title: MCF7_TMXplusFasting_INPUT

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis and duplicates were marked by PICARD/GATK markDuplicates
Enrichment over input control was determined using MACS2 (q < 0.001, narrowPeak mode). Only peaks not overlapping with the ENCODE hg38/GRCh38 blacklisted regions, were retained.
Assembly: hg38/GRCh38
Supplementary files format and content: .bed, narrowPeaks

growth_protocol: MCF7 cells have been cultured in RPMI + 10% FBS + 1% Pen/Strep, at 5% CO2 and 37°C before being xenografted in eight-week-old female athymic nude mice. A the end of 4 cycles of fasting and tamoxifen, mice were sacrificed and MCF7 tumours removed, snap-frozen and further processed for multimomic analysis

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009). In brief, MCF7 tumours were fixed in 2mM of DSG for 20min at RT, followed by 1% formaldehyde for 25 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 15 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Scientific) were conjugated to 5µL of ERa, H3K27ac, GR, PR and c-JUN antibodies.
Illumina

treatment_protocol: Control (no treatment); Tamoxifen (30mg/Kg, 5 days/week, 4 weeks); Fasting (water-only diet, 48h, once a week); TMX+Fasting (combination of the previous treatments)

value: WT

value: Tamoxifen+Fasting (TMX+Fasting)


title: CnR_H3K4me3_R-Suz12KO_DMSO_rep2

status: Public on Oct 14 2025

type: SRA

city: London

first: Aina

middle: Maria

last: Mas

address: Chester Beatty Laboratories, 237 Fulham Rd.

country: United Kingdom

institute: Institute of Cancer Research

library_source: genomic

data_processing:
ChIP and CUT&RUN sequencing reads were trimmed and filtered for quality and adapter content using v0.4.5 of TrimGalore with a quality setting of 15 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), and running version 1.15 of Cutadapt and version 0.11.5 of FastQC.
Trimmed reads were aligned to mouse assembly mm10 with v2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Mapped reads were deduplicated using MarkDuplicates in v2.16.0 of Picard Tools.
Except for H3K9me3 CUT&RUN samples, data were normalized to sequencing depth (to ten million uniquely mapped reads) and normalized bigwig files were created using DeepTools v3.3.0 by running BamCoverage.
For H3K9me3, 10,000bp windows were generated from the mm10 genome using BedTools v2.27.1 by running Makewindows, and bins containing H3K27me3 peaks were removed by running Intersect with the setting -v. BedTools Multicov was used to count aligned reads from H3K9me3 bam files over the 10,000bp windows, and size factors were estimated with the estimateSizeFactorsForMatrix function in DESeq2 v1.34.0. Size factors were used when running deepTools BamCoverage to create normalized bigwig files. For a list of scaling factors and validation of normalizations, refer to Supplementary Fig. 1.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells were cultured in serum/LIF medium (Glasgow Minimum Essential Media (GMEM) supplemented with 10% heat-inactivated Fetal Bovine Serum (HI-FBS), 1% Penicillin/Streptomycin, 2mM L-glutamine, 1 mM Sodium Pyruvate (Gibco), 0.1 mM MEM Non-essential amino acids (Gibco), 100μM ß-Mercaptoethanol (Gibco) and Leukemia Inhibitory Factor (LIF, produced in the lab))

extract_protocol:
Native cells were harvested and 0.4x10^6 cells/per sample were used using standard CUT&RUN protocol: https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn
Histone modifications were mapped with the standard CUT&RUN library prep protocol:  https://www.protocols.io/view/library-prep-for-cut-amp-run-with- nebnext-ultra-ii-wvgfe3w (2019)

treatment_protocol: Cells were treated with either dTAG13 or DMSO for 24hrs. KDM4-specific inhibitor QC6352 treatment for 96hrs

tag: cell line

tag: cell type

value: Mouse embryonic stem cells

tag: antibody

value: H3K4me3, CST-C42D8

tag: genotype

value: RBBP5-FKBP + Suz12 KO (RS)

tag: treatment

value: DMSO


title: TCM_2A

city: Columbus

first: Stanley

last: Huang

state: Ohio

address: 2255 Kenny Road

department: Department of Microbial Infection and Immunity

country: USA

institute: The Ohio State University

library_source: transcriptomic

data_processing:
We used HISAT to align the clean reads to the reference genome and then used StringTie to assemble. We used Bowtie2 to compare clean reads to the reference sequence, and then use RSEM to calculate the expression of genes and transcripts. We used Bowtie2 to align the clean reads to the gene reference sequence, and then count the coverage of the gene.
Assembly: mm10
Supplementary files format and content: includes FPKM for each sample

molecule: total RNA

source_name: Bone marrow

growth_protocol: Bone marrow cells were differentiated in the presence of recombinant mouse M-CSF (20 ng/ml) in complete medium (RPMI 1640 containing 10 mM glucose, 2 mM L-glutamine, 100 U/mL of penicillin/streptomycin and 10% FBS) for 7 days. Fresh complete medium with M-CSF was supplemented on day 6 prior to use.

extract_protocol:
Firstly, the biotin-labeled Ribo-Zero rRNA Removal Kit is used to remove ribosome rRNA of total RNA.Then the un-purified RNA is fragmented under a certain temperature and ion environment. Random primers and reverse transcriptase of TruSeq® Stranded kit are used to synthesize the first-strand cDNA. cDNA library sequencing was performed using Illumina HiSeq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Day 7 bone marrow-derived macrophages were washed and cultured with or without 70% YUMM1.7 tumor cell-conditioned medium (TCM); or stimulated with IL-4 (20 ng/mL), LPS (10 ng/ml) plus IFN-γ (50 ng/ml) for 24 h at a density of 2 million cells per well in a 6-well plate.

tag: tissue

value: Bone marrow

value: WT TCM


title: CnR_H3K4me3_Rbbp5-FKBP_dTAG_rep1


title: fed sample2

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Library name: F2_S2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) using default setting.
The counts matrices were then analyzed in Seurat and batch correction was performed using the Harmony algorithm before creating a UMAP and performing clustering analysis.
Assembly: BDGP6.32
Supplementary files format and content: normalized count matrix, text file
Supplementary files format and content: cell annotation, text file

organism: Drosophila melanogaster

source_name: Whole-body without head

growth_protocol: All flies were kept on standard cornmeal fly food. Crosses were grown at 18°C to inactivate Gal4. Adult offspring flies were collected within 48 hours after emerging, kept at 18°C for another 48 hours and then incubated at 29°C for 7 days to induce transgene expression.

extract_protocol:
Whole-body flies without heads were flash-frozen using liquid nitrogen and were homogenized in 1ml dounce in buffer of 250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCl, 5mM MgCl, 0.1% Triton-X, 0.5% RNasin plus (Promega, N2615), 1X protease inhibitor (Promega, G652A), 0.1 mM DTT, then filtered through 40 um cell strainer and 40 um Flowmi (BelArt, H13680-0040). Samples were centrifuged, washed, and resuspended in 1 X PBS with 0.5% BSA and 0.5% RNasin plus. The suspension was filtered again with 40 um Flowmi immediately before FACS sorting. Nuclei were stained with DRAQ7TM Dye (Invitrogen, D15106) and sorted using Sony SH800Z Cell Sorter at Systems Biology Flow Cytometry Facility at Harvard Medical School. After sorting, nuclei were collected and re-suspend at 700-800 cells/µl in 1 X PBS buffer with 0.5% BSA and 0.5% RNasin plus. snRNAseq was performed according to the 10X genomics protocol (Chromium Next GEM Single Cell 3’_v3.1_Rev_D)
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1

treatment_protocol: Female flies were incubated for 7 days at 29°C

value: Whole-body without head

value: PromE-gal4, Tub-gal80ts

value: Female flies were incubated for 5 days at 29°C


title: MCF7_Fasting_INPUT

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

organism: Homo sapiens

source_name: Breast cancer

value: Breast cancer

value: xenograft

value: Fasting (48h water-only diet)


title: CnR_H3K4me3_RS_S12NSUV2_dTAG_rep2

value: RS + S12N:SUV2


title: CnR_H3K4me3_RS_S12NSD2_DMSO_rep1

value: RS + S12N:SD2


title: TCM_1A


title: MCF7_TMX_INPUT

value: Tamoxifen (30mg/Kg) (TMX)


title: CnR_H3K4me3_RS_S12NSUV2_DMSO_rep1


title: fed sample1

description:
Library name: F1_S1
10x Genomics


title: Phase1_aRUNX1_sgMed12_ChIP_rep2

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

department: Immunology

country: Japan

institute: Tokai Univ

description: Library name: Phase1_aRUNX1_sgMed12_ChIP_rep2

data_processing:
ChIP-seq; Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample. ChIP-seq data were mapped to the mouse genome bulid NCBI37/mm10 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t -best -strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC genome browser (http://genome.ucsc.edu). ChIP peaks were identified with findPeaks.pl against a matched control sample using the setting “-P .1 -LP .1 -poisson .1 -style factor”. The identified peaks were annotated to genes with the annotatePeaks.pl command against the mm10 genomic build in the HOMER package. Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score <15, were considered for further analysis.
Assembly: mm10
Supplementary files format and content: txt files for IDR ChIP peaks

source_name: Fetal liver

growth_protocol: Cas9-expressing lymphoid progenitor (Cas9-LP) cell lines were established from fetal liver progenitors of Ebf1-deficient;Rosa26-Cas9 knock-in mice as a previous report (Hirano et al eLife). Cas9-LPs were cultured in IMDM (Wako) with 10% fetal bovine serum (Sigma-Aldrich), penicillin-streptomycin-glutamine (Gibco), 50 uM b-mercaptoethanol (Sigma-Aldrich), 10 ng/ml mouse SCF (PeproTech), 10 ng/ml human Flt3L (PeproTech), 10 ng/ml human IL-7 (PeproTech) with mitomycin C (Wako) treated OP9.

extract_protocol:
Ten million of Cas9-LPs with or without Notch stimulation were fixed with 1 mg/ml disuccinimidyl glutarate (Thermo Scientific) in PBS for 30 min at room temperature followed by an additional 10 min with addition of formaldehyde up to 1 %. The reaction was quenched by addition of 1/10 volume of 0.125 M glycine and the cells were washed with cold PBS. Pelleted nuclei were dissolved in lysis buffer (0.5 % SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl [pH 8.0], and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30 sec sonication followed by 30 sec rest, with high power.
ChIP-seq libraries were constructed using NEBNext Ultra Ⅱ DNA Library Prep with Sample Purification Beads (E7103S, NEB) and NEBNext Multiplex Oligos for Illumina (E7500S, NEB) and sequenced on Illumina NextSeq500 in single read mode with the read length of 75 nt.

treatment_protocol: Cas9-LPs were transduced with retroviral vectors encoding sgRNA-hNGFR. They were transferred onto OP9 or OP9-DLL4 for 3-5 days after infection, then CD25 and CD44 profiles on sgRNA+ retrovirus-infected cells were analyzed. For QuantSeq 3’ mRNA sequencing, Cas9-LPs were infected with sgRNA-hNGFR. Five days after sgRNA transduction, sgRNA-introduced hNGFR+CD45+ lymphoid progenitor cells were sorted on a BD FACSAria.

value: Fetal liver

tag: chip antibody

value: anti-RUNX1 (abcam; ab23980)

value: Cultured on OP9-DLL4


title: Ctrl_3A

value: WT naive


title: TRAP1_KO_TCM_1A

value: TRAP1 KO


title: MCF7_Control_INPUT

value: WT

value: Control (no treatments)


title: CnR_H3K4me3_R-Suz12KO_DMSO_rep1

value: Mouse embryonic stem cells

value: H3K4me3, CST-C42D8

value: RBBP5-FKBP + Suz12 KO (RS)

value: DMSO


title: Phase1_aRUNX1_sgMed12_ChIP_rep1

description: Library name: Phase1_aRUNX1_sgMed12_ChIP_rep1


title: Ctrl_1A

value: Bone marrow


title: Phase1_aRUNX1_sgCont_ChIP_rep2

description: Library name: Phase1_aRUNX1_sgCont_ChIP_rep2


title: MCF7_TMXplusFasting_PR_Rep3

value: Breast cancer

value: xenograft

value: Tamoxifen+Fasting (TMX+Fasting)


title: MCF7_TMXplusFasting_PR_Rep2


title: CnR_H3K4me3_Suz12KO_S12NSUV2dead_rep2

value: Suz12 KO + S12N:SUV2*


title: CnR_H3K4me3_Rbbp5-FKBP_DMSO_rep1


title: ATM_Young_ctrl_3

city: Minneapolis

first: In Hwa

last: Jang

state: Minnesota

address: 100 Church Street SE

institute: University of Minnesota

data_processing:
First, FastQC was used to assess the quality of the raw reads. Then, Skewer (PMID: 24925680) was used to trim and filter off the sequencing adaptors and low-quality bases (mean quality>20, N ratio<15%, post-trimming length>18nt), and trimmed reads were mapped to mouse genome GRCm39 (mm39) using BWA (PMID: 19451168). BigWig file was generated fro each sampels in RPM sacle.
Assembly: mm39
Supplementary files format and content: bigwig

source_name: Visceral white adipose tissue

growth_protocol: All mice were housed in specific pathogen-free facilities in cage racks that deliver HEPA-filtered air to each cage with free access to sterile water at the University of Minnesota. Sentinel mice in our animal rooms were negative for currently tested standard murine pathogens at various times while the studies were performed.

