title: human monocytes-derived DC_40891-mature

last: Tran

address: 1441 Eastlake Ave

institute: University of Southern California

description:
Dan_15
human monocytes-derived DC_40891-matured by KR-luc tumor lysate and TNFalpha, IL-6,IL-1beta

data_processing:
Paired-end reads were trimmed with trimmomatic v/0.36, and alignment and gene counts generated against the GRCh38.p12 genome assembly using the annotation GeneCode release 28 by STAR v2.6.0b with default options and quantmode=GeneCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited csv file includes raw counts for each Sample
Supplementary files format and content: tab-delimited csv file include TPM values for each Sample
Supplementary files format and content: tab-delimited csv file include CPM values for each Sample
Supplementary files format and content: tab-delimited csv file include RPKM values for each Sample

growth_protocol: cell lines were cultured in DMEM media with 10% FBS and 1% pen/strep

extract_protocol:
RNA was extracted utilizing QIAGEN RNeasy Midi Kit (Cat#75144) according to the manufacturer’s instructions.
Illumina TruSeq Stranded mRNA Library Prep Kit was used by NOVOGENE.
End repair, A-tailing, adaptor ligation

treatment_protocol: For transduction of CFD-containing lentiviruses, GBM cells in baseline DMEM media were incubated with indicated lentiviral constructs for 24hrs., followed by media replacement to RPMI 1640 supplemented with 10% FBS, 1% pen/strep and 3µg/µl puromycin for selection. On day 7 after transduction, cells were passaged into RPMI 1640 media supplemented with 10% FBS and 1% pen/strep without puromycin until analysis. For all of the samples from three cell human GBM cell lines, are derived from in vitro reprogramming by indicated factors for 7 days.

tag: cell line_name

tag: group


title: ES 1

status: Public on Oct 23 2024

type: SRA

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: ES.merged.bw

library_source: genomic

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
Replicates wre merged together, bigwig files were produced by deeptools
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

growth_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). All the ESC cell 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 . E14 mouse Nr1h2-activated embryonic stem cells (NrESC) were cultured in mouse ESC medium supplemented with 10µM T0901317 (MedChemExpress, HY-10626). E14 mouse expanded potential stem cells (ESC) were cultured on gelatin-coated plates in EPSC medium with DMEM/F-12 basal media (Thermo Fisher Scientific) supplemented with 20% knockout serum replacement (Thermo Fisher Scientific), 1X NEAA (Thermo Fisher Scientific), 1X L-glutamine (Thermo Fisher Scientific), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific), 10^3 units/ mL recombinant mouse LIF (Sigma-Aldrich), 3 µM CHIR99021(Tocris) and 1 µM PD0325901 (Tocris), 4 µM JNK Inhibitor VIII (Tocris), 10 µM SB203580 (Tocris), 0.3 µM A-419259 (Santa Cruz) and 5 µM XAV939 (Tocris).

extract_protocol:
Chormatin was using Illumina tagment DNA TDE1 Enzyme and Buffer kit as per manufacturer's instructions.
Library was prepared using Nextera DNA library preparation kit as per manufacturer's instructions.

tag: cell line

tag: cell type

value: ESC


title: mouse_3mth _PBMC

city: Saint Louis

first: David

last: Gutmann

address: 660 S. Euclid Ave

country: USA

institute: Washington University in St. Louis School of Medicine

description:
F/M
10x Genomics

library_source: transcriptomic single cell

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
genome build: mm10-2020-A for mus musculus , GRCh38-2020-A for homo sapiens
single cell data were processed using Partek® Flow® (Version 10.0) https://www.partek.com/partek-flow/. Gene expression and TCR V(D)J data were overlaid by R scRepertoire package.
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by CPM (counts per million) normalization. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat3 integration method to produce batch-corrected data. PCA analysis followed by graph-based clustering using Louvain algorithm, and t-SNE/ UMAP generation employing Euclidean distance, were conducted on the first 20 principal components of the integrated expression data. Differential analyses were performed using gene specific analysis (GSA). Pathway analyses were performed using DAVID Bioinformatics platform.
Assembly: mm10-2020-A for mus musculus, GRCh38-2020-A for homo sapines
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

molecule: total RNA

source_name: blood

extract_protocol:
De-identified human PA samples (4 female sporadic PAs and 1 female NF1-PA; clinical information in Supplemental Table 3) were obtained under an approved Human Studies Protocol as dissociated frozen tumor single cells from the St. Louis Children’s Hospital Pediatric Tumor Bank. The frozen dissociated tumor single cells were thawed and resuspended in DMEM.The cells were then stained with 7-Aminoactinomycin D (7-AAD) (Fisher Scientific, A1310) for sorting using the MoFlo (Siteman Flow Cytometry Core at the Washington University in St Louis). Live cells were collected and submitted for single cell RNA sequencing (scRNA-seq).  Nf1-OPG optic nerves and meningeal duras were collected separately from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo. Live cells were collected and sent for scRNA sequencing with TCR V(D)J enrichment.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

tag: tissue

value: blood

tag: age

value: 12 weeks

tag: Sex

value: mixed

tag: genotype


title: LPS 1d_3

city: Shenyang

first: Jianjun

last: Chang

state: Liaoning

address: No. 77 Puhe Road, Shenyang North New Area, China

country: China

institute: China Medical University

library_source: transcriptomic

data_processing:
The sequencing library was then subjected to sequencing on a Novaseq PE150 System (Illumina) and performed by Shanghai Personal Biotechnology Cp. Ltd (Shanghai, China).
The filtered Reads were aligned to the reference genome using the upgrade version of TopHat2, HISAT2 software, with the objective of achieving a sequence mapping rate exceeding 90%.
The reads were uniformly distributed across all expressed genes.
HTSeq was used to statistically compare the read count value of each gene, as the original expression amount of the gene.
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each sample

source_name: brain

extract_protocol:
On day 1 after PBS/LPS injection or day 7 after LPS injection, mice were anesthetized and sacrificed, and fresh PVT tissues were collected. Total RNA was extracted using the Trizol Reagent. The concentration, quality, and integrity of the extracted RNA were evaluated using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA).
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) following manufacturer's protocols.

value: brain

value: WT

tag: treatment

value: LPS for 1 day


title: LPS 1d_2


title: ES 2

description: ES.merged.bw


title: mouse_Dura

description:
F/M
10x Genomics

source_name: meningeal dura

value: meningeal dura


title: WGBS_ESC

data_processing:
Raw paired-end reads were aligned to the mouse mm10 genome reference with Bismark/Bowtie2 mode with default parameters. Duplicate reads were removed by the command deduplicate_bismark from Bismark. The methylation calls were extracted and bedGraph files were produced by bismak_methylation_extractor.
Assembly: mm10
Supplementary files format and content: bismark.coverage

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, 69556), followed by sonication to generate ~200bp fragments using Bioruptor® Pico (Diagenode, B01080010).
Libraries were prepared using Premium WGBS Kit (Whole Genome Bisulfite Sequencing) (Diagenode, C02030034). All procedures follow manufacturer’s instructions.


title: EGBS_NrESC

value: NrESC


title: Nr1h2_NrES_Sample

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
bigwig files were produced by deeptools
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
8 million cells were cross-linked with 1% formaldehyde for 15min at room temperature, with the formaldehyde then quenched by the addition of 200 mM glycine and cells then washed once with ice-cold PBS. Cell lysis and chromatin shearing was performed using Diagenode Chromatin EasyShear kit - Low SDS. Sonication was conducted using Diagenode Biorupter Pico using 4 cycles of low frequency, 30s pulses on with 30s pulses off. The chromatin solution was clarified by centrifugation at 20,000 g at 4°C for 45 mins and then pre-cleared with Dynabeads G (Life Technologies) for 2 hrs. The pre-cleared chromatin sample was incubated with 50 μl of Dynabeads G loaded with 5 μg antibody overnight. The beads were then washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and once with TE buffer (PH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 min at 68°C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 μg/ml Pronase at 42°C for 2 hr followed by 67°C for 6 hr. The samples were then extracted with QIAGEN MiniElute column, and re-suspended in TE buffer.
The ChIP-Seq libraries were prepared using  Accel-NGS® 2S Plus DNA Library Kit

tag: chip antibody

value: Anti-NR1H2 antibody (Novus Biologicals, NB100-1464)


title: human monocytes-derived DC_40762-mature

city: Los Angeles

state: CA

department: Department of Neurological Surgery

description:
Dan_14
human monocytes-derived DC_40762-matured by KR-luc tumor lysate and TNFalpha, IL-6,IL-1beta

molecule: polyA RNA

organism: Homo sapiens


title: WGBS_EPSC_T09

value: EPSC with T09


title: Nr1h2_NrES_Input


title: human monocytes-derived DC_40173-mature

description:
Dan_13
human monocytes-derived DC_40173-matured by KR-luc tumor lysate and TNFalpha, IL-6,IL-1beta


description:
Dan_12
human monocytes-derived DC_40891-imature


title: PBS 1d_2

value: PBS for 1 day


title: EP 1

description: EP.merged.bw

value: EPSC


title: WGBS_EPSC


title: Nr1h2_NrEPSC_Sample


description:
Dan_11
human monocytes-derived DC_40762-imature


title: CAFs, Vec, 72 h, IP

first: Qijun

last: Wu

address: No. 36, San Hao Street

institute: Shengjing Hospital of China Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output
Discard a paired reads if either one read contains adapter contamination;Discard a paired reads if the proportion of low quality (Phred quality <15) bases is over 40% in either one read
Reference genome and gene model annotation files were downloaded from genome websitedirectly. Index of the reference genome was built using BWA (0.7.17) and clean reads werealigned to the reference genome using BWA mem (0.7.17)
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: cancer-associated fibroblasts

extract_protocol:
Cross-linking of DNA with formaldehyde was performed. After cell lysis, chromatin was sonicated using an ultrasonicator
The ChIP-Seq library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution and quantified by QPCR.

value: cancer-associated fibroblasts


title: PBS 1d_1


title: EP 2

description: EP.merged.bw


description:
Dan_10
human monocytes-derived DC_40173-imature


title: Nr1h2_NrEPSC_Input


title: NCI-H660, Input

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

data_processing:
Basecalling was performed by Illumina Real Time Analysis (RTA) v2.11.3 with default settings
Demultiplexing was perfoemed by Illumina bcl2fastq v2.20.0.422 using parameters --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --barcode-mismatch 1
Raw reads were aligned to the hg38 (human) reference genome using BWA-MEM software (version 0.7.17) with default parameters. Alignments with mapping quality less than 60 were filtered out (leaving only uniquely mapped reads) and subsequently sam files were converted to bam files using Samtools software (version 1.1.2).
Narrow peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAMPE -g 2.9e9 --keep-dup=1 -B -q 0.05. Broad peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAM --broad -g 2.9e9 --keep-dup 1 --broad-cutoff 0.05. Bedtools intersect (v2.28.0) program suite was used to generate shared (-wa -u -f 0.5 -F 0.5 -e) and unique (-v -f 0.5 -F 0.5 -e) peak set between samples.
Deeptools (v2.30.0) program suite was used to generate bigWig files.
HOMER (v4.11) program suite was used to annotate peaks and perform motif enrichment analysis.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Prostate

growth_protocol: NCI-H660 (ATCC cat. #CRL-5813) cell line was cultured in HITES medium following ATCC recommendation in humidified atmospheric air with 5% CO2 at 37°C.

