title: Huh1_siHNF4A_H3K27me3_rep3

city: HUDDINGE

first: Lin

last: Chen

address: Blickagången 16, Flemingsberg,Neo

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: Library name: siHNF4A_H3K27me3_rep3

data_processing:
Computations of mice data were performed using resources provided by Galaxy. The computations of human data was enabled by resources in project sens2024555 provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) at UPPMAX, funded by the Swedish Research Council through grant agreement no. 2022-06725. Analysis was conducted as previously described. Sequencing files (fastq files) provided by NOVOGENE (Cambridge, United Kingdom), along with raw data from published ChIP-seq datasets (KDM6A: GSE95890; HNF4A: GSE31477), were aligned to the NCBI38/mm10 version of the mouse reference genome or GRCh38/hg38 using Bowtie2. Peaks were identified using the HOMER package. Peak heights were normalized to the total number of uniquely mapped reads and displayed in the Integrative Genomics Viewer (IGV) as the number of tags per 10 million tags. For statistical analysis of the peaks, raw tag counts were imported into R and Bioconductor, and the edgeR package was used to identify potential differential-binding sites.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Huh1 cells were crosslinked with 1% formaldehyde (ThermoFisher, 28906) in PBS for 10 minutes for histone modifications. The reaction was stopped with glycine at a final concentration of 0.125 M for 5 minutes. Liver pieces were disaggregated in ice-cold PBS with protease inhibitor using a Dounce Homogenizer, first with a loose pestle and then with a tight pestle (Fisher Science, FB56691). Nuclei were isolated using three lysis buffers: lysis buffer 1 (50 mM Hepes–KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100), lysis buffer 2 (10 mM Tris–HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and lysis buffer 3 (10 mM Tris–HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, and 0.5% N-Lauroylsarcosine). The samples were then sonicated for 30 minutes (30 seconds ON/30 seconds OFF) using the Bioruptor Pico (Diagenode).
For ChIP-seq sample preparation, the same ChIP protocol was followed, but the ChIP DNA was purified using the ChIP DNA Clean and Concentrator Capped Zymo-Spin I (Zymo Research) purification kit. Two to four ChIPs were pooled during the final purification step to obtain concentrated material. For library preparation and sequencing, 2–10 ng of ChIPed DNA was processed using the Rubicon ThruPLEX DNA-seq kit (TAKARA) following standard protocols, and sequenced on the NovaSeq X Plus Series (150PE reads, NOVOGENE, United Kingdom).


title: Huh1_siHNF4A_H3K27me3_rep4

status: Public on Feb 19 2026

type: SRA

description: Library name: siHNF4A_H3K27me3_rep4

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line


title: Thalamus, VLP, OCD, Pair 1, HUID 1413

city: Pittsburgh

first: Susanne

last: Ahmari

state: PA

address: 450 Technology Dr Suite 223

department: Psychiatry

country: USA

institute: University of Pittsburgh

description: S2 flow cell

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 22.0.1
Sequence reads were mapped to GRCh38.106 using CLC Genomics Workbench. Mapping parameters: mismatch cost = 2, insertion or deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
Read count extraction and normalization was performed using CLC Genomics Workbench
Assembly: GRCh38.p13
Assembly: Ensemble Archive Release v106
Supplementary files format and content: comma-separated values files include raw and normalized (TPM, RPKM) counts for each sample

molecule: total RNA

source_name: Thalamus

extract_protocol:
RNA was extracted using an RNeasy Plus Micro kit (Qiagen)
RNA libraries for RNAseq were generated using Illumina TruSeq Stranded Total RNA kit following manufacturer protocols

tag: tissue

value: Thalamus

tag: nucleus

value: VLP

tag: hemisphere

value: right

tag: diagnosis group

value: OCD

tag: subject id

value: HUID 1413

tag: subject pair

value: Pair 1


title: IMG WT rep 1

city: Tampa

first: Jessica

last: Wohlfahrt

state: FL

address: 4202 E Fowler Ave

institute: University of South Florida

description: Library name: WT1

data_processing:
Results were analyzed by the Zymo bioinformatics team using the Zymo Research RNA-Seq pipeline (v2.1.0) adapted from nf-core/rnaseq pipeline (v1.4.2) and built using Nextflow (v21.10.5) to provide differentially expressed genes, normalized counts, and data visualizations.
Sequences were quality controlled with FastQC (v0.11.9), trimmed by Trim Galore! (v0.6.6), and aligned to the reference genome by STAR (v2.6.1d).
SAMtools (v1.9) was used to filter and index BAM file and quality control of the library was ensured by RSeQC (v4.0.0) as well as QualiMap (v2.2.2-dev).
Picard tools (v2.23.9) was used to mark duplicate reads, and a complexity estimate of the library was completed using Preseq (v2.0.3). Additional quality control was completed at this stage using dupRadar (v1.18.0).
Alignment to genes was completed using featureCounts (v2.0.1) and UCSC genome browser RepeatMasker rRNA tracks for rRNA genes.
DESeq2 (v1.28.0) was used to determine differential expression of genes with enrichment analysis by g:Profiler python API (v1.0.0). Data visualization and quality control were completed using MultiQC (v1.9).
Assembly: GRCm39
Supplementary files format and content: Microsoft Excel Worksheet includes normalized counts for each sample

organism: Mus musculus

source_name: IMG

growth_protocol: Both wildtype (WT) and the Kdm5b knockout pool (KOp) cells of an adult-derived mouse microglia cell line (IMG, Sigma-Aldrich, SCC134) were grown in triplicate in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 U/mL streptomycin at 37°C and 5% CO2.

extract_protocol:
500ng RNA was extracted and purified by the Zymo Research Total RNA-Seq Service using the KingFisher Flex (Thermo) with the Quick-RNA MagBead kit (R2132, Zymo) and the RNA Clean & Concentrator MagBead kit (R1081, Zymo).
RNA libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (R3000, Zymo Research) following the manufacturer’s instructions (v1.3.0). D1000 ScreenTape Assay on TapeStation (Agilent) was used to confirm library construction.

value: IMG

tag: cell type

value: microglia

tag: genotype

value: wild-type


title: Huh1_siHNF4A_H3K27me3_rep2

description: Library name: siHNF4A_H3K27me3_rep2


title: IMG WT rep 2

description: Library name: WT2


title: CSEKO6, Ang II

city: Beijing

first: ying

last: zhao

state: Beijing

address: 167, Beilishi Road, Xicheng District, Beijing

country: China

institute: Fuwai Hospital, Chinese Academy of Medical Sciences

description:
Library name: CSEKO6, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEKO6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: wig files were generated using …; Scores represent …
Supplementary files format and content: peak text files

source_name: Primary

growth_protocol: Primary vsmc were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), then incubated at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Ang II (1uM), 24h

value: Primary

value: Smooth Muscle Cells

value: CSE KO

tag: treatment

value: Ang II

tag: batch


title: Thalamus, VLP, CON, Pair 1, HUID 1159

description: S2 flow cell

value: CON

value: HUID 1159


title: Huh1_siKDM6A_H3K27me3_rep3

description: Library name: siKDM6A_H3K27me3_rep3


title: Huh1_siKDM6A_H3K27me3_rep4

description: Library name: siKDM6A_H3K27me3_rep4


title: Huh1_siHNF4A_H3K27me3_rep1

description: Library name: siHNF4A_H3K27me3_rep1


title: Huh1_siKDM6A_H3K27me3_rep2

description: Library name: siKDM6A_H3K27me3_rep2


title: CSEKO4, Ang II

description:
Library name: CSEKO4, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEKO4


title: Thalamus, VA, OCD, Pair 9, HUID 13125

description: S2 flow cell

value: VA

value: Pair 9


title: Huh1_siKDM6A_H3K27me3_rep1

description: Library name: siKDM6A_H3K27me3_rep1


title: Huh1_siLuc_H3K27me3_rep4

description: Library name: siLuc_H3K27me3_rep4


title: Thalamus, VA, CON, Pair 9, HUID 1637

description: S2 flow cell

value: Thalamus

value: HUID 1637


title: Huh1_siLuc_H3K27me3_rep3

description: Library name: siLuc_H3K27me3_rep3


title: CSEKO5, Ang II

description:
Library name: CSEKO5, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEKO5


title: CSEKO2, Ang II

description:
Library name: CSEKO2, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEKO2


title: Thalamus, VA, OCD, Pair 8, HUID 13173

description: S2 flow cell

value: right

value: Pair 8


title: Huh1_siHNF4A_H3K27ac_rep4

description: Library name: siHNF4A_H3K27ac_rep4


title: CSEKO3, Ang II

description:
Library name: CSEKO3, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEKO3


title: Huh1_siLuc_H3K27me3_rep1

description: Library name: siLuc_H3K27me3_rep1


title: Huh1_siHNF4A_H3K27ac_rep2

description: Library name: siHNF4A_H3K27ac_rep2


title: Huh1_siKDM6A_H3K27ac_rep4

description: Library name: siKDM6A_H3K27ac_rep4


title: Thalamus, VA, CON, Pair 7, HUID 1083

description: S2 flow cell

value: HUID 1083

value: Pair 7


title: Huh1_siLuc_H3K27me3_rep2

description: Library name: siLuc_H3K27me3_rep2


title: Huh1_siHNF4A_H3K27ac_rep3

description: Library name: siHNF4A_H3K27ac_rep3


title: CSEWT6, Ang II

description:
Library name: CSEWT6, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEWT6

value: CSE WT


title: CSEKO1, Ang II

description:
Library name: CSEKO1, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEKO1


title: Huh1_siKDM6A_H3K27ac_rep3

description: Library name: siKDM6A_H3K27ac_rep3


title: Thalamus, VA, OCD, Pair 6, HUID 13051

description: S2 flow cell

value: OCD

value: Pair 6


title: Huh1_siKDM6A_H3K27ac_rep2

description: Library name: siKDM6A_H3K27ac_rep2


title: Thalamus, VA, OCD, Pair 5, HUID 1785

description: S2 flow cell

value: HUID 1785

value: Pair 5


title: Thalamus, VA, OCD, Pair 7, HUID 13022

description: S2 flow cell


title: CSEWT4, Ang II

description:
Library name: CSEWT4, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEWT4

value: Primary

value: Smooth Muscle Cells


title: Huh1_siKDM6A_H3K27ac_rep1

description: Library name: siKDM6A_H3K27ac_rep1


title: CSEWT5, Ang II

description:
Library name: CSEWT5, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEWT5

value: Ang II


title: Huh1_siHNF4A_H3K27ac_rep1

description: Library name: siHNF4A_H3K27ac_rep1


title: Huh1_siLuc_H3K27ac_rep3

description: Library name: siLuc_H3K27ac_rep3


title: Huh1_siLuc_H3K27ac_rep2

description: Library name: siLuc_H3K27ac_rep2


title: CSEWT3, Ang II

description:
Library name: CSEWT3, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEWT3


title: Thalamus, VA, OCD, Pair 4, HUID 1505

description: S2 flow cell

value: HUID 1505

value: Pair 4


title: CSEWT2, Ang II

description:
Library name: CSEWT2, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEWT2


title: Huh1_siLuc_H3K27ac_rep1

description: Library name: siLuc_H3K27ac_rep1


title: Huh1_siLuc_H3K27ac_rep4

description: Library name: siLuc_H3K27ac_rep4


title: Thalamus, VA, CON, Pair 5, HUID 1543

description: S2 flow cell

value: VA

value: CON

value: HUID 1543


title: scRNA-seq of Ixodes scapularis adult female salivary glands group 2 replicate 2

