title: genomic DNA from peripheral blood SP30

type: genomic

city: Changsha

first: Shijia

last: Rao

state: Hunan

address: Renmin Road

department: dermatology

country: China

institute: Second Xiangya hospital

description:
sepsis perpheral blood sample
SAMPLE 172

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data was extracted with the champ R package, the results were not normalized.
Average Beta or normalized (provide the normalization method) Average Beta

label: Cy5 and Cy3

source_name: genomic DNA from peripheral blood SP30

label_protocol: Standard Illumina Protocol

growth_protocol: no

extract_protocol: We extracted peripheral blood genomic DNA with GeneJET Whole Blood Genomic DNA Purification Mini Kit (Thermo Fisher Scientific). An EZ DNA Methylation Kit (Zymo Research) was used for DNA samples bisulfite conversion.

treatment_protocol: no

tag: gender

value: female

tag: sample type

value: blood

tag: disease state

value: sepsis


title: PoolG_DBA_Lamin_Zygote_rep2

status: Public on Apr 10 2025

type: SRA

city: Munich

first: Maria-Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description: Low-input LaminB1 DamID

library_source: genomic

data_processing:
Samples were sequenced using Illumina HiSeq4000 or HiSeq2500 platforms in 150 bp PE mode but only read1 was used for downstream analysis. For pre-processing of reads, first 6 random bases were discarded using trimmomatic (version 0.39). Subsequently, the reads were demultiplexed according to DamID indexes using fastx barcode splitter and the additional 15 bp of adaptors were trimmed using trimmomatic. The pre-processed reads starting with GATC were then mapped to the mm10 using bowtie2 (version 2.5.1) with default parameters. Reads aligning to the genome with quality score below 30 were discarded using samtools (version 1.17). Duplicates were removed using picard (version 3.0.0) to finally obtain unique GATC reads.
The computation of OE (Observed/Expected) values were performed in 100-kb genomic bins. To distinguish LAD domains from inter-LADs, a two-state hidden Markov model (HMM) was applied to non-zero OE mean values.
Assembly: mm10
Supplementary files format and content: Dam-LaminB1 observed over expected (OE) values calculated in 100-kb genomic bins provided in bedgraph files and LAD domain coordinates are provided in bed files.
Supplementary files format and content: Mean OE and LAD coordinates files are available on Rep 1 samples.
Library strategy: DamID-seq

molecule: genomic DNA

organism: Mus musculus

source_name: Zygote

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Zona pellucida was removed by treatment with 0.5% pronase in M2 at 37 °C. Polar bodies were separated from the embryos by gentle pipetting after trypsin treatment and discarded. For each replicate, a pool of 10-20 blastomeres (10 to 20 zygotes or 5 to 10 2-cell embryos) were collected in 2 μL DamID buffer (10 mM TRIS acetate pH 7.5, 10 mM magnesium acetate, 50 mM potassium acetate) and stored at -80 °C until downstream processing.
Approximately 300 ng of PCR purified DNA was end-repaired using an End-It DNA End-Repair Kit. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Between steps, the DNA was purified with Agencourt AMPure XP beads with a 1.8 x bead volume and a 1.0 x bead volume after the ligation reaction. After adapter ligation, DNA was PCR amplified with Illumina primers for 8 cycles.

treatment_protocol: For DamID, early zygotes (18 h post hCG) were isolated and injected with 250 ng/μL Tir1, 50 ng/μL membrane-eGFP and 10 ng/μL AID-Dam-LaminB1 along with mRNA encoding candidate protein(s) and cultured in auxin (500μM)-containing medium. For mapping LADs in zygotic stage, auxin was removed from 22 h and late zygotes were collected at 28–30 h post hCG. For DamID in late 2-cell stage, auxin was washed out from 42 to 48-50 h post hCG and embryos were cultured in KSOM. The mRNA concentration of candidate proteins was decided based on size of the ORF to ensure roughly equimolar expression. For EZH2 inhibition experiment in zygote, embryos were treated with 0.01% DMSO (as control) or 5 μΜ GSK343 (Selleckchem, #S7164) from 18 h to 28 h post hCG.

tag: tissue

value: Zygote

tag: genotype

value: (C57BL/6J xCBA) x DBA/2J

tag: mrna injected


title: PoolG_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolG_DBA_Lamin_Zygote.bedgraph
PoolG_DBA_Lamin_Zygote_LAD_coordinates.bed


title: C2C12, 28C, WT, 12h, rep1

city: Princeton

first: Aaron

middle: E

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

country: USA

institute: Princeton University

library_source: transcriptomic

data_processing:
Reads were demultiplexed using Picard v2.25.6, from within viral-ngs v2.1.33 with the read structure ‘5S8B15M8B101T’ and Q20M1 mismatch tolerance.
Demultiplexed reads were mapped to the mouse genome mm39 using STAR v2.7.10a.
Uniquely mapped reads were counted based on the GENCODE comprehensive gene annotation on the primary assembly using htseq-count v1.99.2.
Assembly: mm39, GENCODE release M28
Supplementary files format and content: Counts matrix of genes (mm39, M28) x all 45 samples

molecule: total RNA

growth_protocol: C2C12 mouse myoblast cells were maintained in DMEM supplemented with 20% heat-inactivated fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen) and phenol-chloroform purification.
Starting from 50 ng total RNA per sample, we performed bulk RNA barcoding and sequencing (BRB-Seq) with minor modifications. We performed reverse transcription with SuperScript IV (Invitrogen) and a uniquely barcoded oligo(dT)30 primer for each sample, modified to use Illumina TruSeq Read 1 priming site instead of Nextera Read 1. Following the remainder of the standard BRB-Seq protocol, we pooled up to 24 barcoded first-strand cDNAs into a single tube, synthesized second-strand cDNA with Gubler-Hoffman nick translation, and tagmented cDNA pools with Tn5 produced in-house. We performed 14 cycles of PCR using a P5-containing primer and a unique multiplexed i7 indexing primer (Chromium i7 Multiplex Kit, 10X Genomics). We purified and size-selected libraries with 0.65X SPRIselect (Beckman Coulter) and then 0.7X SPRIselect. We sequenced all pools on a NovaSeq SP v1.5 flowcell (Illumina) with 28 cycles of Read 1, 8 cycles of Read i7, and 101 cycles of Read 2.

treatment_protocol: C2C12 mouse myoblast cells were plated at 50,000 cells/well in 24-well plates and cultured at 37 °C overnight. The following day, cells were transfected with either 250 ng of CHIKV-D-SGR WT or GAA using Lipofectamine 2000 (1:2, Invitrogen), or mock treated (Lipofectamine 2000 only). Cells were then inucbated at 37 °C or 28 °C, for 12 h or 24 h.

tag: cell line

tag: cell type

value: myoblast

tag: temperature

tag: chikv

value: WT

tag: time

tag: replicate


title: C2C12, 28C, mock, 24h, rep1

value: mock


title: PoolF_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: 1200 ng/μL Kdm6a, 800 ng/μL Kdm6b


title: genomic DNA from peripheral blood SP29

description:
sepsis perpheral blood sample
SAMPLE 171

organism: Homo sapiens

source_name: genomic DNA from peripheral blood SP29

value: male

tag: age


title: C2C12, 28C, GAA, 12h, rep1

value: GAA


title: Primed_KD_D5_sgPOU5F1_3

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description:
Primed_KD_D5_sgPOU5F1_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

data_processing:
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.12) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.7.10b)
HTSeq (v0.13.5) were perfomed for counting reads with the GENCODE (version 35) annotation gtf file.
To normalized read counts, R (v4.1) and its package DESeq2 (v1.26.0) were performed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including DESeq2 nomalized count values for each sample.

growth_protocol: Primed human pluripotent stem cells (hPSCs) were maintained in StemFiT AK02N media (Ajinomoto) on iMatrix-511-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2. Naive hiPSCs were maintained media consisting of NDiff227 supplemented with 1 μM PD325901, 2 μM XAV939 (WAKO), 2 μM Gö6983 (Sigma-Aldrich), 10 ng/mL of LIF, 1/30 volume of Geltrex (Thermo Fisher Scientific) in a humidified incubator with 5% O2 and 5% CO2.

extract_protocol:
RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) following the manufacturer's recommendations. RNA was quantified with the Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit RNA (Thermo).
Illumina Stranded Total RNA Library Prep

treatment_protocol: For inducing the knockdown, 1 μg/mL of DOX were added. For endoderm differentiation, the primed hiPSCs were treated with differentiation media 1 (DM1), which consisted of DMEM/F-12 (Thermo Fisher Scientific), 2% B27 supplement (Thermo Fisher Scientific), 1% MEM Non-Essential Amino Acids (NEAA, Thermo Fisher Scientific) and 0.1 mM 2-mercaptoethanol (2-ME, Thermo Fisher Scientific) supplemented with 100 ng/mL Activin A (Nacalai tesque), 3 μM CHIR99021 (Nacalai tesque), 20 ng/mL bFGF (Nacalai tesque) and 50 nM PI-103 (Cayman Chemical). Twenty-four hours later, after washing with DMEM/F-12, the media was replaced with DM1 supplemented with 100 ng/mL Activin A and 250 nM LDN193189 (Stemgent). Two days later, after washing with DMEM/F-12, the media was replaced with DM1 containing 100 ng/mL Activin A until another 48 hours passed. For mesoderm differentiation, primed hiPSCs were cultured in DM1 containing 30 ng/mL Activin A, 40 ng/mL BMP4 (Peprotech), 6 μM CHIR99021, 20 ng/mL bFGF and 100 nM PIK-90 (MedChemExpress) for 24 hours. Then, after washing with DMEM/F-12, the media was replaced with DM1 supplemented with 40 ng/mL BMP4, 1 μM A83-01, and 4 μM CHIR99021, and the cells were maintained for 48 hours. Two days later, the cells were washed once with DMEM/F-12 and then cultured in DM1 supplemented with 40 ng/mL BMP4 for 48 hours. For neuroectoderm differentiation, primed iPSCs were cultured in Glasgow's MEM (WAKO) containing 8% Knockout serum replacement (KSR, Thermo Fisher Scientific), 1 mM sodium pyruvate (Sigma-Aldrich), 1% NEAA and 0.1 mM 2-ME, 1 μM A83-01 and 250 nM LDN193189 for 5 days. For the last disrupting the homeostasis of EIF3D’s target pathways, we replaced the media with StemFit AK02N containing (1) six factors consisting of 10 μM SC79 (Sigma-Aldrich), 10 μM MHY1485 (MedChemExpress), 1 μM A83-01, 2 μM CHIR99021, 50 ng/mL EGF (WAKO), and 1 μM Nutlin-3a (Sigma-Aldrich), (2) five factors (excluding Nutlin-3a from six factors) or (3) 1 μM Nutlin-3a alone.

