title: WT

city: Changchun

first: Qilin

address: 1500 Tsinghua Road

institute: Jilin University

data_processing:
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters. The processed reads from each sample were aligned using HISAT2 against the reference genome. The gene expression analyses were performed with StringTie(v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples. Thousands of independent statistical hypothesis testing was conducted on DEGs, separately. Then a p-value was obtained, which was corrected by FDR method. And Corrected P-value (q-value) was calculated by correcting using BH method. p-value or q-value were used to conduct significance analysis. Parameters for classifying significantly DEGs are ≥2-fold differences (|log2FC|≥1, FC: the fold change of expressions) in the transcript abundance and p ≤ 0.05. The annotation of the DEGs were perfomed based on the information obtained from the database  of ENSEMBL, NCBI, Uniprot, GO, and KEGG.
Assembly: m39
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: Condyle

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen). Total RNA samples that meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio >1.8.
RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China). The triplicate samples of all assays were constructed an independent library, and do the following sequencing and analysis. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed  mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single “A” base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA. The final libraries were quantified using KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer. After quantitative reverse transcription-polymerase chain reaction (RT-qPCR) validation, libraries were subjected to paired-end sequencing with pair end 150-base pair reading length on an Illumina NovaSeq sequencer (Illumina).

value: Condyle


title: HE

status: Public on Mar 19 2024

type: SRA

last: Liu

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype


title: HO


title: Cultured astrocytes WT2

city: Atlanta

first: Fu Hung

last: Shiu

email: fshiu@emory.edu, fshiu@mgh.harvard.edu

state: GA

address: 615 Michael Street Suite 361

country: USA

institute: Emory

data_processing:
Reads were trimmed aligned to the mouse genome GRCM38(mm9) using TopHat2
Quality checks were conducted on the raw reads and the trimmed reads
The number of sequence reads for each gene was quantified using "featureCounts" function
Assembly: mm9
Supplementary files format and content: Raw counts are included in each sample

molecule: polyA RNA

source_name: Brain

extract_protocol:
Cultured astrocytes were homogenized in TRIzol (200 μL). Chloroform (800 μL) was added followed by centrifugation. The top aqueous layer was transferred to a new tube and sodium acetate solution (3M, 20 μL), glycogen (5 mg/ml, 4 μL), and isopropanol (200 μL) were added. The samples were stored overnight at − 80°C, followed by centrifugation. The pellet was washed in 75% ethanol and centrifuged again. The RNA pellet was then dissolved in nuclease-freewater (30 μL).
Bulk RNA-seq libraries were created with the NEB Next Ultra II kit using poly-A selection and sequenced to a depth of 40 million paired-end reads per sample (20 million in each direction)

value: Brain

tag: cell type

value: Astrocytes

value: WT


title: buccal DNA 220

type: genomic

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

hyb_protocol: none provided

scan_protocol: Buccal DNAm was assessed on the MethylationEPIC BeadChips, measuring over 850,000 CpGs at a nucleotide resolution, at the Fred Hutchinson Cancer Research Center Genomics Resource. In brief, 500ng of DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) following the Illumina-specified instructions.  Converted DNAs were applied to Illumina Infinium Methylation EPIC 8-Sample Beadchips following the Infinium HD Methylation 15019521v01 protocol.  Processed BeadChips were scanned using the Illumina iScan+ with ICS v3.3.28 and intensity data was extracted with Illumina GenomeStudio software (GenomeStudio v2011.1 with Methylation Analysis Module v1.9.0).

data_processing:
Data normalization and QC were performed using ChAMP: non-CpG probes, probes with a beadcount <3 in at least 5% of samples, probes annotated to SNPs, probes with a detection p-value > 0.01 in one or more samples, cross-hybridizing probes, and probes on X/Y chromosomes were removed and remaining probes (n=746,421) were normalized using via functional normalization.
functional normalized beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: buccal swab

label_protocol: none provided

extract_protocol: Buccal DNA was extracted using the Maxwell® 16 Instrument (Promega AS3000) and   Maxwell® 16 Blood DNA Extraction Kit (Promega AS1010). Proteinase K (Promega   20mg/ml) was added to 15ml conicals containing 4 swabs and ~1.6ml SLB. Tubes were   vortexed to collect SLB at bottom. Tubes were incubated in s 56°C water bath for 1 hr  and then vortexed. Lysate (800ul) was added to well #7 of the Maxwell® 16 Blood DNA  cartridge. The remaining lysate was stored for a second DNA extraction. Alcohol Wash  Buffer (2 parts Milli-Q water, 1 part 100% EtOH, 1 part 100% isopropanol) was added to  wells #4, #5 and #6. Cartridges were processed using the Buffy Coat Protocol on the  Maxwell® 16 Instrument and eluted in 400ul elution buffer. Purity was measured by  spectrophotometer and concentration measured with the Quant-iT PicoGreen dsDNA  Assay (Invitrogen® P7589).

treatment_protocol: Patients were instructed not to eat or drink at least 30 minutes before buccal sample   collection. Buccal DNA was collected using 4 Sterile HydraFlock® Large Tip Flocked  Swabs (Puritan 253406H). Each swab was applied to the inside of the child’s cheek and  rolled up and down for 30-60 seconds, making certain to roll the swab over the entire  inner cheek and upper gum. Swabs were placed together in a 15 ml conical tube  containing 1600ul of 1X Saliva Lysis Buffer (SLB) before capping tube and vortexing for  10 seconds. The swabs were frozen upright in SLB at -20°C within 1 week from sampling  and stored until DNA extraction.  2X Saliva Lysis Buffer: 0.3 M TRIS-HCl; 0.67 M urea;   0.67 M NaOAc;  0.6% sodium dodecyl sulfate;  3.3 mM EDTA;  30% ethanol)

