title: sir4∆_mutpromoter_Rpb3FLAG input rep1

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hml@2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir4delta::k.l.URA3; RPB3-RxFLAG-KanMX; hmrdelta::HygMX; matdelta::k.l.LEU2


title: S32_WT3 IR

status: Public on May 09 2023

type: SRA

city: Tel-Aviv

first: Amit

last: Levon

address: Ramat Aviv

country: Israel

institute: Tel-Aviv University

description: S32_FKDL202582263-1a-GD05-AK7117_H7YKLDSXY_L4

library_source: transcriptomic

data_processing:
Adaptor clipping and leading and trailing low quality or N bases trimming was done using Trimmomatic v0.36 in paired-end mode.
The processed reads were aligned to the human genome (hg19) using Rsubread v2.0.0 ‘align’ function (sortReadsByCoordinates=True, detectSV=False) in paired-end mode, with the human UCSC refseq genes (hg19) GTF as an external annotation file.
Split samples S18-S28 were merged into one bam file, using the Samtools v1.3.1 ‘merge’ command.
Gene expression was calculated using Rsubread ‘featureCounts’ (countMultiMappingReads=False) in paired end mode to count the number of reads that map to each gene, with the GENCODE GRCh37 (hg19) v25 GTF as an external annotation file.
The reads were then normalized by TPM (Transcripts Per Kilobase Million) using the total exonic length acquired from the same GENCODE database.
In order to remain with only genes that have been robustly expressed in the samples, we continued only with genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts only for genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset (txt file).

molecule: total RNA

organism: Homo sapiens

source_name: Skin primary fibroblasts

growth_protocol: Cells were grown in complete Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 1% (v/v) penicillin/streptomycin and 1% (v/v) L-glutamine. The cultures were maintained at 37°C in a humidified atmosphere with 5% CO2 and 3% O2

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (QIAGEN) and purified with the MiRNeasy Kit (QIAGEN), according to the manufacturer’s protocol. The RNA purity (260/230 and 280/260) was measured by nanodop.  RNA concentration was measured by Qbit and the integrity was measured using the Tapstation instrument. The purified RNA was used for subsequent library preparation and sequencing.
Library preparation was performed Using the mRNA Tecan Genomics Universal Plus mRNA-Seq with NuQuant (includes UDI-UMI) kit.

treatment_protocol: For IR-induced senescence, cells were exposed to 10Gy X-rays using the Faxitron (X-ray) cabinet providing 0.5 Gy/min, and harvested 10 days later .

tag: cell type

value: Human-derived skin fibroblasts

tag: strain

tag: genotype/variation

value: WT

tag: treatment

value: IR (10 Gy)


title: Day 60 human CD4+_2

city: Melbourne

first: Zhoujie

last: Ding

state: VIC

address: 89 Commercial Road

country: Australia

institute: Monash University

data_processing:
Reads were aligned  with  package rnasik 1.5.4 and used iGenomes, GRCm38 build as reference
Gene read counts were converted to log 2 counts per million, quantile normalized and precision weighted with the Voom function of the Limma package through Degust
Genes were filtered from downstream analysis if they did not have a CPM (counts per million mapped reads) value of at least 2 in at least 3 sample libraries. Immunoglobulin genes were excluded from expression analysis.
Genome_build: GRCm38 build
Supplementary_files_format_and_content: CountMatrix_hierarchical_clustering.csv is Matrix table (CSV) with normalised counts for genes with FDR<0.05 across all samples
Supplementary_files_format_and_content: Day60negative_vs_Day60positive.csv is matrix table (CSV) with normalised counts comparing samples that are Day 60 human CD4+ with Day 60 human CD4-
Supplementary_files_format_and_content: Day60negative_vs_Day270positive.csv matrix table (CSV) with normalised counts comparing samples that are Day 270 human CD4+ with Day 60 human CD4-

organism: Mus musculus

source_name: plasma cells from bone marrow

extract_protocol:
RNA was isolated from cells with Qiagen RNeasy Micro Kits according to the manufacturer’s instructions.
TruSeq RNA Library Prep Kit

tag: tissue

value: bone marrow

value: plasma

tag: genotype


title: MAT_mutpromoter_Rpb3FLAG ChIP rep2

city: Berkeley

first: Eliana

middle: Rose

last: Bondra

state: California

address: 440 Barker Hall

department: Molecular and Cell Biology

country: USA

institute: University of California, Berkeley

library_source: genomic

data_processing:
FASTQ generation using Illumina Casava v2.2.
Raw reads were mapped to SacCer3 genome modified to include the mutant promoter site where applicable, and mat∆hmr∆ or hml∆mat∆, using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
PCR duplicates were removed using, sequentially, SAMtools -fixmate -sort -markdup
bedgraph files were generated that included reads between 0-500bp (average fragment size from sonication) and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Assembly: SacCer3 (modified)
Supplementary files format and content: bedgraph (normalized to genome-wide median)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented by sonication. IPs were performed using 5mL mouse monoclonal anti-FLAG® M2 antibody (MilliporeSigma, product no F1804) and 50uL DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D).   DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

tag: cell line

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1; MATalpha-Rap1*bs; RPB3-3xFLAG-KanMX

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: sir4∆_mutpromoter_Rpb3FLAG input rep2


title: sir4∆_mutpromoter_Rpb3FLAG ChIP rep1


title: sir4∆_mutpromoter_Rpb3FLAG ChIP rep2


title: Untagged ZFP661-3HA mESCs, ChIP anti-HA

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

description: ChIP-seq

data_processing:
Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. The resulting clean reads were mapped onto the mouse genome (mm10) using BWA with default parameters, and only uniquely mapped reads (with tag X0:i:1) were retained for downstream analyses.
MACS2 (v2.2.7.1) was used to call peaks with one duplicated tag kept, fragment length 200bp for single-end reads, and the threshold q ≤ 0.01. Peaks that overlapped (overlap represents any bases of a peak sharing with other peaks/regions) with the regions on ENCODE blacklist (Amemiya et al. 2019) were filtered out. During peak calling, ChIP inputs were used as controls for all factors except for ZFP661. For ZFP661 in ZFP661-3HA OE mESCs, ChIP input and the corresponding ChIP in EV control mESCs using anti-HA antibodies (referred to as HA-ChIP) were used as controls to detect peaks (referred to as input-peaks and HA-peaks), respectively. Only HA-peaks that overlapped with input-peaks were retained as reliable peaks for downstream analyses. For ZFP661 in endogenous tagged ZFP661-3HA mESCs, HA-ChIP in un-tagged mESCs were used as ChIP input to detect peaks. For H3K9me3, the peak regions from MACS2 output were used directly. For other factors, the 50 bp flanking regions of ChIP summits (i.e., summits ± 50 bp) were used as refined peak regions for downstream analyses.
To generate high-quality and consistent ChIP peak lists, peaks from two biological replicates in the same condition (i.e., WT or Zfp661 KO, EV control or ZFP661-3HA OE) were combined by retaining peaks in replicate 1 that overlapped with peaks in replicate 2. As ZFP661 expressed at low level in mESCs, the following steps were employed to generate a high-quality peak list for ZFP661 in ZFP661-3HA mESC: ZFP661 peaks in ZFP661-3HA mESCs were detected using a relatively loose threshold (q ≤ 0.1), and only peaks that overlapped with consistent ZFP661 peaks in ZFP661-3HA OE mESCs were retained. To generate consistent ChIP signal (i.e., bigwig) files, deepTools (v3.5.1) was used with the parameters “--normalizeUsing CPM --binSize 10 –extendReads” (CPM represents counts per million) and with chrM and regions on ENCODE blacklist excluded. The ChIP signals were normalized by subtracting the ChIP input in each biological replicate (for ZFP661, subtracted by HA-ChIP), and then the two biological replicates were averaged to generate a consistent bigwig file for each factor.
Assembly: mm10
Supplementary files format and content: bigwig signal files (.bw), MACS2 peak files (.NarrowPeak), tar of consistent bigwig files (.tar), and tar of consistent peak files (.tar).

source_name: JM8.F6 mESCs

growth_protocol: Cells were cultured in a 37 °C humidified incubator with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.4M glycine for 5 min.
ChIP assays were performed according to the ENCODE protocol with modifications. 20M cells/ChIP were used for ZFP661-3HA (anti-HA: Abcam, ab9110), CTCF (anti-CTCF: Millipore, 07-729), RAD21 (Anti-RAD21: Abcam, ab992) and KAP1 (anti-KAP1: Abcam, ab22553), and 10M cells/ChIP were used for H3K9me3 (anti-H3K9me3: Abcam, ab8898). 5 μg of antibodies were used for each ChIP. ChIP DNA was purified, and 10 μl (or up to 50 ng) of ChIP DNA was used as input to construct ChIP library using ThruPLEX DNA-Seq Kit (Takara, R400676). The ChIP inputs from the same biological replicate were evenly sampled and pooled together to construct the corresponding ChIP input library.