extract_protocol:
Cells were processed for ChIPseq following published protocol (PMID: 20680851) with the following antibodies: FOXA2 (5µg, R&D #AF2400-SP. 10 million cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Cells were collected. Chromatin was sonicated to approximately 500bp.
For ChIP-seq, sequencing libraries (100 ng DNA per sample) were constructed using the KAPA library Prep Kit (Roche, Cat KK8510) with Illumina TruSeq indexes. Libraries were assessed for quality using gel electrophoresis and libraries passing quality control (e.g., no primer dimers) were quantified using the KAPA Library Quantification Kit for Illumina (Roche, Cat KK4824). Libraries were sequenced using the Illumina NextSeq 500 (75 bp single-end reads; cell lines).

value: Prostate

value: Neuroendocrine prostate cancer

value: none (input)


title: PBS 1d_3


title: Liver, RD, H3K27me3, 2879

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet

data_processing:
FastQC for quality control of Fastq files
Mapped with bowtie2 (options: --threads 4 —very-sensitive)
SAM files converted to BAM files with samtools
Enriched peaks were called using MACS2 (options: callpeak --gsize 1.87e9 --broad --broad-cutoff 0.05 --f BAMPE)
Assembly: mm10
Supplementary files format and content: Peak files in xls format

source_name: Liver

growth_protocol: Mouse were kept for 52 weeks in either a RD or a WD.

extract_protocol:
Liver and tumour tissues were pulverised before lysis on cell lysis buffer at 4ºC for 5-10 minutes. Nuclei were pelleted and resuspended in 1xPBS and the volume corresponding to 50-70 mg of tissue was used for chromatin extraction by adding nuclei lysis buffer at 4ºC for 5 minutes.
Chromatin was sonicated on a Covaris E220 device (PIP: 105, Duty factor: 2, Cycles/burst: 200, Duration: 5 min). ChIP was performed with antibodies for rabbit anti-H3K27Ac (Abcam, ab4729) and rabbit anti-H3K27Me3 (Abcam, ab192985). ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645)

treatment_protocol: 200 mg of fresh liver and tumour tissue was first dissected into smaller pieces and then fixed for 15 min in 1 ml fixing solution (1% formaldehyde, 50 mM HEPES–KOH, 100 mM NaCl, 1 mM ethylenediaminetetraacetic acid (EDTA), 0.5 mM EGTA) at RT with gentle mixing. Crosslinking was stopped by adding 1/20 volume of 2.5 M glycine for 5 min at RT. Samples were then washed 2 × 5 min at 4 °C with cold 1 × PBS containing protease inhibitor cocktail (Roche, #4693132001), snap frozen and stored at −80 °C until awaiting further processing

value: Liver

tag: strain

value: DIAMOND

value: male

tag: diet

value: RD


title: Nr1h2_EPSC_Sample


title: LN827_hSPI1+hIKZF1_CD45+_bulk

description:
Dan_9
LN827 transfected with  pSF-hSPI1,  pSF_hIKZF1, CD45 positive sorted by FACS

source_name: GBM

value: GBM


title: LPS 1d_1

value: brain

value: WT


title: Liver, RD, H3K27Ac, 2879


title: NCI-H660, FOXA2, ChIP

value: FOXA2 (R&D #AF2400-SP)


title: Liver, RD, input, 2819-2879

value: Input


title: LN827_hSPI1_CD45+_bulk

description:
Dan_8
LN827 transfected with  pSF-hSPI1, CD45 positive sorted by FACS


title: Nr1h2_EPSC_Input


title: HLCs,WT,T28,3

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

institute: CIMA

data_processing:
Samples were aligned to the Human genome (GRCh38) with STAR (v2.6.1). Gene expression was quantified with Subread/1.6.3
Downstream analyses were performed in R (v3.6.2). Data transformation, normalization, and differential gene expression analysis were performed with DESeq2 or MaSigPro. Genes were considered adjusted p value (p-adj)<0.05 and absolute log transformed fold-change (|log2FC|)>1, unless otherwise indicated. vst expression values were used for data visualization and unsupervised analysis.
Assembly: GRCh38_Gencode32
Supplementary files format and content: tab-delimited text file includes filtered raw counts (filtered to have counts >0 at least in one sample) samples
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: Blood

growth_protocol: Two hiPSC lines were used in this work: hiPSC.PH1, that was derived from peripheral blood lymphocytes (PBL) obtained from a patient diagnosed with primary hyperoxaluria type 1 (PH1) with a p.I244T (c.731T>C) mutation in the AGXT gene, and ChiPSC18 derived from Human skin fibroblasts from a healthy individual. The hiPSC.PH1 line is registered at the Spanish National Cell Bank, and the ChiPSC18 is from Takara BioEurope AB, Göteborg, Sweden (Cat. No.Y00305). Both hiPSC lines were routinely propagated in static culture conditions (T-flasks) in Cellartis® DEF-CS Xeno-Free 500 Culture System (Cat. No. Y30045, Takara BioEurope AB, Göteborg, Sweden) at 37°C in a humidified atmosphere with 5% (v/v) CO2, as described previously, and according to manufacturing instructions. Briefly, hiPSC were split typically every 3-4 days at 80-90% confluency and seeded at 3-4 × 104 cell/cm2, the culture medium was changed every day. Cells were dislodged by rinsing with Dulbecco phosphate-buffered saline (DPBS, Thermo Fisher Scientific, Waltham, Massachusetts, EUA) and incubation with Versene (Thermo Fisher Scientific, Waltham, Massachusetts, EUA) for 20 min at 37°C, sedimented by centrifugation and the pellet resuspended in Cellartis® DEF-CS Xeno-Free 500 culture media. Cell concentration and viability were determined using the Trypan Blue exclusion method in a Fuchs-Rosenthal hemocytometer, as described elsewhere.

extract_protocol:
Cells from static culture, dissociated with TrypLE Select (Gibco Life Technologies) for 5 min at 37°C, and aggregates collected from the bioreactor were centrifuged at 300 x g for 5 min. These pellets were washed with DPBS, snap-freezed with liquid nitrogen and kept at -80°C. mRNA was extracted using the High Pure RNA Isolation kit (Roche) according to manufacturer’s instructions.
Roughly 100ng of total RNA were used for the transcriptomic interrogation of samples using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus according to the manufacturer’s instructions. Briefly, cytoplasmic and mitochondrial rRNAs as well as beta globin transcripts were depleted from the samples. The remaining RNA was fragmented and reverse-transcribed. A second strand cDNA synthesis step removed the RNA template while incorporating dUTP in place of dTTP in order to preserve strand specificity. Next, double-stranded cDNA was A-tailed, then ligated to Illumina anchors bearing T-overhangs. PCR-amplification of the library allowed the barcoding of the samples with 10bp dual indexes and the completion of Illumina sequences for cluster generation. Libraries were quantified with Qubit dsDNA HS Assay Kit and their profile was examined using Agilent’s HS D1000 ScreenTape Assay. Sequencing was carried out in an Illumina NextSeq500 using single-end, dual-index sequencing (Rd1: 71 cycles; i7: 10 cycles; i5: 10 cycles) at a depth of 30 million reads per sample.

treatment_protocol: Hepatocyte differentiation was performed in stirred tank bioreactors (DasGip CellFerm-Pro bioreactor system, Eppendorf AG, Hamburg, Germany) operated in perfusion. Bioreactor cultures were performed in a working volume of 200 mL using flat bottom bioreactor vessels equipped with trapezoid shaped paddle impellers with long arms as previously reported. hiPSC were inoculated at a density of 2.5 × 105 cell/mL as single cells and cultured in Cellartis® DEF-CS Xeno-Free 3D Spheroid Culture Medium (Cat. No. Y30047, Takara BioEuropeAB, Göteborg, Sweden) as described elsewhere. During the expansion step (from day -4 to day 0, Fig. 1A) cells were cultured at 37oC with a surface aeration rate of 0.1 vvm with of 5% (v/v) CO2 and DO of 4%O2 (18% of air with 21% of oxygen). The stirring rate was set to 80 rpm. A metallic microsparger (of 10-30 μm pore size) was connected in the outlet perfusion line as cell retention device to prevent aggregate loss. Perfusion was initiated 24 hours post-inoculation and was operated by automated gravimetric control, as described before at a constant dilution rate (1.3 day-1) for 4 days. After expansion, the hepatic differentiation step was initiated (additional 21 days of culture time)[...] During the progenitor’s stage from day 4 to day 14 of differentiation, cells were cultured under two different conditions, in STB_21%O2 with atmospheric DO (21%O2) and in STB_4%O2 under physiological levels of DO (4%O2) both at 37 °C with a surface aeration rate of 0.1 vvm and 5% CO2. From day 1 to day 4 and from day 14 to day 21 of hepatic differentiation cells in both STB_21%O2 and STB_4%O2 conditions were cultured with atmospheric DO (21%O2) at 37°C; surface aeration rate: 0.1 vvm; CO2: 5% (v/v). Stirring rate was set to 80 rpm.

value: Blood

value: peripheral blood lymphocytes (PBL)


title: LN827_pSF_bulk

description:
Dan_7
LN827 transfected with empty pSF

value: pSF


title: Nr1h2_E2iES_Input

value: ESC


title: HLCs,WT,T28,2


title: Liver, RD, H3K27me3, 2819


title: LN308_hSPI1+hIKZF1_CD45+_bulk

description:
Dan_6
LN308 transfected with  pSF-hSPI1,  pSF_hIKZF1, CD45 positive sorted by FACS


title: Liver, RD, H3K27Ac, 2819


title: H3K27ac_NrES_Sample

value: NrESC

value: Anti-Histone H3 (acetyl K27) antibody (Abcam, ab4729)


title: PH1-HLC,Normoxia,T4,1


title: Liver, HCC, H3K27Ac, 2896

value: WD


title: PH1-HLC,Normoxia,T4,2


title: Nr1h2_2iES_Sample

value: Anti-NR1H2 antibody (Novus Biologicals, NB100-1464)


title: PH1-HLC,Normoxia,T21,2


title: Liver, HCC, input, 2882-2896

value: Liver


title: Liver, HCC, H3K27me3, 2896

value: DIAMOND


title: H3K27ac_NrES_Input


title: LN308_pSF_bulk

description:
Dan_4
LN308 transfected with empty pSF


title: LN428_hSPI1+hIKZF1_CD45+_bulk

description:
Dan_3
LN428 transfected with  pSF-hSPI1,  pSF_hIKZF1, CD45 positive sorted by FACS


title: PH1-HLC,Normoxia,T21,1


title: PH1-HLC,Normoxia,T14,2


title: Liver, HCC, H3K27Ac, 2882

value: male


title: LN428_hSPI1_CD45+_bulk

description:
Dan_2
LN428 transfected with  pSF-hSPI1, CD45 positive sorted by FACS


title: Liver, HCC, H3K27me3, 2882


title: H3K27ac_EPSC_Input

value: EPSC


title: LN308_hSPI1_CD45+_bulk

description:
Dan_5
LN308 transfected with  pSF-hSPI1, CD45 positive sorted by FACS

value: GBM


title: Liver, FL, H3K27Ac, 2896


title: H3K27ac_EPSC_Sample


title: PH1-HLC,Normoxia,T0,2


title: Liver, FL, H3K27me3, 2896


title: LN428_pSF_bulk

description:
Dan_1
LN428 transfected with empty pSF


title: K521R_ATF4kd_Rep2

city: New Delhi

first: Sanjeev

last: Das

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Oncology Laboratory

country: India

institute: National Institute of Immunology

data_processing:
Quality assessment of the raw fastq reads of the sample was performed using FastQC v.0.11.9 (default parameters). The raw fastq reads were preprocessed using Fastp v.0.20.1 (parameters: --trim_poly_g --cut_front --cut_tail --average_qual 30), followed by quality re-assessment using FastQC and summarization using MultiQC.
Assembly: The rRNA filtered reads were aligned to the STAR indexed Homo sapiens (hg38) genome using STAR aligner v 2.7.9a [4] (parameters: --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM --outFilterScoreMinOverLread 0.5 --outFilterMatchNminOverLread 0.5 --outSAMattributes Standard --outSAMattributes NH HI AS NM MD).
Supplementary files format and content: Tab-delimited text file inclues FPKM value for each sample.

