrity.
A total amount of 1 μg RNA per sample was used as input material for the RNA samplepreparations.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in FirstStrand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using randomhexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNAsynthesis was subsequently performed using DNA Polymerase I and RNase H. Remainingoverhangs were converted into blunt ends via exonuclease/polymerase activities. Afteradenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated toprepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp inlength, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase,Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPureXP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: splenic B cells

tag: disease state

value: control


title: 1008_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 8_BL


title: Irf5 KO BMM

description:
Library name: KO_BMM
Gene expression data

value: Primary BMM

value: M-CSF


title: WT_2

description: Library name: WT spleen B-2


title: MGUS_18

description: Library name: sample 46


title: Wild-type OC

description:
Library name: WT_OC
Gene expression data

value: Wild-type


title: 1007_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 7_D4


title: WT_1

description: Library name: WT spleen B-1


title: MGUS_17

description: Library name: sample 45


title: Wild-type POC

description:
Library name: WT_Pre_OC
Gene expression data

value: Primary POC


title: 1007_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 7_BL


title: LF_5

description: Library name: fibrosis spleen B-5

value: fibrosis


title: MGUS_16

description: Library name: sample 44


title: Wild-type BMM

description:
Library name: WT_BMM
Gene expression data


title: 1006_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 6_D8


title: LF_4

description: Library name: fibrosis spleen B-4


title: Restricted-fed sow 14

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Library name: RES14

data_processing:
After sequencing, base calling (BCL) files were converted to FASTQ files using bcl2fastq2 (lllumina). The “dirty” raw reads, defined as reads that contain adapters, high content of N bases and low-quality reads were removed by SOAPnuke (BGI-Shenzhen, China) by BGI, with the following parameters (-l 15 -q 0.2 -n 0.05 -i).
Next, the clean reads were aligned to the pig reference genome (scrofa.Sscrofa11.1) using HISAT2 (v2.2.1), applying the following parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000.
Afterwards, the uniquely mapped reads were extracted using Samtools (v1.16.1), followed by deduplication using UMI-tools (v1.1.4) with default parameters.
Gene counts were obtained using featureCounts (v1.6.2) with the parameters: -p -T4 -t exon -g gene_id -a -o. Genes with an average read count of less than 5 across all animals were discarded, and normalization was performed using the negative binomial distribution implemented in the Bioconductor package DESeq.
Assembly: scrofa.Sscrofa11.1
Supplementary files format and content: Raw counts using featureCounts

organism: Sus scrofa

source_name: Ovarian granulosa cell

extract_protocol:
Total RNA of the mural granulosa cells (GCs) from each sow was extracted using the TRIzol method following the manufacturer’s instructions. The RNA Integrity Number (RIN) was assessed using the Agilent 2100 Bioanalyzer. In this study, the mean RIN was 7.30 ± 0.60 (± SD), and none of the RNA samples used in this study had a RIN below 5. One sample of the FF group, FF09, was excluded based on its low RIN number, and therefore subsequqently not taken along.
rRNAs were removed from total RNA, followed by fragmentation (to 200~500 nucleotides). The first-strand cDNA was synthesized using a random hexamer-primer, and dTTP was substituted by dUTP during the synthesis of the second strand. Next, the short fragments were purified and treated with elution buffer to facilitate end repair, followed by the addition of a single nucleotide A (adenine). After that, the adapters were connected to the fragments, and UNG (uracil-N-glycosylase) was used to degrade the second strand. After agarose gel electrophoresis, the suitable fragments were selected for several rounds of PCR amplification.

treatment_protocol: Female pigs were fed either a full (FF; 6.5 kg/day) or a restricted diet  (RES; 3.25 kg/day) during the last 2 weeks of lactation and then were fully fed for 2 days post-weaning before ovary collection.

value: Ovarian granulosa cell

tag: strain

value: Large White times Norwegian Landrace

value: Wild type

value: Restricted diet (3.25kg/day)

tag: time

value: Day 2 post-weaning


title: LF_3

description: Library name: fibrosis spleen B-3

tag: tissue


title: Restricted-fed sow 13

description: Library name: RES13


title: LF_2

description: Library name: fibrosis spleen B-2


title: MGUS_13

description: Library name: sample 41

value: bone marrow


title: Restricted-fed sow 12

description: Library name: RES12


title: MGUS_15

description: Library name: sample 43


title: 1005_non-IMV_DC

description: Library name: Cytostorm RNA SEQ 5_DC

value: non-IMV

value: DC


title: MGUS_14

description: Library name: sample 42


title: 1006_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 6_D4

value: PBMC


title: LF_1

description: Library name: fibrosis spleen B-1


title: MGUS_12

description: Library name: sample 40

value: Myeloma Plasma Cell


title: 203973690061_R01C01_PD916_CNG

value: Anterior cingulate

tag: regiondescription

tag: plate

value: Imperial Brain Bank

value: male

value: FALSE


title: SMM_14

description: Library name: sample 62


title: 1006_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 6_BL

value: BL


title: Restricted-fed sow 11

description: Library name: RES11


title: 1005_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 5_BL


title: Healthy_subject7

tag: Sex

value: Female

value: Peripheral blood mononuclear cells (PBMCs)


title: 203973690005_R06C01_PD793_CNG

tag: centre

value: female


title: MGUS_11

description: Library name: sample 39

tag: cell line

tag: cell type


title: 1004_non-IMV

description: Library name: Cytostorm RNA SEQ 4


title: Restricted-fed sow 10

description: Library name: RES10

value: Ovarian granulosa cell

value: Large White times Norwegian Landrace

tag: genotype


title: MGUS_10

description: Library name: sample 38


title: Restricted-fed sow 9

description: Library name: RES9

value: Wild type

value: Restricted diet (3.25kg/day)


title: 1011_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 11_D8

tag: group


title: 1003_non-IMV_D8

description: Library name: Cytostorm RNA SEQ 3_D8


title: Healthy_subject3

value: Male


title: Male_Placenta_High_GenX_Rep_5

city: Research Triangle Park

first: Suzanne

last: Fenton

state: North Carolina

address: 111 TW ALEXANDER DR

department: Mechanistic Toxicology Branch

institute: Division of the National Toxicology Program, National Institute of Environmental Health Sciences

description: 21546_1226_Male_Placenta_High_GenX_5_Rep_5

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Annotation was derived in R from the Affymetrix annotation file MTA-1_0.na36.mm10.transcript.csv. For each transcript, the raw intensities were background adjusted and RMA normalized.