value: JM8.F6 mESCs

value: mouse embryonic stem cells

tag: chip antibody

value: HA (Abcam, ab9110)


title: CPSF3-AGH, 12h auxin, input,  replicate 2

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description: cpsf3 auxin inducible degron

data_processing:
ChIP-seq fastq files were aligned to the mm10 assembly with BWA MEM.
Peak calls were performed with macs3 callpeak function with --broad option, mouse genome effective size and corresponding background reads.
Visualization tracks were generated with bedtools genomecov (−bg −scale) with scaling factor being 106 per number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).
Assembly: mm10

source_name: R1 CPSF3-AGH

growth_protocol: R1 mESCs were grown in monolayer in 2i + LIF medium

extract_protocol:
Cells were fixed on plate in 1% formaldehyde (in PBS) at room temperature for 10 mins with agitation. Glycine at a final concentration of 0.125M was added to quench fixation. After cell lysis, chromatin was sheared using the Covaris for 5 minutes per sample.
NEBNext library prep

value: R1 CPSF3-AGH

value: ESC

value: auxin, 500uM, 12h


title: CTR_24h_m5

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

description:
1048_0065
1048_0065

data_processing:
reads passing quality control filter were mapped against or GRCm38 (mouse data) reference genomes using STAR (v2.5.2b)
Gene expression levels were quantified based on genome annotation files from Ensembl version 86 using RSEM (v1.3.0) and featureCounts (v1.5.1). For additional quality control we used FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.0.0).
Assembly: GRCm38 (mouse data)
Supplementary files format and content: 1048_uReads.txt containts tab delimited normalized read counts per gene (row) for all samples (column).
Supplementary files format and content: 1048_uTPM.txt containts tab delimited normalized TPM per gene (row) for all samples (column).

source_name: Liver

extract_protocol:
Three PCLS slides per donor per assay condition have been pooled to ensure to get enough material for RNA Sequencing. After homogenization and lysis using in Qiazol buffer (Qiagen, Venlo, the   Netherlands), samples were mixed with 1/5th volume of chloroform (Sigma) and separated using phase extraction tubes. The RNA was then isolated with the RNeasy Lipid Tissue Mini Kit (Qiagen, Venlo, the  Netherlands) or the FavorPrep TM Tissue Total RNA Mini Kit (Favorgen, Vienna, Austria).  RNA samples were quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 96-channel Fragment Analyzer (Agilent), respectively.
Total RNA was normalized on the MicroLab STAR automated liquid platform (Hamilton). 100ng input was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the QIAseq FastSelect RNA removal Kit (Qiagen) upstream and the NEBNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). Fragmentation time was set to 15min. A total of 12 PCR cycles was used for the index PCR while the final libraries were eluted in 25 µL. Of note, the only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) at the double-stranded cDNA purification step, instead of the recommended SPRIselect Beads. Total RNA sequencing libraries were quantified by the fluorescence dye-based methodology High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 100.3 nM. Total RNA libraries were also assessed for size distribution and adapter dimer presence by the High Sensitivity NGS Fragment DNF-474 Kit on a 96-channel Fragment Analyzer (Agilent). Sequencing libraries were normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina).
The library pool was subsequently clustered on an S2 Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2x100 bp length (Read parameters: Rd1: 101, Rd2: 8, Rd3: 8, Rd4: 101) reaching a target depth of approximately 60 million Pass-Filter reads per sample (6.5% CV, see).

treatment_protocol:
Glucose_24h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

tag: gender

value: Male

tag: animal id

value: Liver

value: CTR

tag: timepoint


title: G_24h_m5

description:
1048_0066
1048_0066

treatment_protocol:
Glucose_24h_36mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: G


title: Day 270 human CD4+_3


title: Day 270 human CD4+_2


title: S31_WT2 IR

description: S31_FKDL202582263-1a-GH04-7UDI193_H7YKLDSXY_L4

value: Human-derived skin fibroblasts


title: sir4∆_wtpromoter_Rpb3FLAG ChIP rep2

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; RPB3-3xFLAG-KanMX; hmrdelta::HygMX; matdelta::k.l.LEU2


title: S30_WT1 IR

description: S30_FKDL202582263-1a-GG04-AK4966_H7YKLDSXY_L4

value: WT

value: IR (10 Gy)


title: GFIPO_48h_m4

description:
1048_0064
1048_0064

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Palmitic Acid_48h_Oleic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIPO


title: sir4∆_wtpromoter_Rpb3FLAG input rep2


title: Day 60 human CD4-_3

value: bone marrow

value: plasma


title: sir4∆_wtpromoter_Rpb3FLAG input rep1


title: S28_WT4 R4

description: S28_FKDL202582264-1a-GH02-AK8390_HC5KJDSXY_L4

value: No treatment


title: GFIP_48h_m4

description:
1048_0062
1048_0062

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Palmitic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIP


title: GFIO_48h_m4

description:
1048_0063
1048_0063

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Oleic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIO


title: Day 270 human CD4-_3


title: S29_WT1 R5

description: S29_FKDL202582263-1a-GC05-AK985_H7YKLDSXY_L4


title: GF_48h_m4

description:
1048_0060
1048_0060

treatment_protocol:
Glucose_48h_36mM_Fructose_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GF


title: SIR_mutpromoter_Rpb3FLAG input rep2

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; RPB3-3xFLAG-KanMX; hmrdelta::HygMX; matdelta::k.l.LEU2


title: sir4∆_wtpromoter_Rpb3FLAG ChIP rep1

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: S25_WT1 R4

description: S25_FKDL202582264-1a-GE02-AK845_HC5KJDSXY_L4


title: Day 60 human CD4-_2


title: GFI_48h_m4

description:
1048_0061
1048_0061

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Male

value: Liver

value: GFI


title: S24_WT4 R3

description: S24_FKDL202582264-1a-GD02-AK8389_HC5KJDSXY_L4

value: Human-derived skin fibroblasts


title: SIR_mutpromoter_Rpb3FLAG ChIP rep2

value: Saccharomyces cerevisiae


title: Day 60 human CD4+_1


title: S27_WT3 R4

description: S27_FKDL202582264-1a-GG02-AK5010_HC5KJDSXY_L4


title: S26_WT2 R4

description: S26_FKDL202582264-1a-GF02-7UDI286_HC5KJDSXY_L4


title: G_48h_m4

description:
1048_0058
1048_0058

treatment_protocol:
Glucose_48h_36mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: G


title: F_48h_m4

description:
1048_0059
1048_0059

treatment_protocol:
Fructose_48h_Glucose_48h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: F


title: Day 60 human CD4-_1


title: Day 270 human CD4-_2


title: SIR_mutpromoter_Rpb3FLAG ChIP rep1


title: S23_WT3 R3

description: S23_FKDL202582264-1a-GC02-7UDI293_HC5KJDSXY_L4

value: WT


title: CTR_48h_m4

description:
1048_0057
1048_0057

treatment_protocol:
Glucose_48h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: CTR


title: SIR_mutpromoter_Rpb3FLAG input rep1


title: S22_WT2 R3

description: S22_FKDL202582264-1a-GB02-AK4999_HC5KJDSXY_L4


title: GFIPO_24h_m4

description:
1048_0056
1048_0056

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Palmitic Acid_24h_Oleic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIPO


title: SIR_wtpromoter_Rpb3FLAG input rep2

value: matdelta::klLEU2 ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX; RPB3-3xFLAG-KanMX


title: S21_WT1 R3

description: S21_DKDL202003221-1a-GA02-AK7156_H73F3DSXY_L4

value: No treatment


title: Day 270 human CD4+_1

value: bone marrow

value: plasma


title: SIR_wtpromoter_Rpb3FLAG ChIP rep2


title: Day 270 human CD4-_1


title: GFIO_24h_m4

description:
1048_0055
1048_0055

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Oleic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIO


title: SIR_wtpromoter_Rpb3FLAG input rep1


title: GFIP_24h_m4

description:
1048_0054
1048_0054

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Palmitic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIP


title: GFI_24h_m4

description:
1048_0053
1048_0053

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).