extract_protocol:
ATAC-seq kit (Activemotif, 53150) was used for ATAC-seq library preparation. In brief, ATMs (live CD45+ CD11b+ SiglecF- F4/80+ cells) were sorted using a BD FACS Aria II instrument. Cells were washed with ice-cold PBS to remove any debris and 10^6 cells were resuspended in 100μl ice-cold ATAC lysis buffer. Then, cells were gently pipetted up and down and incubated on ice for 5min. These cells were centrifuged at 500xg for 10min at 4°C and supernatant was discarded. Next, 50μl of tagmentation master mix containing buffer, 10xPBS, 1% Digitonin, 10% Tween 20, H2O and assembled transposome was added to each sample. Samples were incubated at 37°C for 30 min in a thermomixer set at 800rpm. Then, tagmented DNA was extracted and amplified (72°C for 5min; 98°C for 30 sec; 12 cycles of 98°C for 10sec, 63°C for 30sec, 72°C for 1min) for library preparation. Lastly, 1.2x SPRI bead solution was added to samples for left side size selection
Library quality was checked with Agilent High Sensitivity DNA Bioanalysis chip. Libraries were sequenced via 150 bp paired-end sequencing using the Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were naturally aged to appropriate ages and intraperitoneally injected with 0.1mg/kg LPS 4 hours prior to the endpoint. Young mice were defined as 4 months old and old mice were defined as 21 to 24 months old.

value: Visceral white adipose tissue

value: Sorted adipose tissue macrophages

value: GDF3 fl/-

value: Young


title: MCF7_Control_Rep1

data_processing:
Sequencing data were aligned to the human reference genome hg38 using HISAT2 (v2.1.0), and the number of reads per gene was measured with HTSeq count (v0.5.3)
Assembly: hg38/GRCh38
Supplementary files format and content: .tsv, gene count values for each sample

molecule: polyA RNA

growth_protocol: MCF7 cells were xenografted in mice and 2 weeks after 4 week cycle of treatment was performed: Control (ad libitum diet); Tamoxifen (30mg/Kg; 5 days a week), fasting (water-only diet 48h/week) and combination of tamoxifen and fasting

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen, Germany) following manufacturer´s instructions.
Illumina

value: Control (ad libitum diet)


title: Phase1_aRUNX1_sgCont_ChIP_rep1

description: Library name: Phase1_aRUNX1_sgCont_ChIP_rep1

value: Fetal liver

value: anti-RUNX1 (abcam; ab23980)

value: Cultured on OP9-DLL4


title: ATM_Young_ctrl_2


title: Phase1_aMed12_sgCbfb_ChIP_rep1

description: Library name: Phase1_aMed12_sgCbfb_ChIP_rep1

value: anti-Med12 (Bethyl; A300-774A)


title: MCF7_Fasting_PR_Rep2

value: WT

value: Fasting (48h water-only diet)


title: MCF7_TMXplusFasting_PR_Rep1


title: CnR_H3K4me3_Suz12KO_S12NSUV2_rep2

value: Mouse embryonic stem cells

value: H3K4me3, CST-C42D8

value: Suz12 KO + S12N:SUV2


title: ATM_Young_ctrl_1


title: CnR_H3K4me3_Suz12KO_S12NSD2dead_rep2

value: Suz12 KO + S12N:SD2*


title: Phase1_aMed12_sgCont_ChIP_rep2

description: Library name: Phase1_aMed12_sgCont_ChIP_rep2


title: ATM_Old_mKO_3

value: LysMcre/cre; GDF3 fl/fl

value: Old


title: MCF7_Fasting_PR_Rep1

value: Breast cancer

value: xenograft


title: CnR_H3K4me3_Suz12KO_S12NSD2_rep2

value: Suz12 KO + S12N:SD2


title: Ctrl_2A

value: Bone marrow

value: WT naive


title: Phase1_aMed12_sgCbfb_ChIP_rep2

description: Library name: Phase1_aMed12_sgCbfb_ChIP_rep2

value: Fetal liver


title: Phase1_aMed12_sgCont_ChIP_rep1

description: Library name: Phase1_aMed12_sgCont_ChIP_rep1


title: CnR_H3K4me3_Suz12KO_WT_rep2

value: Suz12 KO + WT


title: CnR_H3K4me3_Suz12KO_rep2

value: Suz12 KO


title: ATM_Old_mKO_1

value: Visceral white adipose tissue

value: Sorted adipose tissue macrophages


title: MCF7_TMX_PR_Rep3

value: WT

value: Tamoxifen (30mg/Kg) (TMX)


title: ATM_Old_mKO_2


title: MCF7_TMX_PR_Rep2


title: CnR_H3K4me3_WT_mESC_rep2

value: Mouse embryonic stem cells

value: H3K4me3, CST-C42D8


title: ATM_Old_ctrl_4

value: GDF3 fl/fl


title: MCF7_TMX_PR_Rep1


title: LP_aRUNX1_sgCTCF_ChIP_rep1

description: Library name: LP_aRUNX1_sgCTCF_ChIP_rep1

value: LP

value: anti-RUNX1 (abcam; ab23980)

value: Cultured on OP9


title: LP_aRUNX1_sgCont_ChIP_rep2

description: Library name: LP_aRUNX1_sgCont_ChIP_rep2


title: ATM_Old_ctrl_3

value: LysMcre/cre

value: Old


title: MCF7_Fasting_PR_Rep3

value: Breast cancer

value: xenograft

value: Fasting (48h water-only diet)


title: CnR_H3K4me3_Suz12KO_S12NSUV2dead_rep1

value: Suz12 KO + S12N:SUV2*


title: MCF7_Control_PR_Rep3

value: Control (no treatments)


title: ATM_Old_ctrl_1

value: Visceral white adipose tissue


title: PCL treated 3

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

institute: Brunel University London

description: Pseudomonas aeruginosa PA-W23

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3)
Read mapping was performed with HISAT
Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R and were normalized using edgeR’s Trimmed Mean of M values algorithm.  Subsequent values were then converted to counts per million (cpm).
Assembly: GCA_003833705.1
Supplementary files format and content: raw_counts.tsv includes a tab-delimited matrix with headers with the raw read values for each gene in each sample and condition
Supplementary files format and content: normalised_counts.tsv includes a tab-delimited matrix with headers with the normalised read values for each gene in each sample and condition

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: PA-W23 cultures (3 biological replicates per condition) were grown to mid‐exponential phase (OD600 0.6–0.7) in 20 ml Starvation media (10% LB + 90% M9 Minimal Media).

extract_protocol:
Cultures were harvested by centrifugation (or direct resuspension for desiccated cells) in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: 0.5 g of PCL beads were added to 3 of the cultures as treatment.

value: bacteria


title: MCF7_Control_PR_Rep2

value: WT


title: PCL treated 2

description: Pseudomonas aeruginosa PA-W23


title: MCF7_TMXplusFasting_cJUN_Rep3

value: Tamoxifen+Fasting (TMX+Fasting)


title: CnR_H3K4me3_Suz12KO_S12NSD2_rep1

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SD2


title: Phase2_aNotch1_ChIP_rep1

description: Library name: Phase2_aNotch1-IC_ChIP_rep1

value: Fetal liver

value: anti-Notch1-IC (a mixture of abcam; ab27526 amd CST; 4147)

value: Cultured on OP9-DLL4


title: LP_aRUNX1_sgCTCF_ChIP_rep2

description: Library name: LP_aRUNX1_sgCTCF_ChIP_rep2

value: LP

value: anti-RUNX1 (abcam; ab23980)

value: Cultured on OP9


title: PCL treated 1

description: Pseudomonas aeruginosa PA-W23


title: MCF7_TMXplusFasting_cJUN_Rep2

value: Breast cancer


title: CnR_H3K4me3_Suz12KO_WT_rep1

value: H3K4me3, CST-C42D8

value: Suz12 KO + WT


title: Phase1_aNotch1_ChIP_rep1

description: Library name: Phase1_aNotch1-IC_ChIP_rep1


title: CnR_H3K4me3_WT_mESC_rep1


title: Phase1_aNotch1_ChIP_rep2

description: Library name: Phase1_aNotch1-IC_ChIP_rep2


title: Control culture 2

description: Pseudomonas aeruginosa PA-W23


title: MCF7_TMXplusFasting_cJUN_Rep1

value: xenograft


title: Control culture 3

description: Pseudomonas aeruginosa PA-W23


title: MCF7_Fasting_cJUN_Rep3

value: Fasting (48h water-only diet)


title: Control culture 1

description: Pseudomonas aeruginosa PA-W23


title: MCF7_Fasting_cJUN_Rep2


title: CnR_H3K9me3_RS_S12NSUV2_dTAG_rep2

value: RS + S12N:SUV2


title: CnR_H3K4me3_Suz12KO_rep1

value: Suz12 KO


title: LP_aNotch1_ChIP_rep1

description: Library name: LP_aNotch1-IC_ChIP_rep1


title: CnR_H3K4me3_Suz12KO_S12NSUV2_rep1

value: Suz12 KO + S12N:SUV2


title: CnR_H3K9me3_R-Suz12KO_dTAG_rep2

value: RBBP5-FKBP + Suz12 KO (RS)


title: LP_aNotch1_ChIP_rep2

description: Library name: LP_aNotch1-IC_ChIP_rep2


title: LP_aRUNX1_sgCont_ChIP_rep1

description: Library name: LP_aRUNX1_sgCont_ChIP_rep1


title: Phase2_aNotch1_ChIP_rep2

description: Library name: Phase2_aNotch1-IC_ChIP_rep2


title: CnR_H3K4me3_Suz12KO_S12NSD2dead_rep1

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SD2*


title: MCF7_Control_PR_Rep1

value: WT

value: Control (no treatments)


title: MCF7_Fasting_cJUN_Rep1


title: hippocampus,BTBR,rep4

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Library name: B4

data_processing:
The reads quality was evaluated using FastQC (version 0.11.2; Babraham Institute, Cambridge, UK)
Reads were mapped to the mouse genome (Genome Reference Consortium mouse GRCm38) using the sRNAbench command line tool with ‘genome mapping mode’ from the sRNAtoolbox suite of software.
the sRNAbench pipeline first aligns all of the reads to the reference genome using the Bowtie aligner, then the coordinates are compared to the miRBase annotation version 21. A read is assigned to the reference RNA if its coordinates lie completely within the chromosome coordinates of the reference RNA.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with raw count values for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from single mouse tissues, using Qiazol and miRNeasy spin column (Qiagen), with DNase1 on column treatment, according to the manufacturer’s protocols (Qiagen). RNA concentration was determined by the NanoDrop 1000 analysis (Thermo Fisher Scientific). RNA quality was assessed by gel electrophoresis and by measuring 260/280 and 260/230 absorbance ratios.
MicroRNA-Seq library preparation was performed using the Illumina TruSeq Small RNA Library Preparation kits (Illumina, San Diego, USA), according to manufacturer instructions. An average number of 15 million reads was obtained per sample.

value: hippocampus

value: BTBR T+ Itpr3tf/J


title: ShamNormalChow0132L

city: Madison

first: Cara

middle: L

last: Green

state: WI

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

description: Library name: 0132L

data_processing:
Analysis of significantly differentially expressed genes (DEGs) was completed in R version 4.4.1 using edgeR and limma packages and Empirical Bayes Linear modeling to detect signficance between contrasts of interest. Gene names were converted to gene symbol and Entrez ID formats using the mygene package.
Assembly: Mus musculus GRCm39 reference genome (NCBI assembly accession GCA_000001635.9)
Supplementary files format and content: Processed data file containing log2 fold-changes, gene IDs and unadjusted and Benjamini-Hochberg adjusted p-values and F-statistics. Processed Data.xlsx
Supplementary files format and content: Raw reads file. raw_rnaseq_data.xlsx

source_name: Liver

growth_protocol: Male C57BL/6J mice were purchased from Jackson Laboratories at five weeks of age and preconditioned on a high-fat WD (Inotiv TD.88137; 42% calories from fat; 15% calories from protein; 43% calories from carbohydrates) for 12 weeks to induce obesity and glucose intolerance. Mice were housed in groups of two and had ad libitum access to food and water in a climate-controlled environment with a 12-hour light/dark cycle. All procedures were approved by the Institutional Animal Care and Use Committee (UW-Madison and William S. Middleton Memorial Veteran’s Hospital), and animals were cared for according to guidelines set forth by the American Association for Laboratory Animal Science in an AALAC-accredited facility.