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

description:
Library name: SCL_G2_2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were demultiplexed and processed using the Cell Ranger Software Suite (10x Genomics). Cell Ranger (v7.0.1) was used to perform sample demultiplexing, barcode processing,  and alignments, as well as counting of single-cell barcode and unique molecular identifier (UMI) gene counting. The 'cellranger count' function was applied for alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting. The genome of Ixodes scapularis reference genome (ASM1692078v2) was used as the reference genome for the alignment.  Following generation of gene-cell matrices from Cell Ranger, further analysis was performed using Seurat v4.3, an R package for analysis of single cell RNAseq data. Sample-specific low-quality cells were excluded based on a threshold set at three median absolute deviations (MAD) from the median of the overall cell population, applied to both UMI and feature counts. Quality control was not applied to exclude cells with high mitochondrial gene content, because mitochondrial genes were expected to be upregulated in feeding groups.  The gene expression matrix was then normalized and scaled. Variable features were identified using the 'vst' method in the 'FindVariableFeatures' function. Dimensionality reduction was performed using principal component analysis (PCA). The most significant principal components were selected for downstream analyses. Based on these components, shared nearest neighbor (SNN) graph-based clustering was performed. Clusters were visualized using Uniform Manifold Approximation and Projection (UMAP). For each cluster, differential gene expression was performed to identify cluster-specific marker genes. These markers were used to annotate cell clusters based on known marker genes for cell types.
Assembly: Ixodes scapularis reference genome (ASM1692078v2)
Supplementary files format and content: *filtered_feature_bc_matrix.zip

organism: Ixodes scapularis

source_name: salivary glands

extract_protocol:
The Ixodes scapularis ticks used in this study were obtained from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Prior to infestation, unfed ticks were maintained at 21°C and 85% relative humidity. One day before feeding, female ticks were paired with males to allow mating. Adult ticks were placed on the outer ear of four naïve female New Zealand rabbits, restricted by orthopedic stockinets that were glued in place. A total of 20 female and 20 male ticks (40 ticks per ear, 80 ticks per rabbit) were allowed to attach. To classify ticks by blood-feeding index, partially fed ticks were collected from the host based on engorgement size, sorted by weight, and divided into biological triplicates: an unfed group (UF) (15 females per replicate, weighing 1.6 mg in average), group G2 (5 females per replicate, weighing 7.2 mg in average), and group G5 (4 females per replicate, weighting 41.5 mg in average). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, 70% ethanol, and a final rinse with nuclease-free water. Ticks were dissected within two hours of removal. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization.
The single cell suspensions were loaded (7,000 cells) onto a Chromium Controller for GEM (Gel Bead-In-EMulsion) generation in triplicate for three groups and barcoding using the Chromium Single Cell 3’ Reagent Kits according to the manufacturer's protocol (10x Genomics). After cDNA synthesis, amplification, and library construction, the libraries were sequenced by the Illumina NovaSeq 6000 System.

value: salivary glands

tag: group

tag: Sex

value: female


title: Huh1_siHNF4A_H3K4me2_rep3

description: Library name: siHNF4A_H3K4me2_rep3


title: CSEWT1, Ang II

description:
Library name: CSEWT1, Ang II
Column name in raw_FPKMs_All_Samples. txt: Ao_CSEWT1


title: Thalamus, VA, OCD, Pair 3, HUID 1435

description: S2 flow cell

value: Thalamus

value: right

value: HUID 1435

value: Pair 3


title: Huh1_siHNF4A_H3K4me2_rep2

description: Library name: siHNF4A_H3K4me2_rep2


title: CD36CKO-whole heart-replicate-3

city: Houston

first: Tamer

last: Mohamed

state: TX

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

description: Library name: C03

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The error rate for each base can be transformed by the Phred score as in equation 1. "e" represents sequencing error rate, "Qphred" represents base quality values of Illumina platforms (equation 1: Qphred = -10log10(e)).
GC content distribution detects potential AT/GC separation, which affects subsequent gene expression quantification. In view of random fragmentation and biological law of G/C-A/T content, G and C, A and T should be respectively equal, and the content should be stable throughout the entire sequencing process for non-stranded library(Parkhomchuk et al., 2009) (If the library is strand-specific, AT separation or GC separation may occur). A large variation of sequencing error in the first 6-7 bases is allowed considering the use of random primer in library construction, in which it is normal that the first few bases have certain preference in existing high-throughput sequencing technology.
The sequencing reads/raw reads often contain low quality reads or reads with adapters, which will affect the quality of downstream analysis. To avoid this, it is necessary to filter the raw reads and obtain the clean reads.
Assembly: Alignments were made with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons.
Supplementary files format and content: xlxs data sheet including fpkm values for each sample

source_name: Whole heart tissue

extract_protocol:
RNA was isolated from the pups’ hearts extracted at P1 by using the Qiagen miRNeasy Micro Kit (Cat# 210874), following the manufacturer’s protocol after homogenizing tissue in Qiazol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Whole heart tissue

value: Cardiac specific CD36KO


title: Huh1_siKDM6A_H3K4me2_rep4

description: Library name: siKDM6A_H3K4me2_rep4


title: Huh1_siHNF4A_H3K4me2_rep1

description: Library name: siHNF4A_H3K4me2_rep1


title: CD36CKO-whole heart-replicate-2

description: Library name: C02


title: Thalamus, VA, CON, Pair 3, HUID 13032

description: S2 flow cell


title: Huh1_siHNF4A_H3K4me2_rep4

description: Library name: siHNF4A_H3K4me2_rep4


title: Huh1_siKDM6A_H3K4me2_rep3

description: Library name: siKDM6A_H3K4me2_rep3


title: Huh1_siLuc_H3K4me2_rep4

description: Library name: siLuc_H3K4me2_rep4


title: Thalamus, VA, CON, Pair 4, HUID 1092

description: S2 flow cell

value: HUID 1092


title: CD36KO-whole heart-replicate-3

description: Library name: B03

value: Whole body CD36KO


title: Huh1_siKDM6A_H3K4me2_rep1

description: Library name: siKDM6A_H3K4me2_rep1


title: Huh1_siKDM6A_H3K4me2_rep2

description: Library name: siKDM6A_H3K4me2_rep2


title: Huh1_siLuc_H3K4me2_rep3

description: Library name: siLuc_H3K4me2_rep3


title: CD36CKO-whole heart-replicate-1

description: Library name: C01


title: Huh1_siLuc_H3K4me2_rep2

description: Library name: siLuc_H3K4me2_rep2


title: Thalamus, VA, OCD, Pair 11, HUID 13169

description: S2 flow cell

value: OCD

value: Pair 11


title: Huh1_siLuc_H3K4me2_rep1

description: Library name: siLuc_H3K4me2_rep1


title: Huh1_siHNF4A_H3K4me1_rep4

description: Library name: siHNF4A_H3K4me1_rep4


title: CD36KO-whole heart-replicate-2

description: Library name: B02


title: Thalamus, VA, OCD, Pair 2, HUID 1424

description: S2 flow cell

value: HUID 1424

value: Pair 2


title: Thalamus, VA, CON, Pair 11, HUID 1834

description: S2 flow cell

value: VA

value: HUID 1834


title: CD36KO-whole heart-replicate-1

description: Library name: B01


title: Thalamus, VA, CON, Pair 2, HUID 1293

description: S2 flow cell

value: CON

value: HUID 1293


title: Huh1_siHNF4A_H3K4me1_rep3

description: Library name: siHNF4A_H3K4me1_rep3


title: WT-whole heart-replicate-3

description: Library name: A03

value: wild-type


title: Thalamus, VA, OCD, Pair 10, HUID 13154

description: S2 flow cell

value: Thalamus

value: Pair 10


title: Huh1_siHNF4A_H3K4me1_rep2

description: Library name: siHNF4A_H3K4me1_rep2


title: WT-whole heart-replicate-2

description: Library name: A02


title: Huh1_siHNF4A_H3K4me1_rep1

description: Library name: siHNF4A_H3K4me1_rep1


title: Thalamus, VA, CON, Pair 10, HUID 1282

description: S2 flow cell

value: right

value: HUID 1282


title: Huh1_siKDM6A_H3K4me1_rep2

description: Library name: siKDM6A_H3K4me1_rep2


title: Huh1_siKDM6A_H3K4me1_rep4

description: Library name: siKDM6A_H3K4me1_rep4


title: Huh1_siKDM6A_H3K4me1_rep1

description: Library name: siKDM6A_H3K4me1_rep1


title: Huh1_siLuc_H3K4me1_rep4

description: Library name: siLuc_H3K4me1_rep4


title: Thalamus, VA, OCD, Pair 1, HUID 1413

description: S2 flow cell

value: HUID 1413

value: Pair 1


title: Thalamus, VA, CON, Pair 1, HUID 1159

description: S2 flow cell

value: HUID 1159


title: Huh1_siLuc_H3K4me1_rep2

description: Library name: siLuc_H3K4me1_rep2


title: Huh1_siLuc_H3K4me1_rep1

description: Library name: siLuc_H3K4me1_rep1


title: Huh1_siLuc_H3K4me1_rep3

description: Library name: siLuc_H3K4me1_rep3


title: Thalamus, MDPC, OCD, Pair 9, HUID 13125

description: S2 flow cell

value: MDPC

value: Pair 9


title: Huh1_siKDM6A_H3K4me1_rep3

description: Library name: siKDM6A_H3K4me1_rep3


title: WT-whole heart-replicate-1

description: Library name: A01

value: Whole heart tissue


title: HROhep03_siHNF4A_H3K27me3_rep4

description: Library name: siHNF4A_H3K27me3_rep4

extract_protocol:
Fresh liver tissues (chopped into small pieces) and HROhep03 cells were crosslinked with 1% formaldehyde (ThermoFisher, 28906) in PBS for 10 minutes for histone modifications. For transcription factors (TFs), tissues/cells were double crosslinked with 2 mM disuccinimidyl glutarate (DSG) (ThermoFisher, 20593) for 30 minutes, followed by 1% formaldehyde for 10 minutes. The reaction was stopped with glycine at a final concentration of 0.125 M for 5 minutes. Liver pieces were disaggregated in ice-cold PBS with protease inhibitor using a Dounce Homogenizer, first with a loose pestle and then with a tight pestle (Fisher Science, FB56691). Nuclei were isolated using three lysis buffers: lysis buffer 1 (50 mM Hepes–KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100), lysis buffer 2 (10 mM Tris–HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and lysis buffer 3 (10 mM Tris–HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, and 0.5% N-Lauroylsarcosine). The samples were then sonicated for 30 minutes (30 seconds ON/30 seconds OFF) using the Bioruptor Pico (Diagenode).
For ChIP-seq sample preparation, the same ChIP protocol was followed, but the ChIP DNA was purified using the ChIP DNA Clean and Concentrator Capped Zymo-Spin I (Zymo Research) purification kit. Two to four ChIPs were pooled during the final purification step to obtain concentrated material. For library preparation and sequencing, 2–10 ng of ChIPed DNA was processed using the Rubicon ThruPLEX DNA-seq kit (TAKARA) following standard protocols, and sequenced on the NovaSeq X Plus Series (150PE reads, NOVOGENE, United Kingdom).