growth_protocol: All HT29 cells were cultured in DMEM supplemented with 10% FBS (Invitrogen), 100 U/mL penicillin and 100μg/mL streptomycin at 37°C.

extract_protocol:
Extraction was carried out by Trizol method. Extracted RNA quantity is checked on Qubit flurometer (Thermofisher #Q33238) using RNA HS assay kit (Thermofisher #Q32851) following manufacturer’s protocol. To measure the purity of the extraction we also measured the concentration of the samples on Nanodrop 1000.
The library preparation was carried out using NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760S/L). Final libraries were quantified using Qubit 4.0 fluorometer (Thermofisher #Q33238) using DNA HS assay kit (Thermofisher #Q32851) following manufacturer’s protocol. Obtained results are presented below in the table. To identify the insert size of the library, we queried it on Tapestation 4150 (Agilent) utilizing high sensitive D1000 screentapes (Agilent # 5067- 5582) following manufacturers’ protocol.
All libraries pass QC parameters and will be further taken for RNA-sequencing. Libraries that display adapters will be cleaned on the day of sequencing to protect the library stability.

treatment_protocol: The cell lines were treated with genotoxic stress 5FU

value: Colon adenocarcenoma cells

value: PARP1/ATF4 knockdown


title: PH1-HLC,Normoxia,T0,1


title: PH1-HLC,Normoxia,T14,1


title: H3K27ac_2iES_Input


title: H3K27ac_NrEPSC_Input


title: PH1-HLC,Hypoxia,T4,2


title: H3K27ac_NrEPSC_Sample


title: K521R_ATF4kd_Rep1


title: E14_EP_blastoid_GOOD

data_processing:
Alignment and UMI counting were performed by using Cellranger program with default parameters and mouse mm10 reference genome.
Feature-barcode count matrix obtained from Cellranger were used for the downstream analyses using Seurat
Assembly: mm10

source_name: Blastoid

growth_protocol: E14 mouse expanded potential stem cells (ESC) were cultured on gelatin-coated plates in EPSC medium with DMEM/F-12 basal media (Thermo Fisher Scientific) supplemented with 20% knockout serum replacement (Thermo Fisher Scientific), 1X NEAA (Thermo Fisher Scientific), 1X L-glutamine (Thermo Fisher Scientific), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific), 10^3 units/ mL recombinant mouse LIF (Sigma-Aldrich), 3 µM CHIR99021(Tocris) and 1 µM PD0325901 (Tocris), 4 µM JNK Inhibitor VIII (Tocris), 10 µM SB203580 (Tocris), 0.3 µM A-419259 (Santa Cruz) and 5 µM XAV939 (Tocris).. The cells were incubated at 37oC with 5% CO2 and replaced with fresh media every 24 hours. Cells were routinely passaged every two to three days.

extract_protocol:
Blastoids were washed three times in PBS containing 0.04% BSA before incubation in digestion mix of 0.5X versene (Lonza) 0.5X Acumax (Innovative Cell Tech), and 0.05X Dnase (STEMCELL Technologies) at 37 oC for 30min with agitation. Single cell suspensions were centrifuged, and the resultant cell pellets were washed three times and resuspended in PBS + 0.04% BSA.
The single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121) as per manufacturer's instructions.

treatment_protocol: Blastoid formation was performed on 6-well AggreWell 400 plates (STEMCELL Technologies). Following the manufacturer’s procedures, AggreWells were prepared using Anti-Adherence Rinsing Solution (STEMCELL Technologies). EPSC colonies were dissociated into single cells by incubation with Accutase. Approximate 35,000 cells (5 cells per microwell) were seeded. Blastoid seeding medium was used to culture the cells for the first 24 hours (Day 0 to Day 1). Blastoid seeding medium is composed of 25% TSC basal medium, 25% N2B27 basal medium (Takara Bio), 50% KSOM (Millipore), 12.5 ng/mL rhFGF4 (R&D Systems), 0.5 ug/mL heparin, 3 µM CHIR99021 AND 2 µM Y-27632 (Reagents Direct). The cells were then incubated at 37oC with 5% CO2. Blastoid seeding medium was replaced with complete blastoid medium 24 hours after cell seeding. Complete blastoid medium is composed of 25% TSC basal medium, 25% N2B27 basal medium, 50% KSOM, 12.5 ng/mL rhFGF4, 0.5 ug/mL heparin, 3 µM CHIR9902, 5 ng/mL BMP4 (Proteintech) and 0.5 µM A83-01 (Axon Medchem). On Day 5, blastoids were manually picked for further analysis. Blastoids were harvested on Day 5 of differentiation and separated into type I to III according to their morphological features.

tag: developmental stage

value: Blastoid


title: Liver, FL, H3K27me3, 2882


title: PH1-HLC,Hypoxia,T4,1


title: K521R_Rep3

value: PARP1 knockdown


title: E14_EP_blastoid_BAD


title: K521R_Rep2


title: Liver, FL, H3K27Ac, 2882


title: E14_EP_blastoid_AVG


title: Liver, HCC, input, 2889

value: Input


title: K521R_Rep1


title: H3K27ac_2iES_Sample


title: PH1-HLC,Hypoxia,T21,2

value: Blood

value: peripheral blood lymphocytes (PBL)


title: PH1-HLC,Hypoxia,T21,1


title: Liver, HCC, H3K27me3, 2889


title: Liver, HCC, H3K27Ac, 2889


title: Control_Rep3

value: WT


title: PH1-HLC,Hypoxia,T14,2


title: Control_Rep2


title: CellTag_Day5_Bad_Blastoid__undiluted


title: CellTag_Day5_Average_Blastoid__undiluted


title: Liver, FL, input, 2889


title: Liver, FL, H3K27Ac, 2889


title: siNT_D2

data_processing:
Libraries were mapped to mm9 genome using STAR.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Counts table were obtained using HTSeq
Assembly: mm9
Supplementary files format and content: Tab delimieted text table containing the read counts for each gene in each sample

source_name: siNT derived D2-blastoid

growth_protocol: E14 mouse embryonic stem cells (ESC) were cultured on gelatin-coated plates in ESC medium with DMEM basal medium (Thermo Fisher Scientific) supplemented with 15% ESC-screened FBS (Thermo Fisher Scientific), 1X NEAA (Thermo Fisher Scientific), 1X L-glutamine (Thermo Fisher Scientific), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific), 10^3 units/ mL recombinant mouse LIF (Sigma-Aldrich), 3 µM CHIR99021(Tocris) and 1 µM PD0325901 (Tocris). The cells were incubated at 37oC with 5% CO2 and replaced with fresh media every 24 hours. Mouse ESC were converted to expanded potential stem cells (EPSC) through culturing in EPSC medium for 5 passages in gelatin-coated 6-well plates as previously reported. EPSC medium is made up of DMEM/F-12 basal media supplemented with 20% knockout serum replacement (Thermo Fisher Scientific), 1X L-glutamine, 1X NEAA, 0.1 mM 2-mercaptoethanol, 10^3 units/ mL recombinant mouse LIF, 3 µM CHIR99021, 1 µM PD0325901, 4 µM JNK Inhibitor VIII (Tocris), 10 µM SB203580 (Tocris), 0.3 µM A-419259 (Santa Cruz) and 5 µM XAV939 (Tocris). Cells were routinely passaged every two to three days.

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen). Contaminating DNA was removed by DNaseI (Ambion) treatment, and the RNA was further purified using the QIAGEN RNeasy Kit.
The RNA-Seq libraries were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Cat No. 7420) as per manufacturer's instructions.

treatment_protocol: Blastoid formation was performed on 6-well AggreWell 400 plates (STEMCELL Technologies). Following the manufacturer’s procedures, AggreWells were prepared using Anti-Adherence Rinsing Solution (STEMCELL Technologies). EPSC colonies were dissociated into single cells by incubation with Accutase. Approximate 35,000 cells (5 cells per microwell) were seeded. Blastoid seeding medium was used to culture the cells for the first 24 hours (Day 0 to Day 1). Blastoid seeding medium is composed of 25% TSC basal medium, 25% N2B27 basal medium (Takara Bio), 50% KSOM (Millipore), 12.5 ng/mL rhFGF4 (R&D Systems), 0.5 ug/mL heparin, 3 µM CHIR99021 AND 2 µM Y-27632 (Reagents Direct). The cells were then incubated at 37oC with 5% CO2. Blastoid seeding medium was replaced with complete blastoid medium 24 hours after cell seeding. Complete blastoid medium is composed of 25% TSC basal medium, 25% N2B27 basal medium, 50% KSOM, 12.5 ng/mL rhFGF4, 0.5 ug/mL heparin, 3 µM CHIR9902, 5 ng/mL BMP4 (Proteintech) and 0.5 µM A83-01 (Axon Medchem). On Day 5, blastoids were manually picked for further analysis. For knockdown experiments in blastoid, EPSC were transfected with DharmaFECT1 (Horizon) following manufacturer’s instructions, and seeded into Aggrewell-400. Blastoid aggregates were harvested 48-hour post-transfection. For Nr1h2 activation experiments in ESC or EPSC, 1uM/mL T0901317 was added into culture media. Cells were harvested 3 days after treatment.

value: siNT derived D2-blastoid


title: Sample 109

city: Santander

first: Enrique

last: García Nieto

state: Cantabria

address: C. Cardenal Herrera Oria, s/n

institute: Instituto de Investigación Marqués de Valdecilla

data_processing:
Genes were quantified using RSEM (version 1.3.0) with default parameters.
The human gene annotation file was downloaded from gencode release 36 (https://www.gencodegenes.org/).
Mapping and quantification quality checking were performed with GEMTools (https://gemtools.github.io/) and custom python scripts.
A multidimensional scaling plot was performed to inspect sample similarities using the ‘voom’ transformed counts and the top 500 most variable genes.
Assembly: Human reference genome (GRCh38)
Supplementary files format and content: EGN_RNAseq_Normalized_data: Excel file incuding gene normalized expression for each sample.
Supplementary files format and content: EGN_RNAseq_Processed_data: Differential gene expression (IMID-NAFLD vs. Classic-NAFLD) adjusted for BMI, sex, and fibrosis severity.