extract_protocol:
Mice were euthanized at 14 weeks post-operatively using cervical dislocation after a 16-hour fast and a 4-hour refeed. Tissues were flash-frozen in liquid nitrogen. Liver samples for RNA extraction were processed using the PureLinkTM RNA mini kit (Invitrogen; Carlsbad, CA) .
The UW-Madison Biotechnology Gene Expression Center (Research Resource Identifier - RRID:SCR_017757) was utilized for RNA library preparation and the DNA Sequencing Facility (RRID:SCR_017759) for sequencing. Each submitted RNA sample was assayed on NanoDrop One Spectrophotometer and Agilent 4200Tapestaion to assess purity and integrity. RNA samples that met Illumina’s “TruSeq Stranded mRNA Reference Guide” (Document# 1000000040498 v00, October 2017) quality criteria were prepared for sequencing. Briefly, 1ug total RNA sample was enriched for mRNA by oligo (dT) selection, followed by fragmentation using divalent cations under elevated temperature. Double-stranded cDNA was synthesized using SuperScript II RT (Invitrogen, Carlsbad, CA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA Polymerase I and RNAse H for removal of mRNA. Double-stranded cDNA was purified with SPRI beads (Beckman Coulter Genomics, San Jose, CA), followed by incubation with Klenow DNA Polymerase and Adenine to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments. DNA fragments were ligated to Illumina unique dual index (UDI) adapters, which have a single ‘T’ base (Thymine) overhang at their 3’end. Following ligation, cDNA was purified 2x with SPRI beads, and PCR-amplified (11 cycles) with PhusionTM DNA Polymerase followed by a final purification with SPRI beads. Quality and quantity of the finished libraries were assayed on Agilent 4200Tapestation using  D1000 Screentape and Agilent BioMek Synergy H1 Plate Reader with Picogreen reagent, respectively. Paired end 150bp sequencing was carried out on an Illumina NovaSeqX Plus sequencer with libraries multiplexed across six lanes on a 10B flowcell.

treatment_protocol: At 17 weeks of age, mice were weight matched and randomized into either a Sham or SG surgical group as previously described.97 In brief, mice were placed on a recovery gel diet from 48 hours prior to surgery to 6 days post-surgery before going on their respective diets (Clear H20, Westbrook, ME). Mice were anesthetized with isoflurane under sterile conditions. At the time of surgery, mice received weight-based saline, norocillin, and buprenorphine (Ethiqua XR; Fidelis Animal Health, North Brunswick, NJ). SG consisted of a midline laparotomy, short vessel ligation, and removal of roughly 75% of the stomach and the entirety non-glandular stomach using a linear cutting stapler (Medtronic, Minneapolis, MN). Sham surgery similarly consisted of a laparotomy, short vessel ligation, and manipulation of the stomach along the would-be staple line. . On the morning of post-operative day 7, mice were equally placed into one of four diet groups: continued WD (TD.88137; 42% calories from fat, 42.7% calories from carbohydrates, 15.2% calories from protein) or one of three isocaloric, natural-sourced protein diets (Table S1). The three protein diet groups were as follows: high protein (Inotiv, TD.22029; 36% calories from protein), medium protein (Inotiv, TD.180161; 21% calories from protein), and low protein (Inotiv, TD.10192; 7% calories from protein). The carbohydrate percentage was altered to account for the differences in calories from protein.

value: Liver


title: CnR_H3K9me3_Rbbp5-FKBP_dTAG_rep2


title: CnR_H3K9me3_RS_S12NSUV2_DMSO_rep2

value: DMSO


title: MCF7_TMX_cJUN_Rep3

value: Breast cancer

value: Tamoxifen (30mg/Kg) (TMX)


title: MCF7_TMX_cJUN_Rep2


title: ShamNormalChow0130L

description: Library name: 0130L


title: ShamNormalChow0131L

description: Library name: 0131L


title: hippocampus,BTBR,rep1

description: Library name: B1


title: ShamNormalChow0129L

description: Library name: 0129L


title: CnR_H3K9me3_R-Suz12KO_DMSO_rep2


title: MCF7_TMX_cJUN_Rep1


title: MCF7_Control_cJUN_Rep3


title: ShamNormalChow0128L

description: Library name: 0128L


title: MCF7_Control_cJUN_Rep2


title: hippocampus,WT,rep3

description: Library name: C3


title: ShamNormalChow0125L

description: Library name: 0125L


title: CnR_H3K9me3_Rbbp5-FKBP_DMSO_rep2


title: SleeveNormalChow0133L

description: Library name: 0133L


title: CnR_H3K9me3_Rbbp5-FKBP_dTAG_rep1


title: CnR_H3K9me3_RS_S12NSUV2_dTAG_rep1


title: Sleeve7Protein0124L

description: Library name: 0124L


title: hippocampus,WT,rep1

description: Library name: C1


title: hippocampus,WT,rep2

description: Library name: C2


title: CnR_H3K9me3_R-Suz12KO_dTAG_rep1


title: CnR_H3K9me3_RS_S12NSUV2_DMSO_rep1


title: hippocampus,BTBR,rep3

description: Library name: B3


title: MCF7_Control_cJUN_Rep1


title: Sleeve7Protein0122L

description: Library name: 0122L


title: MCF7_TMXplusFasting_GR_Rep3

value: Tamoxifen+Fasting (TMX+Fasting)


title: MCF7_TMXplusFasting_GR_Rep2

value: xenograft


title: Mutant, scRNA

city: Augusta

first: Kai

last: Jiao

state: GA

address: 1120 15th Street, Rm. CA4098

department: Center for Biotechnology and Genomic Medicine

institute: Augusta University

description: Library name: Kai_M1

data_processing:
fastq files were processed with Cellranger-7.1.0 count pipeline
Assembly: mm10
Supplementary files format and content: seurat_object.rds, seurat object in RDS format with gene expression counts and  metadata

source_name: Mouse embryonic tissues (PA3-6 trunk region + outflow tract)

extract_protocol:
Single cells were obtained by digestion tissues with 0.125% Trypsin digestion for 3-5 minutes followed by cell sorting.
10xGenomics Single Cell 3ʹ v3 Reagent Kits


title: Sleeve7Protein0121L

description: Library name: 0121L


title: CnR_H3K9me3_Rbbp5-FKBP_DMSO_rep1


title: hippocampus,WT,rep4

description: Library name: C4


title: CnR_H3K9me3_R-Suz12KO_DMSO_rep1


title: MCF7_TMXplusFasting_GR_Rep1


title: Control, scRNA

description: Library name: Kai_C1

value: Mouse embryonic tissues (PA3-6 trunk region + outflow tract)


title: MCF7_Fasting_GR_Rep3

value: Fasting (48h water-only diet)


title: Late_Vehicle_6

first: Sandrine

last: Géranton

address: Medawar Building, Malet Place

department: Cell and Developmental Biology

institute: University College London

description: Library name: Sample_24

data_processing:
Sequencing reads concatenated where relevant and trimmed (TRIMMOMATIC; v0.39) using a sliding window Q > 20 across 4 bases. Standard Illumina adapter sequences removed: mismatch 2 and min length 8. All other default parameters used.
Trimmed sequences aligned with mm10 full reference genome (HISAT2; v2.2.1) using default alignment values.
Features summarised using Rsubreads version 2.20. Gene counts and normalisation performed using edgeR in Rstudio version 4.2 or higher using default parameters.
Assembly: mm10
Supplementary files format and content: csv file with rows representing gene ID (in ENTREZ and symbol formats as outlined in the corresponding column header) and columns as samples outlined in the samples library name column. Data are the log(2) counts per million transcripts normalised to each library size.

source_name: Spinal cord (L4-L6)

growth_protocol: Mice were kept in a temperature and light controlled environment with free access to food and water. Housed in social groups of 2-4 per cage and purchased from Charles River, U.K.

extract_protocol:
Total RNA extracted from L4-L6 spinal cord using Qiagen Allprep DNA/RNA/miRNA kit
mRNA sequencing libraries were prepared using the NEBNext Ultra II Directional Library Preparation Kit as recommended with a fragment size of 300bp (94°C for 10 minutes) for 13 cycles. Libraries were quantified using a Qubit 2.0 spectrophotometer.

treatment_protocol: Mice received either VPG-SAFit2 (100 mg/kg) or VPG-vehicle on days 3 and 4 (Early treatment) or days 20 and 27 (Late treatment) after knee joint administration of sodium iodoacetate (1 mg)

value: Spinal cord (L4-L6)

tag: age

value: 12-14 weeks when collected

tag: strain

value: wildtype

value: Vehicle

tag: batch

value: Late


title: CnR_H3K9me3_Suz12KO_S12NSUV2dead_I100nM_rep2

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2*

value: KDM4-specific inhibitor QC6352


title: Sleeve7Protein0119L

description: Library name: 0119L


title: Late_SAFit2_5

description: Library name: Sample_23


title: MCF7_Fasting_GR_Rep2

value: WT


title: hippocampus,BTBR,rep2

description: Library name: B2

value: hippocampus

value: BTBR T+ Itpr3tf/J


title: Late_SAFit2_4

description: Library name: Sample_22


title: Sleeve7Protein0118L

description: Library name: 0118L

value: Liver


title: MCF7_Fasting_GR_Rep1

value: Breast cancer


title: Late_Vehicle_5

description: Library name: Sample_20


title: CnR_H3K9me3_Suz12KO_S12NSUV2dead_rep2


title: CnR_H3K9me3_Suz12KO_S12NSUV2_rep2

value: Suz12 KO + S12N:SUV2


title: Sleeve7Protein0117L

description: Library name: 0117L


title: Sham7Protein0116L

description: Library name: 0116L


title: Late_SAFit2_3

description: Library name: Sample_19


title: CnR_H3K9me3_Suz12KO_WT_rep2

value: Suz12 KO + WT


title: MCF7_TMX_GR_Rep2

value: xenograft

value: Tamoxifen (30mg/Kg) (TMX)


title: Late_Vehicle_4

description: Library name: Sample_18

value: Spinal cord (L4-L6)


title: MCF7_TMX_GR_Rep1


title: Sham7Protein0115L

description: Library name: 0115L


title: Sham7Protein0114L

description: Library name: 0114L


title: CnR_H3K9me3_Suz12KO_rep2

value: Suz12 KO


title: Late_SAFit2_2

description: Library name: Sample_17

value: 12-14 weeks when collected

value: wildtype


title: MCF7_Control_GR_Rep3

value: Control (no treatments)


title: Sham7Protein0113L

description: Library name: 0113L


title: Sleeve7Protein0120L

description: Library name: 0120L


title: MCF7_Control_GR_Rep2


title: CnR_H3K9me3_Suz12KO_S12NSUV2dead_I100nM_rep1

value: Mouse embryonic stem cells


title: Sham7Protein0112L

description: Library name: 0112L


title: MCF7_Control_GR_Rep1


title: Late_Vehicle_2

description: Library name: Sample_15

value: Vehicle

value: Late


title: MCF7_TMX_GR_Rep3

value: WT


title: Sham7Protein0111L

description: Library name: 0111L


title: CnR_H3K9me3_Suz12KO_S12NSUV2_I50nM_rep1

value: KDM4-specific inhibitor QC6352


title: Late_SAFit2_1

description: Library name: Sample_14


title: Sham7Protein0110L

description: Library name: 0110L


title: MCF7_TMXplusFasting_H3K27ac_Rep6

value: Tamoxifen+Fasting (TMX+Fasting)


title: CnR_H3K9me3_Suz12KO_S12NSUV2dead_rep1

value: Suz12 KO + S12N:SUV2*


title: Late_Vehicle_1

description: Library name: Sample_13


title: MCF7_TMXplusFasting_H3K27ac_Rep5

value: Breast cancer


title: Sham7Protein0109L

description: Library name: 0109L

value: Liver


title: Early_Vehicle_6

description: Library name: Sample_12

value: Early


title: MCF7_TMXplusFasting_H3K27ac_Rep4

value: xenograft


title: CnR_H3K9me3_Suz12KO_S12NSUV2_rep1

value: Suz12 KO + S12N:SUV2


title: Sleeve21Protein0108L

description: Library name: 0108L


title: CnR_H3K9me3_Suz12KO_WT_rep1

value: Suz12 KO + WT


title: CnR_H3K9me3_WT_mESC_rep2


title: CnR_H3K9me3_Suz12KO_rep1

value: Suz12 KO


title: MCF7_TMXplusFasting_H3K27ac_Rep3


title: Sleeve21Protein0107L

description: Library name: 0107L


title: MCF7_TMXplusFasting_H3K27ac_Rep2


title: Sleeve21Protein0106L

description: Library name: 0106L


title: CnR_H3K9me3_WT_mESC_rep1


title: Early_Vehicle_4

description: Library name: Sample_9

value: Spinal cord (L4-L6)