title: Thalamus, MDPC, CON, Pair 9, HUID 1637

description: S2 flow cell

value: HUID 1637


title: RPE, Ctrl1

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

country: South Korea

institute: UNIST

data_processing:
Gene expression matrices were generated using Cell Ranger 6.0.1 from 10x Genomics with the mouse genome reference data (mm10).
All raw files were mapped to the human genome reference data (GRCh38) using STAR (version 2.7.3a). After evaluating quality of the raw data by FastQ Screen (version 0.14.1), we calculated TPM (transcripts per millions) using RSEM (RNA-Seq by Expectation-Maximization) (version 1.3.1).
STAR (version 2.7.10b) was used to map the raw sequencing data to the mouse genome reference data (GRCm39). FastQ Screen (version 0.14.1) was used to check the raw data quality. Transcripts per million (TPM) were obtained using RNA-Seq by Expectation-Maximization (RSEM) (version 1.3.1).
Assembly: mm10
Assembly: GRCh38
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: tab-delimited text file includes TPM count for each Sample

source_name: eye

extract_protocol:
RPE cells were carefully dissociated using a papain solution (20 U/ml) supplemented with DNase-I (2000 U/ml) in Earle’s balanced salt solution (EBSS) and incubated in a water bath at 37 °C for 30 minutes. The dissociated single RPE cell pellet was washed with PBS and collected after centrifugation at 1200 RPM for 3 min. The RPE samples were then filtered through a 30 µm cell strainer (Miltenyi Biotech, Cat. #130-098-458) and washed twice with cold Ca²⁺- and Mg²⁺-free 0.04% BSA/PBS at 300g for 5 minutes at 4°C. The samples were gently resuspended in cold Ca²⁺- and Mg²⁺-free 0.04% BSA/PBS and counted using a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems) after acridine orange (AO) and propidium iodide (PI) staining (Logos Biosystems, Cat. #F23001).
Cells were harvested after 5 days and total RNA was isolated using QIAzol Lysis Reagent (QIAZEN). Total RNA concentration was measured using the Quant-IT RiboGreen Assay (Invitrogen, #R11490). To assess RNA integrity, samples were analyzed using the TapeStation RNA ScreenTape system (Agilent, #5067-5576) and only RNA samples with an RNA Integrity Number (RIN) greater than 7.0 were selected for RNA library preparation. For each sample, 1 µg of total RNA was used to construct libraries using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2101). Poly-A mRNA was isolated using poly-T coated magnetic beads and fragmented at high temperatures in the presence of divalent cations.
The eyeballs were trimmed to remove surrounding muscle and anterior segments were dissected. After carefully removing the retina, lysis buffer was gently applied to the eye cup and RNA was extracted following the manufacturer’s instructions for the RNeasy Mini Kit (QIAGEN).
scRNA-seq libraries were prepared using the 10x Chromium Controller and Next GEM Single Cell 5’ Reagent v2 kits (10x Genomics, PN-1000244), following the 10x Chromium Single Cell 5’ v2 protocol. Cell suspension with a target recovery of 10,000 cells was combined with a reverse transcription master mix and loaded onto a Single Cell K-Chip (10x Genomics, PN-1000286) together with single cell 5′ gel beads and partitioning oil to generate gel beads-in-emulsion (GEMs), in which RNA transcripts from individual cells were uniquely barcoded and reverse transcribed. The resulting barcoded full-length cDNA was amplified by PCR, and for 5’ Gene Expression Library preparation, the cDNA underwent enzymatic fragmentation, end repair, A-tailing, adapter ligation, and index PCR. The purified libraries were quantified by the qPCR Qualification Protocol Guide (KAPA), evaluated for quality with the Agilent 4200 TapeStation (Agilent Technologies), and sequenced on the Illumina HiSeq platform (Illumina).
cDNA library was generated from the fragmented RNA with SuperScript II reverse transcriptase (Invitrogen, 18064014). Quantification of the prepared libraries was performed using the KAPA Library Quantification Kit for Illumina platforms according to the manufacturer's protocol (KAPA BIOSYSTEMS, #KK4854). Library quality was assessed using the TapeStation D1000 ScreenTape (Agilent, #5067-5582). The indexed libraries were then sequenced on an Illumina NovaSeqX platform (Illumina) with paired-end 2×100 bp reads performed by Macrogen Incorporated.
The sequencing library was then constructed using the SMARTer Stranded RNA-Seq Kit according to the manufacturer’s instructions. Library quantification, quality assessment, and sequencing on Illumina NovaSeqX platform were performed as described above.

tag: strain

value: eye

value: RPE

tag: condition

value: old mice treated without TRULI


title: RPE, TRULI2

value: old mice treated with TRULI


title: RPE, Ctrl2


title: HROhep03_siHNF4A_H3K27me3_rep2

description: Library name: siHNF4A_H3K27me3_rep2


title: Thalamus, MDPC, OCD, Pair 8, HUID 13173

description: S2 flow cell

value: OCD

value: Pair 8


title: HROhep03_siKDM6A_H3K27me3_rep4

description: Library name: siKDM6A_H3K27me3_rep4


title: HROhep03_siHNF4A_H3K27me3_rep1

description: Library name: siHNF4A_H3K27me3_rep1


title: HROhep03_siHNF4A_H3K27me3_rep3

description: Library name: siHNF4A_H3K27me3_rep3


title: HROhep03_siKDM6A_H3K27me3_rep3

description: Library name: siKDM6A_H3K27me3_rep3


title: 4_HiC_OHSC_rep2

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

data_processing:
cutadapt
STAR alignment (RNA-seq)
featureCount, gene-level extraction (RNA-seq)
HiCUP v 0.7.2 (Hi-C)
Juicer 1.6 (Hi-C)
Assembly: mm10
Supplementary files format and content: gene count text file
Supplementary files format and content: Juicer hic file, binary

source_name: Bone marrow

extract_protocol:
RNA was purified with TRIzol TM Reagent (Invitrogen, 15596026) and Direct-zol RNA microprep (Zymo R2060)
RNA-seq libraries were constructed using SMART-seq v4 Ultra Low Input RNA Kit (634891, TaKaRa)
Hi-C: DNA was purified with 1.6 SPRIselect beads (B23318, Beckman Coulter)
Hi-C: Libraries were prepared with TruSeq Nano DNA Low Throughpout Library Kit (20015964, Illumina)

value: Bone marrow

value: Hematopoietic stem cell

value: WT

value: Old


title: RPE, TRULI1


title: Thalamus, MDPC, CON, Pair 8, HUID 13237

description: S2 flow cell

value: Thalamus

value: right

value: CON


title: HROhep03_siKDM6A_H3K27me3_rep2

description: Library name: siKDM6A_H3K27me3_rep2


title: HROhep03_siKDM6A_H3K27me3_rep1

description: Library name: siKDM6A_H3K27me3_rep1


title: 3_HiC_OHSC_rep1


title: Thalamus, MDPC, OCD, Pair 7, HUID 13022

description: S2 flow cell

value: MDPC

value: Pair 7


title: HROhep03_siLuc_H3K27me3_rep4

description: Library name: siLuc_H3K27me3_rep4


title: Thalamus, MDPC, CON, Pair 7, HUID 1083

description: S2 flow cell

value: HUID 1083


title: HROhep03_siLuc_H3K27me3_rep3

description: Library name: siLuc_H3K27me3_rep3


title: HROhep03_siHNF4A_H3K27ac_rep4

description: Library name: siHNF4A_H3K27ac_rep4


title: HROhep03_siLuc_H3K27me3_rep2

description: Library name: siLuc_H3K27me3_rep2


title: Thalamus, MDPC, OCD, Pair 6, HUID 13051

description: S2 flow cell

value: Pair 6


title: 1_HiC_YHSC_rep1

value: Young


title: 2_HiC_YHSC_rep2


title: HROhep03_siLuc_H3K27me3_rep1

description: Library name: siLuc_H3K27me3_rep1


title: Thalamus, MDPC, CON, Pair 6, HUID 1391

description: S2 flow cell

value: HUID 1391


title: HROhep03_siHNF4A_H3K27ac_rep2

description: Library name: siHNF4A_H3K27ac_rep2


title: Thalamus, MDPC, OCD, Pair 5, HUID 1785

description: S2 flow cell

value: HUID 1785

value: Pair 5


title: HROhep03_siHNF4A_H3K27ac_rep3

description: Library name: siHNF4A_H3K27ac_rep3


title: HROhep03_siHNF4A_H3K27ac_rep1

description: Library name: siHNF4A_H3K27ac_rep1


title: Thalamus, MDPC, CON, Pair 5, HUID 1543

description: S2 flow cell

value: HUID 1543


title: transplant_HSC_Btaf1_shRNA1_rep2

molecule: polyA RNA


title: transplant_HSC_Btaf1_shRNA2_rep1


title: Thalamus, MDPC, CON, Pair 4, HUID 1092

description: S2 flow cell

value: HUID 1092

value: Pair 4


title: transplant_HSC_shControl_rep2

value: Bone marrow

value: Hematopoietic stem cell

value: control


title: HROhep03_siKDM6A_H3K27ac_rep3

description: Library name: siKDM6A_H3K27ac_rep3


title: HROhep03_siLuc_H3K27ac_rep2

description: Library name: siLuc_H3K27ac_rep2


title: HROhep03_siKDM6A_H3K27ac_rep1

description: Library name: siKDM6A_H3K27ac_rep1


title: HROhep03_siKDM6A_H3K27ac_rep4

description: Library name: siKDM6A_H3K27ac_rep4


title: transplant_HSC_Btaf1_shRNA1_rep1

value: WT


title: HROhep03_siLuc_H3K27ac_rep4

description: Library name: siLuc_H3K27ac_rep4


title: transplant_HSC_Btaf1_shRNA2_rep2


title: HROhep03_siHNF4A_H3K4me2_rep3

description: Library name: siHNF4A_H3K4me2_rep3


title: in_vitro_Btaf1_shRNA2_rep2


title: HROhep03_siLuc_H3K27ac_rep3

description: Library name: siLuc_H3K27ac_rep3


title: Thalamus, MDPC, OCD, Pair 3, HUID 1435

description: S2 flow cell

value: Thalamus

value: right

value: OCD

value: HUID 1435

value: Pair 3


title: HROhep03_siLuc_H3K27ac_rep1

description: Library name: siLuc_H3K27ac_rep1


title: HROhep03_siHNF4A_H3K4me2_rep4

description: Library name: siHNF4A_H3K4me2_rep4


title: HROhep03_siKDM6A_H3K27ac_rep2

description: Library name: siKDM6A_H3K27ac_rep2


title: Thalamus, MDPC, CON, Pair 3, HUID 13032

description: S2 flow cell

value: MDPC

value: CON


title: transplant_HSC_shControl_rep1


title: HROhep03_siHNF4A_H3K4me2_rep2

description: Library name: siHNF4A_H3K4me2_rep2


title: in_vitro_Btaf1_shRNA2_rep1


title: HROhep03_siKDM6A_H3K4me2_rep4

description: Library name: siKDM6A_H3K4me2_rep4


title: Thalamus, MDPC, OCD, Pair 2, HUID 1424

description: S2 flow cell

value: HUID 1424

value: Pair 2


title: in_vitro_Btaf1_shRNA1_rep2


title: Thalamus, MDPC, OCD, Pair 4, HUID 1505

description: S2 flow cell

value: HUID 1505


title: HROhep03_siKDM6A_H3K4me2_rep3

description: Library name: siKDM6A_H3K4me2_rep3


title: HROhep03_siKDM6A_H3K4me2_rep1

description: Library name: siKDM6A_H3K4me2_rep1


title: HROhep03_siKDM6A_H3K4me2_rep2

description: Library name: siKDM6A_H3K4me2_rep2


title: HROhep03_siHNF4A_H3K4me2_rep1

description: Library name: siHNF4A_H3K4me2_rep1


title: Thalamus, MDPC, OCD, Pair 11, HUID 13169

description: S2 flow cell

value: Pair 11


title: in_vitro_Btaf1_shRNA1_rep1


title: Thalamus, MDPC, CON, Pair 2, HUID 1293

description: S2 flow cell

value: HUID 1293


title: HROhep03_siLuc_H3K4me2_rep4

description: Library name: siLuc_H3K4me2_rep4


title: Thalamus, MDPC, CON, Pair 11, HUID 1834

description: S2 flow cell

value: HUID 1834


title: Thalamus, MDPC, OCD, Pair 10, HUID 13154

description: S2 flow cell

value: Pair 10


title: HROhep03_siLuc_H3K4me2_rep3

description: Library name: siLuc_H3K4me2_rep3


title: HROhep03_siLuc_H3K4me2_rep1

description: Library name: siLuc_H3K4me2_rep1


title: in_vitro_shControl_rep2

value: Bone marrow

value: Hematopoietic stem cell


title: HROhep03_siHNF4A_H3K4me1_rep3

description: Library name: siHNF4A_H3K4me1_rep3


title: Thalamus, MDPC, CON, Pair 10, HUID 1282

description: S2 flow cell

value: HUID 1282


title: HROhep03_siLuc_H3K4me2_rep2

description: Library name: siLuc_H3K4me2_rep2


title: Thalamus, MDPC, OCD, Pair 1, HUID 1413

description: S2 flow cell

value: Thalamus

value: HUID 1413

value: Pair 1


title: HROhep03_siHNF4A_H3K4me1_rep4

description: Library name: siHNF4A_H3K4me1_rep4


title: Pan02 tumor, GITR

city: Bern

first: Hanne

last: Hillen

address: Murtenstrasse 31

department: IGMP

country: Switzerland

institute: University Bern

data_processing:
Raw reads were aligned using a pre-built reference for mouse genomes, refdata-gex-mm10-2020-A; Mouse reference, mm10 (GENCODE vM23/Ensembl 98) using CellRanger (version 7.1, 10× Genomics Inc., Pleasanton, CA, USA)
Assembly: refdata-gex-mm10-2020-A; Mouse reference, mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: The output of CellRanger was three GZ files, namely barcodes.tsv.gz, features.tsv.gz and matrix.tsv.gz and contains all the output information required for downstream analysis.