tag: Sex

value: F

tag: age days

tag: dataset

tag: smoking


title: H3K4me3 E14 wild-type 9d, rep2

city: Berlin

first: Maximilian

last: Stötzel

state: Berlin

address: Ihnestraße 65

department: Meissner

country: Germany

institute: Max-Planck-Institute for molecular genetics

library_source: genomic

data_processing:
The raw CnT files were trimmed using trim_galore (cutadapt version 2.4) in the paired mode with default parameters.The trimmed reads were aligned to the mm10 genome using bowtie2 (v 2.5.0) with paramters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 and filtered according to their mapping quality (>= 2) using samtools (v 1.17) .
Additonally, the data  was aligned to the E.coli genome using bowtie2 with parameters --end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700. The resulting numbers of mapped reads were used for Spike-In calibration.
Peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Coverage files were created using deepTools' (v 3.5.1) bamCoverage (smoothing window 300bp and CPM normalization). The coverage levels were spike-In calibrated during this step.
Assembly: mm10
Supplementary files format and content: bigWig coverage files, spike-in calibrated, CPM normalized, smoothed (binsize 300bp)
Library strategy: CUT&TAG

source_name: embryonic stem cell

extract_protocol: NOT PROVIDED; REQUESTED

treatment_protocol: Cells were cultured without or in presence of the mTOR inhibitor Ink128

value: embryonic stem cell

value: E14 wild-type

tag: treatment

value: mTORi


title: H3K4me3 E14 wild-type 9d, rep1


title: buccal DNA 219

value: M


title: buccal DNA 217


title: buccal DNA 218


title: buccal DNA 216


title: H3K4me3 E14 wild-type 96hR, rep2


title: H3K4me3 E14 wild-type 96hR, rep1


title: H3K4me3 E14 wild-type 96hP, rep2


title: buccal DNA 214


title: buccal DNA 215


title: buccal DNA 213


title: H3K4me3 E14 wild-type 72hR, rep2


title: buccal DNA 212


title: H3K4me3 E14 wild-type 72hR, rep1


title: buccal DNA 221


title: H3K4me3 E14 wild-type 96hP, rep1


title: Cultured astrocytes WT3


title: buccal DNA 210


title: buccal DNA 209


title: H3K4me3 E14 wild-type 72hP, rep2


title: H3K4me3 E14 wild-type 72hP, rep1


title: Cultured astrocytes WT1


title: buccal DNA 208


title: H3K4me3 E14 wild-type 48hR, rep2


title: buccal DNA 211


title: H3K4me3 E14 wild-type 6hR, rep2


title: buccal DNA 207


title: buccal DNA 205


title: H3K4me3 E14 wild-type 48hR, rep1


title: H3K4me3 E14 wild-type 48hP, rep2


title: buccal DNA 204


title: buccal DNA 203


title: H3K4me3 E14 wild-type 48hP, rep1


title: buccal DNA 206


title: H3K4me3 E14 wild-type 24hR, rep2


title: buccal DNA 202


title: H3K4me3 E14 wild-type 24hP, rep2


title: H3K4me3 E14 wild-type 24hR, rep1


title: buccal DNA 201


title: buccal DNA 200


title: H3K4me3 E14 wild-type 24hP, rep1


title: buccal DNA 198


title: H3K4me3 E14 wild-type 6hR, rep1


title: buccal DNA 199


title: H3K4me3 E14 wild-type 15d, rep2


title: H3K4me3 E14 wild-type 15d, rep1


title: WS, iPS-macrophage, oxLDL, pos, 4

status: Public on Mar 20 2024

city: Chiba

first: Naoya

last: Takayama

state: Chiba

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

department: Graduate School of Medicine

country: Japan

institute: Chiba University

data_processing:
Sequences were aligned to human genome sequences (hg19) with Bowtie2(default setting) . Mapped reads are subsampled with samtools to make numbers of reads same in all samples.
Macs2(ver2.2.6) was used to call peaks with nomodel, narrow peak option. With a q-value cutoff of 0.01
The catalogue of all peaks called in any samples was produced by merging all called peaks that overlapped by, at least, one base pair using the Bedtools merge function.
The Bedtools map function was used to count the reads at each region in the catalog using bed files of each sample.
The read count matrix of each sample was used for the detection of differentially accessible regions (DARs) by using DESeq2.
Assembly: hg19

source_name: iPSC-derived macrophages

extract_protocol:
On day 21 of differentiation, healthy-, WS- and gcWS-iMφs were stained with anti-CD14 and anti-CD11b antibodies, incubated for 30 min on ice, and washed and sorted into 5,000 CD14+ CD11b+ cells in PBS containing 2% FBS.
Library preparation for ATAC-seq was performed on 10,000 cells with a Nextera DNA Sample Preparation kit (cat. #FC-121-1030, Illumina)