value: Day 5

value: Primed iPSC

value: POU5F1 knockdown

tag: treatment

value: DOX+


title: Primed_KD_D5_sgPOU5F1_2

description:
Primed_KD_D5_sgPOU5F1_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolH_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolH_DBA_Lamin_Zygote.bedgraph
PoolH_DBA_Lamin_Zygote_LAD_coordinates.bed

value: 1200 ng/μL Kdm3a, 1500 ng/μL Kdm3b


title: genomic DNA from peripheral blood SP28

description:
sepsis perpheral blood sample
SAMPLE 170

source_name: genomic DNA from peripheral blood SP28


title: PoolF_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: Primed_KD_D5_sgPOU5F1_1

description:
Primed_KD_D5_sgPOU5F1_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: Differentiation_NE_3

description:
Differentiation_NE_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Ectoderm like cell


title: genomic DNA from peripheral blood SP27

description:
sepsis perpheral blood sample
SAMPLE 169

source_name: genomic DNA from peripheral blood SP27


title: PoolF_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Naïve_gfi1cko_ATAC_day30_biol rep1

city: Birmingham

first: Oluwagbemiga

last: Ojo

state: Alabama

department: Radiation Oncology

institute: University of Alabama, at Birmingham

description:
KO_naiveA3
KO_naiveA.narrowpeak

data_processing:
Quality and adapter trimming-TrimGalore v0.6.10
Sequence alignment- Bowtie2 v2.4.3 (bowtie2-p 10 --very-sensitive -k 10 -X 2000)
Peak calling-Genrich v0.6.1 (genrich -t rep1.bam rep2.bam -o sample/ -f sample.log -j -r -e chrM -E Blacklist -s 10 -v )
Conversion of bedgraph-ish file to bedgraph
Generation of bigwig file-bedGraphToBigWig v2.9
Genereration of merged peak files-cat peak1 peak2 > merged.peak
Sorting of merged peak files-sort -k1,1 -k2,2n
Generation of merged bed file-Bedtools v2.28 (bedtools -I merged.peak > merged.bed)
Conversion of merged bed file to SAF format-awk 'OFS="\t" {print $1"_"$2+1"_"$3, $1, $2+1, $3, "."}' merged.bed > merged.saf
Generation of count matrix-featureCounts -p --countReadPairs -a merged.saf -F SAF -o outputdirectory/output.txt bamdirectory/*.bam
Assembly: mm10
Supplementary files format and content: bigWig file for genome browser visualization
Supplementary files format and content: narrowpeak files contains reproducible accessible regions in biological duplicate samples
Supplementary files format and content: delimited text file includes count matrix for each sample

source_name: Spleen

extract_protocol:
Single cell suspension was prepared from spleens of day 30 LCMV clone 13 infected mice or from uninfected mice for naive samples. GP33+ antigen specific CD8+ T cells were FACS sorted and the assay for transposase-accessible chromatin with high sequencing was performed on the cells according to the published protocol (Grandi, F.C., Modi, H., Kampman, L. et al. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 17, 1518–1552 (2022). https://doi.org/10.1038/s41596-022-00692-9). Briefly, nuclei was isolated from FACS sorted antigen specific CD8+ T cell subsets and treated with Tn5 transposase for 30 mins at 37 degrees celsius. Transposed DNA was isolated, PCR amplified using barcoded primers.
Eluted DNA was PCR amplified with barcoded primers. Amplified DNA was purified with AMPure XP magnetic beads.

value: Spleen

value: day 0

value: Naive CD8+ T cell

value: Gfi1 Knockout

tag: infection

value: Uninfected


title: Naïve_gfi1cko_ATAC_day30_biol rep2

description:
KO_naiveB3
KO_naiveB.narrowpeak


title: Differentiation_NE_2

description:
Differentiation_NE_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: Primed_KD_D5_sgSOX2_1

description:
Primed_KD_D5_sgSOX2_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: SOX2 knockdown


title: genomic DNA from peripheral blood SP24

description:
sepsis perpheral blood sample
SAMPLE 167

source_name: genomic DNA from peripheral blood SP24

value: female

value: blood

value: sepsis


title: Transitional_gfi1cko_ATAC_day30_biol rep2

description:
KO2_DP
KO_DP.narrowpeak

value: day 30

value: Ly108+CX3CR1+ GP33+ CD8+ T cell

value: LCMV clone 13


title: PoolE_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: Zygote

value: (C57BL/6J xCBA) x DBA/2J

value: 600 ng/μL NLS Actin R62D, 600 ng/μL Hdac3


title: Differentiation_NE_1

description:
Differentiation_NE_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Day 5

value: WT


title: Transitional_gfi1cko_ATAC_day30_biol rep1

description:
KO1_DP
KO_DP.narrowpeak

value: Spleen


title: genomic DNA from peripheral blood SP25

description:
sepsis perpheral blood sample
SAMPLE 168

source_name: genomic DNA from peripheral blood SP25

value: male


title: genomic DNA from peripheral blood SP22

description:
sepsis perpheral blood sample
SAMPLE 166

source_name: genomic DNA from peripheral blood SP22


title: Progenitor_gfi1cko_ATAC_day30_biol rep2

description:
KO2_Prog
KO_Prog.narrowpeak

value: Ly108+CX3CR1- GP33+ CD8+ T cell


title: PoolE_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: genomic DNA from peripheral blood SP20

description:
sepsis perpheral blood sample
SAMPLE 165

source_name: genomic DNA from peripheral blood SP20


title: PoolE_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolE_DBA_Lamin_Zygote.bedgraph
PoolE_DBA_Lamin_Zygote_LAD_coordinates.bed


title: genomic DNA from peripheral blood SP19

description:
sepsis perpheral blood sample
SAMPLE 164

source_name: genomic DNA from peripheral blood SP19


title: Progenitor_gfi1cko_ATAC_day30_biol rep1

description:
KO1_Prog
KO_Prog.narrowpeak

value: Gfi1 Knockout


title: PoolD_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: 1200 ng/μL DN NM1, 1200 ng/μL DN MyosinVb


title: Naïve_wildtype_ATAC_day30_biol rep2

description:
WT_naiveB3
WT_naiveB.narrowpeak

value: day 0

value: Naive CD8+ T cell

value: Wildtype

value: Uninfected


title: genomic DNA from peripheral blood SP18

description:
sepsis perpheral blood sample
SAMPLE 163

source_name: genomic DNA from peripheral blood SP18

value: blood

value: sepsis


title: Differentiation_ME_2

description:
Differentiation_ME_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Mesoderm like cell


title: Naïve_wildtype_ATAC_day30_biol rep1

description:
WT_naiveA3
WT_naiveA.narrowpeak


title: PoolD_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID

value: Zygote


title: PoolF_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolF_DBA_Lamin_Zygote.bedgraph
PoolF_DBA_Lamin_Zygote_LAD_coordinates.bed

value: (C57BL/6J xCBA) x DBA/2J

value: 1200 ng/μL Kdm6a, 800 ng/μL Kdm6b


title: Terminally_exhausted_wildtype_ATAC_day30_biol rep2

description:
WT2_DN
WT_DN.narrowpeak

value: day 30

value: Ly108-CX3CR1- GP33+ CD8+ T cell

value: LCMV clone 13


title: PoolD_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolD_DBA_Lamin_Zygote.bedgraph
PoolD_DBA_Lamin_Zygote_LAD_coordinates.bed


title: genomic DNA from peripheral blood SP17

description:
sepsis perpheral blood sample
SAMPLE 162

source_name: genomic DNA from peripheral blood SP17

value: male


title: Differentiation_EN_2

description:
Differentiation_EN_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Day 5

value: Endoderm like cell

value: WT


title: Differentiation_EN_3

description:
Differentiation_EN_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: genomic DNA from peripheral blood SP16.1

description:
sepsis perpheral blood sample
SAMPLE 161


title: Terminally_exhausted_wildtype_ATAC_day30_biol rep1

description:
WT1_DN
WT_DN.narrowpeak

value: Spleen


title: PoolC_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: 2500 ng/μL Tpr, 600 ng/μL DN Nup98


title: genomic DNA from peripheral blood SP15

description:
sepsis perpheral blood sample
SAMPLE 160

source_name: genomic DNA from peripheral blood SP15

value: female


title: Differentiation_EN_1

description:
Differentiation_EN_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: Primed_iPS_3

description:
Primed_iPS_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Primed iPSC


title: PoolC_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Transitional_wildtype_ATAC_day30_biol rep2

description:
WT2_DP
WT_DP.narrowpeak

value: Ly108+CX3CR1+ GP33+ CD8+ T cell

value: Wildtype


title: Differentiation_ME_3

description:
Differentiation_ME_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Mesoderm like cell


title: genomic DNA from peripheral blood SP14

description:
sepsis perpheral blood sample
SAMPLE 159

source_name: genomic DNA from peripheral blood SP14

value: blood

value: sepsis


title: PoolC_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolC_DBA_Lamin_Zygote.bedgraph
PoolC_DBA_Lamin_Zygote_LAD_coordinates.bed

value: Zygote

value: (C57BL/6J xCBA) x DBA/2J


title: genomic DNA from peripheral blood SP12

description:
sepsis perpheral blood sample
SAMPLE 158

source_name: genomic DNA from peripheral blood SP12


title: Primed_iPS_2

description:
Primed_iPS_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolB_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: 1000 ng/μL Exportin6, 1000 ng/μL cVCA actin


title: Differentiation_ME_1

description:
Differentiation_ME_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolB_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: w1118, Listeria monocytogenes rep3

city: Tampere

first: Matthew

middle: K

last: Maasdorp

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description: Library name: WT_LM3

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference 3 genome using HHisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie [3](v1.3.3b).
FeatureCounts [4] v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to th
Assembly: The reference used for mapping was the Drosophila melanogaster (bdgp6_gca_000001215_4).
Supplementary files format and content: Text file containing normalized read counts for genes in all samples (FPKMs)