growth_protocol: Liver biopsies were obtained percutaneously with a Tru-Cut biopsy needle following a standard procedure in patients with suspected significant liver fibrosis according to liver stiffness measurement (LSM).

extract_protocol:
Freshly frozen biopsies were disrupted using Kimble® Pellet Pestle® Cordless Motor (DWK Life Sciences, Cat. No.: 749540-0000). RNA extraction was performed using the PureLink™ RNA Mini Kit (Invitrogen, Cat. No.: 12183018A) adding an extrapurification process with the PureLink™ DNase Set (Invitrogen, Cat. No.: 12185010).
RNA-seq reads were mapped against the human reference genome (GRCh38) using STAR (version 2.5.3a) with ENCODE parameters.

treatment_protocol: Total RNA was obtained from freshly frozen biopsies

value: Female

tag: case/control

value: classic-NAFLD

tag: disease

value: NAFLD/NASH

tag: fibrosis degree

tag: obesity

value: yes

value: No

tag: hypertension

tag: fasting glycemia

tag: total cholesterol

tag: hdl-cholesterol

tag: ldl-cholesterol

tag: tryglicerides


title: PH1-HLC,Hypoxia,T0,1

tag: tissue

tag: cell line


title: siNr1_D2

source_name: siNr1h2 derived D2-blastoid

tag: cell type

value: siNr1h2 derived D2-blastoid


title: PH1-HLC,Hypoxia,T0,2


title: Sample 108

value: Liver

tag: Sex

value: no


title: ESCT09

source_name: ESC treated with T09

value: ESC

tag: treatment

value: treated with T09


title: HLCs,WT,T28,1


title: Liver, RD, input, 2845

tag: strain

value: DIAMOND

value: male

tag: diet

value: RD

tag: chip antibody


title: CHiPSC,Normoxia,T4

value: Blood


title: Sample 107

tag: case/control

value: IMID-NAFLD

tag: disease

value: NAFLD & Spondylitis


title: CHiPSC,Normoxia,T21

value: peripheral blood lymphocytes (PBL)


title: Liver, RD, H3K27me3, 2845


title: ESC

source_name: ESC

tag: developmental stage


title: Liver, RD, H3K27Ac, 2845


title: EPT09_Gd

source_name: EPSC treated with T09 derived Type I blastoid

value: EPSC


title: Liver, FL, H3K27me3, 2889

value: WD


title: Liver, FL, 2991

data_processing:
FastQC for quality control of Fastq files
Mapping of reads with STAR (options: --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 --outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantMode GeneCounts)
Assembly: mm10
Supplementary files format and content: Read counts per gene obtained by STAR in txt format

extract_protocol:
total RNA extacted using RNeasy Plus Universal minikit
RNA was enriched for mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) followed by the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770)


title: PH1-HLC,Hypoxia,T14,1


title: CHiPSC,Normoxia,T14


title: Control_Rep1

value: Colon adenocarcenoma cells

tag: genotype

value: WT


title: Sample 105

value: Female

value: NAFLD & IBD

tag: fibrosis degree

tag: obesity

value: No

tag: hypertension

tag: fasting glycemia


title: CellTag_Day5_Good_Blastoid__undiluted

value: Blastoid


title: EPT09Bad

source_name: EPSC treated with T09 derived Type III blastoid


title: CHiPSC,Normoxia,T0


title: EPSCT09

source_name: EPSC treated with T09


title: Sample 103

value: Liver

value: Male

value: no

value: yes

tag: total cholesterol

tag: hdl-cholesterol

tag: ldl-cholesterol

tag: tryglicerides


title: CHiPSC,Hypoxia,T4

tag: tissue

tag: cell line


title: EPSC

source_name: ESC-derived EPSC

tag: cell type

value: ESC-derived EPSC


title: Liver, RD 2845

tag: strain

value: DIAMOND

tag: Sex

value: male

tag: diet

value: RD


title: Liver, FL, 2894


title: Liver, FL, 2896


title: CHiPSC,Hypoxia,T21

value: Blood

value: peripheral blood lymphocytes (PBL)


title: Sample 106

tag: case/control

value: IMID-NAFLD

tag: disease

value: NAFLD & Psoriasis


title: Sample 101


title: Potato stolon, AN2-3

city: qiqihar city

first: Kaixin

last: Ding

state: heilongjiang province

address: Longsha District

institute: Keshan Branch of Heilongjiang Academy of Agricultural Sciences

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2 2 . FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 . PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 5 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO 6 , KEGG 7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software 8-9 . The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: SolTub_3.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Solanum tuberosum

source_name: Potato stolon

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

value: Potato stolon

tag: treatment


title: CHiPSC,Hypoxia,T14


title: Liver, HCC, 2896

value: WD


title: CHiPSC,Hypoxia,T0


title: Sample 100

value: Female

value: NAFLD & IBD

tag: fibrosis degree


title: Sample 104

tag: obesity


title: Potato stolon, AN1-3


title: Liver, FL, 2889


title: Sample 98

value: No

tag: hypertension


title: Potato stolon, AN1-2


title: Potato stolon, AN2-1


title: Liver, HCC, 2889

value: Liver


title: Sample 97

value: Male

tag: fasting glycemia


title: Sample 102

value: NAFLD & Hidradenitis

tag: total cholesterol


title: Potato stolon, AN1-1


title: Sample 95

value: classic-NAFLD

value: NAFLD/NASH

value: yes

value: no

tag: hdl-cholesterol


title: Liver, FL, 2882

value: DIAMOND

value: male


title: Potato stolon, AN2-2


title: Liver, HCC, 2882


title: Liver, RD, 2879

value: RD


title: Potato stolon, AN0-2


title: Liver, RD, 2892


title: Sample 94

value: IMID-NAFLD

value: NAFLD & Spondylitis

tag: ldl-cholesterol


title: Liver, HCC, 2893


title: Sample 93

value: NAFLD & Psoriasis

tag: tryglicerides


title: Liver, FL, 2893

tag: tissue

value: WD


title: Potato stolon, AN0-1

value: Potato stolon


title: Sample 92

value: Female

value: NAFLD & IBD


title: Liver, RD, 2819

value: Liver


title: SUM_4

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Equus caballus reference genome (EquCab3.0) Bowtie2 (2.2.2)
Mapped reads were used for annotation against equine mature and precursor miRNAs listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as TMM-adjusted Counts Per Million (CPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: EquCab3.0
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Equus caballus

source_name: Follicular fluid

extract_protocol:
For EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 OC using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 ×g for 70 min. Finally, EVs were resuspended in 500 µL of PBS and stored in −80 °C until further characterization and analysis.
Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Follicular fluid

value: Extracellular Vesicles

tag: breeding season

value: Summer


title: SUM_3

tag: cell type


title: Sample 96

value: NAFLD & Hidradenitis


title: SUM_1


title: SUM_2


title: Potato stolon, AN0-3


title: Liver, RD, 2812

tag: strain


title: Sample 90

tag: Sex

value: Male

value: yes

value: No


title: SOV_4

value: Spring ovulatory


title: Liver, HCC, 2841

value: DIAMOND

value: male

tag: diet


title: Sample 91

tag: case/control

value: IMID-NAFLD


title: Sample 99

tag: disease


title: NrESC_Type_I

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: NrESC derived blastoids

growth_protocol: E14 mouse Nr1h2-activated embryonic stem cells (mNrESCs) 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), 10µM T0901317 (MedChemExpress, HY-10626). and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the ESC cell 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 .

extract_protocol:
Blastoids were washed three times in PBS containing 0.04% BSA before incubation in digestion mix of 0.5X versene (Lonza) 0.5X Accumax (Innovative Cell Tech), and 0.05X Dnase (STEMCELL Technologies) at 37 oC for 30min with agitation. Single cell suspensions were centrifuged, and the resultant cell pellets were washed three times and resuspended in PBS + 0.04% BSA.
The single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121) as per manufacturer's instructions.

treatment_protocol: NrESCs (ESC+T09). Blastoid formation was performed on 6-well AggreWell 400 plates (STEMCELL Technologies). Following the manufacturer’s procedures, AggreWells were prepared using Anti-Adherence Rinsing Solution (STEMCELL Technologies). ESC colonies were dissociated into single cells by incubation with Accutase. Approximate 35,000 cells (5 cells per microwell) were seeded. Blastoid seeding medium was used to culture the cells for the first 24 hours (Day 0 to Day 1). Blastoid seeding medium is composed of 25% TSC basal medium, 25% N2B27 basal medium (Takara Bio), 50% KSOM (Millipore), 12.5 ng/mL rhFGF4 (R&D Systems), 0.5 ug/mL heparin, 3 µM CHIR99021 AND 2 µM Y-27632 (Reagents Direct). The cells were then incubated at 37oC with 5% CO2. Blastoid seeding medium was replaced with complete blastoid medium 24 hours after cell seeding. Complete blastoid medium is composed of 25% TSC basal medium, 25% N2B27 basal medium, 50% KSOM, 12.5 ng/mL rhFGF4, 0.5 ug/mL heparin, 3 µM CHIR9902, 5 ng/mL BMP4 (Proteintech) and 0.5 µM A83-01 (Axon Medchem). On Day 5, blastoids were manually picked for further analysis. Blastoids were harvested on Day 5 of differentiation.

value: NrESC derived blastoids


title: Sample 89

value: NAFLD & Psoriasis


title: Sample 87

value: no


title: SOV_3


title: Sample 86

value: Female


title: SOV_2


title: NrESC_Type_III

description: 10x Genomics


title: SOV_1


title: Sample 85

value: classic-NAFLD

value: NAFLD/NASH


title: SAN_4

value: Follicular fluid

value: Spring anovulatory


title: Sample 84

value: Liver


title: Tobacco leaf tissue - KY_rep2

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM （http://deweylab.github.io/RSEM/）establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Tobacco K326 Reference Genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome）
Supplementary files format and content: all_ express.txt includes 9 transcriptome sequencing materials and 69500 gene expressions. The file can be opened in Excel for viewing.

organism: Nicotiana tabacum

source_name: Tobacco leaf tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq  sequencing library was sequenced with the Illumina NovaSeq Xquencer (2 × 150bp read length)

value: Tobacco leaf tissue

tag: cell line

value: genotype

tag: genotype

value: KY


title: Tobacco leaf tissue - KY_rep3


title: Liver, FL, 2841

value: WD


title: SAN_3

value: Extracellular Vesicles


title: Sample 88

value: Male

tag: fibrosis degree

tag: obesity

value: yes

value: No


title: Tobacco leaf tissue - KY_rep1


title: SAN_2


title: NrESC_Type_II

description: 10x Genomics

value: NrESC derived blastoids


title: Sample 83

value: IMID-NAFLD

value: NAFLD & Psoriasis

tag: hypertension

tag: fasting glycemia


title: SAN_1


title: FOV_4

value: Fall ovulatory


title: Tobacco leaf tissue - Y_rep1

value: Y


title: Sample 82

value: Female

value: NAFLD & IBD

value: no

tag: total cholesterol

tag: hdl-cholesterol


title: FOV_3

value: Follicular fluid


title: Tobacco leaf tissue - Y_rep3

value: Tobacco leaf tissue


title: Sample 79

value: Liver

tag: ldl-cholesterol

tag: tryglicerides


title: HUVEC, FGF2, 3

city: Chiba-shi

first: Kentaro

last: Kosaka

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba University Graduate School of Medicine

data_processing:
TopHat (version 2.1.1; with default parameters) was used to map to the reference genome (UCSC/hg19) with annotation data from iGenomes (Illumina).
Levels of gene expression were quantified using Cuffdiff (Cufflinks version 2.2.1; with default parameters).
Assembly: hg19
Supplementary files format and content: .xlsx and FPKM

source_name: HUVECs

extract_protocol:
Total RNA from HUVEC treated with PBS, iMPs, PRP or FGF2 was isolated using an RNeasy Micro Kit (QIAGEN)
~10 ng total RNA was used as input for cDNA conversion using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (cat. #634890, Takara Bio). cDNA was fragmented using an S220 Focused-ultrasonicator (Covaris). The cDNA library was then amplified using a NEBNext® Ultra™ DNA Library Prep Kit for Illumina (cat. #E7370L, New England Biolabs).