title: SIR_wtpromoter_Rpb3FLAG ChIP rep1

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: S19_AT3 R3

description: S19_DKDL202003221-1a-GG01-AK7155_H73F3DSXY_L4

value: AT


title: S18_AT2 R3

description: S18_DKDL202003221-1a-GF01-7UDI214_H73F3DSXY_L4


title: mouse M6 33 months old

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to mm10 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_mm9 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

source_name: colon biopsy

extract_protocol:
Puregene-Gentra DNA extraction
Two micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: microbiome

value: specific pathogen-free

tag: interleukin 10

value: wild type

tag: drug treatment


title: mouse M11 4 months old


title: mouse F17 4 months old


title: mouse M7 33 months old


title: F_24h_m4

description:
1048_0051
1048_0051

treatment_protocol:
Fructose_24h_Glucose_24h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Male

value: Liver


title: MAT_wtpromoter_Taf1FLAG input rep2

value: Saccharomyces cerevisiae

value: hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1; MATalpha, TAF1-3xFLAG-KanMX


title: MAT_wtpromoter_Taf1FLAG ChIP rep2


title: S16_WT4 R2

description: S16_FKDL202582263-1a-GA03-AK7240_H7YKLDSXY_L4

value: Human-derived skin fibroblasts

value: WT


title: mouse F16 4 months old


title: MAT_wtpromoter_Taf1FLAG input rep1


title: mouse F13 30 months old


title: S20_AT4 R3

description: S20_DKDL202003221-1a-GH01-AK2418_H73F3DSXY_L4


title: G_24h_m4

description:
1048_0050
1048_0050

value: G


title: CTR_24h_m4

description:
1048_0049
1048_0049

value: CTR


title: S14_WT2 R2

description: S14_FKDL202582263-1a-GG02-AK5010_H7YKLDSXY_L4

value: No treatment


title: specific pathogen-free wild type azoxymethane mouse C6M3

value: azoxymethane 10 mg/kg 6 weekly i.p injections


title: MAT_mutpromoter_Taf1FLAG input rep1

value: hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1; MATalpha-Rap1*bs, TAF1-3xFLAG-KanMX


title: GFIPO_48h_m3

description:
1048_0048
1048_0048

value: GFIPO


title: S17_AT1 R3

description: S17_FKDL202582263-1a-GB03-7UDI276_H7YKLDSXY_L4


title: MAT_wtpromoter_Taf1FLAG ChIP rep1


title: GF_24h_m4

description:
1048_0052
1048_0052

treatment_protocol:
Glucose_24h_36mM_Fructose_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GF


title: GFIO_48h_m3

description:
1048_0047
1048_0047

value: GFIO


title: S13_WT1 R2

description: S13_FKDL202582263-1a-GF02-7UDI286_H7YKLDSXY_L4

treatment_protocol: For IR-induced senescence, cells were exposed to 10Gy X-rays using the Faxitron (X-ray) cabinet providing 0.5 Gy/min, and harvested 10 days later .


title: MAT_mutpromoter_Taf1FLAG ChIP rep1

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: specific pathogen-free wild type azoxymethane mouse C6M1

value: specific pathogen-free


title: GFIP_48h_m3

description:
1048_0046
1048_0046

value: GFIP


title: specific pathogen-free wild type azoxymethane mouse C5M3

value: wild type


title: S12_AT4 R2

description: S12_FKDL202582263-1a-GE02-AK845_H7YKLDSXY_L4

value: AT


title: GFI_48h_m3

description:
1048_0045
1048_0045

value: Male

value: Liver

value: GFI


title: sir4∆_mutpromoter_Taf1FLAG ChIP rep2

value: Saccharomyces cerevisiae

value: , hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; matdelta::k.l.LEU2


title: S15_WT3 R2

description: S15_FKDL202582263-1a-GH02-AK8390_H7YKLDSXY_L4

value: Human-derived skin fibroblasts

value: WT


title: sir4∆_wtpromoter_Taf1FLAG input rep2

value: , hmlalpha2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir3delta::klURA3; matdelta::k.l.LEU2


title: specific pathogen-free wild type azoxymethane mouse C4M1

value: azoxymethane 10 mg/kg 6 weekly i.p injections


title: S9_AT1 R2

description: S9_FKDL202582263-1a-GB02-AK4999_H7YKLDSXY_L4

value: No treatment


title: GF_48h_m3

description:
1048_0044
1048_0044

value: GF


title: sir4∆_wtpromoter_Taf1FLAG ChIP rep2


title: F_48h_m3

description:
1048_0043
1048_0043

value: F


title: specific pathogen-free Il10KO mouse C5M4

value: KO


title: S8_WT4 R1

description: S8_DKDL202003220-1a-GA02-AK7156_H73F3DSXY_L3


title: sir4∆_wtpromoter_Taf1FLAG input rep1


title: S7_WT3 R1

description: S7_DKDL202003220-1a-GH01-AK2418_H73F3DSXY_L3


title: specific pathogen-free Il10KO mouse C5M3

value: specific pathogen-free


title: specific pathogen-free wild type azoxymethane mouse C5M1


title: CTR_48h_m3

description:
1048_0041
1048_0041

value: CTR


title: specific pathogen-free Il10KO mouse C4M5


title: GFIO_24h_m3

description:
1048_0039
1048_0039

value: GFIO


title: S5_WT1 R1

description: S5_DKDL202003220-1a-GF01-7UDI214_H73F3DSXY_L3


title: S4_AT4 R1

description: S4_FKDL202582263-1a-GE01-AK706_H7YKLDSXY_L4

value: AT


title: S11_AT3 R2

description: S11_FKDL202582263-1a-GD02-AK8389_H7YKLDSXY_L4


title: specific pathogen-free Il10KO mouse C5M1


title: S6_WT2 R1

description: S6_DKDL202003220-1a-GG01-AK7155_H73F3DSXY_L3


title: sir4∆_mutpromoter_Taf1FLAG input rep2


title: specific pathogen-free Il10KO mouse C4M2


title: SIR_mutpromoter_Taf1FLAG input rep1

value: , hmlalpha2delta*Rap1bs-mutation::CRE, ura3-1; 3xV5_Rap1-N-terminal ; matdelta::k.l.LEU2


title: S10_AT2 R2

description: S10_FKDL202582263-1a-GC02-7UDI293_H7YKLDSXY_L4


title: GFIP_24h_m3

description:
1048_0038
1048_0038

value: Male

value: Liver

value: GFIP


title: sir4∆_wtpromoter_Taf1FLAG ChIP rep1

value: Saccharomyces cerevisiae

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: specific pathogen-free wild type azoxymethane mouse C4M2

value: wild type


title: SIR_mutpromoter_Taf1FLAG ChIP rep2


title: SIR_mutpromoter_Taf1FLAG input rep2


title: S3_AT3 R1

description: S3_FKDL202582263-1a-GD01-AK7110_H7YKLDSXY_L4

value: Human-derived skin fibroblasts


title: specific pathogen-free Il10KO mouse C4M1


title: specific pathogen-free Il10KO azoxymethane mouse C3M2

value: azoxymethane 10 mg/kg 6 weekly i.p injections


title: GF_24h_m3

description:
1048_0036
1048_0036


title: G_48h_m3

description:
1048_0042
1048_0042

value: G


title: S2_AT2 R1

description: S2_FKDL202582263-1a-GC01-7UDI311_H7YKLDSXY_L4

value: No treatment


title: specific pathogen-free Il10KO azoxymethane mouse C3M1


title: SIR_wtpromoter_Taf1FLAG input rep2

value: matdelta::klLEU2 , hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal


title: SIR_wtpromoter_Taf1FLAG ChIP rep2


title: GFIPO_24h_m3

description:
1048_0040
1048_0040

value: GFIPO


title: S1_AT1 R1

description: S1_FKDL202582263-1a-GB01-7UDI285_H7YKLDSXY_L4


title: F_24h_m3

description:
1048_0035
1048_0035

value: F


title: SIR_wtpromoter_Taf1FLAG input rep1


title: specific pathogen-free Il10KO azoxymethane mouse C1M3

value: specific pathogen-free

value: KO


title: MDA-MB-231 cells-DAC+DEX, 1

city: Hsinchu

first: Yi-Chen

last: Huang

state: Hsinchu

address: No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu City 300044 , Taiwan (R.O.C.)

department: college of life science

country: Taiwan

institute: National Tsing Hua University

data_processing:
Data obtained from high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format
FastQC and MultiQC were used to check FASTQ files for quality
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate low-quality bases.
The obtained high-quality data (clean reads) were used for subsequent analysis.
Read pairs from each sample were aligned to the reference human genome GRCh38. “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological triplicates
Differentially expressed genes (DEGs) in two conditions were analyzed with R using DESeq2 (with biological triplicates). The gene set enrichment analysis (GSEA)60 was performed to identify enriched biological functions and activated pathways from the molecular signature database (MSigDB).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: epithelial cell

growth_protocol: MDA-MB-231 cells were maintained in DMEM containing 8% fetal bovine serum (FBS; HyClone) and 1× penicillin streptomycin (Invitrogen) at 37°C in an atmosphere containing 5% CO2.

extract_protocol:
RNA was extracted from cells using TRIzol (Invitrogen), cleaned up using the RNeasy Mini Kit (Qiagen), and subjected to RNA-seq analysis (BIOTOOLS, Taiwan)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: MDA-MB-231 cells were treated with DMSO, 10 μM DAC, 1 μM DEX, or DAC+DEX for 6 days

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: wtpromoter_Sir3-13xMyc input rep 2

data_processing:
FASTQ generation using Illumina Casava v2.2.
Raw reads were mapped to SacCer3 genome modified to include the mutant promoter site using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were generated that included reads between 0-500bp (average fragment size from sonication) and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Assembly: SacCer3 (modified)
Supplementary files format and content: bedgraph (normalized to genome-wide median)

growth_protocol: Yeast were cultured at 30° in YPD.