label: biotin

label_protocol: Total RNA (25 ng/sample) was first amplified and labeled using the Affymetrix WT Plus Reagent Kit (WT Plus Kit) per manufacturer’s instructions.

growth_protocol: On embryoinic day E 11.5 or E 17.5 pregnant dams were weighed and humanely euthanized by swift decapitation. The uterus was removed and the placentas from viable embryos were collected in succession within a uterine horn and immediately snap frozen in liquid nitrogen (n = 2-5 placentas/litter). For placentas collected at E 17.5, a portion of fetal tissue corresponding to each snap frozen placenta was reserved and genotyped by PCR amplification of the sex determining region-Y (SRY) gene. Sex determination was not conducted for placentas collected at E 11.5 as the embryo gametes are not yet fully developed.

extract_protocol: For placentas collected at E 11.5, three placentas per litter were pooled to achieve sufficient tissue mass for the RNA extraction protocol (> 0.5 mg). For placentas collected at E 17.5, no more than one placenta from each sex was used from a given litter. Snap frozen tissues were weighed then homogenized using a FastPrep-24™ 5G (MP Biomedicals, Valiant Co., Ltd, China) in Buffer RLT (Qiagen, Hilden, Germany) within 2mL, 2.4mm metal bead homogenization tubes (Thermo Fisher Scientific, Waltham, MA). Homogenized placenta samples were snap frozen and stored at -80°C prior to RNA extraction. RNA was extracted using RNeasy kits following manufacturer’s protocols (Qiagen, Hilden, Germany). Resulting purified RNA was subjected to quality control assessments using a NanoDrop™ 2000/2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer High Sensitivity RNA Analysis (Agilent, Santa Clara, CA). All RNA samples used for transcriptomics analysis had a 260/280 ratio > 2.0 and RIN > 5.0. RNA isolates were diluted to a standard concentration of 100 ng RNA/ 1 µL H2O.

treatment_protocol: Pregnant CD-1 mice were exposed via daily oral gavage from embryonic day (E) 1.5 to E 11.5 (early developmental gestation) or E 17.5 (mature gestation) to PFOA (0, 1, or 5 mg/kg) or GenX (0, 2, or 10 mg/kg). A total N = 4-5 per treatment group (exposure chemical, dose, and duration) were used in the current study.

value: placenta

tag: age

value: embryonic day 17.5

tag: treatment

value: GenX

tag: dose

value: 10 mg/kg/day

tag: outlier

value: No


title: MGUS_9

description: Library name: sample 37

value: bone marrow

value: Myeloma Plasma Cell


title: SMM_7

description: Library name: sample 55


title: Restricted-fed sow 8

description: Library name: RES8

value: Day 2 post-weaning


title: 1003_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 3_D4

value: PBMC

value: non-IMV

tag: time point


title: MGUS_8

description: Library name: sample 36


title: Restricted-fed sow 7

description: Library name: RES7


title: 1003_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 3_BL

value: BL


title: MGUS_7

description: Library name: sample 35


title: Restricted-fed sow 6

description: Library name: RES6


title: 1002_IMV_D8

description: Library name: Cytostorm RNA SEQ 2_D8

value: IMV


title: Healthy_subject1

value: Female

tag: age (years)

value: Peripheral blood mononuclear cells (PBMCs)

tag: subject group


title: Male_Placenta_High_GenX_Rep_3

description: 21544_1226_Male_Placenta_High_GenX_3_Rep_3

tag: strain


title: MGUS_6

description: Library name: sample 34

tag: tissue


title: 1002_IMV_D4

description: Library name: Cytostorm RNA SEQ 2_D4


title: Restricted-fed sow 5

description: Library name: RES5

value: Ovarian granulosa cell

value: Large White times Norwegian Landrace

value: Wild type

tag: time


title: Male_Placenta_High_GenX_Rep_4

description: 21545_1226_Male_Placenta_High_GenX_4_Rep_4

value: placenta

value: Male


title: Male_Placenta_High_GenX_Rep_1

description: 21542_1226_Male_Placenta_High_GenX_1_Rep_1

value: embryonic day 17.5

value: GenX


title: HACAT cells,control,2

description:
Library name: SIMPLE 2
K2:fpkm

value: HACAT

value: Immortalized Human Keratinocytes

value: WT


title: MGUS_5

description: Library name: sample 33

value: bone marrow

value: Myeloma Plasma Cell


title: 1002_IMV_BL

description: Library name: Cytostorm RNA SEQ 2_BL

value: PBMC


title: Restricted-fed sow 4

description: Library name: RES4

value: Restricted diet (3.25kg/day)

value: Day 2 post-weaning


title: MGUS_4

description: Library name: sample 32


title: Restricted-fed sow 3

description: Library name: RES3


title: 1001_non-IMV_D4

description: Library name: Cytostorm RNA SEQ 1_D4

value: non-IMV


title: SMM_1_RR

description: Library name: sample 49


title: Irf5 KO POC

description:
Library name: KO_Pre_OC
Gene expression data

value: Bone marrow-derived

value: Primary cell

value: Primary POC

value: Irf5 knockout

value: M-CSF/RANKL


title: MGUS_3

description: Library name: sample 31


title: Restricted-fed sow 2

description: Library name: RES2

value: Ovarian granulosa cell

value: Large White times Norwegian Landrace

value: Wild type


title: WT_4

description: Library name: WT spleen B-4

value: splenic B cells

tag: disease state

value: control


title: 1001_non-IMV_BL

description: Library name: Cytostorm RNA SEQ 1_BL

value: BL


title: Restricted-fed sow 1

description: Library name: RES1


title: Human ascending aortic SMC SMAD3 variant sample 3

city: London

first: Paulina

middle: M

last: Kowalewska

state: Ontario

address: 1151 Richmond Street

department: Robarts Research Institute

country: Canada

institute: The University of Western Ontario

description: Library name: LDS3_C

data_processing:
After separating the multiplexed sequencing data, adapter sequences were removed using Trim Galore and the individual libraries were converted to the FASTQ format.
TopHat v.2.0.11 was used to align transcriptomic sequence reads to the human genome (hg19) and the resulting alignment files were reconstructed using Bowtie2.
The read counts of each transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample, expressed as RPKM. Transcripts expressed below 0.5 RPKM across all samples were not included in bioinformatics analyses.
Assembly: hg19
Supplementary files format and content: csv file includes RPKM values for each sample