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Drosophila melanogaster flies were grown from egg to adults at 25°C at LD12:12

extract_protocol:
RNA was extracted using TRI reagent (MRC, Fisher Scientific), according to manufacturer's protocol
Sequencing and initial bioinformatics analysis was carried out by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

value: whole fly

value: Listeria monocytogenes


title: Effector_wildtype_ATAC_day30_biol rep1

description:
WT1_Eff
WT_Eff.narrowpeak

value: day 30

value: Ly108-CX3CR1+ GP33+ CD8+ T cell

value: LCMV clone 13


title: Primed_iPS_1

description:
Primed_iPS_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Day 5

value: WT


title: genomic DNA from peripheral blood SP11

description:
sepsis perpheral blood sample
SAMPLE 157

source_name: genomic DNA from peripheral blood SP11

value: female


title: Effector_wildtype_ATAC_day30_biol rep2

description:
WT2_Eff
WT_Eff.narrowpeak

value: Spleen


title: PoolB_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID

source_name: Zygote


title: Transitional_wildtype_ATAC_day30_biol rep1

description:
WT1_DP
WT_DP.narrowpeak

value: Ly108+CX3CR1+ GP33+ CD8+ T cell


title: genomic DNA from peripheral blood SP9

description:
sepsis perpheral blood sample
SAMPLE 155

source_name: genomic DNA from peripheral blood SP9

value: male


title: genomic DNA from peripheral blood SP10

description:
sepsis perpheral blood sample
SAMPLE 156

source_name: genomic DNA from peripheral blood SP10


title: w1118, Listeria monocytogenes rep2

description: Library name: WT_LM2


title: Progenitor_wildtype_ATAC_day30_biol rep1

description:
WT1_Prog
WT_Prog.narrowpeak

value: Ly108+CX3CR1- GP33+ CD8+ T cell

value: Wildtype


title: PoolB_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolB_DBA_Lamin_Zygote.bedgraph
PoolB_DBA_Lamin_Zygote_LAD_coordinates.bed


title: w1118, Listeria monocytogenes rep1

description: Library name: WT_LM1


title: genomic DNA from peripheral blood SP7

description:
sepsis perpheral blood sample
SAMPLE 154

source_name: genomic DNA from peripheral blood SP7

value: blood

value: sepsis


title: PoolA_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: Zygote

value: (C57BL/6J xCBA) x DBA/2J

value: 100 ng/μL DN Baf, 800 ng/μL DN Prr14, 400 ng/μL DN Syne1


title: Progenitor_wildtype_ATAC_day30_biol rep2

description:
WT2_prog
WT_Prog.narrowpeak

source_name: Spleen


title: genomic DNA from peripheral blood SP6

description:
sepsis perpheral blood sample
SAMPLE 153

source_name: genomic DNA from peripheral blood SP6


title: w1118, uninfected, rep3

description: Library name: WT_CTRL3

value: whole fly

value: uninfected


title: PoolA_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: D283_treat_k9me3_3 (CUT&RUN)

city: Ann Arbor

first: Sriram

last: Venneti

state: Michigan

address: 1500 E Medical Center Dr

department: Pathology

institute: University of Michigan

data_processing:
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference human (hg38) assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.
Assembly: hg38
Supplementary files format and content: bigwigs
Library strategy: CUT&RUN

growth_protocol: D283 cells were mantained in MEM medium supplimented with 10%FBS

extract_protocol:
CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 50bp reads on an Illumina NextSeq1000 instrument.

treatment_protocol: 10uM IDH1 inhibitor

value: IDH1 inhibitor


title: genomic DNA from peripheral blood SP5

description:
sepsis perpheral blood sample
SAMPLE 152

source_name: genomic DNA from peripheral blood SP5


title: w1118, uninfected, rep2

description: Library name: WT_CTRL2


title: PoolA_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolA_DBA_Lamin_Zygote.bedgraph
PoolA_DBA_Lamin_Zygote_LAD_coordinates.bed


title: genomic DNA from peripheral blood SP4

description:
sepsis perpheral blood sample
SAMPLE 151

source_name: genomic DNA from peripheral blood SP4


title: D283_treat_k9me3_1 (CUT&RUN)


title: w1118, uninfected, rep1

description: Library name: WT_CTRL1


title: IbinBKO, Listeria monocytogenes, rep3

description: Library name: IBINL_LM3

value: IbinBKO

value: Listeria monocytogenes


title: genomic DNA from peripheral blood DE24

description:
drug eruption perpheral blood sample
SAMPLE 148

source_name: genomic DNA from peripheral blood DE24

value: drug eruption


title: Control_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: D283_ctrl_k9me3_2 (CUT&RUN)

value: DMSO


title: genomic DNA from peripheral blood SP2

description:
sepsis perpheral blood sample
SAMPLE 150

source_name: genomic DNA from peripheral blood SP2


title: R12038 uninfected monocytes

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to  GRCh38 genome build
Gene counts were obtained using featureCounts on GENCODE v31 annotations
Assembly: GRCh38
Supplementary files format and content: gene_counts

source_name: PBMC

growth_protocol: 10% FBS in RPMI media supplemented with HEPES

extract_protocol: DiD hi monocytes were sorted using flow cytometer. After sorting, monocytes were incubated for 24 hours before cell lysis using trizol.

treatment_protocol: Infected with DiD-labelled dengue virus

tag: cells

value: monocytes


title: IbinBKO, Listeria monocytogenes, rep1

description: Library name: IBINL_LM1


title: D283_ctrl_k9me3_3 (CUT&RUN)


title: IbinBKO, uninfected, rep3

description: Library name: IBINL_CTRL3


title: Control_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: IbinBKO, uninfected, rep2

description: Library name: IBINL_CTRL2


title: D283_treat_k27me3_2 (CUT&RUN)


title: genomic DNA from peripheral blood DE23

description:
drug eruption perpheral blood sample
SAMPLE 147

source_name: genomic DNA from peripheral blood DE23


title: R12040 infected monocytes

value: infected


title: genomic DNA from peripheral blood DE21

description:
drug eruption perpheral blood sample
SAMPLE 145

source_name: genomic DNA from peripheral blood DE21

value: male


title: R12035 infected monocytes


title: IbinBKO, uninfected, rep1

description: Library name: IBINL_CTRL1


title: D283_treat_k27me3_1 (CUT&RUN)


title: R12033 uninfected monocytes


title: D283_treat_k27me3_3 (CUT&RUN)


title: genomic DNA from peripheral blood DE20

description:
drug eruption perpheral blood sample
SAMPLE 144

source_name: genomic DNA from peripheral blood DE20


title: IbinAKO, Listeria monocytogenes, rep3

description: Library name: IBIN_LM3

value: IbinAKO


title: D283_treat_k9me3_2 (CUT&RUN)


title: R12030 infected monocytes


title: Control_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Control_DBA_Lamin_Zygote.bedgraph
Control_DBA_Lamin_Zygote_LAD_coordinates.bed


title: D283_ctrl_k9me3_1 (CUT&RUN)


title: genomic DNA from peripheral blood SP1

description:
sepsis perpheral blood sample
SAMPLE 149

source_name: genomic DNA from peripheral blood SP1


title: IbinBKO, Listeria monocytogenes, rep2

description: Library name: IBINL_LM2

source_name: whole fly


title: genomic DNA from peripheral blood DE19

description:
drug eruption perpheral blood sample
SAMPLE 143

source_name: genomic DNA from peripheral blood DE19

value: female


title: genomic DNA from peripheral blood DE22

description:
drug eruption perpheral blood sample
SAMPLE 146

source_name: genomic DNA from peripheral blood DE22

value: blood


title: R12028_R uninfected monocytes


title: D283_ctrl_k27me3_2 (CUT&RUN)


title: IbinAKO, Listeria monocytogenes, rep1

description: Library name: IBIN_LM1


title: genomic DNA from peripheral blood DE18

description:
drug eruption perpheral blood sample
SAMPLE 142

source_name: genomic DNA from peripheral blood DE18


title: D283_ctrl_k27me3_1 (CUT&RUN)


title: IbinAKO, Listeria monocytogenes, rep2

description: Library name: IBIN_LM2


title: IbinAKO, uninfected, rep3

description: Library name: IBIN_CTRL3


title: genomic DNA from peripheral blood DE17

description:
drug eruption perpheral blood sample
SAMPLE 141

source_name: genomic DNA from peripheral blood DE17


title: genomic DNA from peripheral blood DE16

description:
drug eruption perpheral blood sample
SAMPLE 140

source_name: genomic DNA from peripheral blood DE16


title: genomic DNA from peripheral blood DE15

description:
drug eruption perpheral blood sample
SAMPLE 139

source_name: genomic DNA from peripheral blood DE15


title: D283_treat_k4me3_2 (CUT&RUN)


title: D283_ctrl_k27me3_3 (CUT&RUN)


title: R12020 infected monocytes


title: IbinAKO;IbinBKO, Listeria monocytogenes, rep3

description: Library name: DM_LM3

value: IbinAKO;IbinBKO


title: D283_ctrl_k4me3_3 (CUT&RUN)


title: IbinAKO, uninfected, rep2

description: Library name: IBIN_CTRL2


title: genomic DNA from peripheral blood DE14

description:
drug eruption perpheral blood sample
SAMPLE 138

source_name: genomic DNA from peripheral blood DE14


title: R12023 uninfected monocytes


title: R12025 infected monocytes


title: D283_treat_k4me3_1 (CUT&RUN)


title: R12018 uninfected monocytes


title: R11434

data_processing:
FASTQ files were mapped using STAR to  GRCh38 genome build
Gene counts were obtained using featureCounts on GENCODE v31 annotations
Assembly: GRCh38
Supplementary files format and content: genecounts_20220406.txt

extract_protocol:
Total RNA was extracted from bulk cells in two steps, RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) and the aqueous phase was processed using Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). Purified RNA samples were quality checked using Agilent RNA 6000 Pico assay (Agilent Technologies, Paolo Alto, CA). Reverse transcription and amplification were performed according to established method (Picelli et al., 2014).
cDNA was synthesized from 2ng of purified total RNA using modified oligo(dT) primers along with 1ul of a 1: 50,000 dilution of ERCC RNA Spike in control (Ambion® Thermo Fisher Scientific). To generate sufficient quantities of cDNA for downstream library preparation steps, 13 cycles of PCR amplification was performed. The quantity and integrity of cDNA was assessed using DNA High Sensitivity Reagent Kit, Perkin Elmer LabChip GX (PerkinElmer, Waltham, MA, USA). Subsequently, pooled cDNA libraries were prepared (250 pg of cDNA per sample) using Nextera XT Kit (Illumina, San Diego, CA, USA) with dual indices for de-multiplexing. The libraries were qPCR quantified (Kapa Biosystems, Wilmington, MA) to ascertain the loading concentration. Samples were subjected to an indexed PE sequencing run of 2x151 cycles on an Illumina HiSeq 4000.