value: HUVECs

tag: treatment


title: Tobacco leaf tissue - Y_rep2

tag: tissue

value: genotype


title: Sample 81

source_name: Liver

value: classic-NAFLD

value: NAFLD/NASH


title: Tobacco leaf tissue - K326_rep3


title: FOV_1

tag: cell type

value: Extracellular Vesicles

tag: breeding season


title: Sample 78

tag: Sex

value: yes

value: No


title: Sample 77

tag: case/control


title: HUVEC, FGF2, 2


title: FOV_2


title: HUVEC, PRP, 3

value: PRP


title: Sample 80

value: IMID-NAFLD

tag: disease


title: HUVEC, FGF2, 1


title: Tobacco leaf tissue - K326_rep1

tag: cell line


title: Nanopore whole genome cytosine modifications (CBM3_2)

city: Bath

first: Adele

last: Murrell

address: Claverton Down

department: Life Sciences Department

country: United Kingdom

institute: University of Bath

description: BedMethyl format file of cytosine modifications in a whole mouse genome dataset. Produced using modkit pileup (0.2.4) with soft masking.

data_processing:
Base-calling and aligment was performed using dorado basecaller
Sorting and indexing of alignment files using samtools
Extraction of modified bases using modkit pileup
Assembly: mm39
Supplementary files format and content: BedMethyl format. See: https://nanoporetech.github.io/modkit/quick_start.html

source_name: Cerebellum

extract_protocol:
Cerebellum tissues were obtained from two 8-week-old female C57BL/6J mice, from which high molecular weight genomic DNA was extracted using the QIAGEN MagAttract HMW DNA Kit (QIAGEN, 67563).
Cerebellar gDNA was sheared using a Covaris g-TUBE (Covaris, 520079) to a target length of 8 kb. Whole genome sequencing (WGS) libraries were prepared in duplicate for each biological replicate, using the Ligation Sequencing Kit V14 standard protocol (Oxford Nanopore Technologies, SQK-LSK114) with reagents from the NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing (New England Biolabs, E7180S). 150 ng of each sample was loaded onto PromethION (Oxford Nanopore Technologies, PRO-SEQ048) flow cells (Oxford Nanopore Technologies, FLO-PRO114HD). All sequencing runs were manually stopped after 72 hours.

value: Cerebellum

tag: strain

tag: age

value: 8 weeks


title: HUVEC, PRP, 2


title: Sample 76

value: Male

value: NAFLD & Psoriasis

tag: fibrosis degree

tag: obesity


title: Nanopore whole genome cytosine modifications (CBM3_1)

value: Female


title: Sample 75

value: no

tag: hypertension

tag: fasting glycemia


title: HUVEC, PRP, 1


title: HUVEC, iMPs, 3

value: iMPs


title: Nanopore whole genome cytosine modifications (CBM2_1)


title: Sample 73

value: Liver

value: NAFLD & IBD

tag: total cholesterol

tag: hdl-cholesterol


title: Nanopore whole genome cytosine modifications (CBM2_2)


title: Tobacco leaf tissue - K326_rep2

value: Tobacco leaf tissue

value: genotype

tag: genotype


title: SalhelPOU_cycle4

city: Hong Kong

first: Daisylyn Senna

middle: Young

last: Tan

state: HONG KONG

address: B1202, 9 Lung Wah Strert, Kennedy Town

country: Hong Kong

institute: The University of Hong Kong

description: Enriched sequences bound by 6xHis-Salhel POU protein in the 4th cycle of a high throughput SELEX experiment

data_processing:
Data obtained were sorted based on barcodes for each sample. After discarding low-quality reads, the remaining sequences underwent trimming to eliminate adaptor sequences. The resultant 40-nt region was subjected to further analysis. PWM models were generated using initial seeds identified through Autoseed, which were subsequently refined through expert analysis, in accordance with the approach outlined in (Jolma et al., 2013). Data was visualized as seqlogos generated using the R package ggseqlogo in the manuscript
Assembly: na
Supplementary files format and content: SVG vector file of sequence logos of enriched motifs in 3rd and 4th cycle of SELEX

organism: synthetic construct

source_name: not a cell (synthetic construct)

extract_protocol:
Selection ligands were designed with an 8-bp barcode flanking a 40 bp randomized region. In summary, 50-100 ng of barcoded DNA fragments were introduced into wells containing the target proteins along with 25 μl of binding buffer supplemented with 5 μg/ml poly-dIdC-oligonucleotide (Sigma P4929-25UN) as a competitor. The plate was gently rotated at room temperature for 30 minutes. Following incubation, 150 μl of binding buffer, along with 10 μl of Ni Sepharose® beads previously equilibrated with poly-dIdC, were introduced into the reaction mixture. This mixture was then incubated on a rotor at room temperature for 60 minutes. Unbound oligomers were subsequently removed from the bound beads using a Biotek 405TS washer. Post washing, the bound DNA was eluted in 50 μl of ddH2O. For PCR amplification, 10 μl of bead suspension was utilized. The resulting PCR products served as input oligomers for the subsequent cycle or were purified for sequencing with the NovaSeq 6000 S4 PE150. This experiment involved a total of four cycles.
DNA libraries used already contained illumina adapters and an 8bp barcode

value: not a cell (synthetic construct)

tag: treatment

value: Salhel POU


title: HUVEC, iMPs, 1

value: HUVECs


title: HUVEC, iMPs, 2


title: mOct4POU_cycle4

description: Enriched sequences bound by 6xHis-mOct4 POU protein in the 4th cycle of a high throughput SELEX experiment

value: mOct4 POU


title: Sample 72

tag: tissue

value: classic-NAFLD

value: NAFLD/NASH

value: yes

tag: ldl-cholesterol

tag: tryglicerides


title: Sample 71

tag: Sex

value: No


title: TAU_ANTI_AGG_UNG-1_20C_D1

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
RNA-seq reads were mapped to the C. elegans genome (WBcel235, Ensembl annotation) using HISAT2 (Default: 2.0.5).
Raw read counts were normalized, and subjected to differential expression analysis using the EdgeR  (3.22.5) library by Novogene, USA. In EdgeR, selection criteria were = |log2(FoldChange)| >= 1 & padj <= 0.05.
Differentially expressed genes were determined by comparison to each cohort’s, UNG-1 or NTH-1’s respective, N2 control worms.
The set of significantly differentially expressed genes were those which had counts ≥100, an absolute value log2 fold-change ≥1 and adj-p-value ≤ 0.05.
The collected genes were subjected to overrepresentation analysis using Wormbase enrichment tool, https://wormbase.org/tools/enrichment/tea/tea.cgi
Assembly: WBcel235, Ensembl annotation
Supplementary files format and content: tab-delimited count text files

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Each synchronized strains of C. elegans was grown on three 35mm NGM plates and harvested for RNA isolation at day one stage of the life cycle.

extract_protocol:
Total RNA was extracted by using RNeasy RNA extraction kits (Qiagen).
cDNA library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA) and quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.

treatment_protocol: Worms were collected from plates and washed with M9 buffer 5 times through gravity. Approximately, 5000 worms per genotype were collected.

value: Whole worm

value: Nth-1 X Anti-Tau aggregate

value: Day 1 synchronized worm

tag: treatment (culture_temperature)


title: K521R_ATF4kd_Rep3

tag: cell type

value: Colon adenocarcenoma cells

value: PARP1/ATF4 knockdown


title: Liver, FL, input, 2882-2896

value: Liver

value: DIAMOND

value: male

tag: diet

value: WD

tag: chip antibody

value: Input


title: mOct4POU_cycle3

description: Enriched sequences bound by 6xHis-mOct4 POU protein in the 3rd cycle of a high throughput SELEX experiment

value: not a cell (synthetic construct)


title: HUVEC, PBS, 2

value: HUVECs

value: PBS


title: SBC5 cells, SCLC negative control rep2

type: RNA

city: Kawagoe-shi

first: Nobuyuki

last: Koyama

state: Saitama

address: 1981 Kamoda

institute: Saitama Medical Center, Saitama Medical University

description: miRNA expression data from SBC5 cells transfected with negative control siRNA

hyb_protocol: Using GeneChip Hybridization Oven 645 (Affymetrix), biotin-labeled samples were hybridized for 18h at 48 ℃ according to the manufacturer's instructions. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix) according to the Affymetrix GeneChip Command Console AGCC 4.0 User Manual.

data_processing:
The data were analyzed with Microarray Data Analysis Tool Ver3.2 (Filgen) using Per Array Normalization and Per Gene Normalization methods.
Affymetrix Expression Console Software (Affymetrix)

label: biotin

source_name: Homo sapiens small cell lung cancer negative control siRNA transfection

label_protocol: Using FlashTag TM Biotin HSR RNA Labeling Kit (Affymetrix), biotin-labeled RNAs were prepared according to FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA Arrays User Manual (Affymetrix).

growth_protocol: Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (GE) in a humidified chamber at 37 ℃ under 5% CO2.

extract_protocol: Total RNA was extracted using the illustra RNAspin Mini Isolation Kit (GE).

treatment_protocol: siRNA against the EZH2 gene (Thermo Fisher) and negative control siRNA (Thermo Fisher) were transfected into SBC3 with moderately high EZH2 expression and SBC5 cells with highest EZH2 expression, using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher) according to the manufacturer's protocol.