source_name: Ascending aortic media

growth_protocol: Control and LDS3 smooth muscle cells (cell passage 1) from the first outgrowth of ascending aortic media explants were thawed onto fibronectin-coated (50µg/mL) culture dishes. SMC cultures were maintained in DMEM/F12 media (Gibco) supplemented with SmGM®-2 SingleQuots® bullet kit (Lonza; insulin, hFGF-B, GA 1000, hEGF and 5% FBS).

extract_protocol:
Total RNA was isolated from aortic SMCs with the Qiagen RNeasy kit (Qiagen).
RNA libraries were prepared from total RNA; amplified poly-A mRNAs were fragmented, reverse transcribed and adaptor ligated to produce the final sequencing library.

treatment_protocol: When cells reached ~80% confluence, growth factors were withdrawn and 0.5% FBS was added to the media to render the SMCs quiescent.

value: Ascending aortic media

value: Human ascending aortic smooth muscle cells


title: WT_3

description: Library name: WT spleen B-3


title: MGUS_2

description: Library name: sample 30

value: bone marrow

value: Myeloma Plasma Cell


title: Male_Placenta_High_GenX_Rep_2

description: 21543_1226_Male_Placenta_High_GenX_2_Rep_2

value: placenta

value: embryonic day 17.5

tag: Sex

value: Male

value: GenX

value: 10 mg/kg/day

value: No


title: MGUS_1

description: Library name: sample 29


title: MGUS_19

description: Library name: sample 47


title: Human ascending aortic SMC SMAD3 variant sample 2

description: Library name: LDS3_B


title: Male_Placenta_Low_GenX_Rep_5

description: 21541_1226_Male_Placenta_Low_GenX_5_Rep_5

value: 2 mg/kg/day


title: Full-fed sow 13

description: Library name: FF13

value: Ovarian granulosa cell

value: Standard diet (6.5kg/day)

value: Day 2 post-weaning


title: HD_10

description: Library name: sample 28

value: Healthy Plasma Cell


title: Male_Placenta_Low_GenX_Rep_4

description: 21540_1226_Male_Placenta_Low_GenX_4_Rep_4


title: Human ascending aortic SMC SMAD3 variant sample 1

description: Library name: LDS3_A


title: Male_Placenta_Low_GenX_Rep_2

description: 21538_1226_Male_Placenta_Low_GenX_2_Rep_2


title: HD_9

description: Library name: sample 27


title: Human ascending aortic SMC control sample 3

description: Library name: Control_C

value: Control


title: Male_Placenta_Low_GenX_Rep_3

description: 21539_1226_Male_Placenta_Low_GenX_3_Rep_3


title: Human ascending aortic SMC control sample 2

description: Library name: Control_B


title: HD_8

description: Library name: sample 26


title: Full-fed sow 10

description: Library name: FF10

value: Large White times Norwegian Landrace

value: Wild type


title: Human ascending aortic SMC control sample 1

description: Library name: Control_A

value: Ascending aortic media

value: Human ascending aortic smooth muscle cells


title: Full-fed sow 11

description: Library name: FF11


title: HD_7

description: Library name: sample 25

value: bone marrow


title: Full-fed sow 8

description: Library name: FF8


title: HumanTissue_sRNA_SchizophreniaPool2_6

city: Barcelona

first: Marcos

last: Galán-Ganga

address: C/ Casanova, 143.

department: Biomedicine

institute: University of Barcelona

description: Library name: Human_P2-SCZ6

data_processing:
The quality of the sequenced fastq files was checked using FastQC software (v0.12.1). Adapter trimming was performed with Cutadapt and the trimmed reads were aligned to the human genome (version Ensemble hg 19) using the STAR aligner (v2.7.9a). Quantification and annotation were performed with the ExceRpt tool. We generated ExceRpt count matrices with raw reads of each sRNA biotype in every sample.
Assembly: hg39
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Hippocampal brain tissue

extract_protocol:
Hippocampal sRNA extraction was performed using the miRNeasy mini kit (QIAGEN, 217004) according to the manufacturer’s instructions. All samples were eluted in 40 µL of RNAse-free water and total RNA quantity and quality were measured using a ND-1000 spectrophotometer (Thermo Fisher Scientific) and a TapeStation 4200 (Agilent), respectively. Most of the samples used for the experiments had an RNA integrity number (RIN) of 6 or higher. sRNA fractions were purified from total RNA using the RNA Clean & ConcentratorTM-5 kit (Zymo Research; R1015).
Sequencing libraries were prepared from hippocampal purified sRNAs in a representative subset of control individuals (N = 6) and schizophrenia patients (N = 12, 6 patients from each pool) using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs), according to the manufacturer’s instructions. Individual libraries were subjected to quality analysis using a Bioanalyser 2100 (Agilent Technologies Inc.), and size selection (140–165 bp) was performed in 6% polyacrylamide gel, which corresponded to adapter-ligated constructs derived from the 21 and 30 nt RNA fragments, respectively. Indexed libraries were equimolarly pooled and sequenced in an HiSeq2500 (Illumina) and 50 nt single-end reads were produced.

value: Hippocampal brain tissue

value: Schizophrenia patient


title: HD_6

description: Library name: sample 24

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
RNA-seq: differential gene expression analysis was performed using DESeq2 and GSEA analyses were conducted using ClusterProfiler.
Assembly: GRCh38.p13
Supplementary files format and content: RNA-seq: one excel file containing the cpm for all the samples (divided cell lines and human samples).