tag: group

value: convalescent

tag: disease severity

value: mild


title: D283_ctrl_k4me3_2 (CUT&RUN)


title: IbinAKO;IbinBKO, Listeria monocytogenes, rep2

description: Library name: DM_LM2


title: genomic DNA from peripheral blood DE13

description:
drug eruption perpheral blood sample
SAMPLE 137

source_name: genomic DNA from peripheral blood DE13

tag: gender

tag: sample type


title: D283_treat_k4me3_3 (CUT&RUN)


title: genomic DNA from peripheral blood DE12

description:
drug eruption perpheral blood sample
SAMPLE 136

source_name: genomic DNA from peripheral blood DE12

tag: disease state


title: R11433


title: D283_ctrl_k4me3_1 (CUT&RUN)


title: IbinAKO;IbinBKO, Listeria monocytogenes, rep1

description: Library name: DM_LM1

tag: tissue

tag: genotype


title: IbinAKO, uninfected, rep1

description: Library name: IBIN_CTRL1


title: IbinAKO;IbinBKO, uninfected, rep3

description: Library name: DM_CTRL3


title: D283_cells_IDH1_siRNA_3 (ATAC-seq)

data_processing:
Trimming of Nextera adapter sequences was performed using cutadapt (version 3.4) using the following parameters: “-a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25”. Trimmed reads were aligned to the human (hg38) reference genome using bowtie2 (version 2.4.4) with the following arguments: “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000”.
bigwigs were generated from Bam files using DeepTools’ bamCoverage function (version 3.5.1) with the following arguments: “--binSize 5 --normalizeUsing RPKM --extendReads”. Reads in peaks were counted using DiffBind (version 3.4.11).
Assembly: hg38
Supplementary files format and content: bigwigs

extract_protocol: Cells were processed using the OMNI-ATAC-Seq protocol (Corces et al., 2017)

tag: cell line


title: genomic DNA from peripheral blood DE10

description:
drug eruption perpheral blood sample
SAMPLE 134

source_name: genomic DNA from peripheral blood DE10


title: IbinAKO;IbinBKO, uninfected, rep2

description: Library name: DM_CTRL2


title: genomic DNA from peripheral blood DE11

description:
drug eruption perpheral blood sample
SAMPLE 135

source_name: genomic DNA from peripheral blood DE11


title: genomic DNA from peripheral blood DE9

description:
drug eruption perpheral blood sample
SAMPLE 133

source_name: genomic DNA from peripheral blood DE9


title: IbinAKO;IbinBKO, uninfected, rep1

description: Library name: DM_CTRL1


title: R11430

source_name: PBMC

value: severe


title: D283_cells_IDH1_siRNA_2 (ATAC-seq)


title: D283_cells_IDH1_siRNA_1 (ATAC-seq)


title: R11429


title: genomic DNA from peripheral blood DE8

description:
drug eruption perpheral blood sample
SAMPLE 132

source_name: genomic DNA from peripheral blood DE8


title: D283_cells_3 (ATAC-seq)

value: ctrl


title: R11428


title: R11427


title: genomic DNA from peripheral blood DE7.1

description:
drug eruption perpheral blood sample
SAMPLE 131

source_name: genomic DNA from peripheral blood DE7.1


title: D283_cells_2 (ATAC-seq)


title: R11426


title: TRT3 (J7)

city: Nakhon Ratchasima

first: Chao

last: Ban

address: 111 University Avenue Muang,

country: Thailand

institute: Suranaree University of Technology

description: Library name: J7

data_processing:
The raw sequencing data were processed using SOAPnuke (v1.5.6, RRID:SCR_015025) to eliminate low-quality and adapter-contaminated reads. The filtering criteria were as follows: 1) removal of reads containing adapter sequences, 2) exclusion of reads with more than 5% unknown bases (N), and 3) discarding low-quality reads, defined as those in which more than 20% of the bases had a quality score below 15.
Differential expression analysis between the two groups was performed using DESeq2 version 1.4.5 (Love et al., 2014). The differential genes with a fold-change (FC) of ≥ 1 and an adjusted P value < 0.05 were classified as differentially expressed genes (DEGs).
Assembly: GCA_002263795.2
Supplementary files format and content: Column 1, gene_id; Column 2, gene_symbol; Column 3 - 10,   Sample_TPM: TPM of each gene; Column 11-18, Sample: read_count, count of each gene.

organism: Bos taurus

source_name: Jejunal tissue

extract_protocol:
According to the manufacturer`s instructions, total RNA was obtained from liver tissue using TRIzol reagent (Molecular Research Center, Cincinnati, Ohio, USA)
RNA reverse transcription, library preparation, and RNA sequencing (RNA-seq) were carried out at BGI Co., Ltd. (Shenzhen, China). Briefly, total RNA was enriched for mRNA by poly(A) selection using oligo(dT) magnetic beads, followed by reverse transcription and cDNA synthesis. The resulting double-stranded cDNA underwent end repair, 5'-phosphorylation, and 3'-adenylation to prepare for adapter ligation. The adapter-ligated products were then PCR amplified, denatured, and circularized using bridging primers to create single-stranded circular DNA libraries. Sequencing was performed on the DNBSEQ platform with PE500 (BGI Co., Ltd., Shenzhen, China).

value: Jejunal tissue

tag: breed

value: Holstein

value: DCLI


title: genomic DNA from peripheral blood DE6

description:
drug eruption perpheral blood sample
SAMPLE 130

source_name: genomic DNA from peripheral blood DE6


title: R11432


title: TRT2 (J6)

description: Library name: J6


title: R11425


title: D283_cells_1 (ATAC-seq)


title: TRT1 (J5)

description: Library name: J5


title: PE_H1047R2

city: NanJing

first: Pingping

last: Cao

state: Jiangsu

address: 101 Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

department: Department of Cell Biology

institute: Nanjing Medical University

description:
8-FPKM
gene expression (8).txt

data_processing:
Data Filtering The raw data obtained from sequencing were filtered using SOAPnuke (v1.5.6) to remove: 1) reads containing adapters (adapter contamination); 2) reads with unknown base ‘N’ content greater than 5%; 3) low-quality reads (reads where bases with a quality score below 15 constitute more than 20% of the total bases in the reads), resulting in clean data. Subsequent data analysis, plotting, and mining were performed using Dr. Tom’s multi-omics data mining system (https://biosys.bgi.com).  Differential Gene Analysis Clean data were aligned to the reference genome using HISAT2 (v2.1.0). Clean data were also aligned to the reference gene set provided by Dr. Tom’s multi-omics data mining system using Bowtie2 (v2.3.4.3)[3]. Gene expression quantification was performed using RSEM (v1.3.1)[4], and clustering heatmaps of gene expression across different samples were created using pheatmap (v1.0.8)[5]. Differential gene detection was conducted using DESeq2 (v1.4.5) (or DEGseq or PoissonDis), with conditions set at Q value ≤0.05 or FDR ≤0.001.  KEGG and GO Enrichment Analysis To further explore the gene functions associated with phenotypic changes, we performed GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis on the differentially expressed genes based on the hypergeometric test, using Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution). A threshold of Q value ≤0.05[9] was set, with conditions meeting this threshold defined as significantly enriched among the candidate genes.
Assembly: Human (GRCh38/hg38)
Supplementary files format and content: files include FPKM values for each Sample

growth_protocol: LOVO(PIK3CA-WT、PIK3CA-MUT) cells were maintained in DMEM supplemented with 10% fetal bovine serum  and antibiotics in humidified atmosphere with 5% CO2 at 37°.

extract_protocol:
Sample Disruption and Lysis 1. Place an appropriate amount of tissue sample into a correspondingly numbered grinding tube (tissue ≤30mg, cells ≤1 x 10^7). 2. Add 600 µL Buffer RLT Plus, homogenize with a homogenizer, and let it sit at room temperature for 5 minutes. 3. Centrifuge at 12,000 x g for 3 minutes at room temperature; transfer the entire supernatant to an AllPrep DNA spin column. 4. Centrifuge at 10,000 x g for 30 seconds at room temperature; collect the fluid in the collection tube for RNA purification.  RNA Purification 1. Add an equal volume of 70% ethanol to the collection tube and mix well by pipetting. 2. Transfer 700 µL of the mixture to an RNeasy spin column set up with a collection tube, centrifuge at 10,000 x g for 30 seconds at room temperature; repeat this step until all the mixture has passed through the RNeasy spin column. 3. Add 700 µL Buffer RW1 to the RNeasy spin column, centrifuge at 10,000 x g for 30 seconds at room temperature, discard the waste fluid. 4. Add 500 µL Buffer RPE to the RNeasy spin column, centrifuge at 10,000 x g for 30 seconds at room temperature, discard the waste fluid. 5. Add 500 µL Buffer RPE to the RNeasy spin column, centrifuge at 10,000 x g for 30 seconds at room temperature, discard the waste fluid. 6. Centrifuge at 16,000 x g for 2 minutes at room temperature, transfer the RNeasy spin column to a 1.5 mL centrifuge tube. 7.  Add about 35 µL RNase-free water to the RNeasy spin column, let it sit at room temperature for 1 minute. 8. Centrifuge at 16,000 x g for 2 minutes at room temperature to collect RNA.
1. Sample Testing Select the appropriate testing method for quality control based on the sample and product requirements. 2. mRNA Isolation Take a certain amount of RNA sample, denature it at suitable temperature to open its secondary structure, and enrich mRNA using oligo(dT) magnetic beads. 3. mRNA Fragmentation Add fragmentation reagent to the obtained mRNA from the previous step, react at a suitable temperature for a set period, and fragment the mRNA. 4. cDNA Synthesis Prepare a reaction system for single-strand cDNA synthesis and set the reaction program; prepare a reaction system for double-strand cDNA synthesis and set the reaction program. 5. End Repair, ‘A’ Tailing, and Adaptor Ligation Prepare a reaction system and set the reaction program to repair the ends of the double-stranded cDNA and add an ‘A’ base to the 3’ end; prepare an adaptor ligation reaction system and set the reaction program to ligate the adaptor to the cDNA. 6. PCR Prepare a PCR reaction system and set the reaction program to amplify the product. 7. Library Testing Select the appropriate testing method for quality control of the library based on product requirements. 8. Circularization Denature the PCR products into single strands, then prepare a circularization reaction system and set the reaction program to obtain single-stranded circular products and digest un-circularized linear DNA molecules. 9.Sequencing Single-stranded circular DNA molecules undergo rolling circle replication to form a DNA nano-ball (DNB) containing multiple copies. The obtained DNBs are applied to a high-density DNA nanoarray technology, placed into the mesh-like pores on the chip, and sequenced using the combined probe anchor synthesis technology (cPAS).

treatment_protocol: LOVO PIK3CA wild-type and mutant cells were treated with 0.5 µM palbociclib (MCE) and DMSO as a control for 72 hours, after which the cells were collected for transcriptome sequencing. After treating cells with 0.5 µM palbociclib (MCE) and DMSO as a control for 72 hours, the conditioned medium from senescent cells was collected. Additionally, cells from the control group, consisting of LOVO PIK3CA wild-type and mutant cells, were collected 48 hours post-treatment. LOVO PIK3CA mutant cells were treated with a combination of 0.5 µM palbociclib (MCE)  and 4 µM erlotinib (MCE)  for 48 hours, then the cells were collected for transcriptome sequencing.

tag: cell type

value: Colorectal cancer cell

value: palbociclib+erlotinib


title: PE_H1047R1

description:
7-FPKM
gene expression (8).txt


title: CON4 (J4)

description: Library name: J4

value: CON


title: genomic DNA from peripheral blood DE5

description:
drug eruption perpheral blood sample
SAMPLE 129

source_name: genomic DNA from peripheral blood DE5

value: drug eruption


title: R11423


title: TRT4 (J8)

description: Library name: J8


title: R11424


title: genomic DNA from peripheral blood DE3

description:
drug eruption perpheral blood sample
SAMPLE 127

source_name: genomic DNA from peripheral blood DE3


title: genomic DNA from peripheral blood DE4

description:
drug eruption perpheral blood sample
SAMPLE 128

source_name: genomic DNA from peripheral blood DE4


title: PE_E545K1

description:
5-FPKM
gene expression (8).txt


title: PE_E545K2

description:
6-FPKM
gene expression (8).txt


title: CON2 (J2)

description: Library name: J2


title: CON3 (J3)

description: Library name: J3


title: R11422


title: CON1 (J1)

description: Library name: J1


title: genomic DNA from peripheral blood DE1

description:
drug eruption perpheral blood sample
SAMPLE 125

source_name: genomic DNA from peripheral blood DE1


title: R11376


title: R11374


title: P_H1047R2

description:
4-FPKM
gene expression (8).txt

value: palbociclib


title: P_H1047R1

description:
3-FPKM
gene expression (8).txt


title: limyb-32, rep3

city: Vicosa

first: Elizabeth

middle: Pacheco

last: Fontes

state: Minas Gerais

address: Av. PH Rolfs, S/N

department: Biochemistry

country: Brazil

institute: Universidade Federal de Vicosa

description:
Library name: KnockOut_032_3
treatment3

data_processing:
Reads quality was evaluated by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Illumina adapters were removed using Trimmomatic software41, and low-quality sequencing reads were filtered and trimmed using prinSEQ software package.
Read mapping was performed using the Bowtie 2 program.
The global analysis of differential gene expression (DGE) was performed using the edger package and DEseq2.
The classification of gene ontology (GO) and analysis of enrichment of pathways were performed using the packages GoStats and PathView.
Assembly: Arabidopsis thaliana (TAIR10)
Supplementary files format and content: raw cout reads (txt)