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented by sonication using a BioRuptor. All immunoprecipitations were performed using Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843). DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

value: ADE2, lys2, TRP1, hmlalpha2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal, SIR3-13xMYC-KanMX


title: CTR_24h_m3

description:
1048_0033
1048_0033

treatment_protocol:
Glucose_24h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Male

value: CTR


title: SIR_wtpromoter_Taf1FLAG ChIP rep1


title: specific pathogen-free Il10KO azoxymethane mouse C2M2


title: MDA-MB-231 cells-DAC+DEX, 2


title: MDA-MB-231 cells-DAC+DEX, 3


title: G_24h_m3

description:
1048_0034
1048_0034

treatment_protocol:
Glucose_24h_36mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Liver


title: GFIP_48h_m2

description:
1048_0030
1048_0030

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Palmitic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIP


title: SIR_mutpromoter_Taf1FLAG ChIP rep1

value: Saccharomyces cerevisiae

value: , hmlalpha2delta*Rap1bs-mutation::CRE, ura3-1; 3xV5_Rap1-N-terminal ; matdelta::k.l.LEU2

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: wtpromoter_Sir3-13xMyc ChIP rep 2

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843)


title: specific pathogen-free mouse C3M2

value: wild type


title: MDA-MB-231 cells- 1 μM DEX, 2


title: GFI_24h_m3

description:
1048_0037
1048_0037

value: GFI


title: specific pathogen-free Il10KO azoxymethane mouse C2M1

value: azoxymethane 10 mg/kg 6 weekly i.p injections


title: specific pathogen-free Il10KO azoxymethane mouse C1M1


title: GFIPO_48h_m2

description:
1048_0032
1048_0032

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Palmitic Acid_48h_Oleic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIPO


title: MDA-MB-231 cells- 1 μM DEX, 1


title: MDA-MB-231 cells- 1 μM DEX, 3


title: wtpromoter_Sir3-13xMyc input rep 1


title: mutpromoter_Sir3-13xMyc input rep 2

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal, SIR3-13xMyc-KanMX


title: GFIO_48h_m2

description:
1048_0031
1048_0031

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Oleic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIO


title: F_48h_m2

description:
1048_0027
1048_0027

value: F


title: specific pathogen-free mouse C2M2

value: specific pathogen-free


title: mutpromoter_Sir3-13xMyc ChIP rep 2


title: specific pathogen-free mouse C1M2


title: specific pathogen-free mouse C3M1


title: MDA-MB-231 cells-10 μM DAC, 3

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: GF_48h_m2

description:
1048_0028
1048_0028

treatment_protocol:
Glucose_48h_36mM_Fructose_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Male

value: GF


title: G_48h_m2

description:
1048_0026
1048_0026

treatment_protocol:
Glucose_48h_36mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Liver

value: G


title: GFI_48h_m2

description:
1048_0029
1048_0029

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).


title: MDA-MB-231 cells-10 μM DAC, 2


title: specific pathogen-free mouse C2M1


title: specific pathogen-free mouse C1M1


title: mutpromoter_Sir3-13xMyc ChIP rep 1

value: Saccharomyces cerevisiae


title: MDA-MB-231 cells-10 μM DAC, 1


title: germ-free Il10KO mouse C1F3

value: germ-free

value: KO


title: CTR_48h_m2

description:
1048_0025
1048_0025

treatment_protocol:
Glucose_48h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: CTR


title: GFIPO_24h_m2

description:
1048_0024
1048_0024

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Palmitic Acid_24h_Oleic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).


title: MDA-MB-231 cells-DMSO, 2


title: MDA-MB-231 cells-DMSO, 1


title: wtpromoter_Sir3-13xMyc ChIP rep 1

value: ADE2, lys2, TRP1, hmlalpha2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal, SIR3-13xMYC-KanMX

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843)


title: antiV5-notag_control ChIP

data_processing:
FASTQ generation using Illumina Casava v2.2.
Raw reads were mapped to SacCer3 genome modified to include the mutant promoter site where applicable, using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were generated that included reads between 0-500bp (average fragment size from sonication) and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Assembly: SacCer3 (modified)
Supplementary files format and content: bedgraph (normalized to genome-wide median)

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented by sonication. All immunoprecipitations were performed using 50uL DynaBeads Protein G (ThermoFisher Scientific 10003D) magnetic beads coupled with 5uL monoclonal mouse-anti-V5 antibody (ThermoFisher Scientific R96025)  DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

value: hmlalpha2delta::CRE ADE2, lys2, TRP1, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1

value: DynaBeads Protein G magnetic beads (ThermoFisher Scientific 10003D) and mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: antiV5-notag_control input


title: GFIO_24h_m2

description:
1048_0023
1048_0023

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Oleic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).


title: germ-free Il10KO mouse C1F1


title: germ-free Il10KO mouse C1F2


title: mutpromoter_Sir3-13xMyc input rep 1

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal, SIR3-13xMyc-KanMX


title: MAT_wtpromoter_V5Rap1 input rep2

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX,  3xV5-Rap1


title: MDA-MB-231 cells-DMSO, 3


title: GFIP_24h_m2

description:
1048_0022
1048_0022

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Palmitic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIP


title: germ-free Il10KO mouse C1M3


title: MAT_wtpromoter_V5Rap1 ChIP rep2

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1


title: germ-free Il10KO mouse C1M2


title: t0_DMSO_V5Rap1 sir4delta ChIP rep 1

data_processing:
FASTQ generation using Illumina Casava v2.2.
Raw reads were mapped to a hybrid SacCer3 genome modified to include "UniqueHML" which has synonymos SNPs at HML to distinguish from MAT as well as hmrdelta::Hyg and the S. paradoxus CBS432 genome assembly,  using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
PCR duplicates were removed using, sequentially, SAMtools -fixmate -sort -markdup
bam files were generated using samtools -view -sort -index
samples (121-124,141-144) were also used to generate bedgraphs to compare Rap1 enrichment at MAT in SIR vs sir4delta cells (figure S2H). In these files, bedgraph files were generated that included S. cerevisiae reads only between 0-500bp (average fragment size from sonication) and normalized to the S.cerevisiae genome-wide median (median excluded subtelomeres, chromosome III, and rDNA).
Assembly: SacCer3 (modified)
Supplementary files format and content: bedgraph (normalized to genome-wide median)

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

source_name: Saccharomyces cerevisiae + paradoxus

growth_protocol: Yeast were cultured at 30° in YPD. Cells were grown overnight in YPD, then back-diluted to OD600 ~ 0.1 in 50mL YPD the following day and grown for two-three doublings and then collected at OD600 ~ 0.8.

treatment_protocol: Additions of rapamycin (at a final concentratiion of 7.5uM) were staggered such that all time points were ready at the same OD (~0.8). ~5×108cells were collected for each sample.

value: Saccharomyces cerevisiae + paradoxus

tag: cell line_(strain_-_cerevisiae)

tag: cell line_(strain_-_paradoxus)

tag: genotype (cerevisiae)

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3,  TOR1(S1972I), fpr1::NAT, RPL13A-2xFKBP12::TRP1 Rap1(134)-FRB_2xV5 bar1delta::k.l.URA3 hmlalphadelta::UniqueHMLwithSNPs sir4delta::HIS3; hmrdelta::HygMX

tag: genotype (paradoxus)