value: lung tumor

tag: cell line

value: transfected with negative control siRNA

value: control


title: HUVEC, PBS, 3


title: TAU_AGG_UNG-1_20C_D1

value: Nth-1 X Tau aggregate


title: SBC5 cells, SCLC EZH2 knockdown rep1

description: miRNA expression data from SBC5 cells transfected with EZH2 siRNA

source_name: Homo sapiens small cell lung cancer EZH2 siRNA transfection

value: transfected with EZH2 siRNA


title: TAU_ANTIAGG_BR5271_20C_D1

value: Whole worm

value: Anti-Tau aggregate


title: SalhelPOU_cycle3

description: Enriched sequences bound by 6xHis-Salhel POU protein in the 3rd cycle of a high throughput SELEX experiment

value: Salhel POU


title: HUVEC, PBS, 1


title: Sample 69

value: Female

tag: case/control

value: classic-NAFLD

tag: disease

value: NAFLD/NASH

tag: fibrosis degree

value: yes

value: No


title: SBC3 cells, SCLC EZH2 knockdown rep1

description: miRNA expression data from SBC3 cells transfected with EZH2 siRNA


title: Sample 70

value: Liver

value: IMID-NAFLD

value: NAFLD & IBD

tag: obesity

tag: hypertension

tag: fasting glycemia


title: TAU_AGG_BR5270_20C_D1

tag: genotype

value: Tau aggregate

value: Day 1 synchronized worm


title: Sample 74

value: Male

tag: total cholesterol

tag: hdl-cholesterol


title: Octamer_lib_input_rep2

description: The degenererat Octamer library used (replicate 2)

data_processing:
R packages (QuasR, Biostrings, tidyr, data.table, stringi) were used to process the paired-end sequencing data. The reads were trimmed for adapter sequences using the preprocessReads function. A library file (pseudogenome) with all the theoretically possible sequences in each experiment was created. This file was used as an alignment template for the sequences from the Spec-seq libraries with the qAlign function (Rhisat2 as aligner) resulting in a count matrix where rows are the sequence elements and columns are samples. The relative binding energy of each sequence was calculated using the ln(#Si_unbound)/(#Si_bound)) where #S is the number of read for each sequence.
Assembly: NA
Supplementary files format and content: Read count for each tested sequence and the calculated binding energy

extract_protocol:
Each band was excised and the DNA in the gel was extracted in 150 uL PAGE diffusion buffer [500 mM Ammonium acetate; 10 mM magnesium acetate; 1 mM EDTA; 0.1 % sodium dodecyl sulfate (SDS), pH 8.0]. The samples were then purified using homemade Qiagen PNI binding buffer, PCR purification columns (Tiangen), and eluted in ultrapure water.
6 cycles of PCR were performed using primers containing a unique molecular identifier (UMI) to account for PCR bias. A second round of PCR (28 cycles) was performed using primers compatible with Illumina adapter and containing different indexing barcodes (Primers are in Table S1). The resulting PCR products were combined and gel purified twice and then sent to sequencing
Spec-seq

treatment_protocol: Binding reactions were prepared using different concentrations of protein and 250 nM dsDNA library, in 1x NEB Cutsmart buffer supplemented with 10% glycerol. The reactions were incubated for 1h at 4°C, and then EMSA was performed. After the EMSA, the gels were stained with 3x GelRed®stain (Biotium: 41003) for 15 min and visualized.

value: not a cell (synthetic construct)

tag: treatment


title: Sample 68

tag: tissue

tag: ldl-cholesterol

tag: tryglicerides


title: T3-3

city: Baicheng City

first: Yong

last: Zhao

address: No. 57, Zhongxingxi Road, Baicheng City, Jilin Province, China

institute: Baicheng Normal University

data_processing:
FDR<0.05 and |log2FC|>1
Assembly: Ricinus communis (assembly ASM1957865v1)
Supplementary files format and content: all genes txt  file includes FPKM values and counts for each sample

organism: Ricinus communis

source_name: Root system

extract_protocol:
Total RNA was extracted using a Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit

value: Root system

tag: group

value: Treatment group

value: Removal of 15% PEG-6000 4 days


title: UNG-1_20C_D1

value: Whole worm

value: Nth-1 mutant

tag: treatment (culture_temperature)


title: Octamer_lib_input_rep1

description: The degenererat Octamer library used (replicate 1)

tag: cell type


title: Sample 67

tag: Sex

value: no


title: T3-2


title: T3-1


title: Sample 66

tag: case/control

value: classic-NAFLD


title: SBC3 cells, SCLC negative control rep2

description: miRNA expression data from SBC3 cells transfected with negative control siRNA

value: lung tumor

tag: cell line

value: transfected with negative control siRNA

value: control


title: WT_20C_D1

value: WT


title: TAU_ANTIAGG_UNG-1_22C_D1

value: Ung-1 X Anti-Tau aggregate


title: T2-3

value: 15% PEG-6000 stress for 7days


title: Sox_lib_input_rep1

description: The degenererat Sox library used (replicate 1)


title: Sample 63

value: Liver

value: IMID-NAFLD

tag: disease

value: NAFLD & IBD

tag: fibrosis degree

value: yes

value: No


title: mSox2_Unbound_rep3

description: Unbound sequences from degenerate Sox libraries in binding experiements with  mSox2 (replicate 3)

value: not a cell (synthetic construct)


title: Sample 64

value: Male

tag: obesity

tag: hypertension


title: TAU_ANTIAGG_BR5271_22C_D1

value: Whole worm

tag: genotype

value: Anti-Tau aggregate

value: Day 1 synchronized worm


title: Sample 65

value: Female

value: classic-NAFLD

value: NAFLD/NASH

tag: fasting glycemia

tag: total cholesterol


title: mSox2_Unbound_rep2

description: Unbound sequences from degenerate Sox libraries in binding experiements with  mSox2 (replicate 2)

tag: treatment


title: T2-1

tag: tissue

value: Root system

value: Treatment group

value: 15% PEG-6000 stress for 7 days


title: Sample 62

tag: hdl-cholesterol

tag: ldl-cholesterol


title: mSox2_Bound_rep3

description: Bound sequences from degenerate Sox libraries in binding experiements with  mSox2 (replicate 3)


title: TAU_AGG_BR5270_22C_D1

value: Tau aggregate


title: Sample 61

value: Liver

tag: tryglicerides


title: UNG-1_22C_D1

value: Ung-1 mutant

tag: treatment (culture_temperature)


title: Sox_lib_input_rep2

description: The degenererat Sox library used (replicate 2)

tag: cell type


title: T1-2

tag: group

value: 15% PEG-6000 stress for 3 days


title: WT_22C_D1

value: WT


title: T1-1


title: mSox2_Bound_rep2

description: Bound sequences from degenerate Sox libraries in binding experiements with mSox2 (replicate 2)


title: TAU_AGG_UNG-1_22C_D1

value: Ung-1 X Tau aggregate


title: Sample 60

tag: Sex

tag: case/control

value: yes

value: No


title: Sample 59

value: Male

tag: disease

value: no


title: PchiSox_Unbound_rep3

description: Unbound sequences from degenerate Sox libraries in binding experiements with  Pchi Sox (replicate 3)

value: not a cell (synthetic construct)

value: Pchi Sox


title: mSox2_Unbound_rep1

description: Unbound sequences from degenerate Sox libraries in binding experiements with  mSox2 (replicate 1)


title: Sample 58

value: classic-NAFLD

tag: fibrosis degree


title: Antp_RNAi_29_Rep1

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description: FACS-sorted wing disc associated myoblasts Antp RNAi

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped to the dm6 genome using subread-align (Subread package) on the command line using default parameters
Reads aligning to dm6 (release r6.42) exons were counted using featureCounts (Subread package) on the command line using default paramters
Differentially expressed genes were called using DESeq2 (version 1.34)
Assembly: dm6
Supplementary files format and content: Differentially expressed genes from DESeq2 analyses in tab-delimited plain text format
Supplementary files format and content: Raw exon counts in tab-delimited plain text format

organism: Drosophila melanogaster

source_name: Late larval (0h APF) FACS sorted wing disc associated myoblasts

extract_protocol:
For the wing, disc-associated myoblasts dissociation was performed according to a modified protocol (Khan et al., 2016). 0 h APF Mef2-GAL4, UAS-GFP::Gma/WT or UAS-Antp RNAi expressing larva raised at 29oC were washed in PBS, sterilised with 70% ethanol and dissected in Supplemented Schneider’s Medium (SSM) containing 10% Foetal bovine serum, 2% Penicillin/Streptomycin and 0.02 mg/mL Insulin. 30 to 35 wing discs were collected in ice-cold PBS and dissociated using preheated TrypLE 10x at 30°C for 45 min at 300rpm. The reaction was stopped by adding SSM and the cells were mechanically resuspended by gentle pipetting. Aggregates were removed by filtering cells in a cell strainer (30µm, Miltenyi) and cells were sorted using a FACS AriaII Machine (BD), according to cell viability, size and GFP intensity. Myoblasts were sorted directly in the kit-provided Lysis buffer supplemented with 2-Mercaptoethanol (#M6250, Sigma) and kept at -80°C until RNA extraction, which was preferentially performed the same day. RNA was isolated from the pure myoblast population of approximately 50 000 cells using RNA extraction Microkit (#74004, Qiagen).
Full length cDNA were generated from 2ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: flight muscle myoblasts

value: Mef2-Gal4;UAS-GFPnls;UAS-Antp RNAi


title: T2-2

value: Root system

value: Treatment group


title: CK3-2

value: control group

value: Incubation without PEG-6000 for 11 days


title: CK3-3


title: mSox2_Bound_rep1

description: Bound sequences from degenerate Sox libraries in binding experiements with mSox2 (replicate 1)


title: Sample 57

value: Liver

value: Female

value: IMID-NAFLD

value: NAFLD & Psoriasis

tag: obesity


title: T1-3

value: 15% PEG-6000 stress for 3 days


title: WT_29_Rep2

description: FACS-sorted wing disc associated myoblasts WT

value: Late larval (0h APF) FACS sorted wing disc associated myoblasts

value: Mef2-Gal4;UAS-GFPnls;UAS-Y RNAi


title: CK3-1


title: PchiSox_Unbound_rep2

description: Unbound sequences from degenerate Sox libraries in binding experiements with  Pchi Sox (replicate 2)


title: Sample 56

value: Male

value: NAFLD & IBD

value: yes

value: No

tag: hypertension


title: WT_29_Rep3

value: flight muscle myoblasts

tag: genotype


title: CK2-3

value: Incubation without PEG-6000 for 7 days


title: Sample 55

tag: fasting glycemia


title: PchiSox_Unbound_rep1

description: Unbound sequences from degenerate Sox libraries in binding experiements with  Pchi Sox (replicate 1)

value: not a cell (synthetic construct)

value: Pchi Sox


title: CK2-2

value: Root system

value: control group


title: Antp_RNAi_29_Rep2

value: Mef2-Gal4;UAS-GFPnls;UAS-Antp RNAi


title: Sample 54

value: Liver

value: classic-NAFLD

value: NAFLD/NASH

tag: total cholesterol


title: PchiSox_Bound_rep2

description: Bound sequences from degenerate Sox libraries in binding experiements with  Pchi Sox (replicate 2)

tag: treatment


title: 0501-0002_C2D16

city: London

first: Rose

last: Hodgson

address: 2 Monnery Road

institute: MiNA Therapeutics

hyb_protocol: RNA expression profiling was performed using the nCounter ®PanCancer IO360 Profiling Panel from NanoString (NanoString Technologies, Seattle, USA). The PanCancer IO360 Profiling Panel contains 770 probes. Hybridization was performed according to manufacturer’s instructions. Hybridized probes were then purified and immobilized on a streptavidin-coated cartridge using the nCounter Prep Station (NanoString Technologies).

scan_protocol: Data collection was carried out on the nCounter Digital Analyzer (NanoString Technologies) following the manufacturer’s instructions to count individual fluorescent barcodes and quantify target RNA molecules present in each sample. For each assay, a scan of 490 fields of view was performed.