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown in soil (Metro Mix 366) in a growth chamber at 23 °C, 45% humidity, and 75 µE/m2/s1 light with a 10-h-light/14-h-dark photoperiod.

extract_protocol:
For RNA-seq experiments, we used three biological replicates of a pool of 12-day-old Col-0, LIMYB-32-L1, and LIMYB-32-L3.
Libraries for RNA-seq were prepared with the TrueSeq-RNA Sample Prep Illumina kit (Illumina, cat # 20020595). The paired-end 100-bp protocol was used with the following quality filter parameters.

treatment_protocol: The limyb-32 lines were transformed with pYFP-LIMYB using the floral dip method, generating LIMYB-32-L1 and LIMYB-32-L3 lines. Primary transformants were selected using 30 µgmL-1 hygromycin, and stable transgene insertion was monitored by PCR.

value: leaf

value: tissue

value: Knock out

tag: batch

value: 12 days


title: R11372

value: moderate


title: P_E545K2

description:
2-FPKM
gene expression (8).txt


title: genomic DNA from peripheral blood TL38

description:
T cell lymphoma perpheral blood sample
SAMPLE 124

source_name: genomic DNA from peripheral blood TL38

value: male

value: blood

value: T cell lymphoma


title: limyb-32, rep2

description:
Library name: KnockOut_032_2
treatment3


title: genomic DNA from peripheral blood TL35

description:
T cell lymphoma perpheral blood sample
SAMPLE 123

source_name: genomic DNA from peripheral blood TL35


title: R11371

value: convalescent


title: P_E545K1

description:
1-FPKM
gene expression (8).txt


title: genomic DNA from peripheral blood TL33

description:
T cell lymphoma perpheral blood sample
SAMPLE 122

source_name: genomic DNA from peripheral blood TL33


title: limyb-32, rep1

description:
Library name: KnockOut_032_1
treatment3


title: genomic DNA from peripheral blood DE2

description:
drug eruption perpheral blood sample
SAMPLE 126

source_name: genomic DNA from peripheral blood DE2

value: female


title: R11370


title: genomic DNA from peripheral blood TL32

description:
T cell lymphoma perpheral blood sample
SAMPLE 121

source_name: genomic DNA from peripheral blood TL32


title: cm_LOVO_H1047R_1

description:
17-FPKM
gene expression (18).txt

value: S-CM (Senescence-Conditioned Media)


title: Col-0, rep3

description:
Library name: COLUMBIA_3
control

value: WT


title: cm_LOVO_H1047R_2

description:
18-FPKM
gene expression (18).txt

value: Colorectal cancer cell


title: R11368_R

value: mild


title: Col-0, rep2

description:
Library name: COLUMBIA_2
control


title: R11367


title: Col-0, rep1

description:
Library name: COLUMBIA_1
control


title: R11363


title: cm_LOVO_E545K_2

description:
16-FPKM
gene expression (18).txt


title: genomic DNA from peripheral blood TL26

description:
T cell lymphoma perpheral blood sample
SAMPLE 119

source_name: genomic DNA from peripheral blood TL26


title: cm_LOVO_E545K_1

description:
15-FPKM
gene expression (18).txt


title: genomic DNA from peripheral blood TL25

description:
T cell lymphoma perpheral blood sample
SAMPLE 118

source_name: genomic DNA from peripheral blood TL25


title: R11361

source_name: PBMC

value: severe


title: cm_LOVO_WT_2

description:
14-FPKM
gene expression (18).txt


title: genomic DNA from peripheral blood TL24

description:
T cell lymphoma perpheral blood sample
SAMPLE 117

source_name: genomic DNA from peripheral blood TL24


title: R11360


title: LIMYB-32, L3, rep2

description:
Library name: 032LIMIB-L3_2
treatament2

value: complemented LIMYB


title: cm_LOVO_WT_1

description:
13-FPKM
gene expression (18).txt


title: genomic DNA from peripheral blood TL23

description:
T cell lymphoma perpheral blood sample
SAMPLE 116

source_name: genomic DNA from peripheral blood TL23


title: LIMYB-32, L3, rep1

description:
Library name: 032LIMIB-L3_1
treatament2


title: R11359


title: genomic DNA from peripheral blood TL21

description:
T cell lymphoma perpheral blood sample
SAMPLE 115

source_name: genomic DNA from peripheral blood TL21


title: LIMYB-32, L1, rep3

description:
Library name: 032LIMIB-L1_3
treatament1


title: R11357


title: p_LOVO_H1047R_1

description:
11-FPKM
gene expression (18).txt

value: palbociclib


title: p_LOVO_H1047R_2

description:
12-FPKM
gene expression (18).txt


title: genomic DNA from peripheral blood TL20

description:
T cell lymphoma perpheral blood sample
SAMPLE 114

source_name: genomic DNA from peripheral blood TL20


title: LIMYB-32, L1, rep2

description:
Library name: 032LIMIB-L1_2
treatament1

value: leaf


title: R11356


title: genomic DNA from peripheral blood TL29

description:
T cell lymphoma perpheral blood sample
SAMPLE 120

source_name: genomic DNA from peripheral blood TL29


title: genomic DNA from peripheral blood TL18

description:
T cell lymphoma perpheral blood sample
SAMPLE 113

source_name: genomic DNA from peripheral blood TL18


title: p_LOVO_E545K_1

description:
9-FPKM
gene expression (18).txt


title: LIMYB-32, L3, rep3

description:
Library name: 032LIMIB-L3_3
treatament2

value: tissue


title: R11350_R


title: rsa1 mutants line -- Rep3

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

data_processing:
The raw files were checked for quality using FastQC and then mapped against Arabidopsis genome (TAIR10) using Hisat2. The resulting alignment files were further processed using the Cufflinks-Cuffdiff protocol with default parameters.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Col-0 background

growth_protocol: Seeds of all three genoypes were grown on half strength MS media, straightified for 3 days and then transferred to 20C growth room. Samples were collected after 6 days of transfer.

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen)
libraries were prepared using TruSeq® library preparation kit using using manufacturer's instructions

treatment_protocol: Seeds were grown for 6 days at 20C

value: whole seedlings


title: p_LOVO_WT_2

description:
8-FPKM
gene expression (18).txt


title: R11355


title: genomic DNA from peripheral blood TL17

description:
T cell lymphoma perpheral blood sample
SAMPLE 112

source_name: genomic DNA from peripheral blood TL17


title: genomic DNA from peripheral blood TL16

description:
T cell lymphoma perpheral blood sample
SAMPLE 111

source_name: genomic DNA from peripheral blood TL16


title: rsa1 mutants line -- Rep1


title: genomic DNA from peripheral blood TL15

description:
T cell lymphoma perpheral blood sample
SAMPLE 110

source_name: genomic DNA from peripheral blood TL15


title: p_LOVO_WT_1

description:
7-FPKM
gene expression (18).txt


title: LOVO_H1047R_2

description:
6-FPKM
gene expression (18).txt

value: DMSO


title: R11347

value: acute


title: rsa1 mutants line - Rep3


title: rsa1 mutants line - Rep2


title: R11348_R


title: R11346


title: R11345

value: moderate


title: genomic DNA from peripheral blood TL12

description:
T cell lymphoma perpheral blood sample
SAMPLE 109

source_name: genomic DNA from peripheral blood TL12

value: male

value: blood


title: p_LOVO_E545K_2

description:
10-FPKM
gene expression (18).txt


title: genomic DNA from peripheral blood TL10

description:
T cell lymphoma perpheral blood sample
SAMPLE 107

source_name: genomic DNA from peripheral blood TL10

value: T cell lymphoma


title: genomic DNA from peripheral blood TL11

description:
T cell lymphoma perpheral blood sample
SAMPLE 108

source_name: genomic DNA from peripheral blood TL11


title: LIMYB-32, L1, rep1

description:
Library name: 032LIMIB-L1_1
treatament1

source_name: leaf

value: 12 days


title: LOVO_E545K_2

description:
4-FPKM
gene expression (18).txt


title: LOVO_H1047R_1

description:
5-FPKM
gene expression (18).txt


title: LOVO_E545K_1

description:
3-FPKM
gene expression (18).txt


title: R11343


title: Wild-type Col-0 Rep2


title: rsa1 mutants line - Rep1


title: Wild-type Col-0 Rep3


title: LOVO_WT_1

description:
1-FPKM
gene expression (18).txt


title: rsa1 mutants line -- Rep2


title: Wild-type Col-0 Rep1


title: R11344


title: LOVO_WT_2

description:
2-FPKM
gene expression (18).txt


title: genomic DNA from peripheral blood TL5

description:
T cell lymphoma perpheral blood sample
SAMPLE 104

source_name: genomic DNA from peripheral blood TL5


title: R11340


title: genomic DNA from peripheral blood TL3

description:
T cell lymphoma perpheral blood sample
SAMPLE 103

source_name: genomic DNA from peripheral blood TL3


title: R11337

source_name: PBMC


title: aerial tissure, swp73a/+swp73b, rep2

city: Warszawa

first: Sebastian

middle: Przemyslaw

last: Sacharowski

state: mazowieckie

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

data_processing:
The reads for each sample were aligned to the TAIR10 A. thaliana genome using RNA-STAR (Galaxy Version 2.6.0b-1) with default settings.
After alignment, the data was uploaded to SeqMonk for further processing. Raw counts were obtained using the RNA-Seq quantitation pipeline, which included mRNA quantitation, merging of transcripts and isoforms, and duplication correction.
DESeq2 R package was employed for the differential gene expression analysis.
Assembly: TAIR10
Supplementary files format and content: count text files

source_name: aerial

growth_protocol: Seedlings were grown on half MS medium supplemented with 0.5% sucrose for 3 weeks

extract_protocol:
RNA was extracted using Total RNA Isolation & Purification Kits from Qiagen according to manufacturer protocol
Libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant rRNA Removal protocol and were then single-end sequenced on HiSeq2500

value: aerial


title: aerial tissure, swp73b, rep2


title: genomic DNA from peripheral blood TL1

description:
T cell lymphoma perpheral blood sample
SAMPLE 101

source_name: genomic DNA from peripheral blood TL1

value: female


title: genomic DNA from peripheral blood TL2

description:
T cell lymphoma perpheral blood sample
SAMPLE 102

source_name: genomic DNA from peripheral blood TL2


title: aerial tissure, swp73a/+swp73b, rep1


title: R11335


title: genomic DNA from peripheral blood TL8

description:
T cell lymphoma perpheral blood sample
SAMPLE 106

source_name: genomic DNA from peripheral blood TL8


title: R11333


title: genomic DNA from peripheral blood S50

description:
adult onset still's disease perpheral blood sample
SAMPLE 100

source_name: genomic DNA from peripheral blood S50

value: adult onset still's disease


title: R11330


title: aerial tissure, swp73b rep1


title: genomic DNA from peripheral blood TL7

description:
T cell lymphoma perpheral blood sample
SAMPLE 105

source_name: genomic DNA from peripheral blood TL7


title: genomic DNA from peripheral blood S49

description:
adult onset still's disease perpheral blood sample
SAMPLE 99

source_name: genomic DNA from peripheral blood S49


title: aerial tissure, swp73a, rep2


title: R11339


title: R11326


title: aerial tissure, swp73a, rep1


title: R11328


title: aerial tissure, swp73a/+, rep2


title: aerial tissure, swp73a/+, rep1


title: plasma_control _rep5

type: RNA

city: Beijing

first: ziqian

last: wang

address: No.28 Fu Xing Road, Beijing 100853, China

institute: the PLA general hospital

description:
Gene expression data from plasma of healthy control
Healthy control-5

hyb_protocol: Following labeling, the fragmented cDNA was hybridized with a Clariom D Assay (Human, Affymetrix) for 16 hours at 45 ℃.