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV6

tag: treatment (growth)

value: 60min treatment with DMSO

tag: treatment (antibody)

value: 50uL DynaBeads Protein G (ThermoFisher Scientific 10003D) magnetic beads coupled with 5uL monoclonal mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: MAT_wtpromoter_V5Rap1 ChIP rep1

value: Saccharomyces cerevisiae

tag: treatment


title: t0_DMSO_V5Rap1 sir4delta input rep 2

tag: tissue

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV9


title: t0_DMSO_V5Rap1 sir4delta ChIP rep 2

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV7


title: GFI_24h_m2

description:
1048_0021
1048_0021

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

tag: strain

value: Male

value: Liver

value: GFI


title: GF_24h_m2

description:
1048_0020
1048_0020

treatment_protocol:
Glucose_24h_36mM_Fructose_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GF


title: germ-free Il10KO azoxymethane mouse C5F3

value: germ-free

value: KO

value: azoxymethane 10 mg/kg 6 weekly i.p injections


title: V5_No-tag_control input

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3, matdelta::K.lactisLEU2, TOR1(S1972I), fpr1::NAT, RPL13A-2xFKBP12::TRP1

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV5


title: V5_No-tag_control ChIP

value: Saccharomyces cerevisiae + paradoxus


title: MAT_mutpromoter_V5Rap1 ChIP rep2

tag: cell line

tag: genotype

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1; MATalpha-Rap1*bs

value: DynaBeads Protein G magnetic beads (ThermoFisher Scientific 10003D) and mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: germ-free Il10KO azoxymethane mouse C5F2


title: CTR_24h_m2

description:
1048_0017
1048_0017

tag: gender

value: CTR


title: F_24h_m2

description:
1048_0019
1048_0019

treatment_protocol:
Fructose_24h_Glucose_24h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

tag: animal id

value: F


title: G_24h_m2

description:
1048_0018
1048_0018

value: G

tag: timepoint


title: germ-free Il10KO azoxymethane mouse C5F1

tag: microbiome


title: GFIPO_48h_m1

description:
1048_0016
1048_0016

value: GFIPO


title: germ-free Il10KO azoxymethane mouse C3M1

tag: interleukin 10


title: 60min_V5Rap ChIP rep1

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3,  fpr1::NAT, RPL13A-2xFKBP12::TRP1 Rap1(134)-FRB_2xV5 bar1delta::k.l.URA3 hmlalphadelta::UniqueHMLwithSNPs  TOR1(S1972I); hmrdelta::HygMX

value: 60min treatment with 7.5uM Rapamycin

value: 50uL DynaBeads Protein G (ThermoFisher Scientific 10003D) magnetic beads coupled with 5uL monoclonal mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: MAT_mutpromoter_V5Rap1 ChIP rep1

value: Saccharomyces cerevisiae


title: t0_DMSO_V5Rap1 sir4delta input rep 1

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3,  TOR1(S1972I), fpr1::NAT, RPL13A-2xFKBP12::TRP1 Rap1(134)-FRB_2xV5 bar1delta::k.l.URA3 hmlalphadelta::UniqueHMLwithSNPs sir4delta::HIS3; hmrdelta::HygMX

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV8

value: 60min treatment with DMSO


title: GFIO_48h_m1

description:
1048_0015
1048_0015

value: Male

value: Liver

value: GFIO


title: MAT_wtpromoter_V5Rap1 input rep1

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX,  3xV5-Rap1


title: germ-free Il10KO mouse C1M1

value: germ-free

value: KO

tag: drug treatment


title: germ-free Il10KO azoxymethane mouse C2M2

value: azoxymethane 10 mg/kg 6 weekly i.p injections


title: 45min_V5Rap ChIP rep2

value: Saccharomyces cerevisiae + paradoxus

tag: cell line_(strain_-_cerevisiae)

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV5

value: 45min treatment with 7.5uM Rapamycin


title: MAT_mutpromoter_V5Rap1 input rep2

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1; MATalpha-Rap1*bs


title: GFIP_48h_m1

description:
1048_0014
1048_0014

value: GFIP


title: sir1∆_wtpromoter_V5Rap1 input rep2

value: matdelta::klLEU2 ADE2, lys2, TRP1, hmlat2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX; sir1delta::KanMX


title: germ-free mouse GF8

value: wild type


title: GFI_48h_m1

description:
1048_0013
1048_0013

value: GFI


title: 30min_V5Rap ChIP rep2

tag: cell line_(strain_-_paradoxus)

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3,  fpr1::NAT, RPL13A-2xFKBP12::TRP1 Rap1(134)-FRB_2xV5 bar1delta::k.l.URA3 hmlalphadelta::UniqueHMLwithSNPs  TOR1(S1972I); hmrdelta::HygMX

value: 30min treatment with 7.5uM Rapamycin

value: 50uL DynaBeads Protein G (ThermoFisher Scientific 10003D) magnetic beads coupled with 5uL monoclonal mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: sir1∆_wtpromoter_V5Rap1 ChIP rep2

value: Saccharomyces cerevisiae

value: DynaBeads Protein G magnetic beads (ThermoFisher Scientific 10003D) and mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: sir1∆_wtpromoter_V5Rap1 input rep1


title: germ-free mouse GF7


title: GF_48h_m1

description:
1048_0012
1048_0012

value: Male

value: Liver

value: GF


title: 30min_V5Rap ChIP rep1

tag: genotype (cerevisiae)


title: 60min_V5Rap ChIP rep2

tag: genotype (paradoxus)

value: 60min treatment with 7.5uM Rapamycin


title: sir1∆_wtpromoter_V5Rap1 ChIP rep1


title: MAT_mutpromoter_V5Rap1 input rep1


title: F_48h_m1

description:
1048_0011
1048_0011

treatment_protocol:
Fructose_48h_Glucose_48h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: F


title: germ-free mouse GF6

value: germ-free


title: 20min_V5Rap ChIP rep2

value: Saccharomyces cerevisiae + paradoxus

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV5

tag: treatment (growth)

value: 20min treatment with 7.5uM Rapamycin


title: sir1∆_mutpromoter_V5Rap1 input rep2

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3-1; 3xV5_Rap1-N-terminal ; hmrdelta::HygMX; matdelta::k.l.LEU2; sir1delta::KanMX


title: G_48h_m1

description:
1048_0010
1048_0010

value: G


title: germ-free mouse GF5

value: wild type


title: sir1∆_mutpromoter_V5Rap1 ChIP rep2


title: 20min_V5Rap ChIP rep1

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3,  fpr1::NAT, RPL13A-2xFKBP12::TRP1 Rap1(134)-FRB_2xV5 bar1delta::k.l.URA3 hmlalphadelta::UniqueHMLwithSNPs  TOR1(S1972I); hmrdelta::HygMX

tag: treatment (antibody)


title: 15min_V5Rap ChIP rep2

value: 15min treatment with 7.5uM Rapamycin


title: germ-free mouse GF4


title: CTR_48h_m1

description:
1048_0009
1048_0009

tag: treatment

value: CTR


title: sir1∆_mutpromoter_V5Rap1 input rep1

tag: tissue

value: Saccharomyces cerevisiae


title: GFIPO_24h_m1

description:
1048_0008
1048_0008

tag: strain

value: GFIPO


title: 45min_V5Rap ChIP rep1

value: 45min treatment with 7.5uM Rapamycin

value: 50uL DynaBeads Protein G (ThermoFisher Scientific 10003D) magnetic beads coupled with 5uL monoclonal mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: germ-free mouse GF3


title: germ-free Il10KO azoxymethane mouse C2M1

value: KO

value: azoxymethane 10 mg/kg 6 weekly i.p injections


title: sir1∆_mutpromoter_V5Rap1 ChIP rep1

tag: cell line

value: DynaBeads Protein G magnetic beads (ThermoFisher Scientific 10003D) and mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: sir3∆_mutpromoter_V5Rap1 input rep2

tag: genotype

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir3delta::klURA3; matdelta::k.l.LEU2


title: 15min_V5Rap ChIP rep1

value: Saccharomyces cerevisiae + paradoxus


title: 10min_V5Rap1 ChIP rep2

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV5

value: 10min treatment with 7.5uM Rapamycin


title: GFIO_24h_m1

description:
1048_0007
1048_0007

tag: gender

value: Male

value: Liver

value: GFIO


title: GFIP_24h_m1

description:
1048_0006
1048_0006

tag: animal id

value: GFIP


title: sir3∆_mutpromoter_V5Rap1 ChIP rep2


title: GFI_24h_m1

description:
1048_0005
1048_0005

value: GFI

tag: timepoint


title: sir3∆_mutpromoter_V5Rap1 input rep1


title: GF_24h_m1

description:
1048_0004
1048_0004

value: GF


title: 5min_V5Rap1 ChIP rep2

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3,  fpr1::NAT, RPL13A-2xFKBP12::TRP1 Rap1(134)-FRB_2xV5 bar1delta::k.l.URA3 hmlalphadelta::UniqueHMLwithSNPs  TOR1(S1972I); hmrdelta::HygMX