value: iPSC-derived macrophages

value: oxLDL


title: H3K4me3 E14 wild-type 144hR, rep2


title: buccal DNA 195


title: buccal DNA 197


title: H3K4me3 E14 wild-type 144hR, rep1


title: H3K4me3 E14 wild-type 144hP, rep2


title: buccal DNA 194


title: buccal DNA 196


title: buccal DNA 192


title: H3K4me3 E14 wild-type 12hR, rep2


title: H3K4me3 E14 wild-type 144hP, rep1


title: H3K4me3 E14 wild-type 120hR, rep2


title: buccal DNA 191


title: buccal DNA 190


title: H3K4me3 E14 wild-type 12d, rep2


title: H3K4me3 E14 wild-type 12d, rep1


title: H3K4me3 E14 wild-type 12hR, rep1


title: buccal DNA 189


title: H3K4me3 E14 wild-type 120hR, rep1


title: buccal DNA 188


title: buccal DNA 187


title: buccal DNA 193


title: buccal DNA 185


title: H3K4me3 Tet1/2 DKO 96hR, rep2

value: Tet1/2 DKO


title: buccal DNA 182


title: buccal DNA 183


title: buccal DNA 181


title: H3K4me3 Tet1/2 DKO 96hR, rep1


title: H3K4me3 E14 wild-type 0hP, rep1


title: H3K4me3 Tet1/2 DKO 72hR, rep1


title: buccal DNA 186


title: H3K4me3 E14 wild-type 120hP, rep2


title: H3K4me3 Tet1/2 DKO 72hP, rep2


title: H3K4me3 E14 wild-type 0hP, rep2


title: H3K4me3 Tet1/2 DKO 72hR, rep2


title: buccal DNA 179


title: buccal DNA 184


title: H3K4me3 Tet1/2 DKO 72hP, rep1


title: buccal DNA 178


title: buccal DNA 175


title: buccal DNA 176


title: buccal DNA 177


title: H3K4me3 Tet1/2 DKO 6hR, rep2


title: H3K4me3 Tet1/2 DKO 6hR, rep1


title: H3K4me3 Tet1/2 DKO 48hP, rep2


title: buccal DNA 174


title: H3K4me3 E14 wild-type 120hP, rep1


title: buccal DNA 173


title: H3K4me3 Tet1/2 DKO 48hP, rep1


title: buccal DNA 180


title: buccal DNA 171


title: buccal DNA 172


title: H3K4me3 Tet1/2 DKO 24hR, rep2


title: H3K4me3 Tet1/2 DKO 24hR, rep1


title: H3K4me3 Tet1/2 DKO 24hP, rep2


title: H3K4me3 Tet1/2 DKO 24hP, rep1


title: buccal DNA 167


title: H3K4me3 Tet1/2 DKO 144hR, rep2


title: buccal DNA 170


title: H3K4me3 Tet1/2 DKO 12hR, rep2


title: buccal DNA 165


title: buccal DNA 169


title: H3K4me3 Tet1/2 DKO 12hR, rep1


title: H3K4me3 Tet1/2 DKO 48hR, rep1


title: buccal DNA 164


title: buccal DNA 162


title: buccal DNA 163


title: H3K4me3 Tet1/2 DKO 120hR, rep1


title: H3K4me3 Tet1/2 DKO 0hP, rep2


title: H3K4me3 Tet1/2 DKO 0hP, rep1


title: H3K4me3 Tet1/2 DKO 120hR, rep2


title: buccal DNA 160


title: H3K4me1 E14 wild-type 9d, rep2


title: buccal DNA 161


title: buccal DNA 166


title: buccal DNA 168


title: buccal DNA 158


title: H3K4me3 Tet1/2 DKO 144hR, rep1


title: H3K4me1 E14 wild-type 96hR, rep1


title: buccal DNA 155


title: buccal DNA 154


title: H3K4me1 E14 wild-type 96hP, rep1


title: buccal DNA 156


title: buccal DNA 153


title: H3K4me1 E14 wild-type 96hR, rep2


title: H3K4me1 E14 wild-type 72hR, rep2


title: H3K4me1 E14 wild-type 72hR, rep1


title: buccal DNA 152


title: H3K4me1 E14 wild-type 72hP, rep1


title: buccal DNA 151


title: H3K4me1 E14 wild-type 6hR, rep2


title: buccal DNA 150


title: H3K4me1 E14 wild-type 48hR, rep2


title: H3K4me1 E14 wild-type 6hR, rep1


title: buccal DNA 149


title: H3K4me1 E14 wild-type 72hP, rep2


title: buccal DNA 148


title: buccal DNA 147


title: H3K4me1 E14 wild-type 48hR, rep1


title: H3K4me1 E14 wild-type 9d, rep1


title: H3K4me1 E14 wild-type 48hP, rep1


title: buccal DNA 159


title: H3K4me1 E14 wild-type 96hP, rep2


title: buccal DNA 146


title: H3K4me1 E14 wild-type 24hR, rep2


title: buccal DNA 144


title: buccal DNA 145


title: H3K4me1 E14 wild-type 24hR, rep1


title: H3K4me1 E14 wild-type 24hP, rep2


title: buccal DNA 141


title: H3K4me1 E14 wild-type 24hP, rep1


title: H3K4me1 E14 wild-type 15d, rep2


title: buccal DNA 140


title: H3K4me1 E14 wild-type 15d, rep1


title: buccal DNA 142


title: buccal DNA 139


title: H3K4me1 E14 wild-type 144hR, rep2


title: buccal DNA 136


title: buccal DNA 137


title: buccal DNA 135


title: buccal DNA 157


title: H3K4me1 E14 wild-type 144hP, rep2


title: H3K4me1 E14 wild-type 12hR, rep2


title: buccal DNA 134


title: H3K4me1 E14 wild-type 12hR, rep1


title: H3K4me1 E14 wild-type 12d, rep2


title: H3K4me1 E14 wild-type 144hR, rep1


title: LacZOsmostress_Beaf32_rep1

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 42nd and Emile street

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

data_processing:
ChIP-seq data was mapped by Bowtie2 to the genome build dm6 with a quality filter ≥10. Mapped reads of replicates were merged together and BPM (bins per million) normalized.
Peaks were identified by Macs2.
Assembly: dm6

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Kc167 cells were cultured in SFX media at 25°C.

extract_protocol:
After respective treatments, cells were harvested and processed according to experiment. Hi-C and ChIP-seq cells were crosslinked with 1% formaldehyde for 10 min followed by 5 min glycine treatment to quench crosslinking reaction, flash freezed and stored at -80°C.
Cells were washed with Buffer A (10 mM Hepes pH 7.9, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X100) and Buffer B (10 mM Hepes pH 7.9, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X100) for 10 min each. These cells were resuspended in sonication buffer (1X TE, 1X SDS, 1mMPMSF). chromatin was sheared with a Bioruptor sonication device (Diagenode) to an average fragment size of 300-500 bp (25 cycles; 30 sec on / 30 sec off). Sheared chromatin was pulled down by respective antibodies and used for library preparation. These libraries were sequenced and analyzed.