data_processing: The quality control enable to keep good quality data with a binding density that range between 0.05 to 2.25. The linearity of positive controls was checked using the R2 of regression between the counts and the concentration of positive controls. No samples were removed from analysis based on a threshold of R2 < 0.75. Unwanted variation was determined by specifying the following housekeeping genes as controlGenes within the DESeq2 v1.36.0 estimateSizeFactors function and as negative control genes within RUVSeq v1.30.0 function RUVg: “UBB”, “PUM1”, “TLK2”, “DNAJC14”, “SF3A1”, “POLR2A”, “SDHA”, “STK11IP”, “NRDE2”, “TBP”, “OAZ1”, “TBC1D10B”, “GUSB”, “PSMC4”, “TMUB2”, “MRPL19”, “G6PD”,”ERCC3”. These factors were included in both data normalisation and transformation by Variance Stabilising transformation (VST) for data visualisation.

source_name: Breast

extract_protocol: RNA was extracted from FFPE tissues using QIAGEN RNeasy FFPE extraction kits (QIAGEN GmbH, Hilden, Germany). Annotations from the pathologist performing H&E staining were used to guide removal of normal tissue from the slides by spectrophotometry prior to nucleic acid extraction, which occurred after tissue deparaffinization and lysis. Each extracted RNA was independently quantified using a NanoDrop spectrophotometer (NanoDrop Technologies, Oxfordshire, UK) and quality checked (Agilent Bioanalyzer, Santa Clara, United States). Degradation assessment was quantified as the percentage of RNA fragments smaller than 300 base pairs using RNA 6000 Nano Kit (Agilent Bioanalyzer, Santa Clara, United States). Good sample quality was defined as less than 50% of RNA fragments of 50 to 300 base pairs in size.

tag: outcome

value: PD


title: PchiSox_Bound_rep1

description: Bound sequences from degenerate Sox libraries in binding experiements with Pchi Sox (replicate 1)


title: CK2-1

tag: tissue


title: 0501-0002_Screening


title: CK1-3

value: Incubation without PEG-6000 for 3 days


title: SalhelSox-I_Unound_rep3

description: Unbound sequences from degenerate Sox libraries in binding experiements with Salhel Sox-I  (replicate 3)

value: Salhel Sox-I


title: Sample 53

value: Female

tag: hdl-cholesterol

tag: ldl-cholesterol


title: Sample 52

value: Male

value: IMID-NAFLD

value: NAFLD & IBD

value: no

tag: tryglicerides


title: Sample 51

value: yes

value: No


title: 0501-0001_Screening

source_name: IntrahepaticCholangiocarcinoma


title: CK1-1


title: PchiSox_Bound_rep3

description: Bound sequences from degenerate Sox libraries in binding experiements with  Pchi Sox (replicate 3)

tag: cell type

value: not a cell (synthetic construct)

value: Pchi Sox


title: Sample 50


title: SalhelSox-I_Unound_rep1

description: Unbound sequences from degenerate Sox libraries in binding experiements with Salhel Sox-I (replicate 1)


title: SalhelSox-I_Bound_rep3

description: Bound sequences from degenerate Sox libraries in binding experiements with Salhel Sox-I (replicate 3)


title: 0107-0001_C2D16

source_name: RectalCancer

value: SD


title: SalhelSox-I_Bound_rep2

description: Bound sequences from degenerate Sox libraries in binding experiements with Salhel Sox-I (replicate 2)


title: Sample 49


title: 0103-0001_C2D16

source_name: Pancreatic


title: Sample 48

value: NAFLD & Spondylitis


title: 0107-0001_Screening


title: Sample 47

value: Liver


title: SalhelSox-I_Bound_rep1

description: Bound sequences from degenerate Sox libraries in binding experiements with Salhel Sox-I (replicate 1)


title: MIME26_YM1_0

city: New York

first: MATTHEW

middle: Dae-Young

last: PARK

state: NY

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

description: 10X Genomics

data_processing:
Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted.
From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
Assembly: Gene expression reads were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output.
Supplementary files format and content: Barcode.tsv, features.tsv, and matrix.mtx files are made available for each sample.

source_name: Lung

extract_protocol:
Lymphoid cells and myeloid cells were separately sorted and barcoded with 10x Cellplex oligos before being encapsulated using the 10X Chromium 3’ v3 chemistry kit according to manufacturer’s instructions. Cells sorted from the same genotype were barcoded and pooled into individual lanes. A total of 12,000 cells were loaded per lane from each condition. For scRNA-seq of BM of naïve, tumor- bearing and IL-4c treated mice, bone marrow myeloid cells and were sorted for sequencing. Due to their abundance in bone marrow, neutrophils were separately sorted and then recombined back with the above cells at a 1:10 ratio.
All sequencing libraries were prepared per manufacturer instructions.
After stringent cDNA and sequencing library quality control with the CybrGreen qPCR library quantification assay, samples were sequenced at a depth of 100 million reads per library with a 75-cycle kit on an Illumina Nextseq 550.

value: Lung

tag: cell line

value: KP

value: Immune Myeloid

value: WT

tag: group

value: young


title: MIME26_YM2_0

description: 10X Genomics


title: 0103-0001_Screening

value: PD


title: MIME26_YM3_0

description: 10X Genomics


title: 0012-0003_C2D16


title: 0501-0001_C2D16


title: CK1-2

value: Root system

value: control group

value: Incubation without PEG-6000 for 3 days


title: mOct4POU_Unbound_rep3

description: Unbound sequences from degenerate Octamer libraries in binding experiements with mOct4 POU (replicate 3)

value: mOct4 POU


title: MIME26_YL1-3_0

description: 10X Genomics

value: Immune Lymphoid


title: Sample 46

tag: Sex

value: Female

tag: case/control

value: IMID-NAFLD

value: NAFLD & IBD

value: no

value: yes


title: SalhelSox-I_Unound_rep2

description: Unbound sequences from degenerate Sox libraries in binding experiements with Salhel Sox-I (replicate 2)

value: not a cell (synthetic construct)

value: Salhel Sox-I


title: mOct4POU_Unbound_rep2

description: Unbound sequences from degenerate Octamer libraries in binding experiements with mOct4 POU (replicate 2)


title: MIME26_AM3_0

description: 10X Genomics

value: Lung

value: KP

value: old


title: 0012-0003_Screening


title: mOct4POU_Unbound_rep1

description: Unbound sequences from degenerate Octamer libraries in binding experiements with mOct4 POU (replicate 1)


title: MIME26_AM2_0

description: 10X Genomics

value: Immune Myeloid

value: WT


title: Sample 45

value: Liver

tag: disease

value: NAFLD & Hidradenitis

tag: fibrosis degree

value: No


title: 0012-0001_C2D16

value: SD


title: Sample 44

value: Male

tag: obesity

tag: hypertension


title: MIME26_AM1_0

description: 10X Genomics

tag: genotype


title: 0012-0001_Screening


title: mOct4POU_Bound_rep3

description: Bound sequences from degenerate Octamer libraries in binding experiements with mOct4 POU (replicate 3)

value: mOct4 POU


title: HCT116_Bulk_shD1_Reccovery_D28_r2

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

data_processing:
Total methylation levels (mC) were calculated by dividing the sum of all C calls with the sum of all C+T calls, and CpGs with a minimum coverage of 5 were used for downstream analyses.
Methylation domains (PMD, LMR, UMR) were called using MethylSeekR (v1.0). HMD domains were called using the ‘complement’ function in bedtools (v2.25.0) against all the coordinates of PMDs, LMRs, and UMRs and were included if the average DNA methylation (average mC) was  0.8 across the domain
Assembly: hg38
Supplementary files format and content: *Methyl_domain_calls.sort.bed; contains genomic coordinates for all Methyl domains called.
Supplementary files format and content: bw, mC-values for all CpGs that passed QC.
Supplementary files format and content: *.tsv.gz files contain the number or reads methylated and the total number of reads for the respective sample.

growth_protocol: HCT116 colon cancer cell line was purchased from ATCC and maintained according to ATCC recommendations in McCoy's (Gibco 16600-082) media supplemented with 10% Fetal Bovine Serum (Millipore Sigma F0926) and 1% penicillin/streptomycin (Life Technologies, 15140-122) at 5% CO2 and 37C.

extract_protocol:
Cells were lysed overnight at 37°C in 2 mls of TE-SDS buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 0.5% SDS), supplemented with 100 μl of 20 mg/ml proteinase K. DNA was purified by phenol:chloroform extraction in three phases: (1) 100% phenol, (2) phenol:chloroform:isoamyl alcohol (25:24:1), and (3) chloroform:isoamyl alcohol (24:1). For each phase, the aqueous layer was combined with the organic layer in a 1:1 ratio. Samples were quickly shaken, allowed to sit on ice for approximately 5 minutes, and then separated by centrifugation at 1,693 RCF for 5 minutes at 4°C. The top aqueous layer was then transferred to a new tube for the next organic phase. Following extraction, DNA was precipitated with 1/10 volume 3 M sodium acetate pH 4.8 and 2.5 volumes 100% ethanol and stored overnight at -20°C. Precipitated DNA was pelleted by centrifugation at 17,090 RCF for 30 minutes at 4°C. The pelleted DNA was washed twice with 70% ethanol, allowed to dry for 15 minutes, and resuspended in TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). Samples were then treated with 1 mg/ml RNAse A at 37°C for 30 minutes and then re-purified by ethanol precipitation as described.
200 ng of DNA was bisfulfite converted using the EZ DNA Methylation-Gold Kit (Zymo, #D5005) according to manufacturer’s instructions. Input DNA was spiked with unmethylated lambda DNA (0.5%) (Promega, #D1521). Replicate bisulfite libraries were generated with the CEGX TrueMethyl® Whole Genome Kit (CEGX, #CEGXTMWG, v3.1) according to manufacturer’s instructions.
Libraries were sequenced on the Illumina X Ten. Sequencing reads from WGBS data were aligned to the human genome using v1.2 of an internally developed pipeline Meth10X41. This is publicly available and can be downloaded from https://github.com/luuloi/Meth10X.

treatment_protocol: In all cases, Baseline (or NoDox) samples were grown in culture for 2 weeks in the absence of doxycycline, and serve as the baseline methylome control for Knockdown and Recovery samples. Knockdown samples were treated with doxycycline (10 ng/mL) for two weeks to induce expression of the shRNA. Recovery samples were treated with doxycycline for two weeks (to induce knockdown of the target protein), and then doxycycline was removed for an additional two weeks to measure recovery methylation dynamics with re-expression of the either UHRF1 or DNMT1. Transgenes for WT and mutant UHRF1 and DNMT1 were stably introduced into the clonally expanded Cl9 shUHRF1 and Cl3 shDNMT1 cell lines, respectively. Doxycycline treatment (10 ng/mL) over 2 weeks depleted the endogenous enzyme in the presence of the transgene protein cover.

value: Colorectal Carcinoma epithelial cells

value: Doxycycline-inducible shRNA against DNMT1

value: 10 ng/mL Doxycycline for 14 days followed by no doxycycline treatment for an additional 14 days

tag: time (days)


title: Sample 42

data_processing:
Genes were quantified using RSEM (version 1.3.0) with default parameters.
The human gene annotation file was downloaded from gencode release 36 (https://www.gencodegenes.org/).
Mapping and quantification quality checking were performed with GEMTools (https://gemtools.github.io/) and custom python scripts.
A multidimensional scaling plot was performed to inspect sample similarities using the ‘voom’ transformed counts and the top 500 most variable genes.
Assembly: Human reference genome (GRCh38)
Supplementary files format and content: EGN_RNAseq_Normalized_data: Excel file incuding gene normalized expression for each sample.
Supplementary files format and content: EGN_RNAseq_Processed_data: Differential gene expression (IMID-NAFLD vs. Classic-NAFLD) adjusted for BMI, sex, and fibrosis severity.