value: 12-14 weeks when collected


title: Early_SAFit1_5

description: Library name: Sample_8

value: wildtype


title: Sleeve21Protein0105L

description: Library name: 0105L


title: CnR_H3K36me3_Suz12KO_S12NSD2dead_rep2

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SD2*


title: MCF7_TMXplusFasting_H3K27ac_Rep1


title: MCF7_Fasting_H3K27ac_Rep3

value: Fasting (48h water-only diet)


title: Early_Vehicle_3

description: Library name: Sample_7

value: Vehicle


title: Early_SAFit1_4

description: Library name: Sample_6


title: CnR_H3K36me3_Suz12KO_S12NSD2_rep2

value: Suz12 KO + S12N:SD2


title: CnR_H3K36me3_Suz12KO_rep2


title: Early_SAFit1_3

description: Library name: Sample_5


title: MCF7_Fasting_H3K27ac_Rep1

value: WT


title: Early_Vehicle_5

description: Library name: Sample_10


title: Sleeve21Protein0102L

description: Library name: 0102L


title: CnR_H3K36me3_WT_mESC_rep2


title: MCF7_Fasting_H3K27ac_Rep2


title: CnR_H3K36me3_Suz12KO_S12NSD2dead_rep1


title: MCF7_TMX_H3K27ac_Rep3

value: Tamoxifen (30mg/Kg) (TMX)


title: Sleeve21Protein0101L

description: Library name: 0101L


title: Sham21Protein0100L

description: Library name: 0100L


title: Early_Vehicle_1

description: Library name: Sample_3


title: MCF7_TMX_H3K27ac_Rep2

value: Breast cancer


title: CnR_H3K36me3_Suz12KO_S12NSD2_rep1


title: Sham21Protein0099L

description: Library name: 0099L

value: Liver


title: MCF7_TMX_H3K27ac_Rep1


title: Early_SAFit1_2

description: Library name: Sample_2

value: Early


title: Sham21Protein0098L

description: Library name: 0098L


title: MCF7_Control_H3K27ac_Rep3

value: xenograft

value: Control (no treatments)


title: Sham21Protein0096L

description: Library name: 0096L


title: CnR_H3K36me3_WT_mESC_rep1


title: Early_SAFit1_1

description: Library name: Sample_1


title: Early_Vehicle_2

description: Library name: Sample_4


title: Exp2_LP_sgMed12_QuantSeq_rep2

description:
Library name: Exp2_LP_sgMed12_QuantSeq_rep2
Exp2_QuantSeq_TPM_values.txt

data_processing:
Adapter sequences were trimmed from the raw RNA-seq reads with fastp. Trimmed reads of each sample were mapped to the reference mouse genome mm10 using STAR and normalized to one million reads in the original library. Differentially expressed genes (DEGs) were defined with p < 0.05, |log2FC| > 1, and TPM > 10 based on measurements from three biologically independent replicates for each sample type.
Assembly: mm10
Supplementary files format and content: txt files include TPM values for each sample

extract_protocol:
Total RNA was isolated from samples of 3 x 105 cultured cells using a RNeasy Micro Kit (Qiagen).
Five hundred nanograms of total RNA was subjected to the 3’mRNA library preparation with QuantSeq 3’ mRNA-seq Library Prep Kit FWD (LEXOGEN) according to the manufacturer’s instructions. After the PCR step, size distribution and yield of the library was determined by the D1000 high sensitivity tape station (Agilent) or Agilent High Sensitivity DNA kit on the bioanalyzer (Agilent). The pooled libraries were loaded on the Illumina Nextseq500 platform and analyzed by 75bp single read.

value: Fetal liver

value: LP

value: Cultured on OP9


title: MCF7_Control_H3K27ac_Rep1


title: Exp2_LP_sgMed12_QuantSeq_rep3

description:
Library name: Exp2_LP_sgMed12_QuantSeq_rep3
Exp2_QuantSeq_TPM_values.txt


title: CnR_H3K27me3_Suz12KO

value: Suz12 KO


title: Sham21Protein0095L

description: Library name: 0095L


title: CnR_H3K27me3_WT_mESC


title: Sham21Protein0093L

description: Library name: 0093L


title: MCF7_TMXplusFasting_ER_Rep6

value: Tamoxifen+Fasting (TMX+Fasting)


title: Exp2_LP_sgMed12_QuantSeq_rep1

description:
Library name: Exp2_LP_sgMed12_QuantSeq_rep1
Exp2_QuantSeq_TPM_values.txt


title: Exp2_LP_sgCTCF_QuantSeq_rep3

description:
Library name: Exp2_LP_sgCTCF_QuantSeq_rep3
Exp2_QuantSeq_TPM_values.txt


title: Sham21Protein0094L

description: Library name: 0094L


title: ChIP_SUZ12_RS_S12NSD2_dTAG

value: Mouse embryonic stem cells

value: RS + S12N:SD2


title: Sleeve36Protein0090L

description: Library name: 0090L


title: MCF7_TMXplusFasting_ER_Rep5


title: MCF7_TMXplusFasting_ER_Rep4


title: CnR_H3K36me3_Suz12KO_rep1


title: ChIP_SUZ12_RS_S12NSD2_DMSO

value: DMSO


title: Exp2_LP_sgCTCF_QuantSeq_rep2

description:
Library name: Exp2_LP_sgCTCF_QuantSeq_rep2
Exp2_QuantSeq_TPM_values.txt


title: Exp2_LP_sgCTCF_QuantSeq_rep1

description:
Library name: Exp2_LP_sgCTCF_QuantSeq_rep1
Exp2_QuantSeq_TPM_values.txt


title: CnR_H3K27me3_Suz12KO_WT

value: Suz12 KO + WT


title: ChIP_SUZ12_RS_S12NSUV2_dTAG

value: RS + S12N:SUV2


title: Exp2_LP_sgCbfb_QuantSeq_rep3

description:
Library name: Exp2_LP_sgCbfb_QuantSeq_rep3
Exp2_QuantSeq_TPM_values.txt


title: Sleeve36Protein0087L

description: Library name: 0087L


title: MCF7_TMXplusFasting_ER_Rep2

value: WT


title: Sleeve36Protein0085L

description: Library name: 0085L


title: MCF7_TMXplusFasting_ER_Rep1


title: Exp2_LP_sgCbfb_QuantSeq_rep2

description:
Library name: Exp2_LP_sgCbfb_QuantSeq_rep2
Exp2_QuantSeq_TPM_values.txt


title: Exp2_LP_sgCbfb_QuantSeq_rep1

description:
Library name: Exp2_LP_sgCbfb_QuantSeq_rep1
Exp2_QuantSeq_TPM_values.txt


title: MCF7_Fasting_ER_Rep3

value: Fasting (48h water-only diet)


title: ChIP_SUZ12_R-Suz12KO_dTAG

value: RBBP5-FKBP + Suz12 KO (RS)


title: Sham36Protein0082L

description: Library name: 0082L

value: Liver


title: Sham36Protein0083L

description: Library name: 0083L


title: Sleeve36Protein0089L

description: Library name: 0089L


title: MCF7_Fasting_ER_Rep2

value: Breast cancer


title: Exp2_LP_sgCont_QuantSeq_rep3

description:
Library name: Exp2_LP_sgCont_QuantSeq_rep3
Exp2_QuantSeq_TPM_values.txt


title: Sham36Protein0081L

description: Library name: 0081L


title: Exp2_LP_sgCont_QuantSeq_rep2

description:
Library name: Exp2_LP_sgCont_QuantSeq_rep2
Exp2_QuantSeq_TPM_values.txt


title: Sham36Protein0080L

description: Library name: 0080L


title: ChIP_SUZ12_Rbbp5-FKBP_DMSO


title: Exp2_LP_sgCont_QuantSeq_rep1

description:
Library name: Exp2_LP_sgCont_QuantSeq_rep1
Exp2_QuantSeq_TPM_values.txt


title: MCF7_TMXplusFasting_ER_Rep3

value: xenograft


title: MCF7_TMX_ER_Rep3

value: Tamoxifen (30mg/Kg) (TMX)


title: Sleeve21Protein0103L

description: Library name: 0103L


title: Sham36Protein0079L

description: Library name: 0079L


title: Exp1_Phase1_sgCbfb_QuantSeq_rep3

description:
Library name: Exp1_Phase1_sgCbfb_QuantSeq_rep3
Exp1_QuantSeq_TPM_values.txt

value: Fetal liver

value: Cultured on OP9-DLL4


title: ChIP_SUZ12_Suz12KO_S12NSUV2

value: Suz12 KO + S12N:SUV2


title: MCF7_TMX_ER_Rep2


title: CnR_H3K9me3_Suz12KO_S12NSUV2_I50nM_rep2

value: KDM4-specific inhibitor QC6352


title: Sham36Protein0077L

description: Library name: 0077L


title: Exp1_Phase1_sgCbfb_QuantSeq_rep2

description:
Library name: Exp1_Phase1_sgCbfb_QuantSeq_rep2
Exp1_QuantSeq_TPM_values.txt


title: SleeveWD0076L

description: Library name: 0076L


title: ChIP_SUZ12_Rbbp5-FKBP_dTAG


title: Exp1_Phase1_sgCbfb_QuantSeq_rep1

description:
Library name: Exp1_Phase1_sgCbfb_QuantSeq_rep1
Exp1_QuantSeq_TPM_values.txt


title: ChIP_SUZ12_R-Suz12KO_DMSO


title: MCF7_Fasting_ER_Rep1


title: MCF7_Control_ER_Rep3

value: Control (no treatments)


title: Exp1_LP_sgCbfb_QuantSeq_rep3

description:
Library name: Exp1_LP_sgCbfb_QuantSeq_rep3
Exp1_QuantSeq_TPM_values.txt

value: LP

value: Cultured on OP9


title: SleeveWD0075L

description: Library name: 0075L


title: ChIP_SUZ12_Suz12KO_WT

value: Mouse embryonic stem cells


title: Exp1_LP_sgCbfb_QuantSeq_rep2

description:
Library name: Exp1_LP_sgCbfb_QuantSeq_rep2
Exp1_QuantSeq_TPM_values.txt


title: SleeveWD0074L

description: Library name: 0074L


title: ChIP_SUZ12_WT_mESC


title: SleeveWD0073L

description: Library name: 0073L


title: Exp1_LP_sgCbfb_QuantSeq_rep1

description:
Library name: Exp1_LP_sgCbfb_QuantSeq_rep1
Exp1_QuantSeq_TPM_values.txt


title: ChIP_SUZ12_Suz12KO_S12NSD2

value: Suz12 KO + S12N:SD2


title: MCF7_Control_ER_Rep2


title: 54-R

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Quality of reads was assessed using FastQC v0.11.8 and summarized with MultiQC v1.9
After subsampling samples to 30M reads maximum, alignment was done with STAR v2.7.6a against GRCh38
Protein-coding gene quantification was performed using featureCounts v2.0 with ENSEMBL v101 annotations
Genes were filtering with only genes with >20 counts in all samples retained for downstream analysis
The filtered count matrix was normalized using quantile normalization
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: csvs of raw and normalized expression levels

source_name: Primary hepatoblast organoids (HBOs)

growth_protocol: Hepatoblast organoids (HBOs) were established as cell lines by the enzymatic and mechanical dissociation of human foetal liver. The dissociated cells were seeded in 45% hepatoblast organoid complete medium (HBO CM) and 55% matrigel. HBOs have a self-renewal capacity and are passaged regularly every 7 - 10 days.

extract_protocol:
Samples were collected in 250 uL of Total RNA lysis buffer and RNA was extracted according to manufacturer's instructions from the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma, RTN350-1KT). RNA was quantified on a Nanodrop machine.
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Briefly, 300 ng of RNA were used to start with; these were incubated for 10 minutes at 94C to fragment the RNA as in step 1.2.37. 10 cycles were used for the indexing PCR (step 1.9.3). Other than the above, all steps were conducted as per the protocol.

treatment_protocol: 3 Biological replicates from each condition were collected (with the exception of the - RSPO - WNT condition where onlu 2 replicates are available) reflecting three different HBO lines. Control represents HBO CM medium that contains both Wnt3a and R-spondin conditioned media; - WNT + DKK is removal of the Wnt3a medium, and addition of a WNT inhibitor DKK; - RSPO + WNT is removal of R-spondin medium but keeping WNT; and finally - RSPO - WNT is removal of both conditioned media. Where conditioned media was removed, the same proportion of FBS-containing medium was added. Treatment with these conditions lasted for a week and RNA was collected at the end of the treatment.

value: - RSPO + WNT


title: SleeveWD0072L

description: Library name: 0072L


title: submergence condition, ein3eil1 mutant, mock, replication 3

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

country: China

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by fastp for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filitered reads were then mapped to Tair10 using Hisat2
Differential gene expression analysis was done using R package DESeq2
Assembly: TAIR10
Supplementary files format and content: all_genes_expression.csv

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: 4-week-old seedlings grown under air conditions (control) were treated with or without submergence 6 hr, and leaves tissue was collected.Three replicates were prepared for each condition and each line.