source_name: tumor

growth_protocol: C57BL/6 mice were received from Janvier Labs (France) and experimental animals were bred and housed in specific pathogen-free conditions in the Central Animal Facility (CAF). Eight to twelve-week-old age- and sex-matched animals were used. Mice were randomly assigned to different treatment groups prior to tumor injection. Pan02 cells were stored in liquid nitrogen, slowly thawed and cultured in RPMI+10%FCS for 3 days prior to injection. Then, tumors were engrafted by subcutaneous (s.c.) injection of 2 × 10^5 Pan02 cells onto the left flanks of the mice. Tumors were grown for 14 days before harvesting.

extract_protocol:
On day 14 post-tumor-inoculation, mice were euthanized, and the tumors were isolated. Tumors were cut into 2–4 mm pieces and placed into a gentleMACS C tube (Miltenyi). Tumors were enzymatically digested using the gentleMACSTM Dissociator and tumor Dissociation kit (Miltenyi) according to manufacturer’s protocol. Cells were filtered through a 70 µm cell strainer to discard any remaining undigested tissue before proceeding with the FACS staining. Zombie Aqua Viability dye (Zombie dye, BioLegend) and PE-Cy7 anti-CD45.2 (clone 104, Biologend) were used to sort for live immune cells.
Single Cell 3′ v3 performed on a Chromium Controller

treatment_protocol: Mice were treated with intra-peritoneal (i.p.) injection of PBS (control) or agonistic anti-mouse GITR monoclonal antibody (500μg in 200μL i.p.) (clone DTA-1, InVivoMab).

value: tumor

value: cancer cell

value: WT

value: agonistic anti-GITR monoclonal antibody (DTA-1)


title: Pan02 tumor, PBS

value: PBS


title: HROhep03_siHNF4A_H3K4me1_rep1

description: Library name: siHNF4A_H3K4me1_rep1


title: Thalamus, MDMC, OCD, Pair 9, HUID 13125

description: S2 flow cell

value: MDMC

value: right

value: OCD

value: Pair 9


title: in_vitro_shControl_rep1

value: control


title: HROhep03_siHNF4A_H3K4me1_rep2

description: Library name: siHNF4A_H3K4me1_rep2


title: F12-WT, HP1

city: Nijmegen

first: Jonas

last: Gockel

email: jonas-gockel@web.de, jonas.gockel@ru.nl

address: Geert Grooteplein-Zuid 8

country: Netherlands

institute: Radboud University

description: Library name: F12-WT

data_processing:
Sequencing reads were mapped against the reference genome PlasmoDB v26 3D7 with bowtie2 (v2.5.2)
Reads were filtered for mapping quality higher or equal than 30 and mitrochondrial and apicoplast reads were removed with samtools (v1.18)
BigWig files normalised to RPMK were generated with deeptools (v3.5.4)
Bedgraphs were generated for visualisation on UCSC genome browser with bedtools (v2.31.0) normalised to reads per million
Log2 ratio tracks were generated by running the multiBigwigSummary command from deeptools (v3.5.4) using 2000 bp bins on both plusRAPA and noRAPA bigwig files. A pseudocount of 1 was added to all values to prevent divisions by 0, and log2 values were calculated in bash and appended to a new bedGraph file for visualisation on UCSC genome browser.
Averages of 3 replicates were calculated by combining replicate bedgraphs into one file with bedtools unionbedg (v2.31.0), averages per position were calculated and a new bedgraph file was generated.
Assembly: PlasmoDB v26 3D7
Supplementary files format and content: bedGraph
Library strategy: CUT&Tag

organism: Plasmodium falciparum

source_name: F12 WT

growth_protocol: RPMI 1640 medium supplemented with 0.2% NaHCO3, 200 µM hypoxyxanthine and 10% human serum at 37 °C under low oxygen conditions (3% O2, 4% CO2 and 93% N2) in human red blood cells at 5% hematocrit.

extract_protocol:
For nuclei isolation, parasite cultures were lightly crosslinked with 0.1% formaldehyde (Sigma, F8775), incubating for 2 min at 37 °C while shaking. Crosslinking was stopped by addition of glycine to 0.125 M final concentration. Samples were handled on ice from here onwards. Cells were harvested by 440 g centrifugation for 8 min at 4 °C, and washed with ice-cold PBS. Centrifugation was repeated and the pellet was washed with PBS supplemented with 1x EDTA-free Protease Inhibitor (Roche, 04693132001). Parasites were extracted by adding saponin (0.05% total concentration) and incubating at room temperature (RT) for 10 min. Nuclei were isolated by carefully transferring the extracted parasite mixture on top of a 0.25 M to 0.1 M sucrose gradient in cell lysis buffer (10 mM Tris pH 8, 3 mM MgCl2, 0.2% NP-40, 1x EDTA free Protease inhibitor (Roche, 04693132001); 15 mL 0.25 M Sucrose and 17.5 mL 0.1M Sucrose for 50 mL tubes, 4 mL 0.25 M Sucrose and 6 mL 0.1 M Sucrose for 15 mL tubes) and centrifuging for 12 min, 3100 g, 4 °C with acceleration and deceleration set to 1 (Eppendorf 5910 Ri, Rotor S-4x400). Supernatant was removed and nuclei washed in cell lysis buffer (10 min, 3500 g, 4 °C; Heraeus Fresco 21). and were directly used for CUT&Tag. Nuclei were washed with cell lysis buffer containing 20% Glycerol and nuclei pellet was snap frozen in liquid nitrogen prior to storage at -80°C. Nuclei were resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor) containing 0.1% Triton X-100 and permeabilized for 10 min on ice. Meanwhile, nuclei were counted in an automatic hemocytometer (BioRad, TC10 Automated Cell Counter). Nuclei were pelleted by centrifugation (3500 g, 10 min, 4 °C) and resuspended in CUT&Tag wash buffer. Concanavalin A beads (Bangs Laboratories, BP531) were activated by resuspending into 10 volumes of Bead Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), washed once on a magnetic rack and resuspended in the starting volume of bead slurry. Purified nuclei were bound to 10 µL beads per reaction by incubating for 10 min rotating at RT. The supernatant was removed and 50 µL antibody buffer (CUT&Tag wash buffer; 2 mM EDTA, 0.1% BSA) with primary Antibody (0.25 µL polyclonal rabbit αHP1) was added and incubated nutating over night at 4 °C. Unbound primary antibody was removed by washing once with 100 µL CUT&Tag wash buffer and samples were then incubated with secondary antibody (1.2 µg guinea pig anti-rabbit antibody, Antibodies-Online ABIN101961; in 100 µL CUT&Tag wash buffer, 1:100 dilution) for 1h on RT, nutating. The nuclei were washed on a magnetic stand twice with 100 µL CUT&Tag wash buffer and once with 100 µL CUT&Tag 300 Wash Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor). For all following wash steps CUT&Tag 300 wash buffer was used in order to quench potential affinity of protA-Tn5 to accessible chromatin regions. 2.5 µL commercial proteinA/G-Tn5 fusion protein (CUTANA™ pAG-Tn5 for CUT&Tag, Epicypher, 15-1017) was added in 50 µL CUT&Tag 300 wash buffer and incubated nutating for 1 h. Unbound proteinA/G-Tn5 fusion protein was removed by thrice washing with 100 µL CUT&Tag 300 wash buffer. The supernatant was removed and the nuclei were resuspended in 200 µL freshly prepared tagmentation buffer (CUT&Tag 300 wash buffer, 10 mM MgCl2). To perform tagmentation, samples were incubated in a PCR thermocycler (BioRad, T100) at 37 °C for 1h. Tagmentation was stopped and nuclei lysis was facilitated by addition of 10 µL of 0.5M EDTA pH8, 3 µL of 10% SDS and 1 µL of 50 mg/mL proteinase K. Samples were briefly vortexed and then incubated at 55 °C for 1 h. DNA fragments were extracted utilizing the DNA Clean & Concentrator - 5 kit (Zymogen, D4014) following manufactures instructions. DNA was eluted from the column with 26 µL of prewarmed elution buffer and DNA concentrations were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231).
Libraries were generated using maximal 50 ng of extracted DNA from CUT&Tag experiments and tagged fragments were amplified with unique combinations of i5 and i7 barcoded primers, enabling tracing the DNA fragments originating from separate experiments in the sequencing data. PCRs were performed in a total reaction volume of 50 µL using Kapa HiFi polymerase (use non-hotstart version for gap filling; Roche, KK2102) in a thermocycler with the following program: 58 °C for 5 min, 62 °C for 5 min (gap filling), 98 °C for 2 min, 12-16 cycles of 98 °C for 20 second and 62 °C for 10 seconds, 62 °C for 1 min and hold at 4 °C. Post-PCR DNA cleanup was performed by adding 50 µL (1x volume) of AMPure XP bead slurry (Beckman Coulter, A63882) and incubating for 10 min at RT, washing twice with 80% EtOH on a magnetic rack, and eluting in 16.5 µL of 10 mM Tris-HCl pH 8 for 5 min at RT. DNA concentrations of libraries were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231) and library fragment size distribution was accessed by microfluidic gel electrophoresis (Agilent 2100 Bioanalyser) with the corresponding High Sensitivity DNA Kit (Agilent, 5067-4626). Sequencing was performed using an Illumina NextSeq 2000 instrument for 3-10 M reads per CUT&Tag sample; 59bp paired-end reads were generated.

value: F12 WT


title: HROhep03_siKDM6A_H3K4me1_rep4

description: Library name: siKDM6A_H3K4me1_rep4


title: UNC0638, HP1

description: Library name: UNC0638


title: HROhep03_siKDM6A_H3K4me1_rep2

description: Library name: siKDM6A_H3K4me1_rep2


title: HROhep03_siLuc_H3K4me1_rep4

description: Library name: siLuc_H3K4me1_rep4


title: HROhep03_siKDM6A_H3K4me1_rep3

description: Library name: siKDM6A_H3K4me1_rep3


title: HROhep03_siLuc_H3K4me1_rep2

description: Library name: siLuc_H3K4me1_rep2


title: UNC0224, HP1

description: Library name: UNC0224


title: SGC0946, HP1

description: Library name: SGC0946


title: Thalamus, MDMC, OCD, Pair 8, HUID 13173

description: S2 flow cell

value: Pair 8


title: HROhep03_siKDM6A_H3K4me1_rep1

description: Library name: siKDM6A_H3K4me1_rep1


title: Huh1_antiKDM6A_siHNF4A_rep2

description: Library name: Huh1_antiKDM6A_siHNF4A_rep2

data_processing:
Sequencing data was processed using standard pipelines. Sequencing files (fastq files) provided by NOVOGENE (Cambridge, United Kingdom) were aligned to the GRCh38/hg38 version of the human reference genome using Bowtie2. Duplicate reads were removed, and peaks were called using the HOMER package to identify regions of significant enrichment. SEACR is used to call peaks and enriched regions from chromatin profiling data. ChIPseqSpikeInFree is used to normalize Data.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

growth_protocol: HROHep03 cells were maintained in high-glucose DMEM/F12 medium, supplemented with 5% FBS and 1% antibiotics. Cells were incubated at 37°C in an atmosphere of 5% CO2. Huh1 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, D5648, Merck) supplemented with 10% fetal bovine serum (FBS, SH30071.03, HyClone) and 1% Penicillin-Streptomycin (P4458, Merck).