scan_protocol: All arrays were scanned by using Affymetrix GeneChip Command Console (AGCC), which was installed in a GeneChip Scanner 3000 7G.

data_processing: The row data were normalized by using Affymetrix default analysis settings and global scaling. Differentially expressed circRNAs were filtered with the limma R package (version: 3.36.5).

label: biotin

source_name: plasma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Whole blood was collected into EDTA-containing tubes by direct venous puncture. The blood was centrifuged at 2000×g for 15 min, after which the plasma was aliquoted into RNase/DNase-free vials.

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

value: younger than 45 years


title: plasma_patient _rep5

description:
Gene expression data from plasma of early-onset myocardial infarction patient
Early-onset patient-5

treatment_protocol: Whole blood was collected into EDTA-containing tubes by direct venous puncture. The blood was centrifuged at 2000×g for 15 min, after which the plasma was aliquoted into RNase/DNase-free vials.


title: genomic DNA from peripheral blood S45

description:
adult onset still's disease perpheral blood sample
SAMPLE 95

source_name: genomic DNA from peripheral blood S45


title: plasma_control _rep1

description:
Gene expression data from plasma of healthy control
Healthy control-1


title: plasma_control _rep2

description:
Gene expression data from plasma of healthy control
Healthy control-2


title: R11320


title: genomic DNA from peripheral blood S44

description:
adult onset still's disease perpheral blood sample
SAMPLE 94

source_name: genomic DNA from peripheral blood S44


title: plasma_control _rep4

description:
Gene expression data from plasma of healthy control
Healthy control-4


title: plasma_patient _rep4

description:
Gene expression data from plasma of early-onset myocardial infarction patient
Early-onset patient-4


title: aerial tissure, WT, rep2


title: plasma_patient _rep3

description:
Gene expression data from plasma of early-onset myocardial infarction patient
Early-onset patient-3


title: Morula, siNr1h2, Rep2

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

description: Library name: siNr1h2_2

data_processing:
For bulk RNA-seq analysis, reads were mapped to the mm9 genome using STAR with the default parameters. GTF annotation file of genes (mm9) was downloaded from the UCSC genome browser. Cufflinks (v2.2.1) were used for gene assembly and gene quantification to generate fragments per kilobase per million mapped reads (FPKM) table based on mapped bam files and GTF annotation file. Count numbers of transcripts were computed by Htseq software (v0.12.4). DESeq2 was used to perform differential gene analysis for samples with replicates. The cutoff p-value was set as 0.05, and the cutoff fold change was set as 1.5. EdgeR was used to perform differential gene analysis for samples without replicates. The cutoff p-value was set as 0.05. For siNr1h2 embryo and prolonged cultured ESC/NrESC analysis, RSEM was used for the quantification of count numbers of transcripts. K-means gene clusters were identified by R function pheatmap.
Assembly: mm9
Supplementary files format and content: DESeq2 DEG

molecule: polyA RNA

source_name: Morula embryo

extract_protocol:
SMARTPool siNT and siNr1h2 siRNA (Horizon Discovery, D-001206-13, M-042839-01) were used for Nr1h2 knockdown in mouse embryos. Capillary glass tubes (outer diameter 1 mm, inner diameter 0.8 mm, and length 10 cm) with cut diameter 30–70 μm were used. 4–5pL of 100 μM siRNA was injected into fertilized one-cell embryos. Injected embryos were then transferred into a droplet of M16 medium covered with mineral oil in a 30 mm dish, and cultured until morula embryo stage before harvest.
Morulae samples were processed for RNA-seq library preparation using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Preparation Kit, following manufacturers’ instructions.

value: Morula embryo

value: Mouse embryo

value: Wild-type


title: IntestCrypts_2DG_1month_R1_Mouse_3

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_3

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: Murine crypts

growth_protocol: All animal experiments in this study were performed in accordance with protocols approved by the Memorial Sloan Kettering Institutional Animal Care and Use Committee (approval number: 11-06-012). The mice were housed with a 12 h light/dark cycle between 8:00 and 20:00 in a temperature-controlled room (22 ± 1°C) with free access to water and food. Both male and female mice were used in equal proportions for all experiments. .

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: For glycolisis inhibition, mice were injected (intraperitoneally) with 2-deoxyglucose once daily with 500 mg/kg dissolved in PBS. For the vehicle control, mice were injected with PBS. Mice were injected 5 times per week, 4 weeks.

tag: mouse strain

value: Murine crypts

tag: time

value: 500 mg/Kg 2DG


title: plasma_control _rep3

description:
Gene expression data from plasma of healthy control
Healthy control-3

tag: age


title: IntestCrypts_2DG_1month_R1_Mouse_4

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_4

tag: treatment


title: R11312

value: healthy


title: R11322


title: Morula, siNr1h2, Rep1

description: Library name: siNr1h2_1


title: R11319


title: genomic DNA from peripheral blood S48

description:
adult onset still's disease perpheral blood sample
SAMPLE 98

data_processing:
Data was extracted with the champ R package, the results were not normalized.
Average Beta or normalized (provide the normalization method) Average Beta

source_name: genomic DNA from peripheral blood S48

extract_protocol: We extracted peripheral blood genomic DNA with GeneJET Whole Blood Genomic DNA Purification Mini Kit (Thermo Fisher Scientific). An EZ DNA Methylation Kit (Zymo Research) was used for DNA samples bisulfite conversion.


title: genomic DNA from peripheral blood S47

description:
adult onset still's disease perpheral blood sample
SAMPLE 97

source_name: genomic DNA from peripheral blood S47


title: R11311


title: R11325


title: genomic DNA from peripheral blood S42

description:
adult onset still's disease perpheral blood sample
SAMPLE 92

source_name: genomic DNA from peripheral blood S42


title: plasma_patient _rep1

description:
Gene expression data from plasma of early-onset myocardial infarction patient
Early-onset patient-1


title: plasma_patient _rep2

description:
Gene expression data from plasma of early-onset myocardial infarction patient
Early-onset patient-2


title: Morula, siNT, Rep2

description: Library name: siNT_2

value: siNT


title: genomic DNA from peripheral blood S43

description:
adult onset still's disease perpheral blood sample
SAMPLE 93

source_name: genomic DNA from peripheral blood S43


title: IntestCrypts_2DG_1month_R1_Mouse_2

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_2


title: aerial tissure, WT, rep1


title: genomic DNA from peripheral blood S41

description:
adult onset still's disease perpheral blood sample
SAMPLE 91

source_name: genomic DNA from peripheral blood S41


title: R11310

source_name: PBMC


title: Morula, siNT, Rep1

description: Library name: siNT_1


title: IntestCrypts_2DG_1month_R1_Mouse_1

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_1


title: R11308


title: NrESC, Passage 14, Rep 2

description: Library name: Nr_P14_2

data_processing:
For bulk RNA-seq analysis, reads were mapped to the mm9 genome using STAR with the default parameters. GTF annotation file of genes (mm9) was downloaded from the UCSC genome browser. Cufflinks (v2.2.1) were used for gene assembly and gene quantification to generate fragments per kilobase per million mapped reads (FPKM) table based on mapped bam files and GTF annotation file. Count numbers of transcripts were computed by Htseq software (v0.12.4). DESeq2 was used to perform differential gene analysis for samples with replicates. The cutoff p-value was set as 0.05, and the cutoff fold change was set as 1.5. EdgeR was used to perform differential gene analysis for samples without replicates. The cutoff p-value was set as 0.05. For siNr1h2 embryo and prolonged cultured ESC/NrESC analysis, RSEM was used for the quantification of count numbers of transcripts. K-means gene clusters were identified by R function pheatmap.
Assembly: mm9
Supplementary files format and content: Gene count matrix (raw counts and normalized counts)

source_name: E14 ES

extract_protocol:
E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% ES FBS (Gibco), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)),  3 μM CHIR99021 (Tocris) and 1 μM PD0325901 (Tocris). NrESC medium is composed of ESC medium supplemented with 10 µM T0901317. All the ESC lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .
Total RNA was extracted from each sample using Monarch® Total RNA Miniprep Kit (New England Biolabs, T2010S). Isolated RNA was then used for RNA-seq library preparation using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, E7775L), following manufacturer’s instructions.