treatment_protocol: Cells were treated with RNAi for Z4 and LacZ knockdown. Isotonic cells were cultured in normal SFX media, osmostress cells were treated with SFX media supplimented with 300 mM NaCl for 1 hour. After NaCl treatment, recovery cells were washed with PBS and cultured in regular SFX media for 1 hour.

value: Embryo

tag: cell line

value: cell line

tag: chip antibody

value: Beaf32 antibody

value: LacZ RNAi, 300mM NaCl treatment for 1 hour


title: LacZOsmostress_Beaf32_rep2


title: buccal DNA 143


title: buccal DNA 133


title: LacZIsotonic_Beaf32_rep2

value: LacZ RNAi, No NaCl treatment


title: InputLacZOsmostress_Beaf32control_rep2

value: No antibody


title: LacZIsotonic_Beaf32_rep1


title: H3K4me1 E14 wild-type 12d, rep1


title: buccal DNA 132


title: InputLacZOsmostress_Beaf32control_rep1


title: buccal DNA 138


title: InputLacZIsotonic_Beaf32control_rep2


title: InputLacZIsotonic_Beaf32control_rep1


title: buccal DNA 130


title: H3K4me1 E14 wild-type 144hP, rep1


title: H3K4me1 E14 wild-type 120hR, rep1


title: Z4KDOsmostress_rep2

value: RNAPII antibody

value: Z4 RNAi, 300mM NaCl treatment for 1 hour


title: buccal DNA 129


title: Z4KDIsitonic_rep2

value: Z4 RNAi, No NaCl treatment


title: H3K4me1 E14 wild-type 120hP, rep1


title: H3K4me1 E14 wild-type 120hP, rep2


title: buccal DNA 128


title: LacZOsmostress_rep2


title: LacZIsotonic_rep1


title: H3K4me1 E14 wild-type 120hR, rep2


title: buccal DNA 131

value: F


title: H3K4me1 E14 wild-type 0hP, rep1

value: embryonic stem cell


title: LacZIsotonic_rep2


title: buccal DNA 126


title: buccal DNA 125


title: InputZ4KDOsmostress_RNAPIIcontrol_rep1


title: InputZ4KDOsmostress_RNAPIIcontrol_rep2


title: H3K4me1 Tet1/2 DKO 96hR, rep2


title: Z4KDOsmostress_rep1


title: H3K4me1 Tet1/2 DKO 96hR, rep1


title: buccal DNA 124


title: InputZ4KDIsotonic_RNAPIIcontrol_rep1


title: buccal DNA 127


title: H3K4me1 E14 wild-type 0hP, rep2

value: E14 wild-type


title: buccal DNA 123


title: InputLacZOsmostress_RNAPIIcontrol_rep2


title: H3K4me1 Tet1/2 DKO 72hR, rep2

value: mTORi


title: LacZOsmostress_rep1


title: InputLacZOsmostress_RNAPIIcontrol_rep1


title: Z4KDIsotonic_rep1


title: InputZ4KDIsitonic_RNAPIIcontrol_rep2


title: InputLacZIsotonic_RNAPIIcontrol_rep2


title: buccal DNA 122


title: Step Down 10 mM to 2 mM, rep 3 [SD3]

city: Stanford

first: Drew

last: Endy

state: CA

address: 443 Via Ortega, Shriram Center, Room 248

department: Bioengineering

institute: Stanford University

data_processing:
Sequence reads were processed to assess initial read quality using FastQC v0.12.1
Sequence reads were trimmed for low-quality (below Phred score 20) ends and auto-detected adapters using Trim Galore v0.6.10
Reads that became shorter than 20 bp because of either quality or adapter trimming were discarded
Trimmed sequence reads were mapped to the Staphylococcus epidermidis ATCC 12228 genome using Bowtie2 v2.5.1
Mapped reads were counted for genomic features using featureCounts in the Subread package v2.0.6
Assembly: ASM987345v1 (NCBI RefSeq assembly GCF_009873455.1)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Staphylococcus epidermidis ATCC 12228

growth_protocol: We started ATCC 12228 broth cultures using a single colony from a fresh colony plate. We grew broth cultures in fresh tryptic soy broth (TSB) without Dextrose (BD 286220) supplemented with the appropriate carbon source at 37°C with shaking.

extract_protocol:
We harvested RNA using enzymatic lysis (lysostaphin and mutanolysin), mechanical disruption (TissueLyser LT Qiagen 85600), and an RNeasy Mini Kit (Qiagen 74106).  ≥ 500ng of total RNA was used for the construction of sequencing libraries.
We used Novogene Co., LTD (Beijing, China) to carry out our rRNA depletion, cDNA library construction, and sequencing as part of their Prokaryotic RNA Sequencing service.

treatment_protocol: We subjected ATCC 12228 cells to heat shock (from 37°C to 45°C), 20-minute glucose spikes, persistent glucose via batch culture, or a step down in glucose concentration from 10 mM to 2 mM.

value: Prokaryotic

value: WT

value: Step Down 10 mM to 2 mM


title: buccal DNA 120


title: H3K4me1 Tet1/2 DKO 72hP, rep2

value: Tet1/2 DKO


title: H3K4me1 Tet1/2 DKO 72hP, rep1


title: Step Down 10 mM to 2 mM, rep 2 [SD2]


title: Glucose Spike 50 mM, rep 2 [G50_2]

value: Glucose Spike, 50 mM


title: Glucose Spike 50 mM, rep 3 [G50_3]


title: buccal DNA 121

value: M


title: H3K4me1 Tet1/2 DKO 6hR, rep1


title: InputLacZIsotonic_RNAPIIcontrol_rep1

value: Embryo

value: cell line


title: H3K4me1 Tet1/2 DKO 6hR, rep2


title: Hi-C Z4KD Recovery rep2

data_processing:
Sequenced reads were preprocessed, mapped to the Drosophila genome build dm6, filtered for quality score ≥10, and removed of PCR duplicates using HiC-Pro (2.7.2).
Replicates were combined and juicer tools (1.14.08) was used to create .hic files.
Assembly: dm6
Supplementary files format and content: .hic files

growth_protocol: Kc167 cells were cultured in SFX media.