extract_protocol:
RNA was isolated with the MagMAX mirVana total RNA Isolation kit (applied biosystems)
RNA-seq library was prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina).


title: HD_5

description: Library name: sample 23


title: Full-fed sow 7

description: Library name: FF7


title: HumanTissue_sRNA_SchizophreniaPool2_5

description: Library name: Human_P2-SCZ5


title: HD_4

description: Library name: sample 22


title: HumanTissue_sRNA_SchizophreniaPool2_4

description: Library name: Human_P2-SCZ4


title: Full-fed sow 6

description: Library name: FF6


title: HD_3

description: Library name: sample 21


title: Full-fed sow 5

description: Library name: FF5


title: HumanTissue_sRNA_SchizophreniaPool2_3

description: Library name: Human_P2-SCZ3


title: HD_2

description: Library name: sample 20


title: HumanTissue_sRNA_SchizophreniaPool2_2

description: Library name: Human_P2-SCZ2


title: Full-fed sow 4

description: Library name: FF4


title: HD_1

description: Library name: sample 19


title: Full-fed sow 3

description: Library name: FF3


title: HumanTissue_sRNA_SchizophreniaPool2_1

description: Library name: Human_P2-SCZ1


title: MM.1R-IRF-sg2 R3

description: Library name: sample 18

source_name: cell line

value: cell line

value: Multiple Myeloma

value: modified to express Cas9 protein


title: vHipp_ctrl_Saline38

description: Library name: P30210_1072_S146

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
miRNeasy Micro Kit (Qiagen), 100 ng of total RNA was used for construction of sequencing libraries
Illumina Stranded mRNA Prep

value: vHipp

value: ctrl

value: male

value: WT

value: Saline

tag: ID


title: Full-fed sow 2

description: Library name: FF2

value: Ovarian granulosa cell

value: Standard diet (6.5kg/day)

value: Day 2 post-weaning


title: HumanTissue_sRNA_SchizophreniaPool1_6

description: Library name: Human_P1-SCZ6


title: MM.1R-IRF-sg1 R3

description: Library name: sample 17

tag: cell line


title: Male_Placenta_Low_PFOA_Rep_4

description: 21531_1226_Male_Placenta_Low_PFOA_4_Rep_4

value: placenta

value: embryonic day 17.5

value: Male

value: PFOA

value: 1 mg/kg/day

value: No


title: Full-fed sow 1

description: Library name: FF1

value: Large White times Norwegian Landrace

value: Wild type


title: Male_Placenta_High_PFOA_Rep_4

description: 21535_1226_Male_Placenta_High_PFOA_4_Rep_4

value: 5 mg/kg/day


title: Male_Placenta_Low_GenX_Rep_1

description: 21537_1226_Male_Placenta_Low_GenX_1_Rep_1

value: GenX

value: 2 mg/kg/day


title: Male_Placenta_High_PFOA_Rep_5

description: 21536_1226_Male_Placenta_High_PFOA_5_Rep_5


title: HumanTissue_sRNA_SchizophreniaPool1_5

description: Library name: Human_P1-SCZ5

value: Hippocampal brain tissue

value: Schizophrenia patient


title: MM.1R Scr R3

description: Library name: sample 16

value: cell line

tag: cell type

value: Multiple Myeloma

value: modified to express Cas9 protein

value: scramble


title: HeLa cells, Input, for siDC1 batch

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

description: Library name: Sample9

data_processing:
For RNA-seq analysis, raw sequencing reads for shBRD4 HeLa rescued by EGFP-BRD4-WT and EGFP-BRD4-12A samples were trimmed for low-quality nucleotides and adapter sequences using Trim Galore! (v0.6.7). The reads were then aligned to human genome GRCh38/hg38 with HISAT2 (v2.2.1) using the ‘-rna-strandness RF’ parameter and an additional ‘-k 30’ parameter for chromatin RNA analysis. Gene annotation GTF format files for human were downloaded from the ENSEMBL database (https://www.ensembl.org/index.html). Reads counts for genes were obtained using featureCounts (v2.0.2) and then normalized to fragments per kilobase of transcript per million mapped reads (FPKM). Differential expression analysis was performed with the R/Bioconductor package DESeq2 (v1.36.0),using P value < 0.05 and log2 |fold change| > log2 (1.5) threshold.
For ChIP-seq analysis, raw reads were trimmed and aligned to the GRCh38/hg38 human reference genome using Bowtie2 (v2.4.5). Duplicate reads were removed using Picard tools (v.1.88, http://broadinstitute.github.io/picard) and BAM files were generated using Samtools (v1.2). Peak calling was performed using MACS2 (2.2.7.1) with ‘-q 0.01 --extsize 150 --keep-dup 5’ parameters to identify histone and transcription factor ChIP-seq enrichment regions over background. Robust BRD4 peaks intersected from two biological replicates were merged from both the 12A and WT treatments using Bedtools (v2.31.1).
Assembly: Assembly: hg38
Supplementary files format and content: bigWig

source_name: HeLa

growth_protocol: HeLa cell line was cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C under 5% CO2.