extract_protocol:
CUT&TAG sample preparation was performed following protocols from the Fred Hutchinson Cancer Research Center. Approximately 50,000 harvested and counted cells were resuspended in Wash Buffer and mixed with Concanavalin A-coated magnetic beads. The mixture was incubated at room temperature to allow binding. Bead-bound cells were then washed and incubated with a primary antibody(anti-KDM6A, invitrogen, PA5-31828, 1μg) specific to the target protein, followed by a secondary antibody for bridging. Next, the bead-bound cells were incubated with Protein A-Tn5 transposase in the presence of digitonin for tethering. After a brief incubation to allow the transposome to tether to chromatin sites targeted by antibodies, cells were washed and subjected to magnesium activation to induce tagmentation. This step facilitated DNA cleavage and simultaneous tagging with sequencing adapters. Following tagmentation, DNA was purified using SPRI beads and quantified using a fluorometric method.
Libraries were PCR-amplified with barcoded primers, cleaned up, and subjected to quality control checks, including size selection and quantification.


title: Thalamus, MDMC, CON, Pair 8, HUID 13237

description: S2 flow cell

value: CON


title: HROhep03_siLuc_H3K4me1_rep3

description: Library name: siLuc_H3K4me1_rep3


title: Huh1_antiKDM6A_siHNF4A_rep1

description: Library name: Huh1_antiKDM6A_siHNF4A_rep1


title: HROhep03_siLuc_H3K4me1_rep1

description: Library name: siLuc_H3K4me1_rep1


title: Ryuvidine, HP1

description: Library name: Ryuvidine


title: Mocetinostat, HP1

description: Library name: Mocetinostat


title: Thalamus, MDMC, CON, Pair 9, HUID 1637

description: S2 flow cell

value: HUID 1637


title: Huh1_antiKDM6A_siluc_rep4

description: Library name: Huh1_antiKDM6A_siluc_rep4


title: Huh1_antiKDM6A_siHNF4A_rep3

description: Library name: Huh1_antiKDM6A_siHNF4A_rep3


title: Huh1_antiKDM6A_siluc_rep3

description: Library name: Huh1_antiKDM6A_siluc_rep3


title: Thalamus, MDMC, OCD, Pair 6, HUID 1785

description: S2 flow cell

value: Thalamus

value: HUID 1785

value: Pair 6


title: MM_102, HP1

description: Library name: MM_102


title: Huh1_antiKDM6A_siluc_rep2

description: Library name: Huh1_antiKDM6A_siluc_rep2


title: Thalamus, MDMC, OCD, Pair 7, HUID 13022

description: S2 flow cell

value: Pair 7


title: HRO_antiKDM6A_siHNF4A_rep4

description: Library name: HRO_antiKDM6A_siHNF4A_rep4


title: Huh1_antiKDM6A_siHNF4A_rep4

description: Library name: Huh1_antiKDM6A_siHNF4A_rep4


title: Thalamus, MDMC, CON, Pair 7, HUID 1083

description: S2 flow cell

value: HUID 1083


title: Thalamus, MDMC, CON, Pair 6, HUID 1391

description: S2 flow cell

value: HUID 1391


title: Thalamus, MDMC, CON, Pair 5, HUID 1543

description: S2 flow cell

value: HUID 1543

value: Pair 5


title: HRO_antiKDM6A_siHNF4A_rep3

description: Library name: HRO_antiKDM6A_siHNF4A_rep3


title: Thalamus, MDMC, OCD, Pair 6, HUID 13051

description: S2 flow cell

value: MDMC


title: ML_324, HP1

description: Library name: ML_324


title: HRO_antiKDM6A_siluc_rep4

description: Library name: HRO_antiKDM6A_siluc_rep4


title: GSK_J4, HP1

description: Library name: GSK_J4


title: Thalamus, MDMC, OCD, Pair 4, HUID 1505

description: S2 flow cell

value: right

value: HUID 1505

value: Pair 4


title: HRO_antiKDM6A_siluc_rep3

description: Library name: HRO_antiKDM6A_siluc_rep3


title: HRO_antiKDM6A_siHNF4A_rep2

description: Library name: HRO_antiKDM6A_siHNF4A_rep2


title: HRO_antiKDM6A_siluc_rep2

description: Library name: HRO_antiKDM6A_siluc_rep2


title: HRO_antiKDM6A_siluc_rep1

description: Library name: HRO_antiKDM6A_siluc_rep1


title: Thalamus, MDMC, CON, Pair 4, HUID 1092

description: S2 flow cell

value: HUID 1092


title: GSK343, HP1

description: Library name: GSK343

value: F12 WT


title: Thalamus, MDMC, OCD, Pair 3, HUID 1435

description: S2 flow cell

value: OCD

value: HUID 1435

value: Pair 3


title: DMSO, rep2, HP1

description: Library name: DMSO, rep2


title: Huh1_antiKDM6A_siluc_rep1

description: Library name: Huh1_antiKDM6A_siluc_rep1


title: EPZ004777, HP1

description: Library name: EPZ004777


title: Heterochromatin Spreadig Sensor, HP1

description: Library name: HSS_HP1


title: HRO_antiKDM6A_siHNF4A_rep1

description: Library name: HRO_antiKDM6A_siHNF4A_rep1


title: DMSO, rep1, HP1

description: Library name: DMSO, rep1


title: OVCAR8_DHX9i_rep 1

city: Bethesda

first: Tzu-Ting

last: Huang

state: MD

address: 10 Center Dr., Bldg 10, Rm 6B05

institute: National Cancer Institute

description: Library name: 70_OVCAR8_DHX9i_1

data_processing:
Reads were quality-trimmed using Cutadapt v3.4 and aligned to hg38 reference genome using STAR v2.7.9a with GENCODE v38 annotations. Gene expression quantification was performed using STAR/RSEM v1.3.3, followed by quartile normalization and log2 transformation.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

growth_protocol: All cell lines were maintained in RPMI-1640 medium, supplemented with 10% fetal bovine serum, 0.01 mg/mL insulin, and 1% penicillin-streptomycin at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) with on-column DNase treatment.
Library preparation used the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, followed by sequencing on NovaSeq X Plus 10B platform (150 bp paired-end reads, ~50 million reads per sample).

value: ovarian cancer cells

value: 10 uM DHX9i


title: OVCAR8_DMSO_rep 2

description: Library name: 68_OVCAR8_2


title: OVCAR8_DHX9i_rep 3

description: Library name: 72_OVCAR8_DHX9i_3


title: Thalamus, MDMC, OCD, Pair 2, HUID 1424

description: S2 flow cell

value: Thalamus

value: HUID 1424

value: Pair 2


title: OVCAR8_DHX9i_rep 2

description: Library name: 71_OVCAR8_DHX9i_2


title: OVCAR8_DMSO_rep 3

description: Library name: 69_OVCAR8_3


title: OVCAR8_DMSO_rep 1

description: Library name: 67_OVCAR8_1


title: PEO4_DHX9i_rep 3

description: Library name: 60_PEO4_DHX9i_3


title: PEO4_DHX9i_rep 1

description: Library name: 58_PEO4_DHX9i_1


title: BIX01294, HP1

description: Library name: BIX01294


title: Thalamus, MDMC, CON, Pair 2, HUID 1293

description: S2 flow cell

value: CON

value: HUID 1293


title: PEO4_DHX9i_rep 2

description: Library name: 59_PEO4_DHX9i_2


title: Thalamus, MDMC, OCD, Pair 11, HUID 13169

description: S2 flow cell

value: Pair 11


title: caSTAT3+5, donor1 (caS3+5_donor1)

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

description: Library name: caS3+5_donor1

data_processing:
DNBSEQ-T7 was used for base calling.
Sequenced reads were trimmed with low-quality bases using fastp. Read lengths less than 15 nucleotides or a PHRED Quality Score of less than 15 were removed.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.2.1).
Read counts for each gene were calculated using featureCounts of the Subread package (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: Calculated raw read counts for individual genes are shown in a tab-delimited text file.

source_name: CD8+ T cells

growth_protocol: Human T cells were stimulated on day 0 with K562 cells engineered to express an anti-CD3 monoclonal antibody (clone OKT3)-derived scFv fused to the transmembrane and cytoplasmic domains of CD8α, along with CD80 (K562-OKT3/CD80). On day 2, the stimulated T cells were retrovirally transduced with an anti-CD19 CAR construct (FMC63-28z) alone, in combination with caSTAT3, or with both caSTAT3 and caSTAT5. The CAR-T cells were then expanded in vitro in RPMI medium supplemented with 10% FBS and 100 IU/mL recombinant human IL-2.

extract_protocol:
CD8+ CAR-T cell populaiton was isolated by an MA900 Cell Sorter (Sony). Total RNA was isolated from the purified CD8+ T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA libraries were prepared using the MGIEasy Fast RNA Library Prep Set, following the standard protocols for the DNBSEQ-T7 platform.

treatment_protocol: Control, caSTAT3, or caSTAT3+5-expressing CAR-T cells were cultured overnight in cytokine-free medium on day6.

value: CD8+ T cells

value: donor 1


title: caSTAT3+5, donor2 (caS3+5_donor2)

description: Library name: caS3+5_donor2

value: donor 2


title: PEO4_DMSO_rep 3

description: Library name: 57_PEO4_3


title: PEO4_DMSO_rep 1

description: Library name: 55_PEO4_1


title: Thalamus, MDMC, CON, Pair 11, HUID 1834

description: S2 flow cell

value: MDMC

value: right

value: HUID 1834


title: PEO4_DMSO_rep 2

description: Library name: 56_PEO4_2


title: Thalamus, MDMC, CON, Pair 3, HUID 13032

description: S2 flow cell


title: caSTAT3+5, donor3 (caS3+5_donor3)

description: Library name: caS3+5_donor3

value: donor 3


title: OVCAR3_DHX9i_rep 2

description: Library name: 53_OVCAR3_DHX9i_2


title: Thalamus, MDMC, OCD, Pair 10, HUID 13154

description: S2 flow cell

value: OCD

value: Pair 10


title: OVCAR3_DHX9i_rep 1

description: Library name: 52_OVCAR3_DHX9i_1

value: ovarian cancer cells


title: OVCAR3_DHX9i_rep 3

description: Library name: 54_OVCAR3_DHX9i_3

value: 10 uM DHX9i


title: caSTAT3, donor3 (caS3_donor3)

description: Library name: caS3_donor3


title: Thalamus, MDMC, CON, Pair 10, HUID 1282

description: S2 flow cell

value: Thalamus

value: HUID 1282


title: caSTAT3, donor1 (caS3_donor1)

description: Library name: caS3_donor1


title: ARK2_DHX9i_rep 3

description: Library name: 48_ARK2_DHX9i_3

value: endometrial cancer cells


title: OVCAR3_DMSO_rep 2

description: Library name: 50_OVCAR3_2


title: Thalamus, MDMC, OCD, Pair 1, HUID 1413

description: S2 flow cell

value: HUID 1413

value: Pair 1


title: Thalamus, MDMC, CON, Pair 1, HUID 1159

description: S2 flow cell

value: CON

value: HUID 1159


title: caSTAT3, donor2 (caS3_donor2)

description: Library name: caS3_donor2

value: CD8+ T cells


title: ARK2_DHX9i_rep 2

description: Library name: 47_ARK2_DHX9i_2


title: Control, donor3 (Ct_donor3)

description: Library name: Ct_donor3

value: CAR


title: OVCAR3_DMSO_rep 3

description: Library name: 51_OVCAR3_3


title: Control, donor2 (Ct_donor2)

description: Library name: Ct_donor2

value: donor 2


title: ARK2_DMSO_rep 3

description: Library name: 45_ARK2_3


title: ARK2_DHX9i_rep 1

description: Library name: 46_ARK2_DHX9i_1


title: U2OS, galactose, Replicate 3

city: Philadelphia

first: Marni

middle: J

last: Falk

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Sequencing quality was checked with FastQC
Adapter and quality trimming was performed with Trim Galore!
Samples were aligned to hg38 using STAR
Transcripts were quantified using RSEM
Assembly: hg38
Supplementary files format and content: RSEM isoform count files

growth_protocol: Cells were cultured in 100mm dishes with 5.6mM glucoseDMEM-10% FBS-0.2% (v/v) uridine at37℃ with 5% CO2 until about 80% confluency.