extract_protocol:
After respective treatments, cells were harvested and crosslinked with 1% formaldehyde for 10 min followed by 5 min glycine treatment to quench crosslinking reaction, flash freezed and stored at 80°C. These cells were used for HiC library preparation.
Cross-linked cells were incubated for 30 min on ice in HiC lysis buffer (10 mM Tris-HCl at pH 8, 10 mM NaCl, 0.2% NP-40), centrifuged for 5 min at 3500g, resuspended in 190 μL of NEBuffer2 1× (New England BioLabs [NEB]) and 10 μL of 10% SDS, and were then incubated for 10 min at 65°C. After the addition of Triton X-100 and 15-min incubation at 37°C, nuclei were centrifuged for 5 min at 3500g and were resuspended in 300 μL of 1x NEBuffer2. Nuclei were digested overnight using 400 U of the MboI restriction enzyme (NEB). For fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× repair buffer (1.5 μL of 10 mM dCTP, 1.5 μL of 10 mM dGTP, 1.5 μL of 10 mM dTTP, 37.5 μL of 0.4 mM biotin-dATP, 50 U of DNA Polymerase I large [Klenow] fragment in 300 μL NEBunffer2 1×). Ligation was performed for 4 h at 16°C using 10,000 units of T4 DNA ligase (NEB) in 1.2 mL of ligation buffer (120 μL of 10× T4 DNA ligase buffer, 100 μL of 10% Triton X-100, 12 μL of 10 mg/mL BSA, 963 μL of H2O). After reversion of the cross-link, DNA was purified using phenol/chloroform/isoamyl. Purified DNA was sonicated to an average size of 300–400 bp using a Bioruptor (Diagenode; eight cycles of 20 sec on and 60 sec off), and 3 μg of sonicated DNA was used per in situ Hi-C library preparation. Briefly, biotinylated DNA was pulled down using 20 μL of Dynabeads MyOne T1 streptavidin beads in binding buffer (5 mMTris-HCl at pH 7.5, 0.5 mM EDTA, 1 M NaCl). End-repair, A-tailing and Illumina adaptors ligation were performed on the beads using NEBNext library preparation end-repair and A-tailing modules (NEB). Libraries were amplified and sequenced in biological replicates.

tag: restriction enzyme

value: MboI restriction enzyme digested

value: Z4 RNAi, 300mM NaCl treatment for 1hour, recovered in normal media for 1 hour


title: Glucose Spike 50 mM, rep 1 [G50_1]


title: buccal DNA 119


title: Step Down 10 mM to 2 mM, rep 1 [SD1]


title: Hi-C Z4KD Recovery rep1


title: H3K4me1 Tet1/2 DKO 48hR, rep2


title: buccal DNA 117


title: Hi-C Z4KD Osmostress rep2

value: Z4 RNAi, 300mM NaCl treatment for 1hour


title: Glucose Spike 17 mM, rep 3 [G17_3]

value: Glucose Spike, 17 mM


title: H3K4me1 Tet1/2 DKO 48hR, rep1


title: Glucose Spike 17 mM, rep 2 [G17_2]


title: H3K4me1 Tet1/2 DKO 48hP, rep2


title: Hi-C Z4KD Osmostress rep1


title: Glucose Spike 17 mM, rep 1 [G17_1]


title: H3K4me1 Tet1/2 DKO 48hP, rep1


title: buccal DNA 115


title: Hi-C Z4KD Isotonic rep1

value: Z4 RNAi, No NaCl treatment


title: Hi-C Z4KD Isotonic rep2


title: Glucose Spike 10 mM, rep 3 [G10_3]

value: Glucose Spike, 10 mM


title: Glucose Spike 10 mM, rep 2 [G10_2]


title: buccal DNA 118

value: F


title: Hi-C LacZ Recovery rep1

value: LacZ RNAi, 300mM NaCl treatment for 1hour, recovered in normal media for 1 hour


title: Hi-C LacZ Recovery rep2


title: H3K4me1 Tet1/2 DKO 24hR, rep2

value: embryonic stem cell

value: mTORi


title: buccal DNA 112


title: H3K4me1 Tet1/2 DKO 24hP, rep2


title: buccal DNA 114


title: Glucose Spike 10 mM, rep 1 [G10_1]

value: Prokaryotic

value: WT


title: H3K4me1 Tet1/2 DKO 24hR, rep1

value: Tet1/2 DKO


title: buccal DNA 113


title: buccal DNA 116


title: Glucose Spike 5 mM, rep 3 [G5_3]

value: Glucose Spike, 5 mM


title: buccal DNA 111


title: H3K4me1 Tet1/2 DKO 24hP, rep1


title: Glucose Spike 5 mM, rep 2 [G5_2]


title: H3K4me1 Tet1/2 DKO 144hR, rep2


title: Hi-C LacZ Osmostress rep2

value: LacZ RNAi, 300mM NaCl treatment for 1hour


title: Hi-C LacZ Osmostress rep1

value: Embryo


title: buccal DNA 110


title: Glucose Spike 5 mM, rep 1 [G5_1]


title: H3K4me1 Tet1/2 DKO 144hR, rep1


title: Hi-C LacZ Isotonic rep2

value: LacZ RNAi, No NaCl treatment


title: Glucose Spike 2 mM, rep 3 [G2_3]