extract_protocol:
For RNA-seq, Total RNA and RNA associated with different cell fractions were extracted using TRIzol™ reagent (Invitrogen, 15596026) according to the manufacturer’s protocol and quantified using NanoDrop One spectrophotometer (Invitrogen). For ChIP-seq, HeLa cells were resuspended with growth medium into a density of 106 mL-1. Crosslinking was performed by adding 1% formaldehyde (Sigma-Aldrich, F1635) into the cells followed by rotation for 20 min at RT, which was ceased by glycine with a final concentration of 0.125 M followed by rotating for 5 min at RT. Supernatants were removed and cell pellets were rinsed with ice cold PBS twice, then the cells were resuspended with lysis buffer (50 mM HEPES, pH 7.9, 5 mM MgCl2, 0.2% Triton X-100, 20% glycerol, 300 mM NaCl, 1× protease inhibitor) on ice for 10 min. Cell pellets were collected by centrifugation at 4 °C, 500 g for 5 min, then resuspended with SDS lysis buffer (50 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1× protease inhibitor) and kept on ice for 30 min. The lysates were sonicated utilizing a Bioruptor sonicator (Diagenode) at high power for 30 cycles, followed by centrifugation at 17000 × g for 10 min. Supernatants were collected into new tubes. The specified antibodies, BRD4 (E2A7X) Rabbit mAb (Cell Signaling Technology, 13440S) and HA-Tag (C29F4) Rabbit mAb (Cell Signaling Technology, 3724S), were diluted 1:50 in SDS lysis buffer and incubated with a pre-washed mixture of Protein A and G magnetic beads at 4 °C with continuous rotation for a minimum of 2 h. The beads were subsequently washed three times with SDS lysis buffer. Cell lysates were pre-cleaned with washed Protein A and G magnet beads mixture at 4 °C for 1 h with rotation, and 10% of the lysate were kept as the input control. Then, the remaining lysates and antibody-coated beads were incubated at 4 °C overnight with rotation. The beads were washed with rotation sequentially at 4 °C with the following buffers, 5 min for each: twice with SDS lysis buffer, twice with high salt wash buffer (50 mM HEPES, pH 7.5, 350 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), twice with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) and once with TE wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.2% Triton X-100), then eluted with 240 µL elution buffer (100 mM NaHCO3, 1% freshly added SDS) by shaking at 30 °C for 1 h. The eluent was then mixed with 14.4 µL 5 M NaCl and shaken at 65 °C for 4 h to reverse the crosslinks between proteins and DNA. Afterwards, the eluent was treated with 4 µL RNase A (Thermo Scientific, EN0531), shaken at 37 °C for 15 min, then 4 µL proteinase K (Thermo Scientific, 100005393), shaken at 65 °C overnight. The DNA was extracted by DNA clean & concentrator (Zymo Research, D4014) and set aside for subsequent qPCR assay or library preparation.
For RNA-seq, RNA-seq library preparation was performed utilizing VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NR605) following the manufacturer’s protocols with 1 µg initial amount of total RNA for each sample, and sequencing was performed at JMDNA Bio-Medical Technology Corporation on an Illumina NovaSeq 6000 platform. For ChIP-seq, library preparation was performed utilizing VAHTS Universal Pro DNA Library Prep Kit (Vazyme, ND608) following the manufacturer’s protocols with 10 ng initial amount of DNA for each sample, and sequencing was performed at JMDNA Bio-Medical Technology Corporation on an Illumina NovaSeq 6000 platform.

value: HeLa

value: Cervical cancer cells


title: Male_Placenta_High_PFOA_Rep_3

description: 21534_1226_Male_Placenta_High_PFOA_3_Rep_3

value: placenta

value: embryonic day 17.5

value: Male


title: Male_Placenta_Low_PFOA_Rep_3

description: 21530_1226_Male_Placenta_Low_PFOA_3_Rep_3

value: PFOA

value: 1 mg/kg/day

value: No


title: KMS-11-IRF2-sg2 R3

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

institute: CIMA

description: Library name: sample 15

tag: genotype


title: HumanTissue_sRNA_SchizophreniaPool1_4

description: Library name: Human_P1-SCZ4


title: HeLa cells, ChIP 12A, siYTHDC1, rep2

description: Library name: Sample8

value: 12A, siYTHDC1


title: HumanTissue_sRNA_SchizophreniaPool1_3

description: Library name: Human_P1-SCZ3


title: Male_Placenta_Low_PFOA_Rep_2

description: 21529_1226_Male_Placenta_Low_PFOA_2_Rep_2


title: KMS-11-IRF2-sg1 R3

description: Library name: sample 14


title: HeLa cells, ChIP 12A, siYTHDC1, rep1

description: Library name: Sample7


title: HumanTissue_sRNA_SchizophreniaPool1_2

description: Library name: Human_P1-SCZ2


title: Male_Placenta_High_PFOA_Rep_2

description: 21533_1226_Male_Placenta_High_PFOA_2_Rep_2

value: 5 mg/kg/day


title: KMS-11 Scr R3

description: Library name: sample 13


title: HeLa cells, ChIP 12A, mock, rep2

description: Library name: Sample6

value: 12A, mock


title: Full-fed sow 14

description: Library name: FF14

value: Ovarian granulosa cell

value: Large White times Norwegian Landrace

value: Wild type

value: Standard diet (6.5kg/day)

value: Day 2 post-weaning


title: Male_Placenta_High_PFOA_Rep_1

description: 21532_1226_Male_Placenta_High_PFOA_1_Rep_1


title: HumanTissue_sRNA_SchizophreniaPool1_1

description: Library name: Human_P1-SCZ1

value: Hippocampal brain tissue

value: Schizophrenia patient


title: Male_Placenta_Low_PFOA_Rep_1

description: 21528_1226_Male_Placenta_Low_PFOA_1_Rep_1


title: MM.1R-IRF-sg2 R2

description: Library name: sample 12

value: cell line

value: Multiple Myeloma

value: modified to express Cas9 protein


title: HeLa cells, ChIP 12A, mock, rep1

description: Library name: Sample5

value: HeLa

value: Cervical cancer cells


title: HumanTissue_sRNA_ControlPool_6

description: Library name: Human_CTL6

value: Healthy donor


title: MM.1R-IRF-sg1 R2

description: Library name: sample 11


title: HeLa cells, ChIP WT, siYTHDC1, rep2

description: Library name: Sample4

value: WT, siYTHDC1


title: MM.1R Scr R2

description: Library name: sample 10

value: scramble


title: HumanTissue_sRNA_ControlPool_5

description: Library name: Human_CTL5


title: Full-fed sow 12

description: Library name: FF12


title: HeLa cells, ChIP WT, siYTHDC1, rep1

description: Library name: Sample3


title: HumanTissue_sRNA_ControlPool_4

description: Library name: Human_CTL4


title: KMS-11-IRF2-sg2 R2

description: Library name: sample 9


title: HeLa cells, ChIP WT, mock, rep2

description: Library name: Sample2

value: WT, mock


title: Male_Placenta_Cont_Rep_2

value: placenta

value: embryonic day 17.5

value: Male

value: Vehicle control

value: 0 mg/kg/day

value: No


title: HeLa cells, ChIP WT, mock, rep1

description: Library name: Sample1


title: KMS-11-IRF2-sg1 R2

description: Library name: sample 8


title: HumanTissue_sRNA_ControlPool_3

description: Library name: Human_CTL3

value: Hippocampal brain tissue


title: HumanTissue_sRNA_ControlPool_2

description: Library name: Human_CTL2


title: Male_Placenta_Cont_Rep_5


title: KMS-11 Scr R2

description: Library name: sample 7


title: HDF cells overexpressing OCT4, KDM8 and shSOX2 (input)