value: 5min treatment with 7.5uM Rapamycin


title: F_24h_m1

description:
1048_0003
1048_0003

value: F


title: 5min_V5Rap1 ChIP rep1

value: 50uL DynaBeads Protein G (ThermoFisher Scientific 10003D) magnetic beads coupled with 5uL monoclonal mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: t0_DMSO_V5Rap1 input rep 2

value: 60min treatment with DMSO


title: ddm1_Input_set4

city: Vienna

first: Bhagyshree

middle: Babasaheb

last: Jamge

address: Dr. Bohr Gasse -3

country: Austria

institute: Gregor Mendel Institute

description: ChIP

data_processing:
For alignment and quality check of sequenced samples, bedtools v2.27.1 was used to convert the raw BAM files to fastq.
FastQC v0.11.8 (Andrews 2010) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to generate quality reports for all sequencing data.
Reads were trimmed using trim_galore v0.6.5 (DOI:10.5281/zenodo.5127898.)
Reads were aligned to the TAIR10 Arabidopsis genome using Bowtie2 (Langmead and Steven L Salzberg 2013) with default settings
Picard v2.22.8 (broadinstitute.github.io/picard/) was used to mark  duplicated reads.
The bamCompare function from Deeptools was used to normalize ChIP samples to Input or H3. log2 ratio (ChIP/ (Input or H3)) bigwig files.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: 4-5 week old Leaves

growth_protocol: Col-0 wild type (WT) and ddm1(-/-) Arabidopsis thaliana seeds were stratified at 4˚C in the dark for three days. Seeds were sown in soil in the growth chamber under long day (LD) conditions (21˚C; 16 h light/8 h dark). After 4-5 week leaves tissue was freshly harvested.

extract_protocol:
Freshly harvested tissues (0.3 g of tissue was used for each immunoprecipitation) were fixed with 1% formaldehyde for 15 min and the cross-linking reaction was stopped by the addition of 125 mM glycine. . Crosslinked tissues were frozen and ground with a mortar and pestle in liquid nitrogen to obtain a fine powder. Ground tissues were resuspended in M1 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM 2-mercaptoethanol, and protease inhibitor (Roche)), and the suspension was filtered through miracloth. Nuclei were precipitated by centrifugation and washed six times with M2 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM MgCl2, 0.5% Triton X-100, 10 mM 2-mercaptoethanol, and protease inhibitor), and then further washed once with M3 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 10 mM 2-mercaptoethanol, and protease inhibitor). Nuclei pellets were rinsed and resuspended in a sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS, and protease inhibitor) and sonicated with a Covaris E220 High Performance Focused Ultrasonicator for 15 min at 4˚C (Duty factor 5.0; PIP 140.0; Cycles per Burst 200) in 1 ml Covaris milliTUBE. After chromatin shearing, the debris were removed by centrifugation and the solutions containing chromatin fragments were diluted with three times the volume of ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS, and protease inhibitor). After dilution, protein A/G magnetic beads (50 µl for one gram of tissue; Thermo Fisher Scientific) were added to sheared chromatin and incubated at 4˚C for 1 hour with rotation. Pre-cleared samples were collected and incubated with 5 µg of anti-H3 (Abcam, ab1791), anti-H2A.X.3/5, anti-H2A.13, anti-H2A.2, anti-H2A.Z.9, anti-H2A.Z.11, anti-H2A.W.6, anti-H2A.W.7, anti-H1, anti-H3K36me3 (Abcam, ab9050), anti-H3K27me3 (Millipore, 07-449), anti-H3K4me3 (Abcam, ab8580), anti-H3K4me1 (Abcam, ab8895), anti-H3K27me1 (Millipore 17-643), anti-H4K20me1 (Abcam, ab9051), anti-H3K9me1 (Abcam, ab8896) or anti-H3K9me2 (Abcam, ab1220) antibodies at 4˚C overnight with rotation. After incubation, samples were mixed with 30 µl of protein A/G magnetic beads, incubated at 4˚C for 3 hours with rotation, washed twice with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL® CA-630, and 0.1% deoxycholic acid), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Immunoprecipitated DNA was eluted by adding 500 µl of elution buffer (1% SDS and 0.1 M NaHCO3), incubated at 65˚C for 15 min, and mixed with 51 µl of reverse crosslink buffer (40 mM Tris-HCl pH 8.0, 0.2 M NaCl, 10 mM EDTA, 0.04 mg/ml proteinase K (Thermo Fisher Scientific)). The reaction mixture was then incubated at 45˚C for 3 hours and subsequently at 65˚C for 16 hours. After crosslink reversal, DNA was treated with 10 µg of RNaseA (Thermo Fisher Scientific), incubated at room temperature for 30 min, and purified with a MinElute PCR purification kit (Qiagen).
For ChIP-seq, libraries were prepared either with  NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with an Illumina Hiseq 2500 to generate single-end 50 bp reads.

value: ddm1(-/-) 1st generation

value: 4-5 week old Leaves

tag: chip antibody

value: Input


title: ddm1_H3_set4

description: ChIP


title: G_24h_m1

description:
1048_0002
1048_0002

value: G


title: ddm1_H2AW7_set4

description: ChIP


title: ddm1_H2AW7_set3

description: ChIP


title: sir4∆_mutpromoter_V5Rap1 input rep2

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hmlat2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir4delta::k.l.URA3; matdelta::k.l.LEU2


title: t0_DMSO_V5Rap1 input rep 1

value: Saccharomyces cerevisiae + paradoxus

value: Z1.1 ho::HygMX ura3::KanMXBarcode TRP LEU HIS Rap1-2xV5


title: sir4∆_mutpromoter_V5Rap1 ChIP rep2

value: DynaBeads Protein G magnetic beads (ThermoFisher Scientific 10003D) and mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: t0_DMSO_V5Rap1 ChIP rep 2


title: CTR_24h_m1

description:
1048_0001
1048_0001

treatment_protocol:
Glucose_24h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Male

value: Liver

value: CTR


title: ddm1_H3K27me3_set4

description: ChIP


title: ddm1_H3_set3

description: ChIP


title: ddm1_Input_set3

description: ChIP


title: 10min_V5Rap1 ChIP rep1

value: can1-100, his3-11,15, leu2-3,112, lys2, trp1-1, ura3,  fpr1::NAT, RPL13A-2xFKBP12::TRP1 Rap1(134)-FRB_2xV5 bar1delta::k.l.URA3 hmlalphadelta::UniqueHMLwithSNPs  TOR1(S1972I); hmrdelta::HygMX

value: 10min treatment with 7.5uM Rapamycin


title: t0_DMSO_V5Rap1 ChIP rep 1


title: sir4∆_mutpromoter_V5Rap1 input rep1


title: Placenta WT PEGIL11 rep4

city: Parkville

first: Guannan

last: Yang

address: Grattan Street

institute: University of Melbourne

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq 2.20.0.422 pipeline
The sequence reads from all samples were analysed according to AGRF quality  control measures (Australian Genome Research Facility Ltd.). The reads were also screened for the presence of any Illumina adapter/overrepresented sequences and cross-species contamination. The cleaned sequence reads were then aligned against the mm10 genome. The STAR aligner v2.5.3a was used to map reads to the genomic sequences.
mRNA were identified and kept according to MGI-Mouse Gene Expression Database (GXD). Genes with low raw counts (lower than 15 in 13 samples or more) were removed. For each sample, counts were scaled and normalized by TMM (trimmed mean of M-values) and CPM (counts per million) using the R package edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file with raw RNA counts for every gene in total RNA and every sample
Supplementary_files_format_and_content: comma-separated values file with raw RNA counts for every mRNA and every sample
Supplementary_files_format_and_content: comma-separated values file with filtered and normalised CPM values for every mRNA and every sample

source_name: Placenta

growth_protocol: C57BL6 (WEHI, Kew, VIC, Australia), Asc null (kindly provided by Millennium Pharmaceuticals) and Nlrp3 null (kindly provided by the University of Lausanne) female (virgin 8-12 weeks) and male (8-52 weeks) were housed under conventional conditions, had ad libitum food and water and were maintained in a 12h: light-dark cycle.