value: Glucose Spike, 2 mM


title: buccal DNA 109


title: Glucose Spike 2 mM, rep 2 [G2_2]


title: H3K4me1 Tet1/2 DKO 12hR, rep1


title: Z4KD_CAP-H2_rep2

data_processing:
ChIP-seq data was mapped by Bowtie2 to the genome build dm6 with a quality filter ≥10. Mapped reads of replicates were merged together and BPM (bins per million) normalized.
Peaks were identified by Macs2.
Assembly: dm6
Supplementary files format and content: bw

value: cell line

value: CAP-H2 antibody


title: Hi-C LacZ Isotonic rep1

value: MboI restriction enzyme digested


title: buccal DNA 107

value: M


title: Z4KD_CAP-H2_rep1

value: Z4 RNAi, No NaCl treatment


title: buccal DNA 105


title: H3K4me1 Tet1/2 DKO 12hR, rep2


title: LacZOsmostress_Z4_rep2

value: Z4 antibody

value: LacZ RNAi, 300mM NaCl treatment for 1 hour


title: H3K4me1 Tet1/2 DKO 120hR, rep2

value: embryonic stem cell


title: H3K4me1 Tet1/2 DKO 120hR, rep1

value: mTORi


title: buccal DNA 106


title: LacZOsmostress_Z4_rep1


title: H3K4me1 Tet1/2 DKO 0hP, rep2


title: Glucose Spike, 0 mM Control, rep 3 [G0_3]

value: Prokaryotic

value: Glucose Spike, 0 mM


title: Glucose Spike 2 mM, rep 1 [G2_1]

value: WT


title: Glucose Spike, 0 mM Control, rep 2 [G0_2]


title: Glucose Spike, 0 mM Control, rep 1 [G0_1]


title: buccal DNA 103


title: H3K4me1 Tet1/2 DKO 0hP, rep1

value: Tet1/2 DKO


title: 1% Persistent Glucose, rep 2 [C12]

value: 1% Persistent Glucose


title: H3K27ac E14 wild-type 9d, rep2

value: E14 wild-type


title: buccal DNA 104


title: LacZOsmostress_CAP-H2_rep2

value: Embryo


title: LacZOsmostress_CAP-H2_rep1


title: buccal DNA 108


title: buccal DNA 102


title: 1% Persistent Glucose, rep 1 [C11]


title: H3K27ac E14 wild-type 9d, rep1


title: LacZIsotonic_CAP-H2_rep2

value: LacZ RNAi, No NaCl treatment


title: buccal DNA 101


title: LacZIsotonic_CAP-H2_rep1

value: cell line


title: 0.2% Persistent Glucose, rep 2 [A22]

value: 0.2% Persistent Glucose


title: buccal DNA 100


title: H3K27ac E14 wild-type 96hR, rep2


title: 0.2% Persistent Glucose, rep 1 [A21]


title: buccal DNA 99

value: F


title: H3K27ac E14 wild-type 96hR, rep1


title: InputZ4KD_rep2

description: inputOsmostress

value: No antibody


title: InputOsmostress_rep2

description: inputOsmostress


title: H3K27ac E14 wild-type 96hP, rep2


title: H3K27ac E14 wild-type 96hP, rep1


title: Heat-shock, rep 3 [HS3]

value: Heat Shock


title: InputZ4KD_rep1

value: Z4 RNAi, No NaCl treatment


title: buccal DNA 98


title: buccal DNA 96

value: M


title: InputOsmostress_rep1

description: inputOsmostress

value: LacZ RNAi, 300mM NaCl treatment for 1 hour


title: buccal DNA 97


title: Heat-shock, rep 2 [HS2]


title: H3K27ac E14 wild-type 72hR, rep2

value: embryonic stem cell

value: mTORi


title: H3K27ac E14 wild-type 72hR, rep1


title: Heat-shock, rep 1 [HS1]

value: Prokaryotic


title: buccal DNA 95

value: birth


title: H3K27ac E14 wild-type 72hP, rep2


title: InputLacZIsotonic_rep1

description: inputLacZIsotonic


title: Z4KDrep2

data_processing:
ATAC-seq data was trimmed of adapter sequences using cutadapt, aligned to the reference genome dm6 using bowtie2, deduplicated with picard (https://broadinstitute.github.io/picard/).
Peaks identified by macs2 with the extsize 147 and nomodel parameters. Tranposase hypersensitive sites (THSSs) and nucleosomes were separately analyzed by categorizing the reads by insert size (<120 bp v.s. 140-250 bp respectively).
Signal was BPM normalized and we tested for differential peaks by MANorm. Footprint analysis was performed using TOBIAS on Z4 peaks overlapping architectural protein motifs where available in the Jaspar databse (i.e. Beaf-32 and Dref) and ChIP-seq summits for the others.
Assembly: dm6
Supplementary files format and content: bw

extract_protocol:
After respective treatments, cells were harvested and processed according to experiment. Hi-C and ChIP-seq cells were crosslinked with 1% formaldehyde for 10 min followed by 5 min glycine treatment to quench crosslinking reaction, flash freezed and stored at -80°C.
Cell pellets were resuspended in 50 μl Tn5 transposase mixture (2.5 μL Tn5, 25 μL 2X TD buffer, 22.5 μL RNase Free Water), and incubated at 37°C for 30 min. After the reaction, cells were cooled on ice and DNA was purified using the Minelute Kit (QIAGEN). Transposed DNA was eluted in 10 μl of Elution Buffer (10mM Tris, pH8.0) and used for real-time PCR amplification in the reaction mixture (2x KAPA HiFi mix and 1.25 μM indexed primers) using the following conditions: (1) 72°C for 5 min; (2) 98°C for 30 s; (3) 98°C for 10 s, (4) 63°C for 30 s, (5) 72°C for 1 min, (6) Repeat steps 3-4 for 4 times, (7) Hold at 4°C.