city: changchun

first: songqin

last: yang

address: No. 5625, Renmin Street

institute: Changchun Institute of Applied Chemistry

description: Library name: O-KDM8-shSOX20-input

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for raw data filtering: Remove low quality tags as well as contaminants to get clean reads. Software information SOAPnuke Parameter: Clean Parameter: SOAPnuke filter -l 15 -q 0.5 -n 0.01 -Q 2 -c 21.
After filtering, SOAPaligner/SOAP2 (v 2.21t),which allows up to two mismatches in the alignment, is used to align clean data to the reference genome. The unique mapped reads are used for downstream bioinformatic analysis. Parameter：Clean Parameter: soap_mm_gz -p 4 -v 2 -s 35
Peak calling is a tool to identify regions which are enriched. MACS (Model-based Analysis of  ChIP-Seq)  software applied in our workflow uses Dynamic Possion Distribution to calculate p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value< le-5. Thus, MACS assigns each enriched region (Peak) with set of numerical values which are the number of summits, tags, normalized p-value as well as fold enrichment information. The more enriched these regions are, the more likely they are transcription factor binding sites. The score is positively correlated to transcription factor binding intensity.
MAnorm(v1.1) is used to build different enriched peaks of different samples. The significant regions are picked up if |M| ≥ 1 and p-value ≤ 10-5. The gene element annotation of peak or different enrichment peak from different samples is carried out by bedtools intersect mode with overlap 50%.
Assembly: GRCh38
Supplementary files format and content: Raw sequencing data are subjected to quality control and data filtering. Alignment tools are used to align the data to the reference genome. The output of the alignment procedure is stored in a text file (bed format) which will be used for downstream bioinformatic analysis, including read analysis and peak scanning.

source_name: human dermal fibroblasts

extract_protocol:
On day 8 after lentiviral transduction, chromatin immunoprecipitation was performed on HDFs using the CST (#9005) kit following the manufacturer’s instructions.
Library preparation is performed using MGIEasy Universal DNA Library Prep Set (MGI-Shenzhen, China). Firstly, A certain amount of purified ChIPed DNA sample is taken and converted into blunt-end DNA through end repair reaction. Then an adenosine is added to the 3′ ends of the end repaired DNA through A-tailing reaction. Later, library adaptors are connected through adaptor ligation process, Finally, the library products are amplified through PCR reaction and subjected to quality control.

value: human dermal fibroblasts

value: overexpressing OCT4, KDM8 and shSOX2

tag: batch


title: HumanTissue_sRNA_ControlPool_1

description: Library name: Human_CTL1


title: HDF cells overexpressing OCT4, KDM8 and shSOX2 (ChIP)

description: Library name: O-KDM8-shSOX2-ChIP

value: KDM8 (Thermo Fisher Science PA5-44862)


title: MM.1R-IRF-sg2

description: Library name: sample 6

value: cell line

value: Multiple Myeloma

value: modified to express Cas9 protein


title: DiR-ID (DiR-ID, DEX) - rep2

city: Illkirch-Graffenstaden

first: Maximiliano

last: Portal

state: Alsace

address: 1 rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2. Obtained data was further analyzed using fastQC and fastQScreen.
DiR-F, ChIP-seq and FAIRE-seq data was mapped to hg38 using Bowtie2. For peaks/broad region enrichment calling we used PePr pipeline in either sharp peaks (DiR-F, FAIRE, H3K4me1, H3K4me3, H3K9Ac and H3K27Ac) or broad (DiR-F, H3K9me3, H3K27me3 and H3K36me3) mode with 200 window size for DiR-F and FAIRE-seq data and 146 window size for ChiP-seq data with an FDR<0.05. DiR-F data was analyzed in both modes and peaks/regions were collapsed into a single file using intersectBed tool from BedTools. All data obtained from sharp peak detection was further refined using PePr-postprocess. DNAseI footprint analysis was performed over DiR-F detected peaks/regions using wellington_footprints.py from pyDNAse suite using and FDR<0.01 cutoff. mNET-Seq obtained reads were first stripped from adaptors using cutadapt pipeline and obtained reads were mapped to hg38 using Tophat2 under standard conditions for reads longer than 20 nucleotides. For reads smaller than 20 nucleotides reads were mapped using bowtie2 with the following parameters: bowtie2 –k 20 –end-to-end –D 20 –R 3 –N 0 –L 6 –I 5,1,0.50 to ensure that reads of 6-19 nucleotides were mapped at least 20 times when multiple alignment was possible. mNET-Seq datasets were further curated to remove rRNA and tRNA mapping reads using intersectBed from BedTools and 3’-ends position was recorded using bam2wig module from BioToolBox (https://github.com/tjparnell/biotoolbox). Nucleosome mapping was achieved by collapsing ChIP-seq data obtained from input material (mononucleosomes) and processed using Nucwave suite in single-end reads mode. All data analyzed in this section was processed through R (https://cran.r-project.org) and/or DeepTools for visualization purposes.
TARDIS obtained strand-specific RNA-Seq data was mapped to hg38 using HISAT2 and HeLa cells transcriptome reconstructed using Stringtie. Differential analysis was performed using Kallisto/Sleuth pipeline (FDR<0.05) to determine either differential recruitment or differential expression. Triplexator analysis was performed using the following parameters: –l 20 –e 5 –fr on –mrl 7 –mrp 3 –dc –1 using all detected DiR-F peaks/regions as targets and RNAseA treated DiR-ID RNA library as transcript source. For individual transcript analysis we used Triplex Domain Finder using and FDR<0.05, minimum length of 20, maximum error rate of 20, a tolerated number of consecutive events of 2 for 5000 randomization events. All data analyzed in this section was processed through R and/or DeepTools for visualization purposes.
Genome_build: hg38
Supplementary_files_format_and_content: bdg files were generated using bam2wig module from BioToolBox (https://github.com/tjparnell/biotoolbox).