value: E14 ES

value: Embryonic stem cell

value: With T09

tag: passage

value: Passage 14


title: R11309


title: IntestCrypts_2GD_Control_R1_Mouse_2

description: Library name: IntestCrypts_2GD_Control_R1_Mouse_2

value: PBS


title: genomic DNA from peripheral blood S38

description:
adult onset still's disease perpheral blood sample
SAMPLE 88

source_name: genomic DNA from peripheral blood S38

value: blood


title: genomic DNA from peripheral blood S40

description:
adult onset still's disease perpheral blood sample
SAMPLE 90

source_name: genomic DNA from peripheral blood S40


title: NrESC, Passage 12, Rep 2

description: Library name: Nr_P12_2

value: Passage 12


title: IntestCrypts_2DG_Control_R1_Mouse_1

description: Library name: IntestCrypts_2DG_Control_R1_Mouse_1


title: R11304


title: genomic DNA from peripheral blood S37

description:
adult onset still's disease perpheral blood sample
SAMPLE 87

source_name: genomic DNA from peripheral blood S37

value: male


title: IntestCrypts_2GD_Control_R1_Mouse_3

description: Library name: IntestCrypts_2GD_Control_R1_Mouse_3


title: NrESC, Passage 14, Rep 1

description: Library name: Nr_P14_1


title: genomic DNA from peripheral blood S36

description:
adult onset still's disease perpheral blood sample
SAMPLE 86

source_name: genomic DNA from peripheral blood S36

value: adult onset still's disease


title: genomic DNA from peripheral blood S35

description:
adult onset still's disease perpheral blood sample
SAMPLE 85

source_name: genomic DNA from peripheral blood S35

value: female


title: R11306


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep10 - H3K27me3

city: Glasgow

first: Kieran

last: Woolcock

address: Sir Graeme Davies Building, 120 University Place

department: School of Infection & Immunity

country: United Kingdom

institute: University of Glasgow

description:
Library name: H3K27ME3_K1_RA_10
H3K27me3_RA_Normalised_Counts.csv

data_processing:
The fastQ files were quality control checked using FastQC (Andrews, GitHub, v0.11.7) and then aligned to the reference genome and transcriptome GRCh38 (release 102) using Bowtie2 (v2.4.4). Peaks were called using MACS2 (v2.2.8) specifying the appropriate ChIP input for each sample.
The data was batch corrected using the SVA package ComBat-seq based on sample origin and for the fraction of reads within peak regions (FRiPs).
Assembly: GRCh38 (release 102)
Supplementary files format and content: csv file includes normalised counts for each sample in each dataset (H3K4me3 and H3K27me3). Any samples that did not pass QC were removed from the normalised counts files.

source_name: Peripheral Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from fresh human blood samples by density gradient centrifugation using Ficoll® Paque Plus (Sigma-Aldrich). To isolate CD14+ monocytes, the EasySep human CD14 positive selection kit II (StemCell Technologies) was used following manufacturer’s instructions.

extract_protocol:
Cells were fixed in 1% methanol free formaldehyde, and then lysed. Chromatin samples were sonicated into 200-600 bp long fragments. Chromatin was split into the 10% input control, and the rest was used for either H3K4me3 or H3K27me3 chromatin immunoprecipitation. Input and ChIP'd DNA samples were extracted using the Qiagen MinElute PCR purification kit, as per manufacturer’s instructions.
DNA libraries were prepared for sequencing using the NEBNext Ultra II Directional DNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s instructions. Quality control was performed on the DNA libraries using a high sensitivity DNA Chip (Agilent) on the 2100 Bioanalyzer Instrument (Agilent).
ChIP-Seq (Each sample was sequenced to a depth of ~30 million reads, with fragments undergoing single end sequencing of 75 base pair read lengths.)

value: Peripheral Blood

value: Monocyte

tag: subject status

value: Rheumatoid Arthritis


title: genomic DNA from peripheral blood S46

first: Shijia

last: Rao

institute: Second Xiangya hospital

description:
adult onset still's disease perpheral blood sample
SAMPLE 96

source_name: genomic DNA from peripheral blood S46


title: NrESC, Passage 10, Rep 2

description: Library name: Nr_P10_2

value: Wild-type

value: Passage 10


title: NrESC, Passage 12, Rep 1

description: Library name: Nr_P12_1


title: R11303

tag: group

value: healthy


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep10 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_10
H3K4me3_RA_Normalised_Counts.csv


title: genomic DNA from peripheral blood S39

description:
adult onset still's disease perpheral blood sample
SAMPLE 89

source_name: genomic DNA from peripheral blood S39


title: R11300

tag: disease severity


title: NrESC, Passage 8, Rep 2

description: Library name: Nr_P8_2

value: Passage 8


title: NrESC, Passage 10, Rep 1

description: Library name: Nr_P10_1

value: E14 ES


title: R11302


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep10 - Input

description: Library name: Input_K1_RA_10


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep9 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_9
H3K4me3_RA_Normalised_Counts.csv


title: genomic DNA from peripheral blood S34

description:
adult onset still's disease perpheral blood sample
SAMPLE 84

source_name: genomic DNA from peripheral blood S34

tag: gender


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep9 - Input

description: Library name: Input_K1_RA_9


title: genomic DNA from peripheral blood S33

description:
adult onset still's disease perpheral blood sample
SAMPLE 83

source_name: genomic DNA from peripheral blood S33

tag: sample type


title: genomic DNA from peripheral blood S32

description:
adult onset still's disease perpheral blood sample
SAMPLE 82

source_name: genomic DNA from peripheral blood S32

tag: disease state


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep9 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_9
H3K27me3_RA_Normalised_Counts.csv

tag: tissue


title: R11299

value: acute


title: NrESC, Passage 6, Rep 1

description: Library name: Nr_P6_1

value: Embryonic stem cell

tag: genotype

value: With T09

value: Passage 6


title: NrESC, Passage 8, Rep 1

description: Library name: Nr_P8_1

tag: cell line


title: R11298


title: NrESC, Passage 4, Rep 2

description: Library name: Nr_P4_2

value: Passage 4


title: NrESC, Passage 6, Rep 2

description: Library name: Nr_P6_2


title: genomic DNA from peripheral blood S30

description:
adult onset still's disease perpheral blood sample
SAMPLE 80

source_name: genomic DNA from peripheral blood S30

value: blood


title: R11297

value: severe


title: genomic DNA from peripheral blood S31

description:
adult onset still's disease perpheral blood sample
SAMPLE 81

source_name: genomic DNA from peripheral blood S31

value: adult onset still's disease


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep8 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_8
H3K4me3_RA_Normalised_Counts.csv


title: NrESC, Passage 2, Rep 2

description: Library name: Nr_P2_2

value: Passage 2


title: genomic DNA from peripheral blood S29

description:
adult onset still's disease perpheral blood sample
SAMPLE 79

source_name: genomic DNA from peripheral blood S29

value: male


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep7 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_7
H3K27me3_RA_Normalised_Counts.csv

value: Peripheral Blood

value: Monocyte


title: genomic DNA from peripheral blood S28

description:
adult onset still's disease perpheral blood sample
SAMPLE 78

source_name: genomic DNA from peripheral blood S28


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep8 - Input

description: Library name: Input_K1_RA_8

value: Rheumatoid Arthritis


title: R11295

source_name: PBMC


title: NrESC, Passage 4, Rep 1

description: Library name: Nr_P4_1

source_name: E14 ES

value: Wild-type


title: genomic DNA from peripheral blood S27

description:
adult onset still's disease perpheral blood sample
SAMPLE 77

source_name: genomic DNA from peripheral blood S27

value: female


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep7 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_7
H3K4me3_RA_Normalised_Counts.csv


title: R11294


title: R11293


title: NrESC, Passage 2, Rep 1

description: Library name: Nr_P2_1


title: genomic DNA from peripheral blood S26

description:
adult onset still's disease perpheral blood sample
SAMPLE 76

source_name: genomic DNA from peripheral blood S26


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep8 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_8
H3K27me3_RA_Normalised_Counts.csv


title: R11290


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep6 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_6
H3K27me3_RA_Normalised_Counts.csv


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep6 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_6
H3K4me3_RA_Normalised_Counts.csv


title: R11296


title: NrESC, Passage 0, Rep 2

description: Library name: Nr_P0_2

value: Passage 0


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep7 - Input

description: Library name: Input_K1_RA_7


title: genomic DNA from peripheral blood S25

description:
adult onset still's disease perpheral blood sample
SAMPLE 75

source_name: genomic DNA from peripheral blood S25


title: R11292


title: NrESC, Passage 0, Rep 1

description: Library name: Nr_P0_1

value: E14 ES


title: R11289

value: acute

value: mild


title: R11291


title: ESC, Passage 14, Rep 1

description: Library name: ES_P14_1

value: Embryonic stem cell

value: Control

value: Passage 14


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep6 - Input

description: Library name: Input_K1_RA_6


title: genomic DNA from peripheral blood S24

description:
adult onset still's disease perpheral blood sample
SAMPLE 74

source_name: genomic DNA from peripheral blood S24

value: blood


title: R11287


title: ESC, Passage 14, Rep 2

description: Library name: ES_P14_2


title: genomic DNA from peripheral blood S21

description:
adult onset still's disease perpheral blood sample
SAMPLE 71

source_name: genomic DNA from peripheral blood S21


title: genomic DNA from peripheral blood S23

description:
adult onset still's disease perpheral blood sample
SAMPLE 73

source_name: genomic DNA from peripheral blood S23


title: genomic DNA from peripheral blood S20

description:
adult onset still's disease perpheral blood sample
SAMPLE 70

source_name: genomic DNA from peripheral blood S20


title: genomic DNA from peripheral blood S22

description:
adult onset still's disease perpheral blood sample
SAMPLE 72

source_name: genomic DNA from peripheral blood S22


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep5 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_5
H3K27me3_RA_Normalised_Counts.csv

source_name: Peripheral Blood


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep5 - H3K4me3

description:
Library name: H3K4ME3_C1_RA_5
H3K4me3_RA_Normalised_Counts.csv


title: ESC, Passage 12, Rep 2

description: Library name: ES_P12_2

value: Passage 12


title: ESC, Passage 12, Rep 1

description: Library name: ES_P12_1


title: R11284


title: ESC, Passage 10, Rep 2

description: Library name: ES_P10_2

value: Passage 10


title: genomic DNA from peripheral blood S19

description:
adult onset still's disease perpheral blood sample
SAMPLE 69

source_name: genomic DNA from peripheral blood S19

value: adult onset still's disease


title: R11282

value: severe


title: ESC, Passage 10, Rep 1

description: Library name: ES_P10_1


title: R11279


title: genomic DNA from peripheral blood S18

description:
adult onset still's disease perpheral blood sample
SAMPLE 68

source_name: genomic DNA from peripheral blood S18

value: male


title: genomic DNA from peripheral blood S17

description:
adult onset still's disease perpheral blood sample
SAMPLE 67

source_name: genomic DNA from peripheral blood S17


title: ESC, Passage 8, Rep 2

description: Library name: ES_P8_2

value: Passage 8


title: R11276


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep4 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_4
H3K4me3_RA_Normalised_Counts.csv

value: Peripheral Blood

value: Monocyte

value: Rheumatoid Arthritis


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep3 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_3
H3K27me3_RA_Normalised_Counts.csv


title: genomic DNA from peripheral blood S15

description:
adult onset still's disease perpheral blood sample
SAMPLE 65

source_name: genomic DNA from peripheral blood S15


title: R11273


title: ESC, Passage 8, Rep 1

description: Library name: ES_P8_1

value: Wild-type


title: R11263


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep3 - Input

description: Library name: Input_K1_RA_3


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep4 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_4
H3K27me3_RA_Normalised_Counts.csv