value: Z4 RNAi to knockdown Z4


title: H3K27ac E14 wild-type 72hP, rep1


title: H3K27ac E14 wild-type 6hR, rep2


title: buccal DNA 94


title: buccal DNA 92


title: Z4KDrep1


title: LacZrep2

value: LacZ RNAi to knockdown LacZ


title: H3K27ac E14 wild-type 6hR, rep1

value: E14 wild-type


title: MET035

type: RNA

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Fasted Mcl1(L-/-), biological rep4

hyb_protocol: Labeled cRNA was fragmented and prepared for hybridization.

scan_protocol: The Affymetrix Gene Titan system was used to perform the hybridization, washing and scanning of the arrays.

data_processing: Affymetrix CEL files were normalized using Robust Multi-array Average method with a log base 2 transformation. A filtering step was performed to remove low expression probe sets using Partek Genomics Suite version 7.0 (Partek Inc.).

label: biotin

source_name: Liver from Fasted Mcl1(L-/-) mouse

label_protocol: Double-stranded cDNA was synthesized using the GeneChip WT PLUS Reagent Kit (Affymetrix)

growth_protocol: Mcl1(F/F) mice were treated with AAV-LP1-Cre to induce liver-specific deletion of target protein, MCL-1.

extract_protocol: Livers were harvested, washed with PBS, then total RNA was isolated using Trizol according to manufacturer's instructions.

treatment_protocol: Mice were housed with food ad libitum (Fed) or were housed individually in wire-bottom cages without food for 48 hours (Fasted). In all cases water was supplied ad libitum.

tag: diet

value: Fasted

value: Liver


title: InputLacZIsotonic_rep2

description: inputLacZIsotonic

value: Embryo

value: cell line

value: LacZ RNAi, No NaCl treatment


title: H3K27ac E14 wild-type 48hR, rep1


title: H3K27ac E14 wild-type 48hR, rep2


title: MET034

description: Fasted Mcl1(L-/-), biological rep3


title: A15

city: Dongjak-gu

first: Junil

last: Kim

state: Seoul

address: 360 Songdo-ro

department: Department of Bioinformatics

country: South Korea

institute: Soongsil University

data_processing:
The RNA-seq reads were trimmed by BBDuk with quality-trim=20 option. The trimmed reads were mapped to the human reference genome GRCh377 using TopHat. Based on the mapping result, we computed Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks. Differentially expressed genes (DEGs) were obtained by comparing three groups (UCA, UCI, and NC) using EdgeR. Genes with p-value<0.01 and log2fold change > 1 were selected as DEGs. The union of DEGs were clustered using hierarchical clustering and principal component analysis (PC) implemented in MATLAB R2020a. The enriched Gene Ontology and KEGG pathway terms associated with clustered genes were obtained using Enrichr software. Metascape, an enrichment analysis tool was used for obtaining a network representation of enrichment terms.
Assembly: GRCh37

source_name: Colon tissue samples from mucosa with active inflammation

extract_protocol:
We performed RNAseq on total RNA from both areas of the colonic mucosa with active inflammation and without inflammation during the colonoscopy.
RNA quality was assessed by RIN (RNA Integrity Number) algorithm on the Agilent 2100 bioanalyzer. The cDNA library was constructed with 1.0 μg of total RNA using NEBNext Ultra II directional RNA library prep kit for Illumina sequencer. Then, 100bp paired-end sequencing reads were obtained using Illumina NovaSeq 6000. RNA extraction and reverse transcription were conducted following the protocols provided by the manufacturer. Subsequently, the Quantstudio 3 real-time polymerase chain reaction (PCR) system (Applied Biosystems, Waltham, Massachusetts, USA) was used for analysis using 0.1 μg of the synthesized cDNA as a template for the 2X Power SYBR Green PCR Master mix (Applied Biosystems). Specific primer set for each gene from Macrogen (Seoul, Korea) was employed (detailed in Supplementary Table 1). Each PCR was performed after 10 min of pre-denaturation at 95°C, 15 s at 95°C, and 1 min at 60°C; this was repeated 40 times. After the PCR was completed, a melting curve was drawn to check the accuracy of gene amplification. For the internal compensation of gene expression level, the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was also used, and relative gene expression levels were presented as 2-ΔΔCt values.