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000. The integrity of RNA was detected by agarose gel, and the RIN value was determined by Agilent 2100. Using magnetic beads with Oligo (dT) and ployA for A-T base pairing, mRNA can be isolated from total RNA for analysis of transcriptome information. Under the action of reverse transcriptase, six random primers were added to reverse synthesize a single strand of cDNA using mRNA as a template, followed by a two-strand synthesis to form a stable double-stranded structure. The structure of double-stranded cDNA is sticky end. Add End Repair Mix to repair it into a flat end, and then add an "A" base at the 3 'end to connect the Y-shaped connector.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: with 6 hours submergence treatment

value: leaves

value: submergence condition


title: Exp1_Phase1_sgCont_QuantSeq_rep3

description:
Library name: Exp1_Phase1_sgCont_QuantSeq_rep3
Exp1_QuantSeq_TPM_values.txt


title: submergence condition, ein3eil1  mutant, mock, replication 2


title: SleeveWD0071L

description: Library name: 0071L


title: submergence condition, ein3eil1 mutant, mock, replication 1


title: Exp1_Phase1_sgCont_QuantSeq_rep1

description:
Library name: Exp1_Phase1_sgCont_QuantSeq_rep1
Exp1_QuantSeq_TPM_values.txt


title: 57-W

value: - WNT + DKK


title: SleeveWD0070L

description: Library name: 0070L

value: Liver


title: 54-W


title: ChIP_SUZ12_Suz12KO

value: Suz12 KO


title: submergence condition, phya-211 mutant, mock, replication 3


title: 53-W


title: ChIP_SUZ12_Suz12KO_S12N

value: Suz12 KO + S12N


title: Exp1_LP_sgCont_QuantSeq_rep3

description:
Library name: Exp1_LP_sgCont_QuantSeq_rep3
Exp1_QuantSeq_TPM_values.txt


title: submergence condition, phya-211 mutant, mock, replication 2


title: ShamWD0068L

description: Library name: 0068L


title: Exp1_LP_sgCont_QuantSeq_rep2

description:
Library name: Exp1_LP_sgCont_QuantSeq_rep2
Exp1_QuantSeq_TPM_values.txt


title: ShamWD0067L

description: Library name: 0067L


title: ShamWD0066L

description: Library name: 0066L


title: Exp1_LP_sgCont_QuantSeq_rep1

description:
Library name: Exp1_LP_sgCont_QuantSeq_rep1
Exp1_QuantSeq_TPM_values.txt


title: Phase1_input_rep2

description: Library name: Phase1_input_rep2


title: 53-R


title: submergence condition, wild type, mock, replication 2

value: Wild type


title: ShamWD0065L

description: Library name: 0065L


title: SleeveWD0069L

description: Library name: 0069L


title: 54C

value: Control


title: 53-W-R

value: - RSPO - WNT


title: ShamWD0064L

description: Library name: 0064L


title: submergence condition, wild type, mock, replication 1


title: MCF7_TMX_ER_Rep1

value: Breast cancer

value: xenograft

value: WT

value: Tamoxifen (30mg/Kg) (TMX)


title: air condition, ein3eil1 mutant, mock, replication 3

value: air condition


title: Late_Vehicle_3

description: Library name: Sample_16

value: Spinal cord (L4-L6)

value: 12-14 weeks when collected

value: wildtype

value: Vehicle

value: Late


title: ShamWD0063L

description: Library name: 0063L


title: Phase1_input_rep1

description: Library name: Phase1_input_rep1

value: Fetal liver

value: Cultured on OP9-DLL4


title: LP_input_rep2

description: Library name: LP_input_rep2

value: LP

value: Cultured on OP9


title: 53C


title: 57-W-R


title: submergence condition, phya-211 mutant, mock, replication 1

value: leaves

value: submergence condition


title: LP_input_rep1

description: Library name: LP_input_rep1


title: air condition, ein3eil1  mutant, mock, replication 2


title: 57C

value: Control


title: Exp1_Phase1_sgCont_QuantSeq_rep2

description:
Library name: Exp1_Phase1_sgCont_QuantSeq_rep2
Exp1_QuantSeq_TPM_values.txt


title: MCF7_Control_ER_Rep1

value: Breast cancer

value: Control (no treatments)


title: ShamWD0062L

description: Library name: 0062L

value: Liver


title: submergence condition, wild type, mock, replication 3

value: Wild type


title: air condition, ein3eil1 mutant, mock, replication 1

value: air condition


title: ShamWD0061L

description: Library name: 0061L


title: Phase1_ap300_ChIP_rep2

description:
Library name: Phase1_ap300_ChIP_rep2
Phase1_p300_ChIP_IDR_peaks.txt


title: Phase1_ap300_ChIP_rep1

description:
Library name: Phase1_ap300_ChIP_rep1
Phase1_p300_ChIP_IDR_peaks.txt


title: LL_2

first: Ping

address: 800 Rd dong chuan

institute: Shanghai Jiao Tong University

data_processing:
Raw RNA-seq reads were quality checked and trimmed to remove adaptor sequences, contamination and low-quality reads. Trimmed reads from each sample were aligned to the publicly available mouse reference genome using Hisat2 version 2.0.5. Read counts were generated for each gene using featureCounts v1.5.0-p3. The FPKM of each gene was then calculated based on the length of the gene and the number of reads mapped to that gene.
Assembly: mm10
Supplementary files format and content: xls files containing transcriptome data.
Supplementary files format and content: Tab-delimited text filefor each sample

source_name: Hippocampi

extract_protocol:
For RNA-seq, mice were deeply anaesthetised with 0.14 g/kg sodium pentobarbital 24 h after the second hit. Whole hippocampi from 4 groups (3 animals/ group) were rapidly dissected. Total RNA was extracted with TRIzol reagent.
Library preparation and RNA-seq were performed by Novogene using an Illumina HiSeq 2000 platform.

value: brain cells

value: Hippocampi

value: P3 LPS and P14 LPS


title: 57-R

value: - RSPO + WNT


title: air condition, phya-211 mutant, mock, replication 3


title: ChIP_SUZ12_RS_S12NSUV2_DMSO

value: Mouse embryonic stem cells

value: RS + S12N:SUV2

value: DMSO


title: LP_ap300_ChIP_rep1

description:
Library name: LP_ap300_ChIP_rep1
LP_p300_ChIP_IDR_peaks.txt

value: Fetal liver

value: LP


title: Mock H3K9me3 Replicate 2

city: Charlottesville

first: Abigail

last: Whitford

state: Virginia

address: 1340 Jefferson Park Ave, Apt 305

department: Microbiology

institute: University of Virginia

description:
Library name: K
Procssed file aligned to HSV-1 SC16

data_processing:
Pair-ended, partial lane sequencing and de-multiplexing were carried out using NovaSeq (Novogene).
Data analysis was performed using Galaxy, command line and R code, and workflow, adapted from the cited tutorial.
Data was aligned to mouse (mm39) and viral [SC16; KX946970 70] genomes using Bowtie2.
Cutadapt was used to trim i5 and i7 adapters. Bam files were converted to Bed files using samtools.
Bed files were converted to Bedgraph files using bedtools. Bedgraph files were normalized to total mapped reads for host (mouse), virus (SC16), and the K Met Stat panel.
Assembly: mm39 or KX946970 (SC16)
Supplementary files format and content: bedgraph
Library strategy: CUT&Tag

source_name: Superior Cervical Ganglia

growth_protocol: Latent HSV‐1 infection was established in P6‐8 sympathetic neurons from the superior cervical ganglia (SCG). Neurons were cultured for at least two days without antimitotic agents prior to infection. The cultures were infected with Stayput Us11-GFP at an of MOI 5 PFU/cell, (assuming 10,000 cells per well) in Dulbecco’s Phosphate Buffered Saline (DPBS) + CaCl2 + MgCl2 supplemented with 1% fetal bovine serum, 4.5 g/L glucose, and 10 μM acyclovir (ACV) for 4 h at 37°C. The inoculum was replaced with CM1 containing 50 μM ACV. 8 days post-infection, ACV was washed out and replaced with CM1 alone. Latent time point was 10 days post infection .

extract_protocol:
CUT&Tag was carried out on latent neuronal cultures (approximately 1.2 x105 neurons per reaction) using the Epicypher CUTANA CUT&Tag Kit and workflow (14-1102).
Dual-indexed DNA libraries were prepared using the same kit.

treatment_protocol: 600 IU/uL IFNα for 18 hours pre-infection, during infection, and 24 hours post infection only.

value: Superior Cervical Ganglia

value: Primary Cultured Neurons

value: Neurons

value: WT

value: mock

tag: replicate


title: LL_1


title: LS_3

value: P3 LPS and P14 saline


title: air condition, phya-211 mutant, mock, replication 1

value: leaves


title: MCF7_Control_H3K27ac_Rep2

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis and duplicates were marked by PICARD/GATK markDuplicates
Enrichment over input control was determined using MACS2 (q < 0.001, narrowPeak mode). Only peaks not overlapping with the ENCODE hg38/GRCh38 blacklisted regions, were retained.
Assembly: hg38/GRCh38
Supplementary files format and content: .bed, narrowPeaks

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009). In brief, MCF7 tumours were fixed in 2mM of DSG for 20min at RT, followed by 1% formaldehyde for 25 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 15 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Scientific) were conjugated to 5µL of ERa, H3K27ac, GR, PR and c-JUN antibodies.
Illumina

value: Breast cancer

value: xenograft

value: Control (no treatments)


title: IFNα IgG Replicate 2

description:
Library name: J
Procssed file aligned to HSV-1 SC16

value: IFNα

value: IgG


title: Phase1_aMed12_ChIP_rep2

description:
Library name: Phase1_aMed12_ChIP_rep2
Phase1_Med12_ChIP_IDR_peaks.txt

value: anti-Med12 (Bethyl; A300-774A)

value: Cultured on OP9-DLL4


title: air condition, wild type, mock, replication 3

value: Wild type

value: air condition


title: Mock IgG Replicate 2

description:
Library name: I
Procssed file aligned to HSV-1 SC16


title: Phase1_aMed12_ChIP_rep1

description:
Library name: Phase1_aMed12_ChIP_rep1
Phase1_Med12_ChIP_IDR_peaks.txt

value: Fetal liver


title: LS_2

value: brain cells

value: Hippocampi


title: LS_1


title: LL_3

value: P3 LPS and P14 LPS


title: air condition, wild type, mock, replication 2


title: IFNα H3K9me3 Replicate 1

description:
Library name: D
Procssed file aligned to HSV-1 SC16

value: Superior Cervical Ganglia

value: Primary Cultured Neurons

value: Neurons

value: WT


title: LP_aMed12_ChIP_rep2

description:
Library name: LP_aMed12_ChIP_rep2
LP_Med12_ChIP_IDR_peaks.txt

value: LP

value: Cultured on OP9


title: SL_3

value: P3 saline and P14 LPS


title: LP_aMed12_ChIP_rep1

description:
Library name: LP_aMed12_ChIP_rep1
LP_Med12_ChIP_IDR_peaks.txt


title: air condition, wild type, mock, replication 1

value: leaves


title: Mock H3K9me3 Replicate 1

description:
Library name: C
Procssed file aligned to HSV-1 SC16

value: mock


title: SL_2


title: IFNα IgG Replicate 1

description:
Library name: B
Procssed file aligned to HSV-1 SC16

value: IFNα

value: IgG


title: air condition, phya-211 mutant, mock, replication 2


title: IFNα H3K9me3 Replicate 2

description:
Library name: L
Procssed file aligned to HSV-1 SC16


title: Non tranformed calli, rep 2

city: Milano

first: Raul

last: Pirona

address: Via Alfonso Corti 12

institute: IBBA-CNR

description: Library name: WT Rep 2

data_processing:
The quality of the reads was assessed with the software FASTQC. In order to remove adapters and low-quality bases from the reads, a trimming step with TRIMMOMATIC software was performed with the following parameters: minimum length was set to 35 bp and the quality score to 25. The Spliced Transcripts Alignment to a Reference (STAR) software was used to align the reads to the Cynara cardunculus reference genome (V1 from Ensembl Plants). FeatureCounts was used to calculate gene expression values as raw fragment counts. In addition, a normalization was applied to the raw fragment counts by using the Trimmed Mean of M -values (TMM) and the Fragments Per Kilobase Million (FPKM) normalization. The FPKM count matrix was filtered with the HTSfilter package to eliminate the genes that created uninformative signal. The identification of the differentially expressed genes (DEGs) was performed with the package edgeR (Robinson et al. 2009) setting the threshold for significance of False Discovery Rate (FDR, Benjamini–Hochberg correction to p-value) to < 0.05. Finally, a gene was considered differentially expressed if the log (Fold Change, FC) was greater than 1 or smaller than -1.
Assembly: Cynara cardunculus genome (V1 from Ensembl Plants)
Supplementary files format and content: fastq