extract_protocol:
Freshly frozen biopsies were disrupted using Kimble® Pellet Pestle® Cordless Motor (DWK Life Sciences, Cat. No.: 749540-0000). RNA extraction was performed using the PureLink™ RNA Mini Kit (Invitrogen, Cat. No.: 12183018A) adding an extrapurification process with the PureLink™ DNase Set (Invitrogen, Cat. No.: 12185010).
RNA-seq reads were mapped against the human reference genome (GRCh38) using STAR (version 2.5.3a) with ENCODE parameters.

value: Female

value: classic-NAFLD

value: NAFLD/NASH

value: yes

tag: fasting glycemia

tag: total cholesterol


title: MIME26_AL1-3_0

description: 10X Genomics

tag: tissue

value: Lung

value: KP

value: Immune Lymphoid


title: mOct4POU_Bound_rep2

description: Bound sequences from degenerate Octamer libraries in binding experiements with mOct4 POU (replicate 2)

value: not a cell (synthetic construct)

tag: treatment


title: 0008-0002_C2D16

source_name: PancreaticAdenocarcinoma

tag: outcome

value: PD


title: mOct4POU_Bound_rep1

description: Bound sequences from degenerate Octamer libraries in binding experiements with mOct4 POU (replicate 1)


title: SalhelPOU_Unbound_rep3

description: Unbound sequences from degenerate Octamer libraries in binding experiements with Salhel POU (replicate 3)

value: Salhel POU


title: Sample 43

value: Liver

value: no

tag: hdl-cholesterol

tag: ldl-cholesterol

tag: tryglicerides


title: Sample 40

value: No


title: 0008-0002_Screening


title: 0004-0008_C2D16

source_name: Sarcoma


title: HCT116_Bulk_shD1_Knockdown_D14_r2

tag: cell line

tag: cell type

value: 10 ng/mL Doxycycline for 14 days


title: Sample 41

tag: Sex

value: Male

tag: case/control


title: 0004-0008_Screening


title: HCT116_Bulk_shD1_Baseline_D14_r2

value: Colorectal Carcinoma epithelial cells

value: Doxycycline-inducible shRNA against DNMT1

value: No Doxycycyline for 14 days


title: SalhelPOU_Unbound_rep2

description: Unbound sequences from degenerate Octamer libraries in binding experiements with Salhel POU (replicate 2)


title: HCT116_Bulk_shD1_Reccovery_D28_r1

value: 10 ng/mL Doxycycline for 14 days followed by no doxycycline treatment for an additional 14 days


title: Sample 39

value: Female

value: classic-NAFLD

tag: disease

value: NAFLD/NASH

tag: fibrosis degree


title: SalhelPOU_Unbound_rep1

description: Unbound sequences from degenerate Octamer libraries in binding experiements with Salhel POU (replicate 1)


title: Sample 38

value: IMID-NAFLD

value: NAFLD & Spondylitis

tag: obesity

value: yes

tag: hypertension


title: HCT116_Bulk_shD1_Knockdown_D14_r1

tag: genotype

tag: time (days)


title: 0004-0006_C2D16

source_name: Recto-sigmoid

value: PD


title: SalhelPOU_Bound_rep3

description: Bound sequences from degenerate Octamer libraries in binding experiements with Salhel POU (replicate 3)

value: not a cell (synthetic construct)

value: Salhel POU


title: 0004-0006_Screening


title: Sample 37

value: Liver

value: NAFLD & IBD

value: no

tag: fasting glycemia

tag: total cholesterol


title: HCT116_Bulk_shD1_Baseline_D14_r1

tag: treatment


title: 0004-0005_C2D16

tag: outcome


title: SalhelPOU_Bound_rep2

description: Bound sequences from degenerate Octamer libraries in binding experiements with Salhel POU (replicate 2)


title: 0004-0005_Screening


title: SalhelPOU_Bound_rep1

description: Bound sequences from degenerate Octamer libraries in binding experiements with Salhel POU (replicate 1)


title: Sample 36

tag: tissue

value: No

tag: hdl-cholesterol


title: Sample 35

value: Male

tag: ldl-cholesterol

tag: tryglicerides


title: HCT116_Cl9_shU1_Knockdown_D14

tag: cell line

tag: cell type

value: Colorectal Carcinoma epithelial cells

value: Doxycycline-inducible shRNA against UHRF1

value: 10 ng/mL Doxycycline for 14 days


title: 0004-0004_C2D16

source_name: LungMetastaticAtypicalLung

value: PR


title: Liver, 14 days post torpor, Rep2

first: Kurt

last: Weir

address: 733 North Broadway

institute: Johns Hopkins School of Medicine

data_processing:
de novo transcriptome generation with Trinity v2.13.1
alignment with Bowtie2 v2.4.1
quantification with RSEM v1.2.15
Assembly: de novo transcriptome
Supplementary files format and content: .Robj file containing matrix with RSEM expression values for each gene in each sample

organism: Ictidomys tridecemlineatus

source_name: Liver

extract_protocol:
Total RNA was isolated with the miRNeasy micro kit with an optional DNase step, per the manufacturer’s protocol (Qiagen, Hilden, Germany)
The total RNA was used to generate cDNA libraries with the Illumina TruSeq stranded Total RNA kit

tag: condition

value: 14 days post torpor


title: HCT116_Cl9_shU1_Baseline_D14

value: No Doxycycyline for 14 days


title: 0004-0004_Screening


title: Liver, 14 days post torpor, Rep1


title: HCT116_Cl3_shU1_Knockdown_D14


title: Liver, 3 days post torpor, Rep3

value: 3 days post torpor


title: Sample 34

tag: Sex

value: Female

tag: case/control

value: classic-NAFLD

tag: disease

value: NAFLD/NASH


title: Sample 33

value: IMID-NAFLD

value: NAFLD & Hidradenitis

tag: fibrosis degree

tag: obesity

tag: hypertension

value: yes


title: Sample 31

value: Liver

value: NAFLD & IBD

tag: fasting glycemia


title: Sample 32

value: No

tag: total cholesterol


title: 0004-0003_Screening

source_name: Colon

value: SD


title: Liver, 3 days post torpor, Rep2


title: HCT116_Cl3_shU1_Baseline_D14

value: Colorectal Carcinoma epithelial cells

tag: genotype

tag: treatment

tag: time (days)


title: Sample 30

tag: tissue

tag: hdl-cholesterol


title: HCT116_Cl6_shU1_Recovery_D28

value: Doxycycline-inducible shRNA against UHRF1

value: 10 ng/mL Doxycycline for 14 days followed by no doxycycline treatment for an additional 14 days


title: 0004-0002_Screening

source_name: FibrolamellarHCC

tag: outcome


title: Liver, 3 days post torpor, Rep1


title: HCT116_Cl6_shU1_Knockdown_D14

tag: cell line

value: 10 ng/mL Doxycycline for 14 days


title: 0003-0010_C2D16

source_name: Ovarian(HighgradeSerous)

value: PD


title: Liver, Torpor, Rep3

value: Torpor


title: Sample 28

value: Male

tag: ldl-cholesterol

tag: tryglicerides


title: HCT116_Cl3_shU1_Recovery_D28

tag: cell type


title: 0004-0003_C2D16


title: 0003-0010_Screening


title: HCT116_Cl6_shU1_Baseline_D14

value: No Doxycycyline for 14 days


title: Sample 29

tag: Sex

tag: case/control

value: classic-NAFLD


title: Sample 27

value: Female

tag: disease

value: NAFLD & Psoriasis

tag: fibrosis degree


title: 0004-0002_C2D16


title: Liver, Torpor, Rep1

tag: condition


title: st21_dorsal_Dam_rep2

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

institute: The Gurdon Institute

description: Dam-Only control

data_processing:
Analysis was perfomed with damidseq_pipeline script which uses bowtie2 to align reads to given genome, extends the reads until 300bp or the next GATC site, bins the reads into GATC fragments and normalises against Dam-Only control.
Replicates of normalised bedgraphs were quantile normalised to each other, averaged and backtransformed.
Averaged bedgraphs were converted into bigwig format.
Assembly: mm10, dm6, Xla.v9.1
Supplementary files format and content: The processed data are quantile normalised and averaged bigwig files, generated as described.
Library strategy: DamID-Seq

organism: Xenopus laevis

source_name: stage 21 embryos (dorsal injection)

extract_protocol:
For Drosophila DamID, 20-50 third instar larval brains were dissected. For mouse samples, in utero electroporation with DamID plasmids was performed on E13.5 embryos. Electroporated cortex was microdissected. For Xenopus samples, mRNA was injected into stage 11 or stage 21 embryos. All tissue collections were followed by genomic DNA extraction with Qiagen DNAeasy blood and tissue kit and processed for DamID according to previous protocols before library prep.
Samples prepared for Illumina sequencing according to a modified TruSeq protocol.

value: stage 21 embryos (dorsal injection)


title: Sample 26

value: NAFLD/NASH

tag: obesity

value: yes

value: no

tag: hypertension

tag: fasting glycemia


title: Sample 25

value: Liver

value: No

tag: total cholesterol


title: 0003-0009_C2D16

source_name: Ovarian(lowgradeserous)


title: 0003-0009_Screening


title: st21_dorsal_Dam_rep1

description: Dam-Only control


title: st21_dorsal_TAF3_Dam_rep2

description: TAF3-phd(H3K4me3)-Dam fusion


title: Liver, Euthermia, Rep3

value: Euthermia


title: Liver, Prehibernation, Rep1

value: Prehibernation


title: Sample 24

value: IMID-NAFLD

value: NAFLD & IBD


title: 0002-0006_C2D16

source_name: BreastCancer(TripleNeg)

value: PD


title: 0002-0006_Screening


title: 0002-0001_C2D16


title: Liver, Euthermia, Rep2


title: Sample 23

value: NAFLD & Hidradenitis


title: Liver, Euthermia, Rep1


title: Liver, Torpor, Rep2

value: Torpor


title: Sample 22

value: Male


title: HCT116_Cl9_shU1_Recovery_D28

value: Colorectal Carcinoma epithelial cells

tag: genotype

value: Doxycycline-inducible shRNA against UHRF1

tag: treatment

value: 10 ng/mL Doxycycline for 14 days followed by no doxycycline treatment for an additional 14 days

tag: time (days)


title: 0002-0001_Screening

tag: outcome


title: RPE, 14 days post torpor, Rep6

source_name: Retinal pigment epithelium

tag: tissue

value: Retinal pigment epithelium

value: 14 days post torpor


title: st21_ventral_TAF3_Dam_rep2

description: TAF3-phd(H3K4me3)-Dam fusion

source_name: stage 21 embryos (ventral injection)

value: stage 21 embryos (ventral injection)


title: RPE, 14 days post torpor, Rep5


title: st21_ventral_Dam_rep2

description: Dam-Only control