extract_protocol:
Twenty-four hours later, cells were washed with cold PBS twice, then cold 1mL TRIzol® reagent (Invitrogen #15596026) was added. Cells were scraped with cell lifter and homogenized by pipetting up and down several times.
RNA was purified with RNeasy Kits (Qiagen, Hilden Germany, #74004).
Libraries were constructed with the TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: Media was then replaced with 10ml of fresh DMEM-10% FBS with 5.6 mM glucose, 10mM galactose, or 10mM galactose plus drug (cycloheximide, metformin, ONC201 or ONC206).

value: osteosarcoma

value: 10 mM galactose media


title: Control, donor1 (Ct_donor1)

description: Library name: Ct_donor1

value: donor 1


title: U2OS, galactose, Replicate 2


title: MFE280_DHX9i_rep 3

description: Library name: 36_MFE280_DHX9i_3


title: MFE280_DHX9i_rep 1

description: Library name: 34_MFE280_DHX9i_1


title: ARK2_DMSO_rep 1

description: Library name: 43_ARK2_1


title: MFE280_DHX9i_rep 2

description: Library name: 35_MFE280_DHX9i_2


title: PCSK9_mice_LKO_antiCREBH_rep3

description: Library name: LKO_antiCREBH_rep3

data_processing:
Computations of mice data were performed using resources provided by Galaxy. The computations of human data was enabled by resources in project sens2024555 provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) at UPPMAX, funded by the Swedish Research Council through grant agreement no. 2022-06725. Analysis was conducted as previously described. Sequencing files (fastq files) provided by NOVOGENE (Cambridge, United Kingdom), along with raw data from published ChIP-seq datasets (KDM6A: GSE95890; HNF4A: GSE31477), were aligned to the NCBI38/mm10 version of the mouse reference genome or GRCh38/hg38 using Bowtie2. Peaks were identified using the HOMER package. Peak heights were normalized to the total number of uniquely mapped reads and displayed in the Integrative Genomics Viewer (IGV) as the number of tags per 10 million tags. For statistical analysis of the peaks, raw tag counts were imported into R and Bioconductor, and the edgeR package was used to identify potential differential-binding sites.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
For transcription factors (TFs), tissues/cells were double crosslinked with 2 mM disuccinimidyl glutarate (DSG) (ThermoFisher, 20593) for 30 minutes, followed by 1% formaldehyde for 10 minutes. The reaction was stopped with glycine at a final concentration of 0.125 M for 5 minutes. Liver pieces were disaggregated in ice-cold PBS with protease inhibitor using a Dounce Homogenizer, first with a loose pestle and then with a tight pestle (Fisher Science, FB56691). Nuclei were isolated using three lysis buffers: lysis buffer 1 (50 mM Hepes–KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100), lysis buffer 2 (10 mM Tris–HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and lysis buffer 3 (10 mM Tris–HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, and 0.5% N-Lauroylsarcosine). The samples were then sonicated for 30 minutes (30 seconds ON/30 seconds OFF) using the Bioruptor Pico (Diagenode).
For ChIP-seq sample preparation, the same ChIP protocol was followed, but the ChIP DNA was purified using the ChIP DNA Clean and Concentrator Capped Zymo-Spin I (Zymo Research) purification kit. Two to four ChIPs were pooled during the final purification step to obtain concentrated material. For library preparation and sequencing, 2–10 ng of ChIPed DNA was processed using the Rubicon ThruPLEX DNA-seq kit (TAKARA) following standard protocols, and sequenced on the NovaSeq X Plus Series (150PE reads, NOVOGENE, United Kingdom).

value: liver


title: MFE280_DMSO_rep 2

description: Library name: 32_MFE280_2


title: PCSK9_mice_LKO_antiCREBH_rep4

description: Library name: LKO_antiCREBH_rep4


title: U2OS, galactose, Replicate 1


title: MFE280_DMSO_rep 3

description: Library name: 33_MFE280_3


title: MFE280_DMSO_rep 1

description: Library name: 31_MFE280_1


title: U2OS, glucose, Replicate 3

value: 5.6 mM glucose media


title: ARK2_DMSO_rep 2

description: Library name: 44_ARK2_2


title: SJSA1, glucose, Replicate 3


title: KLE_DHX9i_rep 3

description: Library name: 30_KLE_DHX9i_3

source_name: KLE

value: KLE


title: KLE_DHX9i_rep 2

description: Library name: 29_KLE_DHX9i_2

value: 10 uM DHX9i


title: PCSK9_mice_LKO_antiCREBH_rep2

description: Library name: LKO_antiCREBH_rep2


title: SJSA1, glucose, Replicate 1


title: PCSK9_mice_WT_antiCREBH_rep4

description: Library name: WT_antiCREBH_rep4


title: SJSA1, galactose, Replicate 2


title: PCSK9_mice_LKO_antiCREBH_rep1

description: Library name: LKO_antiCREBH_rep1


title: KLE_DHX9i_rep 1

description: Library name: 28_KLE_DHX9i_1


title: SJSA1, galactose, Replicate 1


title: MFE296_DHX9i_rep 3

description: Library name: 24_MFE296_DHX9i_3


title: MFE296_DHX9i_rep 2

description: Library name: 23_MFE296_DHX9i_2


title: MFE296_DHX9i_rep 1

description: Library name: 22_MFE296_DHX9i_1


title: PCSK9_mice_WT_antiCREBH_rep2

description: Library name: WT_antiCREBH_rep2


title: SJSA1, glucose, Replicate 2


title: Saos2, glucose, Replicate 3


title: PCSK9_mice_WT_antiCREBH_rep3

description: Library name: WT_antiCREBH_rep3


title: MFE296_DMSO_rep 3

description: Library name: 21_MFE296_3


title: KLE_DMSO_rep 3

description: Library name: 27_KLE_3


title: MFE296_DMSO_rep 2

description: Library name: 20_MFE296_2


title: Female_PCSK9_LKO_rep4

description: Library name: PCSK9_LKO_rep4

data_processing:
Preprocessed reads were aligned to the hg38/mm10 transcriptome using the HISAT2 program, and read counts were determined using featureCounts v1.5.0-p3. Raw tag counts were imported into R and Bioconductor, and differential gene expression was analyzed using the edgeR package.
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from snap-frozen liver tissues and human cell lines using the E.Z.N.A.® Total RNA Kit I (Omega Bio-tek, R6834-02).
mRNA library preparation, including poly-A enrichment, was carried out using the Novogene NGS RNA Library Prep Set (PT042) following the manufacturer’s protocol.


title: PCSK9_mice_WT_antiCREBH_rep1

description: Library name: WT_antiCREBH_rep1


title: AN3CA_DHX9i_rep 2

description: Library name: 5_AN3CA_DHX9i_2


title: Saos2, glucose, Replicate 1


title: Saos2, glucose, Replicate 2


title: KLE_DMSO_rep 2

description: Library name: 26_KLE_2


title: KLE_DMSO_rep 1

description: Library name: 25_KLE_1


title: Female_PCSK9_LKO_rep3

description: Library name: PCSK9_LKO_rep3


title: AN3CA_DHX9i_rep 3

description: Library name: 6_AN3CA_DHX9i_3


title: Female_PCSK9_LKO_rep2

description: Library name: PCSK9_LKO_rep2


title: AN3CA_DMSO_rep 3

description: Library name: 3_AN3CA_3


title: AN3CA_DHX9i_rep 1

description: Library name: 4_AN3CA_DHX9i_1


title: Saos2, galactose, Replicate 3


title: AN3CA_DMSO_rep 2

description: Library name: 2_AN3CA_2


title: MFE296_DMSO_rep 1

description: Library name: 19_MFE296_1


title: OVCAR3_DMSO_rep 1

description: Library name: 49_OVCAR3_1

value: ovarian cancer cells


title: Saos2, galactose, Replicate 2


title: AN3CA_DMSO_rep 1

description: Library name: 1_AN3CA_1


title: Saos2, galactose, Replicate 1


title: Female_PCSK9_WT_rep3

description: Library name: PCSK9_WT_rep3


title: Rho0, glucose, Replicate 3

value: 143B cells with no mitochondria


title: heart, normal diet, 1,1-DEE treatment-1

city: Jeollanam-do

first: Seung-Rock

address: Seoyang-ro, Hwasun-eup, Hwasun-gun

department: Biochemistry

institute: Chonnam National University Medical school

description:
Library name: Sample 4
2_1_H

data_processing:
Raw sequencing data were assessed for quality using FastQC (v0.11.7). The reads were trimmed using TrimGalore with a quality threshold of > 30. Trimmed reads were aligned to the GRCm38 reference genome using STAR (v2.7.0). The HTseq-count algorithm and ensemble Gencode m25 gene annotations were used to profile the gene expression from the raw read counts. Count data were converted to counts per million (CPM) using EdgeR, with the merging of redundant genes to calculate the average CPM.
Assembly: GRCm38
Supplementary files format and content: xlsx file inclues cpm values for each sample

source_name: Heart

growth_protocol: Eight-week-old male C57BL/6J mice were purchased from Damool Science (Daejeon, Korea) and maintained under specific pathogen-free conditions in the animal facility at the Hwasun Biomedical Convergence Center, Chonnam National University Medical School (Republic of Korea). All animal experiments were reviewed and approved by the Animal Use and Care Committees at Chonnam National University Medical School and were conducted in accordance with institutional guidelines for animal care, as well as the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

extract_protocol:
Total RNA was extracted using Trizol reagent (#155960626; Ambion, Carlsbad, CA, USA).
The mRNA-seq library was constructed using the TruSeq mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions

treatment_protocol: The mice were randomly divided into 2 groups (n = 3) and fed a diet consisting of 70 kcal% carbohydrate, 20 kcal% protein, and 10 kcal% fat. 1,1-DEE was orally administered every other day at a concentration of 100 mg/kg, and the untreated group received equivalent volumes of water

value: Heart


title: Female_PCSK9_WT_rep4

description: Library name: PCSK9_WT_rep4


title: HROHep03_siKDM6A_CREBH_rep3

description: Library name: siKDM6A_CREBH_rep3

data_processing:
Computations of mice data were performed using resources provided by Galaxy. The computations of human data was enabled by resources in project sens2024555 provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) at UPPMAX, funded by the Swedish Research Council through grant agreement no. 2022-06725. Analysis was conducted as previously described. Sequencing files (fastq files) provided by NOVOGENE (Cambridge, United Kingdom), along with raw data from published ChIP-seq datasets (KDM6A: GSE95890; HNF4A: GSE31477), were aligned to the NCBI38/mm10 version of the mouse reference genome or GRCh38/hg38 using Bowtie2. Peaks were identified using the HOMER package. Peak heights were normalized to the total number of uniquely mapped reads and displayed in the Integrative Genomics Viewer (IGV) as the number of tags per 10 million tags. For statistical analysis of the peaks, raw tag counts were imported into R and Bioconductor, and the edgeR package was used to identify potential differential-binding sites.
Assembly: hg38 and mm10
Supplementary files format and content: bigwig