source_name: HeLa cells

extract_protocol:
Input and immunoprecipitated DNA was recovered using Qiagen MinElute kits. mNET-Seq immunoprecipitated material was recovered using Qiagen MinElute kits. DiR-F derived samples were recovered using PAGE electrophoresis. RNA was recovered using Trizol.
DNA libraries were prepared following Diagenode MicroPlex kit instructions. RNA libraries were prepared following TARDIS protocol (Portal MM et al. Nature Protocols. 2016)
DNA or RNA molecules were end-repaired and ligated to DNA/RNA adaptors prior to PCR amplification and further sequencing.

tag: sample type

value: DiR-ID

value: HeLa


title: Male_Placenta_Cont_Rep_4

tag: age

tag: treatment


title: MM.1R-IRF-sg1

description: Library name: sample 5


title: HDF cells overexpressing OCT4 and KDM8 (input)

description: Library name: O-KDM8-input

value: overexpressing OCT4 and KDM8


title: DiR-ID (DiR-ID, DEX) - rep1


title: MM.1R Scr

description: Library name: sample 4

value: scramble


title: HDF cells overexpressing OCT4 and KDM8 (ChIP)

description: Library name: O-KDM8-ChIP


title: Actively transcribed RNA (Tx, DEX) - rep2

value: TARDIS RNA-seq


title: HDF cells, overexpressing OCT4 and KDM8, day 5, O-KDM8-3

description:
Library name: O8_d5_3
O-KDM8-3

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V4.1.2)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
owtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.12)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) (or DEGseq （v1.48.0）or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCh38
Supplementary files format and content: xlsx file includes read count vlaues  for each Sample

extract_protocol:
Total RNA was isolated using the UNIQ-10 Silica-Matrix RNA Purification System (Sangon Biotech, China) following manufacturer-recommended protocols. 0.2 ug of total RNA was used for the construction of sequencing libraries
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).


title: KMS-11-IRF2-sg2

description: Library name: sample 3

value: IRF2-sg2 (transduced with lentiviral particles containing sgRNA-2 against IRF2)


title: Actively transcribed RNA (Tx, DEX) - rep1


title: 203968030087_R01C01_PD820_CNG

city: Exeter

first: Joshua

last: Harvey

address: RILD Building, RD&E, Barrack Road

institute: University of Exeter

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

source_name: Anterior cingulate

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Anterior cingulate

tag: regiondescription

tag: plate

tag: centre

value: Imperial Brain Bank

value: female

tag: thal

value: FALSE


title: KMS-11-IRF2-sg1

description: Library name: sample 2

value: IRF2-sg1 (transduced with lentiviral particles containing sgRNA-1 against IRF2)


title: HDF cells, overexpressing OCT4 and KDM8, day 5, O-KDM8-2

description:
Library name: O8_d5_2
O-KDM8-2

value: human dermal fibroblasts


title: Total RNA (SS, DEX) - Rep2


title: KMS-11 Scr

description: Library name: sample 1

value: scramble (transduced with lentiviral particles of the empty vector)


title: Male_Placenta_Cont_Rep_3

value: placenta

tag: strain

value: embryonic day 17.5

value: Male

value: Vehicle control

tag: dose

value: 0 mg/kg/day

tag: outlier

value: No


title: Female_Placenta_Low_GenX_Rep_4

description: 21516_1226_Female_Placenta_Low_GenX_4_Rep_4

tag: tissue

value: Female

value: GenX

value: 2 mg/kg/day


title: HDF cells, overexpressing OCT4 and KDM8, day 5, O-KDM8-1

description:
Library name: O8_d5_1
O-KDM8-1


title: Male_Placenta_Cont_Rep_1

tag: Sex


title: Total RNA (SS, DEX) - Rep1

value: TARDIS RNA-seq

value: HeLa


title: Female_Placenta_Low_GenX_Rep_3

description: 21515_1226_Female_Placenta_Low_GenX_3_Rep_3


title: Flow2

city: New Haven

first: Yibing

last: Qyang

address: 300 George St

institute: Yale University

description: Library name: Sample2

data_processing:
RNA-seq reads were aligned to the reference genome with STAR(version= 2.7.11a), gene counts were obtained using Subread/featureCounts(v2.0.3), and differential expression was analyzed in R (v4.4.1-foss-2022b) with DESeq2. GO enrichment was performed with clusterProfiler (org.Hs.eg.db, AnnotationDbi, enrichplot, DOSE), and KEGG pathways were analyzed using pathview. P-value less than 0.05 was considered significant.
Assembly: GRCh38
Supplementary files format and content: txt file including raw counts of each sample and gene IDs

source_name: Endothelial Cell

extract_protocol:
After conditioning, ECs from both flow and static grafts were lysed directly in TRIzol. Each RNA sample represented a pooled lysate from three independent batches derived from one HLHS patients. In total, iPSC-ECs from three HLHS patients were used for both flow and static graft conditions.
mRNA is purified, from a normalized input between 10-1000ng of total RNA, using mRNA capture beads prior to fragmentation (Watchmaker mRNA Library Prep Kit).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ T overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution is determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: iPSC-ECs were then seeded onto decellularized human umbilical arteries (dHUAs) and subjected to two hemodynamic conditions: (1) a shear preconditioning protocol designed to mimic IVC hemodynamics (ramping from 1 to 15 dynes/cm² over 36 h, maintaining 15 dynes/cm² for 48 h, then reducing to 5 dynes/cm² for 12 h), and (2) a static condition followed by abrupt exposure to 5 dynes/cm² for 6 h (static + abrupt flow).