title: ESC, Passage 2, Rep 2

description: Library name: ES_P2_2

value: E14 ES

value: Passage 2


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep4 - Input

description: Library name: Input_K1_RA_4


title: genomic DNA from peripheral blood S16

description:
adult onset still's disease perpheral blood sample
SAMPLE 66

source_name: genomic DNA from peripheral blood S16


title: R11268

value: acute

value: moderate


title: ESC, Passage 6, Rep 2

description: Library name: ES_P6_2

value: Embryonic stem cell

value: Control

value: Passage 6


title: R11266


title: ESC, Passage 2, Rep 1

description: Library name: ES_P2_1


title: genomic DNA from peripheral blood S14

description:
adult onset still's disease perpheral blood sample
SAMPLE 64

source_name: genomic DNA from peripheral blood S14

value: blood


title: genomic DNA from peripheral blood S13

description:
adult onset still's disease perpheral blood sample
SAMPLE 63

source_name: genomic DNA from peripheral blood S13

value: female


title: genomic DNA from peripheral blood S10

description:
adult onset still's disease perpheral blood sample
SAMPLE 60

source_name: genomic DNA from peripheral blood S10

value: adult onset still's disease


title: ESC, Passage 6, Rep 1

description: Library name: ES_P6_1

source_name: E14 ES


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep5 - Input

description: Library name: Input_K1_RA_5


title: ESC, Passage 0, Rep 2

description: Library name: ES_P0_2

value: Passage 0


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep3 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_3
H3K4me3_RA_Normalised_Counts.csv


title: genomic DNA from peripheral blood S9

description:
adult onset still's disease perpheral blood sample
SAMPLE 59

source_name: genomic DNA from peripheral blood S9


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep1 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_1
H3K27me3_RA_Normalised_Counts.csv


title: R11265

source_name: PBMC


title: ESC, Passage 0, Rep 1

description: Library name: ES_P0_1


title: R11255


title: R11257

value: severe


title: ESC, Passage 4, Rep 2

description: Library name: ES_P4_2

value: Passage 4


title: ESC, Passage 4, Rep 1

description: Library name: ES_P4_1


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep2 - H3K27me3

description:
Library name: H3K27ME3_K1_RA_2
H3K27me3_RA_Normalised_Counts.csv

value: Peripheral Blood


title: genomic DNA from peripheral blood S12

description:
adult onset still's disease perpheral blood sample
SAMPLE 62

source_name: genomic DNA from peripheral blood S12


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep15 - H3K27me3

description:
Library name: H3K27ME3_K1_HC_5
H3K27me3_RA_Normalised_Counts.csv

value: Monocyte

value: Healthy Control


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep2 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_2
H3K4me3_RA_Normalised_Counts.csv

value: Rheumatoid Arthritis


title: Wild type Cellobiose Rep 3

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

description: Library name: yku70D_Cellobiose_Rep3

data_processing:
Base calling was performed with the Illumina DRAGON Bio-IT Platform v4.1 and demultiplexed fastq files were generated using Illumina bcl-convert v4.0.3 software.
Sequenced reads were trimmed for adapter sequence and aligned to the predicted transcripts from the R. toruloides IFO0880 genome (v4). TPMs were quantified with Salmon v. 1.10.0 with the --validateMappings setting.
Assembly: Rhodosporidium toruloides IFO0880 (NBRC0880) v.4 (https://mycocosm.jgi.doe.gov/Rhoto_IFO0880_4/Rhoto_IFO0880_4.home.html)
Supplementary files format and content: Tab-delimited text file with TPM values for each sample

organism: Rhodotorula toruloides

source_name: Yeast cells

growth_protocol: R. toruloides cells were inoculated into yeast extract peptone dextrose (YPD) medium overnight at 28C with constant shaking at 250rpm in constant light so that cells were in exponential growth phase

extract_protocol:
Cells were harvested by centrifugation and flash frozen using liquid nitrogen. RNA was isolated using the Zymo Quick-RNA Fungal/Bacterial Kit according to manufacturer's protocols. 7.5ug of RNA was DNase treated with Invitrogen DNA-free kit according to manufacturer's protocol. RNA integrity was checked via agarose gel and Bioanalyzer.
RNA were prepared for sequencing using poly-A enrichment and standard Illumina protocols.

treatment_protocol: Cells were washed 3 times in yeast nitrogen base with NH4SO4 w/out amino acids + 12 mM K2HPO4 + 38 mM KH2PO4 + 100nM Fe(II)SO4 pH 6.2 (YNB) medium without a carbon source and then transferred to 100ml YNB lacking a carbon source, YNB 1% succinate, or YNB 1% cellobiose as indicated at 0.1 OD/mL and incubated at 28C in constant light with constant shaking at 250rpm for 8h prior to harvesting for RNAseq.

value: Yeast cells

value: YNB 1% cellobiose


title: cbr1D Cellobiose Rep 3

description: Library name: cbr1D_Cellobiose_Rep3

value: yku70::HygR cbr1::NatR


title: genomic DNA from peripheral blood S11

city: Changsha

address: Renmin Road

description:
adult onset still's disease perpheral blood sample
SAMPLE 61

source_name: genomic DNA from peripheral blood S11


title: Wild type Cellobiose Rep 1

description: Library name: yku70D_Cellobiose_Rep1


title: genomic DNA from peripheral blood S2

description:
adult onset still's disease perpheral blood sample
SAMPLE 52

source_name: genomic DNA from peripheral blood S2


title: R11259

value: acute


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep2 - Input

description: Library name: Input_K1_RA_2


title: cbr1D Succinate Rep 3

description: Library name: cbr1D_Succinate_Rep3

value: YNB 1% succinate


title: R11260


title: Peripheral blood CD14+ monocyte, Rheumatoid Arthritis, Rep1 - H3K4me3

description:
Library name: H3K4ME3_K1_RA_1
H3K4me3_RA_Normalised_Counts.csv


title: genomic DNA from peripheral blood S8

description:
adult onset still's disease perpheral blood sample
SAMPLE 58

source_name: genomic DNA from peripheral blood S8


title: ESC Nr1h2-FLAG + T09 H3K9me3-ChIP (input)

description: Library name: Nr_T_Me3_In

data_processing:
FastQC was used to check the sequence quality. Reads were mapped to the mm9 genome using STAR software with the parameters ‘–alignIntronMax 1 –alignEndsType EndToEnd’. MACS2 were used to call H3K27ac peaks (q-value < 0.05) and Nr1h2 peaks (p-value < 0.01). H3K27ac peaks from samples were merged with bedtools, and read counts for each sample on merged peaks were then calculated using featureCounts. The differential peaks were identified by EdgeR. Significant differential H3K27ac peaks were determined using cutoff p-value < 0.05 and |log2FC| > 1.5. Bigwig files were produced by Deeptools and visualized in WashU Epigenome Browser. Motif enrichment analysis was performed using Homer with function findMotifsGenome.pl. The p-value of known motifs was used for the visualization.  The enrichment analysis of genomic features on differentially upregulated/downregulated Nr1h2 peaks was performed using Fisher’s exact test. The log2-odds ratio and significance p-value was shown in the bar plot. The public ChIP-seq data of Kdm1a (GSE27841) used in Fig. 6 and S6 was downloaded from GEO database. For the analysis of Nr1h2-FLAG and EGFP-FLAG cells, significant differential H3K27ac peaks were determined using cutoff p-value < 0.05 and |log2FC| > 1. Genome-wide H3K9me3 peaks were first determined by MACS2 and featureCounts followed by edgeR workflow similarly using cutoff p-value < 0.05 and |log2FC| > 1. The overlapping peaks with Nr1h2 bound sites were then selected using bedtools intersect function.
Assembly: mm9
Supplementary files format and content: bigwig

source_name: E14 ESC

extract_protocol:
E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% ES FBS (Gibco), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)),  3 μM CHIR99021 (Tocris) and 1 μM PD0325901 (Tocris). NrESC medium is composed of ESC medium supplemented with 10 µM T0901317. All the ESC lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 . Cells were trypsinized, harvested and the cell number was estimated. Cross-linking was performed for 10 × 106 cells using 1% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M Glycine. Crosslinked cells were resuspended in 1 ml of FA lysis buffer (10 mM Tris–Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche)), nutated at 4 °C for 15 min and spun down at 1300 × g for 5 min at 4 °C. Supernatant was removed and the pellet was re-suspended in 1% SDS lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail). After 15 min of incubation, the pellet was spun down and washed two times with 0.1% lysis buffer (50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-1s00, 0.1% NaDOC and protease inhibitor cocktail). Cell pellet was sonicated by Biorupter (Diagenode) for 14 cycles (30 s on and 60 s off for each cycle). Cell debris was removed from the sheared chromatin by centrifugation at 21,000 × g at 4 °C for 30 min. Protein G Dynabeads (Life Technologies) was incubated with antibodies (Nr1h2 ChIP antibody (NB100-1464, Novus Biologicals), FLAG ChIP antibody (F1804, Sigma-Aldrich), H3K9me2 ChIP antibody (Abcam, ab1220), H3K9me3 ChIP antibody (Abcam, ab8898) and H3K27Ac ChIP antibody (ab4729, Abcam)) for 3 h at room temperature and washed three times by PBS with 0.1% TritonX-100. 5% of the sheared chromatin was separated as input while the remaining was subject to overnight incubation with antibody-bound Dynabeads. In total 7 washes were performed to remove unspecific bindings, including three washes with 0.1% SDS lysis buffer, one with 0.1% SDS lysis buffer/0.35 M NaCl, one with 10 mM Tris–Cl (pH 8.0), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and two with TE buffer (pH 8.0). Dynabeads were resuspended in elution buffer (50 mM Tris–HCl (pH 7.5), 10 mM EDTA, 1% SDS) and incubated at 68 °C for 1 h with 1400 rpm shaking. Eluted samples were de-crosslinked at 42 °C for 2 h and 67 °C for 6 h with Pronase (Sigma).
DNA purification was further performed with QIAGEN PCR Purification kit (for inputs) and the QIAGEN MinELute PCR Purification kit (for ChIP samples). Quantitative PCR with CXF384 Real-time System (Bio-Rad) and Kapa SYBR Fast qPCR kit (Kapa Biosystems). For ChIP-seq library preparation, ACCEL-NGS®2S Plus DNA library kit (IDT) and 2S™ Adapter Set A (IDT) was used as per manufacturer’s instruction starting with 5–10 ng DNA for both input and ChIP sample.

value: E14 ESC

value: Embryonic stem cell

value: Wild-type

value: Nr1h2-FLAG overexpression + T09


title: genomic DNA from peripheral blood S7

description:
adult onset still's disease perpheral blood sample
SAMPLE 57

source_name: genomic DNA from peripheral blood S7

value: male

value: blood

value: adult onset still's disease


title: cbr1D Cellobiose Rep 2

description: Library name: cbr1D_Cellobiose_Rep2


title: genomic DNA from peripheral blood N50

description:
normal  perpheral blood sample
SAMPLE 50

source_name: genomic DNA from peripheral blood N50

value: normal


title: ESC Nr1h2-FLAG + T09 H3K9me3-ChIP (antibody)

description: Library name: Nr_T_Me3_Ch


title: genomic DNA from peripheral blood S6

description:
adult onset still's disease perpheral blood sample
SAMPLE 56

source_name: genomic DNA from peripheral blood S6

value: female


title: cbr1D Cellobiose Rep 1

description: Library name: cbr1D_Cellobiose_Rep1


title: ESC Nr1h2-FLAG + T09 H3K27ac-ChIP (input)

description: Library name: Nr_T_Ac_In