title: Female_PCSK9_WT_rep2

description: Library name: PCSK9_WT_rep2


title: HROHep03_siKDM6A_CREBH_rep2

description: Library name: siKDM6A_CREBH_rep2


title: heart, normal diet, non treatment-2

description:
Library name: Sample 2
1_2_H


title: Rho0, glucose, Replicate 1


title: heart, normal diet, non treatment-3

description:
Library name: Sample 3
1_4_H


title: Rho0, glucose, Replicate 2


title: heart, normal diet, 1,1-DEE treatment-2

description:
Library name: Sample 5
2_2_H


title: HROHep03_siKDM6A_CREBH_rep1

description: Library name: siKDM6A_CREBH_rep1


title: heart, normal diet, non treatment-1

description:
Library name: Sample 1
1_1_H


title: heart, normal diet, 1,1-DEE treatment-3

description:
Library name: Sample 6
2_4_H


title: Female_PCSK9_WT_rep1

description: Library name: PCSK9_WT_rep1


title: Rho0, galactose, Replicate 3


title: HROHep03_siLuc_CREBH_rep3

description: Library name: siLuc_CREBH_rep3


title: PCSK9_mice_input

description: Library name: mice_input

extract_protocol:
Huh1 cells were crosslinked with 1% formaldehyde (ThermoFisher, 28906) in PBS for 10 minutes for histone modifications. For transcription factors (TFs), tissues/cells were double crosslinked with 2 mM disuccinimidyl glutarate (DSG) (ThermoFisher, 20593) for 30 minutes, followed by 1% formaldehyde for 10 minutes. The reaction was stopped with glycine at a final concentration of 0.125 M for 5 minutes. Liver pieces were disaggregated in ice-cold PBS with protease inhibitor using a Dounce Homogenizer, first with a loose pestle and then with a tight pestle (Fisher Science, FB56691). Nuclei were isolated using three lysis buffers: lysis buffer 1 (50 mM Hepes–KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100), lysis buffer 2 (10 mM Tris–HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and lysis buffer 3 (10 mM Tris–HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, and 0.5% N-Lauroylsarcosine). The samples were then sonicated for 30 minutes (30 seconds ON/30 seconds OFF) using the Bioruptor Pico (Diagenode).
For ChIP-seq sample preparation, the same ChIP protocol was followed, but the ChIP DNA was purified using the ChIP DNA Clean and Concentrator Capped Zymo-Spin I (Zymo Research) purification kit. Two to four ChIPs were pooled during the final purification step to obtain concentrated material. For library preparation and sequencing, 2–10 ng of ChIPed DNA was processed using the Rubicon ThruPLEX DNA-seq kit (TAKARA) following standard protocols, and sequenced on the NovaSeq X Plus Series (150PE reads, NOVOGENE, United Kingdom).


title: HROHep03_siLuc_CREBH_rep2

description: Library name: siLuc_CREBH_rep2


title: HROHep03_siLuc_CREBH_rep1

description: Library name: siLuc_CREBH_rep1


title: RPE, 3 months, scRNA-seq

description: 10x Genomics

value: eye

value: RPE

value: Old sample

tag: age

value: 3 months


title: ileum, KO+TB, sample 4

city: Madrid

first: María

last: Mittelbrunn

state: Madrid

address: C/ Nicolás Cabrera, 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa

description: Library name: Ileum_845

data_processing:
RNA-sequencing reads were mapped to the Mus musculus reference genome, GRCm39, using STAR v2.5.2 software.
Reads were then preprocessed with STAR v2.5.2 to transform Sequence Alignment/Map files into Binary Alignment/Map files and sorted.
The number of reads covered by each gene is calculated by HTSeq-Count v1.99.2.
The raw counts was obtained using DESeq2 v1.48.1
Assembly: grcm39
Supplementary files format and content: tab-separated value file with the DESeq2 raw counts for each sample
Supplementary files format and content: tab-separated value file the metadata for each sample

source_name: Ileum

extract_protocol:
RNA from mouse ileum was purified using the RNeasy Mini Kit (QIAGEN)
cDNA libraries were prepared from total RNA and, then, validated and quantified by an Qsep400 Analyzer

value: Ileum

value: Tfamfl/flUbCre ERT2

value: Tributyrin


title: ileum, KO+TB, sample 5

description: Library name: Ileum_846


title: Rho0, galactose, Replicate 1


title: Rho0, galactose, Replicate 2


title: Exp2_siMondoA_ChREBP_2

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Library name: Exp2_siMondoA_ChREBP_2

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment was to hg38 with Bowtie 2,  reads >700bp filtered out
Data were aligned using Bowtie2. Bigwig files were produced using bedtools genomecov, and WigToBigWig scripts.
Assembly: Hg38
Supplementary files format and content: Bigwig files are provided for Cut&Run data
Library strategy: CUT&Run

growth_protocol: Human PDAC PSN-1 cells were grown in RPMI supplemented with 10% FBS and pen/strep.

extract_protocol:
For CUT&RUN, cells were processed on an automated system at the Fred Hutch Cancer Center.
KAPA DNA polymerase method for library preparation and 25x25 paired-end sequencing was performed on an Illumina HiSeq 2500 instrument.

treatment_protocol: PSN-1 cells were transfected with the indicated siRNA (siControl, siMondoA) for 48 hours then processed for Cut&Run with the indicated antibody. Experiment 1 (IgG, MondoA, MYC), Experiment 2 (IgG, MNT, ChREBP).

value: PDAC

tag: sample group


title: Huh1_siHNF4A_rep4

description: Library name: Huh1_siHNF4A_rep4

tag: cell line


title: Exp2_siMondoA_MNT_2

description: Library name: Exp2_siMondoA_MNT_2


title: Ileum, control, sample 4

description: Library name: Ileum_844

tag: tissue

value: Tfamfl/fl

value: Standard diet


title: Exp2_siMondoA_ChREBP_1

description: Library name: Exp2_siMondoA_ChREBP_1


title: Q2148, glucose, Replicate 1

value: patient-derived normal skin fibroblast, same individual as 15454


title: Huh1_siHNF4A_rep2

description: Library name: Huh1_siHNF4A_rep2


title: RPE, 24months, scRNA-seq

description: 10x Genomics

value: 24 months


title: Q2148, glucose, Replicate 2

value: 5.6 mM glucose media


title: Q2148, glucose, Replicate 3


title: Female_PCSK9_LKO_rep1

description: Library name: PCSK9_LKO_rep1

value: liver


title: ileum, KO+TB, sample 3

description: Library name: Ileum_826


title: Ileum, control, sample 3

description: Library name: Ileum_825


title: ileum, KO, sample 5

description: Library name: Ileum_842


title: Huh1_siKDM6A_rep4

description: Library name: Huh1_siKDM6A_rep4


title: Huh1_siHNF4A_rep3

description: Library name: Huh1_siHNF4A_rep3


title: Huh1_siHNF4A_rep1

description: Library name: Huh1_siHNF4A_rep1


title: Exp2_siMondoA_MNT_1

description: Library name: Exp2_siMondoA_MNT_1


title: Q2148, galactose, Replicate 3

value: 10 mM galactose media


title: Q2148, galactose, Replicate 2


title: ileum, KO, sample 4

description: Library name: Ileum_824


title: Exp2_siMondoA_IgG_1

description: Library name: Exp2_siMondoA_IgG_1


title: ileum, KO, sample 3

description: Library name: Ileum_823


title: Huh1_siKDM6A_rep3

description: Library name: Huh1_siKDM6A_rep3


title: Q1875p1F, glucose, Replicate 3

value: cybrid osteosarcoma, nuclear DNA 143B, normal mitochondrial DNA Q1875p1F


title: ileum, KO, sample 2

description: Library name: Ileum_818


title: Huh1_siKDM6A_rep2

description: Library name: Huh1_siKDM6A_rep2


title: Exp2_siControl_ChREBP_1

description: Library name: Exp2_siControl_ChREBP_1


title: Q2148, galactose, Replicate 1


title: Exp2_siControl_ChREBP_2

description: Library name: Exp2_siControl_ChREBP_2


title: Huh1_siKDM6A_rep1

description: Library name: Huh1_siKDM6A_rep1


title: Q1875p1F, glucose, Replicate 2


title: Huh1_siLuc_rep4

description: Library name: Huh1_siLuc_rep4


title: Ileum, control, sample 2

description: Library name: Ileum_817


title: Q1875p1F, glucose, Replicate 1


title: ileum, KO+TB, sample 2

description: Library name: Ileum_816


title: Exp2_siControl_MNT_1

description: Library name: Exp2_siControl_MNT_1


title: Huh1_siLuc_rep2

description: Library name: Huh1_siLuc_rep2


title: Huh1_siLuc_rep1

description: Library name: Huh1_siLuc_rep1


title: Exp1_siMondoA_MondoA_2

description: Library name: Exp1_siMondoA_MondoA_2


title: ileum, KO, sample 1

description: Library name: Ileum_815


title: Q1875p1F, galactose, Replicate 2


title: Ileum, control, sample 1

description: Library name: Ileum_809


title: Q1875p1F, galactose, Replicate 1


title: Exp1_siMondoA_MYC_2

description: Library name: Exp1_siMondoA_MYC_2


title: APCknockout Day6 rep 2

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road,

department: Department of Genetics

institute: Rutgers University

description: Library name: Sample 7

data_processing:
Alignment: RNA-seq: Kallisto v0.46.1
RNA-seq Transcript Import: tximport 1.28.0
DESeq2 1.40.1
Assembly: RefSeq mm9
Supplementary files format and content: csv file: FPKM table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments

source_name: Intestinal Mesenchyme

extract_protocol:
QIAGEN RNeasy Micro Kit
Library preparation was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Intestinal Mesenchyme


title: HROhep03_input

city: HUDDINGE

first: Lin

address: Blickagången 16, Flemingsberg,Neo

institute: Karolinska Institutet

description: Library name: hro_input


title: Huh1_input

description: Library name: Huh1_input


title: Exp2_siControl_IgG_1

description: Library name: Exp2_siControl_IgG_1


title: Exp1_siMondoA_MondoA_1

description: Library name: Exp1_siMondoA_MondoA_1


title: Q1875F, glucose, Replicate 2

value: cybrid osteosarcoma, nuclear DNA 143B, patient mitochondrial DNA Q1875F (m.8993T>C)


title: Exp2_siControl_MNT_2

description: Library name: Exp2_siControl_MNT_2


title: Q1875p1F, galactose, Replicate 3


title: Wildtype Control rep 3

description: Library name: Sample 6


title: APCknockout Day6 rep 1

description: Library name: Sample 5


title: Exp1_siMondoA_MYC_1

description: Library name: Exp1_siMondoA_MYC_1


title: Q1875F, galactose, Replicate 3


title: Q1875F, glucose, Replicate 1


title: Q1875F, glucose, Replicate 3


title: APCknockout Day4 rep 2

description: Library name: Sample 3


title: Exp1_siMondoA_IgG_2

description: Library name: Exp1_siMondoA_IgG_2


title: huh7_siHNF4A_rep4(HAKD group)

description: Library name: huh7_HAKD_siHNF4A_rep4


title: ileum, KO+TB, sample 1

description: Library name: Ileum_808


title: Exp1_siMondoA_IgG_1

description: Library name: Exp1_siMondoA_IgG_1


title: Wildtype Control rep 2

description: Library name: Sample 4


title: huh7_siHNF4A_rep3(HAKD group)

description: Library name: huh7_HAKD_siHNF4A_rep3


title: Q1875F, galactose, Replicate 2


title: NHOst, glucose, Replicate 3

source_name: NHOst

value: NHOst

value: normal osteoblast


title: Exp1_siControl_MYC_2

description: Library name: Exp1_siControl_MYC_2


title: Huh1_siLuc_rep3

description: Library name: Huh1_siLuc_rep3


title: Exp1_siControl_MondoA_2

description: Library name: Exp1_siControl_MondoA_2


title: huh7_siHNF4A_rep1(HAKD group)

description: Library name: huh7_HAKD_siHNF4A_rep1


title: Exp1_siControl_MondoA_1

description: Library name: Exp1_siControl_MondoA_1


title: APCknockout Day4 rep 1

description: Library name: Sample 2


title: Q1875F, galactose, Replicate 1


title: Exp1_siControl_MYC_1

description: Library name: Exp1_siControl_MYC_1


title: NHOst, glucose, Replicate 1


title: mice_LKO_H3K27me3_rep3

description: Library name: LKO_H3K27me3_rep3


title: huh7_siLuc_rep1(HAKD group)

description: Library name: huh7_HAKD_siLuc_rep1


title: huh7_siHNF4A_rep2(HAKD group)

description: Library name: huh7_HAKD_siHNF4A_rep2


title: huh7_siLuc_rep4(HAKD group)

description: Library name: huh7_HAKD_siLuc_rep4


title: Wildtype Control rep 1

description: Library name: Sample 1


title: Mice_input

description: Library name: mice_input


title: huh7_siLuc_rep3(HAKD group)

description: Library name: huh7_HAKD_siLuc_rep3


title: huh7_siLuc_rep2(HAKD group)

description: Library name: huh7_HAKD_siLuc_rep2


title: NHOst, galactose, Replicate 3


title: NHOst, glucose, Replicate 2


title: Exp1_siControl_IgG_2

description: Library name: Exp1_siControl_IgG_2


title: Exp1_siControl_IgG_1

description: Library name: Exp1_siControl_IgG_1


title: NHOst, galactose, Replicate 2


title: SBI477_2

description:
Library name: SBI477_2
PSN1_RNASeq_SBI477.txt

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
For RNASeq analysis, low quality reads were filtered out prior to alignment to mm10 using TopHat v2.1.0.
Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1. Normalization and gene expression results were done using EdgeR.
Assembly: hg38
Supplementary files format and content: For RNA-seq data, EdgeR count tables with Log2Fold gene expression changes and adjusted p values.