organism: Cynara cardunculus

source_name: Callus

growth_protocol: Undifferentiated wild type (WT) friable cardoon calluses (“Spagnolo” genotype), along with transgenic SAD-OE overexpressing and FAD-KD silenced cardoon calli (hereafter reported as SAD-OE and FAD-KD) were previously established (Cappetta et al. 2022), and maintenance of calli cultures was made on GB5 medium. Cell suspension cultures were started as previously described (Oliviero et al. 2022) by inoculating 2.0 g of friable callus from SAD-OE and FAD-KD transgenic lines and WT calli in three biological replicates, in a 250 mL Erlenmeyer flask containing 50 mL of GB5 liquid medium, and kept on a gyratory shaker at 100 rpm in the dark at 25 °C. After four cycles of subculturing, 10 days’ time course for growth measurements and for transcriptional analysis was performed on 50 ml liquid culture in triplicates.

extract_protocol:
Total RNAs from calli were extracted in triplicates from three experimental groups: one WT, and two independent transgenic lines carrying the construct pGWB411: SAD (SAD-OE) and pHellsgate12 :: FAD2:2 (FAD-KD), for a total of 9 samples. RNA extraction was performed on100 mg of callus, ground under liquid nitrogen, lysed/homogenized with 1 mL of TRIzol (Thermo Fisher Scientific, #15596026) and, after addition of 0.2 mL of Phenol:Chloroform:Isoamyl-alcohol (25:24:1) and centrifugation (10 min, 13,000× g), the RNA was precipitated from the aqueous phase with 1 volume of isopropanol. Preliminary analysis confirmed that all samples passed the quality control (A260/A280 = 2.10, total RNA amount > 10 µg/sample and RNA integrity number > 9).
Illumina TruSeq RNA Sample Prep kit

value: Callus


title: Phase1_aCTCF_ChIP_rep2

description:
Library name: Phase1_aCTCF_ChIP_rep2
Phase1_CTCF_ChIP_IDR_peaks.txt

value: anti-CTCF (CST; 3418)

value: Cultured on OP9-DLL4


title: Mock IgG Replicate 1

description:
Library name: A
Procssed file aligned to HSV-1 SC16


title: LP_ap300_ChIP_rep2

description:
Library name: LP_ap300_ChIP_rep2
LP_p300_ChIP_IDR_peaks.txt

value: Fetal liver


title: Phase1_aCTCF_ChIP_rep1

description:
Library name: Phase1_aCTCF_ChIP_rep1
Phase1_CTCF_ChIP_IDR_peaks.txt


title: Cat_23_Medulla

city: Lausanne

first: James

middle: Holzwarth

last: A

address: EPFL Innovation Park

country: Switzerland

institute: Nestlé

description: Library name: Cat_23_Medulla

data_processing:
Reads were aligned to the Felis catus 9.0 using RNAstar v2.5.3
Gene count was performed with HTSeq v2.16.2
Assembly: Felis catus genome version 9.0
Supplementary files format and content: htseq counts

organism: Felis catus

source_name: kidney Medulla

extract_protocol:
Total RNA was extracted using the Agencourt RNAdvance Tissue Kit (Beckman Coulter): tissues were disrupted and lyzed using the Fastprep 2 x 1’ at speed 6. 400 μL of lyzate was extracted and eluted in 50μL
The Stranded mRNA Library Prep protocol convert the mRNA in a total RNA sample into a library of template molecules of known strand origin using the reagents provided in an Illumina® Stranded mRNA library prep workflow

value: kidney Medulla

tag: disease stage


title: SS_3

value: brain cells

value: Hippocampi

value: P3 saline and P14 saline


title: Non tranformed calli, rep 1

description: Library name: WT Rep 1


title: SL_1


title: Cat_22_Medulla

description: Library name: Cat_22_Medulla


title: SS_1


title: SS_2


title: Cat_20_Medulla

description: Library name: Cat_20_Medulla


title: SAD-OE transformed calli, rep 2

description: Library name: SAD-OE Rep 2

value: SAD-OE


title: LP_aCTCF_ChIP_rep1

description:
Library name: LP_aCTCF_ChIP_rep1
LP_CTCF_ChIP_IDR_peaks.txt


title: MSS116_1-53_OE_rep3

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

description:
Library name: 4575C
additional_samples_for_GSE303345_count_matrix.txt.gz

data_processing:
Sequencing data was demultiplexed using Illumina's BCL Convert. De-multiplexed read sequences were then aligned to the Saccharomyces cerevisiae (R64-1-1) reference sequence using DRAGEN RNA app on Basespace Sequence Hub. Gene-level read counts were quantified using the featureCounts function from the Rsubread package in R.
Assembly: Saccharomyces cerevisiae R64-1-1
Supplementary files format and content: tab delineated text file matrix_of_counts.txt.gz contains the raw counts for each sample

organism: Saccharomyces cerevisiae

growth_protocol: YPR (1% yeast extract, 2% peptone, 2% raffinose)

extract_protocol:
Cytiva RNAspin Mini Kit
Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina).

treatment_protocol: Induction of corresponding gene was done with the addtion of 1% galactose for 4h

value: carrying a 2u empty plasmid

value: induction of GAL-MTSMSS116 (+/-) with 1% galactose for 4h


title: SAD-OE transformed calli, rep 1

description: Library name: SAD-OE Rep 1


title: Cat_18_Medulla

description: Library name: Cat_18_Medulla


title: Phase1_aRUNX1_ChIP_rep2

description:
Library name: Phase1_aRUNX1_ChIP_rep2
Phase1_RUNX1_ChIP_IDR_peaks.txt

data_processing:
ChIP-seq; Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample. ChIP-seq data were mapped to the mouse genome bulid NCBI37/mm10 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t -best -strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC genome browser (http://genome.ucsc.edu). ChIP peaks were identified with findPeaks.pl against a matched control sample using the setting “-P .1 -LP .1 -poisson .1 -style factor”. The identified peaks were annotated to genes with the annotatePeaks.pl command against the mm10 genomic build in the HOMER package. Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score <15, were considered for further analysis.
Assembly: mm10
Supplementary files format and content: txt files for IDR ChIP peaks

extract_protocol:
Ten million of Cas9-LPs with or without Notch stimulation were fixed with 1 mg/ml disuccinimidyl glutarate (Thermo Scientific) in PBS for 30 min at room temperature followed by an additional 10 min with addition of formaldehyde up to 1 %. The reaction was quenched by addition of 1/10 volume of 0.125 M glycine and the cells were washed with cold PBS. Pelleted nuclei were dissolved in lysis buffer (0.5 % SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl [pH 8.0], and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30 sec sonication followed by 30 sec rest, with high power.
ChIP-seq libraries were constructed using NEBNext Ultra Ⅱ DNA Library Prep with Sample Purification Beads (E7103S, NEB) and NEBNext Multiplex Oligos for Illumina (E7500S, NEB) and sequenced on Illumina NextSeq500 in single read mode with the read length of 75 nt.

value: anti-RUNX1 (abcam; ab23980)


title: Non tranformed calli, rep 3

description: Library name: WT Rep 3

value: WT


title: Phase1_aRUNX1_ChIP_rep1

description:
Library name: Phase1_aRUNX1_ChIP_rep1
Phase1_RUNX1_ChIP_IDR_peaks.txt


title: MSS116_1-53_OE_rep2

description:
Library name: 4575B
additional_samples_for_GSE303345_count_matrix.txt.gz


title: LP_aRUNX1_ChIP_rep2

description:
Library name: LP_aRUNX1_ChIP_rep2
LP_RUNX1_ChIP_IDR_peaks.txt

value: LP

value: Cultured on OP9


title: Cat_17_Medulla

description: Library name: Cat_17_Medulla


title: FAD-KD transformed calli, rep 3

description: Library name: FAD-KO Rep 3

value: FAD-KD


title: MSS116_1-53_OE_rep1

description:
Library name: 4575A
additional_samples_for_GSE303345_count_matrix.txt.gz


title: FAD-KD transformed calli, rep 2

description: Library name: FAD-KO Rep 2


title: Cat_16_Medulla

description: Library name: Cat_16_Medulla


title: MTSMGE1_OE_pdr3_KO_rep3

description: Library name: 4508C

value: nduction of GAL-MTSMGE1 (+/-) with 1% galactose for 4h


title: LP_aRUNX1_ChIP_rep1

description:
Library name: LP_aRUNX1_ChIP_rep1
LP_RUNX1_ChIP_IDR_peaks.txt


title: LP_aCTCF_ChIP_rep2

description:
Library name: LP_aCTCF_ChIP_rep2
LP_CTCF_ChIP_IDR_peaks.txt


title: SAD-OE transformed calli, rep 3

description: Library name: SAD-OE Rep 3

value: Callus


title: Transformed calli with empty vector, rep 3

description: Library name: Empty-Vector Rep 3

value: Empty vector


title: old replicate 5, Input

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

data_processing:
All seqeuncing files were aligned to a combined mouse-human genome
Any read that aligned to the human renome was then removed.
Peaks were called using homer and normazlied to Input.
Assembly: mm10
Supplementary files format and content: .txt and .bw, peaks of each file

source_name: Hepatocytes

extract_protocol:
After ChIP decrosslinking at 65C overnight with RNase A and 2-hours Proteinase K at 37C, DNA was isolated using phenol-chloroform isoamyl alcohol and ethanol precipitation.
After DNA integrity was confirmed, the DNA fragments are repaired, dA-tailed.DNA fragments with A tail are ligated to sequencing adaptor followed by size selection and PCR amplification by Novagene

treatment_protocol: Hepatocytes were isolated from young and old mice using 2-step perfusion methadology. Chromatin were generated and human chromatin were added for 5% spike-in. ChIP for Histone H3 (Abcam ab1791), Histone H3K4me1 (Abcam ab8895), or Histone H3K27ac (Abcam ab4729) with 5ug chromatin and 5ug antibody. IP overnight.

value: Hepatocytes

value: Input


title: MTSMGE1_OE_pdr3_KO_rep2

description: Library name: 4508B


title: young replicate 5, Input


title: Cat_14_Medulla

description: Library name: Cat_14_Medulla

value: kidney Medulla


title: MTSMGE1_OE_pdr3_KO_rep1

description: Library name: 4508A


title: Cat_15_Medulla

description: Library name: Cat_15_Medulla


title: Cat_11_Medulla

description: Library name: Cat_11_Medulla


title: Transformed calli with empty vector, rep 1

description: Library name: Empty-Vector Rep 1


title: MTSMGE1_OE_rep3

description: Library name: 3188C


title: old replicate 4, Input


title: LN6

city: Liverpool

first: Atilla

last: ALTINPINAR

address: 6 West Derby street

institute: University of Liverpool

description: Library name: Sample 12

data_processing:
The raw Fastq files are trimmed using Cutadapt version 1.2.1
The reads are further trimmed using Sickle version 1.200 with a minimum window quality score of 20. Reads shorter than 15 bp after trimming were removed.
The processed reads were then pseudo-aligned to the Ensemble release mus musculus transcriptomes v96 with Kallisto quant version 0.46.1
Read count extraction and normalization were performed using DESe2.
Assembly: mus musculus transcriptomes v96
Supplementary files format and content: tab-delimited tsv files contain abundance, count and length values for each sample

source_name: gastrocnemius muscle

extract_protocol:
RNA was harvested usingTRizol reagent and Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Preparation of dual-indexed, strand-specific RNASeq library from submitted total RNA was performed using the NEBNext polyA selection and Ultra II Directional RNA library preparation kits (New England Biolabs, UK).