value: Endothelial Cell

value: Flow


title: Female_Placenta_Low_GenX_Rep_2

description: 21514_1226_Female_Placenta_Low_GenX_2_Rep_2

value: Yes


title: Female_Placenta_Low_GenX_Rep_5

description: 21517_1226_Female_Placenta_Low_GenX_5_Rep_5


title: Female_Placenta_High_PFOA_Rep_3

description: 21510_1226_Female_Placenta_High_PFOA_3_Rep_3

value: PFOA

value: 5 mg/kg/day


title: Female_Placenta_High_PFOA_Rep_5

description: 21512_1226_Female_Placenta_High_PFOA_5_Rep_5


title: Female_Placenta_High_PFOA_Rep_2

description: 21509_1226_Female_Placenta_High_PFOA_2_Rep_2


title: Female_Placenta_High_GenX_Rep_5

description: 21522_1226_Female_Placenta_High_GenX_5_Rep_5

value: 10 mg/kg/day


title: Female_Placenta_High_GenX_Rep_2

description: 21519_1226_Female_Placenta_High_GenX_2_Rep_2

value: placenta


title: Female_Placenta_High_GenX_Rep_1

description: 21518_1226_Female_Placenta_High_GenX_1_Rep_1

value: embryonic day 17.5


title: SH-SY5Y_BSJ_DMSO_rep4

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description:
Library name: SH-SY5Y_BSJ_DMSO_rep4
SH-SY5Y_BSJ_DMSO_rep4

data_processing:
Reads were quality checked with FastQC (v0.11.7) and aligned to the Homo sapiens reference genome (GRCh38.96) using STAR (v2.7.2b).
Post-alignment, read counts were generated and normalized with edgeR (v3.36.0).
After performing PCA plotting, certain replicates were removed from the analysis as they did not cluster with the other replicates, indicating potential outliers or inconsistencies.
Differential expression analysis was performed using the Limma-Voom pipeline (v3.50.3) with three or four replicates per condition.
Assembly: Homo sapiens GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts per experiment

source_name: bone marrow

extract_protocol:
RNA was isolated as described in the ‘RNA isolation and RT-qPCR’ section. RNA quality was measured using the Fragment analyzer 12 capillary array prior to profiling
A total of 55ng of RNA was used as input for the library preparation with the Illumina Stranded mRNA prep (#20040534). During the library preparation 15 PCR cycles were used. qPCR quantification of the libraries was done using the Kapa Library Quantification Kit for the Illumina LightCycler 480 (Roche diagnostics #07960298001).
RNA-Seq libraries were sequenced on the Illumina NextSeq 2000 platform using the NextSeq 2000 P2 Reagents 100 Cycles single-end kit (Illumina #20100987).

value: bone marrow

value: neuroblast

value: WT

value: DMSO in BSJ-4-116 experiment


title: DiR-ID + RNAseA - rep2

value: DiR-ID


title: HDF cells, overexpressing OCT4 and EGFP, day 5, O-EGFP-3

description:
Library name: O_d5_3
O-EGFP-3

value: human dermal fibroblasts


title: SH-SY5Y_BSJ_DMSO_rep3

description:
Library name: SH-SY5Y_BSJ_DMSO_rep3
SH-SY5Y_BSJ_DMSO_rep3


title: IL-1R1 gKO_F_sham_72h_A142

city: Lexington

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

description:
Library name: A142
Bulk RNA-seq, IL-1R1 gKO, F, sham, 72h

data_processing:
Quality assessment of raw reads with FastQC
Read alignment with STAR to mouse genome
Transcript quantification with Salmon
Gene-level count aggregation with tximeta
Differential expression analysis with DESeq2
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level read counts (salmon.merged.gene_counts.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level TPM values (salmon.merged.gene_tpm.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.

source_name: mouse brain

growth_protocol: 14:10 (light:dark), ad lib food access

extract_protocol:
RNeasy Mini with genomic dna depletion
RNA library preparation was performed by Novogene (Project X202SC24077443-Z01-F001). [Add library prep kit info, e.g., Illumina Stranded mRNA Prep, polyA selection, etc.]

treatment_protocol: Mice underwent closed head injury (CHI) or sham surgery. Brain tissue was collected at 9h, 24h, or 72h post-injury.

value: mouse brain

value: IL-1R1 gKO

value: Female

tag: surgery

value: sham

tag: timepoint

tag: age (months)

value: 5.87 months

tag: animal id

tag: experiment id


title: HDF cells, overexpressing OCT4 and EGFP, day 5, O-EGFP-2

description:
Library name: O_d5_2
O-EGFP-2

tag: cell type


title: Female_Placenta_High_PFOA_Rep_4

description: 21511_1226_Female_Placenta_High_PFOA_4_Rep_4

tag: age

value: No


title: IL-1R1 gKO_M_CHI_24h_A024

description:
Library name: A024
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 24h

value: Male

value: CHI

value: 5.3 months


title: IL-1R1 gKO_F_sham_9h_A169

description:
Library name: A169
Bulk RNA-seq, IL-1R1 gKO, F, sham, 9h

value: 3.3 months


title: RCH-ACV TP53 WT Combination treatment 1

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

institute: Princess Maxima Center

description:
Library name: Sample 19
WT_CMB_R1

data_processing:
Raw data (raw reads) of FASTQ format were processed through fastp
alignment to reference genome (hg38) using the HISAT2 v2.0.5 algorithm program
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped of each gene.
FPKM of each gene was calculated
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: .xls file including FPKM values for each Sample
Supplementary files format and content: .xls file including count values for each sample

source_name: RCH-ACV

growth_protocol: Cells were grown in RPMI (Invitrogen, Thermo Fisher Scientific, Breda, the Netherlands), supplemented with 10% fetal bovine serum (FBS, Greiner Bio-One, Essen, Germany) and 1% penicillin/streptomycin solution (P/S) (Invitrogen) at a cell density between 0.25 and 3x106 cells per milliliter.

extract_protocol:
NucleoSpin RNA isolation kit  (Macherey-Nagel, 740955)
The NEBNext® UltraTM Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: 24-hour treatment with DMSO, 100 nM berzosertib, 4 nM orludodstat, or the combination thereof

tag: cell line

value: RCH-ACV

value: BCP-ALL

tag: genotype

value: TP53 WT

tag: treatment

value: Combination


title: DiR-ID + RNAseA - rep1

tag: sample type

value: HeLa