extract_protocol:
Placenta's were removed, flash frozen on dry ice before RNA was harvested using the RNeasy Mini kit (QIAGEN).
RNA libraries were prepared using Illumina's Ribo-zero Gold protocol

treatment_protocol: Mated female mice received once daily sub-cutaneous injections of 500µg/kg/day PEGIL11 or PEG control from embryonic day (E) 10 to E12 before being killed on E13 and the placenta collected.

value: placenta

tag: age

value: embryonic day 13

value: wild type

value: PEG IL11


title: ddm1_H2AZ11_set2_Rep2

description: ChIP

value: ddm1(-/-) 1st generation

value: 4-5 week old Leaves


title: Placenta WT PEG rep4

value: PEG


title: sir4∆_mutpromoter_V5Rap1 ChIP rep1

value: Saccharomyces cerevisiae


title: sir3∆_mutpromoter_V5Rap1 ChIP rep1

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir3delta::klURA3; matdelta::k.l.LEU2


title: ddm1_H2AW6_set2_Rep1

description: ChIP


title: ddm1_H3K36me3_set2_Rep2

description: ChIP


title: Placenta WT PEGIL11  rep3


title: Placenta WT PEG rep3


title: sir4∆_wtpromoter_V5Rap1 ChIP rep2

value: ADE2, lys2, TRP1, hmlat2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; matdelta::k.l.LEU2


title: Placenta WT PEGIL11  rep2


title: sir4∆_wtpromoter_V5Rap1 ChIP rep1


title: Placenta WT PEG rep2


title: sir4∆_wtpromoter_V5Rap1 input rep1


title: ddm1_H3K9me1_set2_Rep2

description: ChIP


title: ddm1_H3_set2_Rep2

description: ChIP


title: sir3∆_wtpromoter_V5Rap1 input rep2

value: ADE2, lys2, TRP1, hmlalpha2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir3delta::klURA3; matdelta::k.l.LEU2


title: ddm1_H2AZ11_set2_Rep1

description: ChIP


title: Placenta WT PEGIL11  rep1


title: sir3∆_wtpromoter_V5Rap1 ChIP rep2

value: DynaBeads Protein G magnetic beads (ThermoFisher Scientific 10003D) and mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: Placenta WT PEG rep1


title: ddm1_H2AW7_set2_Rep1

description: ChIP


title: sir3∆_wtpromoter_V5Rap1 input rep1


title: sir4∆_wtpromoter_V5Rap1 input rep2


title: Donor AU81709 CAR Stimulated

type: RNA

city: London

first: Simon

last: Thomas

address: The MediaWorks, 191 Wood Lane

country: United Kingdom

institute: Autolus

description: mRNA was extracted following transduction and the indicated treatment of the T cells and assessed for gene expression using Nanostring

hyb_protocol: CodeSet Hybridization Setup MAN-10056 (https://www.nanostring.com/download_file/view/863/3778) + nCounter

scan_protocol: SPRINT® Profiler User Manual MAN-10017 (https://www.nanostring.com/download_file/view/254/3778)

data_processing: Matrix values values were generated by normalization of geometic means of gene expression to defined housekeeping genes utilizing NSolver 4.0 software

source_name: Transduced T cells

growth_protocol: T Cells were maintained in RPMI medium supplemented with 10% fetal calf serum and 100U/ml IL2

extract_protocol: RNA was extracted using a Qiagen RNAeasy mini kit plus DNAse treatment and frozen at -80C until analysis

treatment_protocol: T Cells were stimulated for 24 hours with Milteny Transact then a further 24 hours with IL7 and IL15 and transduced with retrovirus encoding a CD19 CAR or a CD19 CAR + the dSHP module. Four dats following transduction

tag: donor

value: Donor 81709

tag: cell type

value: CAR T cells

tag: condition

value: CAR, Stimulated, 24hr


title: Donor AU81710  CAR + dSHP2 Unstimulated

value: Donor 81710

value: CAR + dSHP2, Unstimulated, 24hr


title: Donor AU81710  CAR Unstimulated

value: CAR, Unstimulated, 24hr


title: Donor AU81709  CAR + dSHP2 Stimulated

value: CAR + dSHP2, Stimulated, 24hr


title: Donor AU81709  CAR + dSHP2 Unstimulated


title: Donor AU81710  CAR Stimulated


title: Donor AU81710 CAR + dSHP2 Stimulated


title: ddm1_H3K36me3_set2_Rep1

description: ChIP


title: sir3∆_wtpromoter_V5Rap1 ChIP rep1


title: Placenta ASC KO PEGIL11  rep4

value: placenta

value: embryonic day 13

value: ASC-/-


title: Placenta ASC KO  PEG rep4

value: ASC -/-


title: ddm1_H3K27me3_set2_Rep2

description: ChIP

value: ddm1(-/-) 1st generation

value: 4-5 week old Leaves


title: Donor AU81709 CAR Unstimulated


title: SIR_mutpromoter_V5Rap1 input rep2

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3-1; 3xV5_Rap1-N-terminal ; matdelta::k.l.LEU2


title: ddm1_H3K27me3_set2_Rep1

description: ChIP


title: ddm1_H3K9me1_set2_Rep1

description: ChIP


title: Placenta ASC KO  PEGIL11 rep3

value: PEG IL11


title: Placenta ASC KO  PEG rep3

value: PEG


title: Donor AU81708 CAR + dSHP2 Stimulated

value: Donor AU81708


title: Donor AU81708  CAR Stimulated

value: CAR T cells


title: ddm1_H3_set2_Rep1

description: ChIP


title: SIR_mutpromoter_V5Rap1 ChIP rep2

value: DynaBeads Protein G magnetic beads (ThermoFisher Scientific 10003D) and mouse-anti-V5 antibody (ThermoFisher Scientific R96025)


title: Placenta ASC KO  PEGIL11 rep2


title: ddm1_H2AZ9_Rep2

description: ChIP


title: SIR_mutpromoter_V5Rap1 input rep1


title: Placenta ASC KO  PEG rep2


title: Placenta ASC KO  PEG rep1


title: SIR_wtpromoter_V5Rap1 ChIP rep2

value: matdelta::klLEU2 ADE2, lys2, TRP1, hmlat2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal


title: Placenta ASC KO  PEGIL11 rep1


title: ddm1_H2AZ9_Rep1

description: ChIP


title: SIR_mutpromoter_V5Rap1 ChIP rep1


title: Donor AU81708  CAR Unstimulated


title: Donor AU81708  CAR + dSHP2 Unstimulated

value: CAR + dSHP2, Unstimulated, 24hr


title: SIR_wtpromoter_V5Rap1 input rep1


title: Donor AU81707  CAR Stimulated

value: Donor AU81707

value: CAR, Stimulated, 24hr


title: Col_H2AW7_set4

description: ChIP

value: WT


title: Donor AU81707 CAR + dSHP2 Stimulated

value: CAR + dSHP2, Stimulated, 24hr


title: Col_H3K27me3_set4

description: ChIP


title: GC-Tfh cells_day 21_rep2

city: Birmingham

first: Fangming

last: Zhu

state: AL

address: 845 19th Street South

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Low quality reads and sequencing adapters were removed using Trim Galore! (v.0.4.4).
Trimmed reads were aligned to the mouse genome mm10 using STAR (v.2.5.4b).
Genes counts were determined using HTSeq-Count (v.0.12.3).
Raw read counts were normalized using the Bioconductor package DESeq2 (v.1.28.1).
Genome_build: Mus Musculus genome (version mm10)
Supplementary_files_format_and_content: Comma-Separated Values File with normalized counts of indicated sample.