value: gastrocnemius muscle

value: Gestational Protein Restriction


title: MTSMGE1_OE_rep2

description: Library name: 3188B


title: old replicate 3, Input


title: MTSMGE1_OE_rep1

description: Library name: 3188A


title: LN5

description: Library name: Sample 11


title: Cat_08_Medulla

description: Library name: Cat_08_Medulla


title: PSD1_OE_pdr3_KO_rep3

description: Library name: 961C

value: nduction of GAL-PSD1 (+/-) with 1% galactose for 4h


title: young replicate 3, Input


title: Cat_07_Medulla

description: Library name: Cat_07_Medulla


title: Cat_06_Medulla

description: Library name: Cat_06_Medulla

value: Control


title: LN4

description: Library name: Sample 10


title: FAD-KD transformed calli, rep 1

description: Library name: FAD-KO Rep 1


title: PSD1_OE_pdr3_KO_rep2

description: Library name: 961B

value: carrying a 2u empty plasmid


title: Cat_05_Medulla

description: Library name: Cat_05_Medulla


title: young replicate 2, Input


title: LN3

description: Library name: Sample 9


title: Transformed calli with empty vector, rep 2

description: Library name: Empty-Vector Rep 2


title: Cat_04_Medulla

description: Library name: Cat_04_Medulla


title: old replicate 2, Input


title: LN2

description: Library name: Sample 8


title: young replicate 4, Input


title: LN1

description: Library name: Sample 7


title: PSD1_OE_pdr3_KO_rep1

description: Library name: 961A


title: Cat_03_Medulla

description: Library name: Cat_03_Medulla


title: PSD1_OE_rep3

description: Library name: 470C


title: Cat_10_Medulla

description: Library name: Cat_10_Medulla


title: PSD1_OE_rep2

description: Library name: 470B


title: NN6

description: Library name: Sample 6

value: control


title: Cat_02_Medulla

description: Library name: Cat_02_Medulla


title: PSD1_OE_rep1

description: Library name: 470A


title: old replicate 5, H3K27Ac

value: H3K27ac (Abcam ab4729)


title: Cat_23_Cortex

description: Library name: Cat_23_Cortex

source_name: kidney Cortex

value: kidney Cortex


title: Cat_01_Medulla

description: Library name: Cat_01_Medulla


title: young replicate 5, H3K27Ac


title: NN5

description: Library name: Sample 5


title: LNCaP, siNC, 96h, rep3

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: Library name: siNC_96h_3

data_processing:
Raw reads were trimmed and filtered for short sequences using cutadapt v.1.8, setting minimum-length option to 18, error-rate 0.2 and overlap 5.
Reads were mapped against the human reference genome (Gencode GRCh38) using STAR aligner (version:2.7.0f_0328) with default parameters.
Using featureCounts, reads were assigned to exonic regions and counted.
Differential expression analysis was done from filtered CPM normalised counts (CPM <1 across half of the samples) using DESeq2 (Bioconductor Release: 3.14) in R version 3.4.1.
Assembly: hg38
Supplementary files format and content: Excel file that includes normalised counts (RPKM) for all samples

source_name: Prostate cancer

growth_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).

extract_protocol:
Total RNA was extracted using Trizol, according to the manufacturer's instructions.
Stranded polyA libraries were prepared according to the Nugen Universal Plus mRNA-seq protocol and included 15 cycles of amplification.

treatment_protocol: LNCaP cells were transfected with siRNAs for 48h or 96h using RNAiMAX.

value: Prostate cancer

value: LNCaP

value: siNC


title: NN4

description: Library name: Sample 4


title: old replicate 4, H3K27Ac


title: LNCaP, siNC, 96h, rep2

description: Library name: siNC_96h_2


title: NN3

description: Library name: Sample 3


title: young replicate 4, H3K27Ac


title: Cat_22_Cortex

description: Library name: Cat_22_Cortex


title: old replicate 1, Input


title: old replicate 3, H3K27Ac


title: NN2

description: Library name: Sample 2


title: LNCaP, siNC, 96h, rep1

description: Library name: siNC_96h_1


title: Cat_21_Cortex

description: Library name: Cat_21_Cortex


title: young replicate 1, Input


title: Cat_20_Cortex

description: Library name: Cat_20_Cortex


title: LNCaP, siNC, 48h, rep3

description: Library name: siNC_48h_3


title: NN1

description: Library name: Sample 1


title: LNCaP, siNC, 48h, rep2

description: Library name: siNC_48h_2


title: Cat_19_Cortex

description: Library name: Cat_19_Cortex


title: old replicate 2, H3K27Ac


title: Mouse spleen 50 UL reaction system scFFPE-ATAC

city: Uppsala

first: Xingqi

last: Chen

address: Husargata

department: Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

description: Library name: Mouse_spleen_50UL_reaction_system_scFFPE-ATAC

library_source: genomic single cell

data_processing:
The scFFPE-ATAC was debarcoded using https://github.com/pengweixing/scFFPE/fastq_debarcoding.allow_mismatch.v3.1.py
Fastq were mapped to hg38 or mm10 using bwa mem
The mapped data were sort and filtered using samtools
The single cell data were processed using the pipeline from https://github.com/pengweixing/scFFPE/tree/main/Snakemake
Assembly: hg38 and mm10
Supplementary files format and content: fragments for downsteream data analysis

source_name: Spleen

extract_protocol:
Before tagmentation, 50,000 purified FFPE single-cell nuclei were centrifuged at 2,000 g for 5 minutes at 4°C and resuspended in 0.1% lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630). The nuclei were then centrifuged again at 2,000 g for 5–10 minutes at 4°C. The nuclei pellet was resuspended in 95 μl of 1× tagmentation buffer (10 mM Tris-HCl, pH 7.5, 5 mM MgCl₂, 10% dimethylformamide, and dH₂O), and 5 μl of barcoded FFPE-Tn5 transposase (2 mM) was added per sample. The reaction mix was gently mixed and incubated at 37°C for 30 minutes at 400 rpm. The reaction was stopped by directly adding EDTA to a final concentration of 30 mM to each sample. All samples were then pooled and centrifuged to obtain a nuclei pellet. Next, three rounds of ligation were performed using the split-and-pool technique in a 96-well plate, with each well containing a ramped specific linker and ligation barcode. Detailed DNA sequences are provided in Supplementary Table 1. In brief, the ligation process was performed as follows: the pooled nuclei were resuspended in 1 mL of 1× NEBuffer 3.1 and mixed with the ligation mix (100 μL of 10× NEBuffer 3.1, 22 μL of 50 mg/mL BSA, 500 μL of 10× T4 DNA ligase buffer, 2,278 μL of ultrapure water, and 100 μL of T4 DNA ligase). A total of 40 μL of this mix was transferred per well, containing 10 μL of the ramped Ligation1 mixture, and incubated at 37°C for 30 minutes at 400 rpm. Then, 10 μL of Blocker-Ligation1 solution (2.64 μL of 100 μM Blocker-Ligation1, 2.50 μL of 10× T4 ligation buffer, and 4.86 μL of ultrapure water) was added per well, and the reactions were incubated at 37°C for 20 minutes at 400 rpm. The samples were then pooled into a 15 mL tube pre-coated with 0.5% BSA, followed by centrifugation at 1,500 g for 10 minutes at 4°C. The second and third ligation reactions were performed identically to the first. After the second and third ligations, blocking reactions were carried out using: 10 μL of Blocker-Ligation2 solution per well (2.64 μL of 100 μM Blocker-Ligation2, 2.50 μL of 10× T4 ligation buffer, and 4.86 μL of ultrapure water); 7.5 μL of Terminator_Ligation3 solution per well (2.64 μL of 100 μM Terminator_Ligation3, 2.50 μL of 0.5 M EDTA, and 2.36 μL of ultrapure water) for reaction termination. After gently mixing, the samples were pooled again into a 15 mL tube pre-coated with 0.5% BSA, followed by centrifugation at 1,500 g for 10 minutes at 4°C. After the third ligation, each nucleus acquired a unique combination of barcodes. Finally, the pellet was resuspended in PBS, nuclei were counted, and the sample was split into tubes containing 30,000–80,000 nuclei for reverse crosslinking.
Single cell FFPE-ATAC DNA library preparation Single-stranded cDNAs are prepared from 0.5–1 μg of purified IVT transcripts using the FirstStrand_cDNA oligo (DNA oligo sequences are provided in Supplementary Table 1). The reaction mixture (11.25 μL), containing 500ng-1 μg of RNA, 1 μL of 100 μM random octamer primer stock, and 0.25 μL of RNase Inhibitor (20 U/μL), is heated at 70°C for 3 minutes, then immediately cooled on ice. Next, the master mix is added, which consists of: • 4 μL of 5× First-Strand Buffer • 2 μL of dNTP Mix • 2 μL of 100 mM DTT • 0.25 μL of RNase Inhibitor (20 U/μL) • 0.5 μL SMART MMLV RT

value: Spleen


title: young replicate 3, H3K27Ac


title: LNCaP, siNC, 48h, rep1

description: Library name: siNC_48h_1


title: Mouse spleen withough gradient centrifugation  scFFPE-ATAC

description: Library name: Mouse_spleen_without_gradient_centrifugation_scFFPE-ATAC


title: Cat_18_Cortex

description: Library name: Cat_18_Cortex


title: Cat_17_Cortex

description: Library name: Cat_17_Cortex


title: old replicate 1, H3K27Ac


title: LNCaP, siPDIA5, 96h, rep3

description: Library name: siPDIA5_96h_3


title: Cat_16_Cortex

description: Library name: Cat_16_Cortex


title: LNCaP, siPDIA5, 96h, rep2

description: Library name: siPDIA5_96h_2


title: scATAC RV  R1

description:
Library name: singlecell-ATAC-Seq mouse spleen with reverse crosslinking 1
singlecell-ATAC-Seq mouse spleen with reverse crosslinking 1

data_processing:
Paired-end trimmed reads are aligned to the genome using Bowtie2 (v2.4.x) with parameters for sensitive, concordant mapping.
The resulting SAM files are converted to BAM, sorted, and duplicates removed using Samtools (v1.15) and Picard (v1.119)
Peaks are called using SEACR (v1.3) with thresholds of 0.01 and 0.05.
Assembly: mm10
Supplementary files format and content: Peaks

extract_protocol:
Nuclei were isolated from snap-frozen FFPE spleen tissues of C57BL/6J mice following the Omni-ATAC-seq protocol. A total of 20,000 to 100,000 DAPI-positive nuclei were counted and collected.
The nuclei were pelleted and resuspended in 1 mL of ATAC-Resuspension Buffer (ATAC-RSB) supplemented with 0.1% Tween-20. Transposition was performed using Tn5 transposase. The tagmented DNA was purified under both reverse crosslinking and non-crosslinking conditions, and subsequently PCR-amplified for 8–15 cycles using indexed primers to introduce sample-specific barcodes. For single-cell ATAC-seq, a combinatorial indexing (split-pool) strategy was employed to profile chromatin accessibility in individual nuclei isolated from FFPE mouse spleen samples. Nuclei were first isolated using a modified Omni-ATAC protocol optimized for FFPE tissue. After DAPI staining and counting, the nuclei were subjected to a three-level barcoding scheme. In the first round, transposition was performed using indexed Tn5 transposase. The nuclei were then split across multiple wells and underwent successive rounds of PCR with unique barcoded primers at each step. This split-pool barcoding enabled the unique indexing of individual nuclei. Libraries were pooled, purified under both reverse crosslinking and non-crosslinking conditions, and sequenced to generate single-nucleus ATAC-seq data.