extract_protocol:
RNA was extracted using Direct-zol miniprep kits (Zymo), and 500ng was used for library generation for sequencing.
Libraries were prepared using the Kapa system, 25x25 paired-end sequencing was performed on an Illumina HiSeq 2500 instrument.

treatment_protocol: Experiment 1: PSN-1 cells were transfected with the indicated siRNA (siControl, siMondoA or siMLX) for 72 hours. Experiment 2: PSN-1 cells were treated with DMSO or SBI-477 (MondoA inhibitor) for 72 hours.

value: MondoA Inhibition


title: huh7_siKDM6A_rep2(KAKD group)

description: Library name: huh7_KAKD_siKDM6A_rep2


title: mice_LKO_H3K27me3_rep2

description: Library name: LKO_H3K27me3_rep2

extract_protocol:
Fresh liver tissues (chopped into small pieces) and HROhep03 cells were crosslinked with 1% formaldehyde (ThermoFisher, 28906) in PBS for 10 minutes for histone modifications. For transcription factors (TFs), tissues/cells were double crosslinked with 2 mM disuccinimidyl glutarate (DSG) (ThermoFisher, 20593) for 30 minutes, followed by 1% formaldehyde for 10 minutes. The reaction was stopped with glycine at a final concentration of 0.125 M for 5 minutes. Liver pieces were disaggregated in ice-cold PBS with protease inhibitor using a Dounce Homogenizer, first with a loose pestle and then with a tight pestle (Fisher Science, FB56691). Nuclei were isolated using three lysis buffers: lysis buffer 1 (50 mM Hepes–KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100), lysis buffer 2 (10 mM Tris–HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and lysis buffer 3 (10 mM Tris–HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, and 0.5% N-Lauroylsarcosine). The samples were then sonicated for 30 minutes (30 seconds ON/30 seconds OFF) using the Bioruptor Pico (Diagenode).
For ChIP-seq sample preparation, the same ChIP protocol was followed, but the ChIP DNA was purified using the ChIP DNA Clean and Concentrator Capped Zymo-Spin I (Zymo Research) purification kit. Two to four ChIPs were pooled during the final purification step to obtain concentrated material. For library preparation and sequencing, 2–10 ng of ChIPed DNA was processed using the Rubicon ThruPLEX DNA-seq kit (TAKARA) following standard protocols, and sequenced on the NovaSeq X Plus Series (150PE reads, NOVOGENE, United Kingdom).


title: SBI477_1

description:
Library name: SBI477_1
PSN1_RNASeq_SBI477.txt


title: huh7_siKDM6A_rep4(KAKD group)

description: Library name: huh7_KAKD_siKDM6A_rep4


title: mice_LKO_H3K27me3_rep1

description: Library name: LKO_H3K27me3_rep1


title: huh7_siKDM6A_rep3(KAKD group)

description: Library name: huh7_KAKD_siKDM6A_rep3


title: mice_LKO_H3K27ac_rep3

description: Library name: LKO_H3K27ac_rep3


title: SBI477_3

description:
Library name: SBI477_3
PSN1_RNASeq_SBI477.txt


title: mice_LKO_H3K27ac_rep2

description: Library name: LKO_H3K27ac_rep2


title: MG63, galactose, Replicate 3

value: osteosarcoma


title: MG63, glucose, Replicate 2


title: huh7_siKDM6A_rep1(KAKD group)

description: Library name: huh7_KAKD_siKDM6A_rep1


title: huh7_siLuc_rep4(KAKD group)

description: Library name: huh7_KAKD_siLuc_rep4


title: MG63, glucose, Replicate 3


title: DMSO_3

description:
Library name: DMSO_3
PSN1_RNASeq_SBI477.txt


title: NHOst, galactose, Replicate 1


title: DMSO_1

description:
Library name: DMSO_1
PSN1_RNASeq_SBI477.txt


title: mice_LKO_H3K27ac_rep1

description: Library name: LKO_H3K27ac_rep1


title: mice_LKO_H3K4me2_rep2

description: Library name: LKO_H3K4me2_rep2


title: MG63, galactose, Replicate 1


title: huh7_siLuc_rep3(KAKD group)

description: Library name: huh7_KAKD_siLuc_rep3


title: mice_LKO_H3K4me2_rep1

description: Library name: LKO_H3K4me2_rep1


title: huh7_siLuc_rep1(KAKD group)

description: Library name: huh7_KAKD_siLuc_rep1


title: DMSO_2

description:
Library name: DMSO_2
PSN1_RNASeq_SBI477.txt


title: mice_LKO_H3K4me2_rep3

description: Library name: LKO_H3K4me2_rep3


title: huh7_siLuc_rep2(KAKD group)

description: Library name: huh7_KAKD_siLuc_rep2


title: MG63, galactose, Replicate 2


title: HRO_HNF4A_knockdown_rep4

description: Library name: HRO_HAKD_rep4


title: siMLX_2

description:
Library name: siMLX_2
PSN1_RNASeq_siRNA.txt

value: siRNA


title: siMLX_3

description:
Library name: siMLX_3
PSN1_RNASeq_siRNA.txt


title: HOS, glucose, Replicate 3

source_name: HOS

value: HOS


title: siMLX_1

description:
Library name: siMLX_1
PSN1_RNASeq_siRNA.txt

value: PDAC


title: mice_LKO_H3K4me1_rep2

description: Library name: LKO_H3K4me1_rep2


title: HRO_HNF4A_knockdown_rep3

description: Library name: HRO_HAKD_rep3


title: mice_LKO_H3K4me1_rep1

description: Library name: LKO_H3K4me1_rep1


title: HRO_HNF4A_knockdown_rep2

description: Library name: HRO_HAKD_rep2


title: HOS, glucose, Replicate 2


title: HOS, galactose, Replicate 3


title: HRO_HNF4A_knockdown_rep1

description: Library name: HRO_HAKD_rep1


title: siMondoA_3

description:
Library name: siMondoA_3
PSN1_RNASeq_siRNA.txt


title: siMondoA_2

description:
Library name: siMondoA_2
PSN1_RNASeq_siRNA.txt


title: mice_LKO_H3K4me1_rep3

description: Library name: LKO_H3K4me1_rep3


title: siMondoA_1

description:
Library name: siMondoA_1
PSN1_RNASeq_siRNA.txt


title: mice_flox_H3K27me3_rep2

description: Library name: flox_H3K27me3_rep2


title: HRO_KDM6A_knockdown_rep4

description: Library name: HRO_KAKD_rep4


title: HOS, galactose, Replicate 1


title: HOS, glucose, Replicate 1


title: hFOB, glucose, Replicate 3

source_name: hFOB

value: hFOB


title: HOS, galactose, Replicate 2


title: mice_flox_H3K27me3_rep3

description: Library name: flox_H3K27me3_rep3


title: HRO_KDM6A_knockdown_rep2

description: Library name: HRO_KAKD_rep2


title: siControl_2

description:
Library name: siControl_2
PSN1_RNASeq_siRNA.txt


title: mice_flox_H3K27me3_rep1

description: Library name: flox_H3K27me3_rep1


title: hFOB, glucose, Replicate 2


title: siControl_3

description:
Library name: siControl_3
PSN1_RNASeq_siRNA.txt


title: siControl_1

description:
Library name: siControl_1
PSN1_RNASeq_siRNA.txt


title: HRO_KDM6A_knockdown_rep1

description: Library name: HRO_KAKD_rep1


title: mice_flox_H3K27ac_rep2

description: Library name: flox_H3K27ac_rep2


title: mice_flox_H3K27ac_rep1

description: Library name: flox_H3K27ac_rep1


title: HRO_KDM6A_knockdown_rep3

description: Library name: HRO_KAKD_rep3


title: RNA-Seq of zebrafish larvae srrm4[y712] mutant replicate 2

first: Tripti

last: Gupta

address: 6 Center Drive

institute: NICHD

description: Library name: srrm4[y712] mutant replicate 2

data_processing:
Alignment of RNA-Seq data was performed with RNA-STAR (version 2.7.3) [1] against the Danio rerio GRCz11 genome build.
Gene-based read quantitation was performed using SubRead featureCounts (version 1.6.4).
Read count normalization was performed using DESeq2.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

organism: Danio rerio

source_name: head

extract_protocol:
RNA was isolated using the Qiagen RNeasy mini kit or Zymo Direct-zol RNA Microprep Kit . 1 microgram of total RNA was used for construction of each library.
Libraries were constructed using the TruSeq stranded mRNA library kit following the manufacturer's protocols.

value: head

value: homozygous mutant


title: RNA-Seq of zebrafish larvae srrm4[y712] mutant replicate 3

description: Library name: srrm4[y712] mutant replicate 3


title: HRO_NC_rep4

last: Chen

description: Library name: HRO_NC_rep4


title: HRO_NC_rep3

description: Library name: HRO_NC_rep3


title: hFOB, galactose, Replicate 3


title: hFOB, galactose, Replicate 2


title: RNA-Seq of zebrafish larvae srrm4[y712] mutant replicate 1

description: Library name: srrm4[y712] mutant replicate 1


title: mice_flox_H3K27ac_rep3

description: Library name: flox_H3K27ac_rep3


title: mice_flox_H3K4me2_rep3

description: Library name: flox_H3K4me2_rep3


title: mice_flox_H3K4me2_rep2

description: Library name: flox_H3K4me2_rep2


title: hFOB, galactose, Replicate 1


title: RNA-Seq of zebrafish larvae srrm4[y712] wild-type replicate 3

description: Library name: srrm4[y712] wild-type replicate 3

value: wild-type


title: HRO_NC_rep2

description: Library name: HRO_NC_rep2


title: hFOB, glucose, Replicate 1

value: 5.6 mM glucose media


title: RNA-Seq of zebrafish larvae srrm4[y712] wild-type replicate 2

description: Library name: srrm4[y712] wild-type replicate 2


title: 15454, metformin, Replicate 2

value: metastatic osteosarcoma lung biopsy, same individual as Q2148

value: metformin


title: mice_flox_H3K4me1_rep3

description: Library name: flox_H3K4me1_rep3

value: liver


title: HUH7_antiKDM6A_siHNF4A_rep3

description: Library name: HUH7_antiKDM6A_siHNF4A_rep3

growth_protocol: HROHep03 cells were maintained in high-glucose DMEM/F12 medium, supplemented with 5% FBS and 1% antibiotics. Cells were incubated at 37°C in an atmosphere of 5% CO2.


title: RNA-Seq of zebrafish larvae srrm4[y712] wild-type replicate 1

description: Library name: srrm4[y712] wild-type replicate 1


title: mice_flox_H3K4me2_rep1

description: Library name: flox_H3K4me2_rep1


title: 15454, metformin, Replicate 3

value: 10 mM galactose media


title: mice_flox_H3K4me1_rep2

description: Library name: flox_H3K4me1_rep2


title: HRO_NC_rep1

description: Library name: HRO_NC_rep1


title: mice_flox_H3K4me1_rep1

description: Library name: flox_H3K4me1_rep1