source_name: mediastinal lymph node

extract_protocol:
Cells were sorted directly into TRIzol-LS Reagent (Invitrogen) and RNA was isolated using miRNeasy Micro Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PR8-OVA flu infected ex vivo OT-II T cells

value: mediastinal lymph node

value: PR8-OVA flu infection day 21


title: SIR_wtpromoter_V5Rap1 ChIP rep1


title: Col_H3_set4

description: ChIP

value: 4-5 week old Leaves


title: GC-Tfh cells_day 21_rep1


title: Donor AU81707  CAR + dSHP2 Unstimulated


title: Col_Input_set4

description: ChIP

value: Input


title: Tigit+CXCR5+ T cells_day 21_rep2


title: Donor AU81707 CAR Unstimulated

value: CAR, Unstimulated, 24hr


title: Col_H2AW7_set3

description: ChIP


title: Donor AU80537 CAR + dSHP2 Stimulated

value: Donor AU80537


title: SIR_wtpromoter_V5Rap1 input rep2

value: Saccharomyces cerevisiae


title: Col_H3_set3

description: ChIP


title: Donor AU80537 CAR Stimulated


title: Input_Vps15LKO

city: Paris

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

country: France

institute: Inserm U1151/CNRS UMR 8253, Necker Enfants Malades Institute (INEM)

data_processing:
Data filtering was performed with SOAPnuke to remove adaptor sequences and low-quality reads. Data filtering parameter was: SOAPnuke filter -l 5 -q 0.5 -n 0.1 -Q 2 -c 40.
Clean reads were aligned to the mm10 mouse genome using Bowtie2 version 2.4.4 and SAMtools version 1.13 was used to index and sort BAM file
Peak calling was performed for all samples with MACS2 version 2.2.7.1 18 ChIP-BMAL1 with the following parameter: callpeak -t -c -f BAM -g mm -p 0.01, H3K27Ac peak calling was performed using: callpeak -t -c -f BAM -g mm –broad, and ChIP-Vps15 was performed using: callpeak -t -c -f BAM -g mm -p 0.001 --broad –nomodel.
Differential peak calling analysis was performed using DiffBind, an R package 19. Differentially bound peaks were annotated, and pathway analysis performed using ChIPseeker and clusterProfiler 20,21. Motif analysis was performed using HOMER with the following parameter: findMotifsGenome.pl -mask -size 200 22
Assembly: mm10
Supplementary files format and content: bed

source_name: Liver, Input

extract_protocol:
Liver powder was fixed for 15min with 1% Formaldehyde and sonicatated to achieve fragments between 100-500bp using a Diagenode Bioruptor Pico Sonicator.
ChIP-DNA was subjected to end-repair and then 3’ adenylated. Adaptors were ligated to ends of the 3’ adenylated fragments. PCR products were purified and selected with Agencourt AMPure XP-Medium kit. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. Library was qualified by Qubit ssDNA kit. Library was then amplified to make DNA nanoballs (DNB). DNBs were loaded into the patterned nanoarray and single end base reads were generated by sequenced combinatorial Probe-Anchor Synthesis.

value: liver

value: none (input)

value: Vps15 liver KO


title: ChIP_Vps15_WT_rep2

source_name: Liver, Vps15


title: Input_WT


title: Tigit+CXCR5+ T cells_day 21_rep1


title: Tigit-CXCR5+ T cells_day 21_rep2


title: Col_Input_set3

description: ChIP


title: Donor AU80537 CAR + dSHP2 Unstimulated

value: CAR T cells


title: Col_H2AZ11_set2_Rep2

description: ChIP


title: ChIP_Vps15_WT_rep1


title: ChIP_H3K27ac_WT_rep2

source_name: Liver, H3K27ac

value: Abcam #ab4729


title: Donor AU80537 CAR Unstimulated


title: Non-Tfh cells_day 21_rep2


title: Tigit-CXCR5+ T cells_day 21_rep1


title: Donor AU80536  CAR + dSHP2 Stimulated

value: Donor AU80536


title: Col_H2AW6_set2_Rep1

description: ChIP


title: Col_H3K36me3_set2_Rep2

description: ChIP


title: ChIP_H3K27ac_WT_rep1


title: Non-Tfh cells_day 21_rep1


title: ChIP_H3K27ac_Vps15LKO_rep2


title: naïve T cells rep2

source_name: spleen

value: naive OT-II T cells

value: spleen

value: no treatment


title: Donor AU80536  CAR Stimulated

value: CAR, Stimulated, 24hr


title: Donor AU80536 CAR + dSHP2 Unstimulated

value: CAR + dSHP2, Unstimulated, 24hr


title: naïve T cells rep1


title: Col_H3K27me3_set2_Rep2

description: ChIP

value: WT


title: ChIP_H3K27ac_Vps15LKO_rep1


title: Col_H3K9me1_set2_Rep2

description: ChIP

value: 4-5 week old Leaves


title: Donor AU80536  CAR Unstimulated


title: ChIP_Bmal1_WT_rep2

source_name: Liver, Bmal1

value: Abcam #ab3350


title: GC-Tfh cells_day 14_rep2

data_processing:
Low quality reads and sequencing adapters were removed using Trim Galore! (v.0.4.4).
Trimmed reads were aligned to the mouse genome mm10 using Bowtie2 (v.2.3.3).
PCR duplicates were removed using Picard (v.2.20.0).
Peak calling was performed using MACS v2 (FDR q-value 0.01).
IDR (v.2.0.3) software was used to find reproducible peaks between sample replicates.
For each experiment, we combined peaks of all samples to create a union peak list and merged overlapping peaks with BedTools (v.2.28.0) merge.
Raw read counts were normalized using the Bioconductor package DESeq2 (v.1.28.1).
Genome_build: Mus Musculus genome (version mm10)
Supplementary_files_format_and_content: Comma-Separated Values File with normalized counts of indicated sample.

extract_protocol:
5 × 105 cells were sorted into 1.5 ml tubes for library construction.
library was prepared as described (Buenrostro, J.D., Wu, B., Chang, H.Y. & Greenleaf, W.J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21 29 21-21 29 29 (2015)).

value: PR8-OVA flu infected ex vivo OT-II T cells

value: mediastinal lymph node

value: PR8-OVA flu infection day 14


title: Col_H3_set2_Rep2

description: ChIP


title: GC-Tfh cells_day 14_rep1


title: sir4∆_mutpromoter_Sua7FLAG ChIP rep1

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hml@2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; SUA7-3xFLAGKanmX

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: Tigit+CXCR5+ T cells_day 14_rep2


title: ChIP_Bmal1_Vps15LKO_rep2

value: liver

value: Vps15 liver KO


title: ChIP_Bmal1_WT_rep1


title: Col_H2AW7_set2_Rep1

description: ChIP


title: Col_H2AZ11_set2_Rep1

description: ChIP


title: sir4∆_mutpromoter_Taf1FLAG input rep1

value: , hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; matdelta::k.l.LEU2


title: ChIP_Bmal1_Vps15LKO_rep1


title: Tigit+CXCR5+ T cells_day 14_rep1


title: Col_H3K36me3_set2_Rep1

description: ChIP


title: ZH11_R_H3K18Ace_input

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

data_processing:
Sequencing reads were mapped to rice reference genome (MSU7) using Bowtie2. ChIP-seq peaks and the signal tracks were generated by MACS2.
Assembly: MSU7
Supplementary files format and content: ChIP-seq signal tracks in bigWig format.

organism: Oryza sativa Japonica Group

source_name: 4-leaf stage seedling

growth_protocol: The rice seeds were sinked in water in the dark for 2-3 days at 37°C, and then 10 days in the hydroculture.

extract_protocol:
The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modiﬁcations. Briefly, 3 g seedling tissue were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by anti-H3K18Ac (A7257, ABclonal). The ChIP DNA was eluted, purified, and dissolved in ddH2O.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

value: 4-leaf stage seedling

tag: chip-seq antibody

value: Normal


title: Tigit-CXCR5+ T cells_day 14_rep2


title: Col_H3K27me3_set2_Rep1

description: ChIP


title: Vps15LKO_rep3

data_processing:
Raw reads were filtered following sequencing, using SOAPnuke parameters: -n 0.03 -I 20 -q 0.4 -A 0.28 to obtain clean reads. Roughly forty-one million clean reads were obtained per sample (Beijing Genomics Institute, China).
FASTQ files were mapped to the ENSEMBL [Mouse GRCm38/mm10] reference using HISAT2 and counted by featureCounts from the Subread R package
Read count normalizations and groups comparisons were performed by three independent and complementary statistical methods: Deseq2, edgeR, LimmaVoom.
Flags were computed from counts normalized to the mean coverage. All normalized counts <20 were considered as background (flag 0) and >=20 as signal (flag=1). P50 lists used for the statistical analysis regroup the genes showing flag=1 for at least half of the compared samples. Direct comparisons were made between WT and Vps15LKO animals to generate lists of differentially expressed genes

source_name: Liver, Vps15LKO

extract_protocol:
Total RNA was isolated from liver tissue using RNAeasy Lipid Tissue Mini Kit (Qiagen)
Oligo dT beds enriched polyA taail and mRNA fragmented before cDNA synthesis with random primers. Adaptors ligated to 3' adenylted cDNA fragments and digested the U-labeled second-strand templae with Uracil-DNA-Glycosylase (UDG) prior to PCR amplification. Library amplified and circularized into DNA nanoball (DNB)


title: Vps15LKO_rep2


title: m331_R_H3K18Ace_input


title: Col_H3K9me1_set2_Rep1

description: ChIP


title: ZH11_R_H3K18Ace_2_IP

value: anti-H3K18Ac (A7257, ABclonal)