title: young replicate 1, H3K27Ac


title: LNCaP, siPDIA5, 96h, rep1

description: Library name: siPDIA5_96h_1


title: scATAC NoRV  R2

description:
Library name: singlecell-ATAC-Seq mouse spleen without reverse crosslinking 2
singlecell-ATAC-Seq mouse spleen without reverse crosslinking 2


title: RV R2

description:
Library name: Bulk ATAC-seq mouse spleen with reverse crosslinking 2
Bulk ATAC-seq mouse spleen with reverse crosslinking 2


title: scATAC NoRV  R1

description:
Library name: singlecell-ATAC-Seq mouse spleen without reverse crosslinking 1
singlecell-ATAC-Seq mouse spleen without reverse crosslinking 1


title: Cat_15_Cortex

description: Library name: Cat_15_Cortex


title: RV R1

description:
Library name: Bulk ATAC-seq mouse spleen with reverse crosslinking 1
Bulk ATAC-seq mouse spleen with reverse crosslinking 1


title: LNCaP, siPDIA5, 48h, rep2

description: Library name: siPDIA5_48h_2


title: Cat_13_Cortex

description: Library name: Cat_13_Cortex


title: NoRV R1

description:
Library name: Bulk ATAC-seq mouse spleen without reverse crosslinking 1
Bulk ATAC-seq mouse spleen without reverse crosslinking 1


title: Cat_14_Cortex

description: Library name: Cat_14_Cortex


title: NoRV R2

description:
Library name: Bulk ATAC-seq mouse spleen without reverse crosslinking 2
Bulk ATAC-seq mouse spleen without reverse crosslinking 2


title: young replicate 2, H3K27Ac


title: LNCaP, siPDIA5, 48h, rep1

description: Library name: siPDIA5_48h_1


title: LNCaP, siPDIA1, 96h, rep3

description: Library name: siPDIA1_96h_3


title: Cat_12_Cortex

description: Library name: Cat_12_Cortex


title: scATAC RV  R2

description:
Library name: singlecell-ATAC-Seq mouse spleen with reverse crosslinking 2
singlecell-ATAC-Seq mouse spleen with reverse crosslinking 2


title: mAT-MSC VAT_25+27

city: Prague

first: Yusuf

middle: Caglar

last: Odabasi

state: Vestec

address: Prumyslova 595

department: BIOCEV

country: Czech Republic

institute: IBT

description:
Library name: 25+27 HFD + Gln_A
25_27_HFD

data_processing:
The quality of raw sequencing reads was evaluated with FastQC v0.12.1 and potential contamination was assessed using FastQ_Screen v0.15.3.
Low-quality reads and adaptors were removed with TrimmomaticSE v0.36 (2), employing the parameters ILLUMINACLIP:/storage/abaffyp/Adapters/Lexogen_quantseq2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Ribosomal and mitochondrial reads were filtered out using SortMeRNA v2.1b.
Aligned reads were converted into BAM files with STAR v2.7.10b, referencing the Mus musculus genome version GRCm38.
Final count tables were generated using the Python script htseq-count v0.11.3, with the annotation file genecode.vM8.gtf and the parameter -m union.
Assembly: Mus musculus genome version GRCm38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Adipose

extract_protocol:
RNA integrity was assessed using a Fragment Analyzer system with the RNA Fragment Kit (Agilent Technologies). All samples had an RNA quality number (RQN) greater than 7.
Sequencing libraries were prepared from 30 ng of total RNA using the QuantSeq 3´ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer’s protocol. The libraries were quantified with the Qubit dsDNA assay kit and Qubit 2 fluorometer (Thermo Fisher Scientific), and their quality was evaluated using a Fragment Analyzer system with the NGS Fragment Kit (Agilent Technologies). Sequencing was performed on a NovaSeq X Plus Sequencing System using the NovaSeq™ X Series 25B Reagent Kit (300 Cyc) using one lane in 2 × 157 bp mode, generating an average of 120 million reads per sample. Only read1 were used for analysis.

value: Adipose

tag: Sex

value: male

value: Glutamine


title: LNCaP, siPDIA1, 96h, rep2

description: Library name: siPDIA1_96h_2


title: Cat_11_Cortex

description: Library name: Cat_11_Cortex


title: Cat_06_Cortex

description: Library name: Cat_06_Cortex


title: LNCaP, siPDIA1, 96h, rep1

description: Library name: siPDIA1_96h_1


title: mAT-MSC VAT_13+15

description:
Library name: 13+15 HFD + Gln_A
13_15_HFD


title: FFPE MouseSpleen

description: Library name: FFPE_Mouse_Spleen

extract_protocol:
Tagmentation and combinatorial indexing via ligation
Before tagmentation, 50,000 purified FFPE single-cell nuclei were centrifuged at 2,000 g for 5 minutes at 4°C and resuspended in 0.1% lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630). The nuclei were then centrifuged again at 2,000 g for 5–10 minutes at 4°C. The nuclei pellet was resuspended in 95 μl of 1× tagmentation buffer (10 mM Tris-HCl, pH 7.5, 5 mM MgCl₂, 10% dimethylformamide, and dH₂O), and 5 μl of barcoded FFPE-Tn5 transposase (2 mM) was added per sample. The reaction mix was gently mixed and incubated at 37°C for 30 minutes at 400 rpm. The reaction was stopped by directly adding EDTA to a final concentration of 30 mM to each sample. All samples were then pooled and centrifuged to obtain a nuclei pellet. Next, three rounds of ligation were performed using the split-and-pool technique in a 96-well plate, with each well containing a ramped specific linker and ligation barcode. Detailed DNA sequences are provided in Supplementary Table 1. In brief, the ligation process was performed as follows: the pooled nuclei were resuspended in 1 mL of 1× NEBuffer 3.1 and mixed with the ligation mix (100 μL of 10× NEBuffer 3.1, 22 μL of 50 mg/mL BSA, 500 μL of 10× T4 DNA ligase buffer, 2,278 μL of ultrapure water, and 100 μL of T4 DNA ligase). A total of 40 μL of this mix was transferred per well, containing 10 μL of the ramped Ligation1 mixture, and incubated at 37°C for 30 minutes at 400 rpm. Then, 10 μL of Blocker-Ligation1 solution (2.64 μL of 100 μM Blocker-Ligation1, 2.50 μL of 10× T4 ligation buffer, and 4.86 μL of ultrapure water) was added per well, and the reactions were incubated at 37°C for 20 minutes at 400 rpm. The samples were then pooled into a 15 mL tube pre-coated with 0.5% BSA, followed by centrifugation at 1,500 g for 10 minutes at 4°C. The second and third ligation reactions were performed identically to the first. After the second and third ligations, blocking reactions were carried out using: 10 μL of Blocker-Ligation2 solution per well (2.64 μL of 100 μM Blocker-Ligation2, 2.50 μL of 10× T4 ligation buffer, and 4.86 μL of ultrapure water); 7.5 μL of Terminator_Ligation3 solution per well (2.64 μL of 100 μM Terminator_Ligation3, 2.50 μL of 0.5 M EDTA, and 2.36 μL of ultrapure water) for reaction termination. After gently mixing, the samples were pooled again into a 15 mL tube pre-coated with 0.5% BSA, followed by centrifugation at 1,500 g for 10 minutes at 4°C. After the third ligation, each nucleus acquired a unique combination of barcodes. Finally, the pellet was resuspended in PBS, nuclei were counted, and the sample was split into tubes containing 30,000–80,000 nuclei for reverse crosslinking.
Reverse-crosslinking, gap filling and in vitro transcription
After the third ligation, reverse cross-linking buffer (50 mM Tris-HCl, pH 8, 250 mM NaCl, 1 mM EDTA, and 1% SDS) and 0.22 mg/mL proteinase K were added to each tube, following previous publications 42, 43. The reaction mixture was incubated in a thermomixer at 1,200 rpm overnight at 65°C. The next day, a second proteinase K digestion was performed at 37°C for 2 hours at 850 rpm to ensure complete protein digestion. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit, following the manufacturer’s instructions. For gap filling, an equal volume of NEBNext High-Fidelity 2X PCR Master Mix was added to the eluted DNA, and the reaction mixture was incubated at 72°C for 8 minutes in a thermal cycler. The sample was then purified using the Qiagen MinElute PCR Purification Kit, following the manufacturer’s instructions. Further DNA purification was carried out using the 1X SPRI beads method to remove fragments shorter than 150 bp. Finally, the DNA was eluted in nuclease-free water. For in vitro transcription (IVT), a T7 RNA synthesis kit (New England Biolabs) was used. The following reagents were mixed:
- 12.4 μL of template DNA
- 2.5 μL of 10X T7 buffer
- 1 μL of DTT
- 2 μL each of ATP, CTP, UTP, and GTP
- 1 μL of T7 mix
- μL of RNase inhibitor (Thermo Fisher Scientific)
The IVT mixture was incubated at 37°C overnight (16 hours), followed by DNase treatment and RNA purification using the ZYMO RNA Purification Kit (RNA Clean & Concentrator-5), according to the manufacturer’s instructions. Finally, RNA was eluted in 20 μL of nuclease-free water. The RNA concentration was measured using NanoDrop, and the sample was either immediately used for DNA library preparation or stored at −80°C for future use.
Single cell FFPE-ATAC DNA library preparation
Single-stranded cDNAs are prepared from 0.5–1 μg of purified IVT transcripts using the FirstStrand_cDNA oligo (DNA oligo sequences are provided in Supplementary Table 1). The reaction mixture (11.25 μL), containing 500ng-1 μg of RNA, 1 μL of 100 μM random octamer primer stock, and 0.25 μL of RNase Inhibitor (20 U/μL), is heated at 70°C for 3 minutes, then immediately cooled on ice. Next, the master mix is added, which consists of:
- 4 μL of 5× First-Strand Buffer
- 2 μL of dNTP Mix
- 2 μL of 100 mM DTT
- 0.25 μL of RNase Inhibitor (20 U/μL)
- 0.5 μL SMART MMLV RT
The reaction is gently mixed and incubated at 42°C for 60 minutes and then at 70°C for 15 minutes. Next, 2.2 μL of 10× RNase H buffer and 0.2 μL of RNase H (5 U/μL) are added to each reaction and incubated at 37°C for 20 minutes. The RNAClean XP beads (1.8X) are used to purify the cDNA reaction mixture, and the cDNA is eluted in Qiagen Elution Buffer. A sequencing library mix is prepared using purified cDNA, NEBNext high-fidelity 2× PCR master mix, and a unique forward (i5) and reverse (i7) primer combination (DNA oligo sequences are provided in Supplementary Table 1). PCR amplification is run with the following cycling program:
- 98°C for 30 seconds
- 12 cycles of:
- 98°C for 20 seconds
- 63°C for 20 seconds
- 72°C for 1 minute
The sample is purified using the Qiagen MinElute PCR Purification Kit and run on a 6% PAGE gel. The gel region corresponding to 250–800 bp is cut, and the gel is made into fine pieces, which are incubated overnight at 55°C in crush-soak buffer (500 mM NaCl, 1 mM EDTA, 0.5% SDS) at 1,200 rpm. The DNA is purified from the gel using Costar spin-X centrifuge tubes and the Zymo ChIP DNA Clean & Concentrator Kit, following the manufacturer's instructions. A high-sensitivity DNA bioanalyzer chip is used to check the DNA size distribution and quantify the DNA concentration of the DNA library. Finally, deep sequencing is performed with NovaSeq  6000 on the mouse and human scFFPE-ATAC samples for single-cell analysis.


title: Cat_05_Cortex

description: Library name: Cat_05_Cortex


title: Cat_09_Cortex

description: Library name: Cat_09_Cortex


title: mAT-MSC VAT_10+12

description:
Library name: 10+12 HFD + Gln_A
10_12_HFD


title: Cat_04_Cortex

description: Library name: Cat_04_Cortex


title: Cat_03_Cortex

description: Library name: Cat_03_Cortex


title: Cat_07_Cortex

description: Library name: Cat_07_Cortex


title: Cat_10_Cortex

description: Library name: Cat_10_Cortex


title: LNCaP, siPDIA1, 48h, rep2

description: Library name: siPDIA1_48h_2


title: mAT-MSC VAT_4+6

description:
Library name: 4+6 HFD + Gln_A
4_6_HFD


title: mAT-MSC VAT_18+20

description:
Library name: 18+20 HFD + Gln_A
18_20_HFD


title: mAT-MSC VAT_23+28

description:
Library name: 23+28 HFD_A
23_28_HFD

value: Ctrl

value: no


title: ApfEIN3-IP-set2

data_processing:
*library strategy: DAP-seq
Trimmomatic software were used to remove adapter and low quality reads.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak.
Reads distributions (from bigwig) across gene are presented as an average plot (average of reads signals across all genes). The deeptools tool is used for this analysis.
Assembly: Alternanthera philoxeroides
Supplementary files format and content: bigwig, narrowpeak

organism: Alternanthera philoxeroides

source_name: shoot

growth_protocol: Alternanthera philoxeroides grown for 4 weeks under normal conditions.

extract_protocol:
ApfEIN3 was fused with Halo-TF and expressed using a TNT SP6 Coupled Wheat Germ Extract System (Promega).
For DNA library construction, genomic DNA was extracted using plant tissue by Hi-Pure Plant Genomic DNA Kit and quantified by Qubit Fluorometer and examined by agarose gel electrophoresis.

treatment_protocol: No treatment

value: shoot

value: wild type


title: Cat_02_Cortex

description: Library name: Cat_02_Cortex


title: LNCaP, siPDIA1, 48h, rep1

description: Library name: siPDIA1_48h_1


title: Cat_01_Cortex

description: Library name: Cat_01_Cortex


title: ApfEIN3-input


title: LNCaP, siPDIA5, 48h, rep3

description: Library name: siPDIA5_48h_3