tag: disease

value: Active ulceraitve colitis

value: colonoscopic biopsy specimens


title: MET036

description: Fasted Mcl1(L-/-), biological rep5


title: buccal DNA 90

value: F


title: H3K27ac E14 wild-type 48hP, rep2


title: buccal DNA 89


title: A14


title: buccal DNA 88


title: MET032

description: Fasted Mcl1(L-/-), biological rep1


title: buccal DNA 93


title: MET031

description: Fed Mcl1(L-/-), biological rep5

source_name: Liver from Fed Mcl1(L-/-) mouse

value: Fed


title: MET029

description: Fed Mcl1(L-/-), biological rep3


title: MET030

description: Fed Mcl1(L-/-), biological rep4


title: buccal DNA 87


title: MET033

description: Fasted Mcl1(L-/-), biological rep2


title: buccal DNA 91

value: M


title: A13


title: LacZrep1


title: MET028

description: Fed Mcl1(L-/-), biological rep2


title: A12


title: buccal DNA 86


title: H3K27ac E14 wild-type 24hR, rep2

value: embryonic stem cell


title: buccal DNA 85


title: A11


title: H3K27ac E14 wild-type 24hP, rep2

value: mTORi


title: H3K27ac E14 wild-type 24hR, rep1


title: A10


title: buccal DNA 83


title: buccal DNA 84


title: H3K27ac E14 wild-type 24hP, rep1


title: H3K27ac E14 wild-type 48hP, rep1


title: A9


title: buccal DNA 82


title: H3K27ac E14 wild-type 15d, rep2


title: MET027

description: Fed Mcl1(L-/-), biological rep1


title: A8


title: MET025

description: Fasted WT, biological rep4

source_name: Liver from Fasted WT mouse

value: WT


title: H3K27ac E14 wild-type 15d, rep1


title: MET023

description: Fasted WT, biological rep2


title: A6


title: A7


title: buccal DNA 80

value: birth


title: MET026

description: Fasted WT, biological rep5


title: MET024

description: Fasted WT, biological rep3


title: H3K27ac E14 wild-type 144hR, rep1


title: buccal DNA 79


title: A5


title: MET022

description: Fasted WT, biological rep1


title: H3K27ac E14 wild-type 144hP, rep2


title: A4


title: buccal DNA 81


title: A3


title: buccal DNA 78


title: buccal DNA 76


title: A2


title: H3K27ac E14 wild-type 144hP, rep1


title: buccal DNA 77


title: aged mouse eAT, epicardial fat 6

first: Suphansa

last: Sawamiphak

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Centrum für Molekulare Medizin

data_processing:
RNA-seq data were processed and analyzed using pseudo-mapping to the mouse transcriptome (GRCm39, Ensembl) and unique transcript counts were performed using Kallisto (v0.46.1).
Transcript level counts were summarized into gene counts using Tximport (v1.22.0), and genes with over 10 counts were maintained.
Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package (version 1.34.0)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values of DESeq2 normalized counts for young mouse eAT and aged mouse eat

source_name: adipose tissue

extract_protocol:
Adipocytes were collected for RNA extraction. Total RNA was prepared using TRIzol (Life Technologies, 15596026)
Libraries were prepared using Illumina Stranded Total RNA (with rRNA depletion)

value: adipose tissue

value: epicardial fat

value: female


title: MET021

description: Fed WT, biological rep5

source_name: Liver from Fed WT mouse


title: buccal DNA 75


title: H3K27ac E14 wild-type 12hR, rep1

value: E14 wild-type


title: MET020

description: Fed WT, biological rep4

value: Liver


title: aged mouse eAT, epicardial fat 5


title: buccal DNA 74


title: I15

source_name: Colon tissue samples from mucosa without active inflammation

value: Inactive ulcerative colitis


title: A1


title: aged mouse eAT, epicardial fat 4


title: H3K27ac E14 wild-type 144hR, rep2


title: H3K27ac E14 wild-type 120hR, rep2


title: H3K27ac E14 wild-type 12d, rep1


title: buccal DNA 73


title: young mouse eAT, epicardial fat 3


title: H3K27ac E14 wild-type 12hR, rep2


title: buccal DNA 72


title: I13


title: MET019

description: Fed WT, biological rep3


title: MET018

description: Fed WT, biological rep2


title: H3K27ac E14 wild-type 120hR, rep1


title: young mouse eAT, epicardial fat 2


title: I12


title: buccal DNA 71


title: young mouse eAT, epicardial fat 1


title: H3K27ac E14 wild-type 120hP, rep2


title: H3K27ac E14 wild-type 12d, rep2


title: MET017

description: Fed WT, biological rep1


title: HKC_sgVHL_sg2_RNA_Rep3

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

description: RNA-seq

data_processing:
The MeRIP and input library reads were aligned to aligned to mycoplasma genome to assess contamination followed by alignment to human reference genome (hg19) with STAR. MarkDuplicates (Picard) was used for identifying and removing duplicates reads. DESeq2 was used to call the differential expression genes (DEG) between Ctrlsg and VHL knockout groups. The m6A peaks were called by MeTDiffpackage with default parameter by combining signals from all the biological triplicates. Homer was used to search for the enriched motif in the m6A peaks, and the m6A peak distribution across the whole transcriptome was called using the Guitar package. A convolutional neural network model (MATK, http://matk.renlab.org/#/home) was used identify the specific m6A site from the detected peaks. Pathway enrichment analysis were performed using Enrichr (https://maayanlab.cloud/Enrichr/enrich).
Assembly: hg19
Supplementary files format and content: m6A bigwig files contain read-depth normalized per-base signal for each m6A sample and replicate.
Supplementary files format and content: Excel files labeled *_MATK.xlsx contain m6A peaks across treatments as determined by MATK.
Supplementary files format and content: Excel files labeled *m6A_peaks_MeTDiff.xlsx contain m6A peaks per treatment as determined by MeTDiff.
Supplementary files format and content: Excel files labeled *diff_peaks_MeTDiff.xlsx contain differential m6A peaks between labeled treatments as determined by MeTDiff. Files are labeled as they were run in MeTDiff: treatment_vs_control.
Supplementary files format and content: Excel files labeled *DESeq2_feature_counts.xlsx contain per-gene counts for each treatment and replicate as determined by DESeq2.
Supplementary files format and content: Excel files labeled *DESeq2_diff_genes.xlsx contain differentially expressed genes between labeled treatments as determined by DESeq2. Files are labeled as they were run in DESeq2: treatment_vs_control. File contains DESeq2 output for both sgVHL_sg1 vs sgCtrl and sgVHL_sg2 vs sgCtrl

source_name: HKC

growth_protocol: HKC cells are obtained from Dr. Kimryn Rathmell from Vanderbilt University. All the cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco, 11995073) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. The cells were incubated at 37 °C in a humidified atmosphere containing 5% CO2. Mycoplasma testing was routinely carried out with MycoAlert® PLUS Mycoplasma Detection Kit (Lonza, LT07-703) to ensure cells are mycoplasma free.

extract_protocol:
Cellular RNA was extracted using the RNeasy mini kit (Qiagen, 74104) according to the manufacturer’s instructions. Complementary DNA (cDNA) was synthesized iScript Reverse Transcription Supermix (Bio-Rad, 1708841). RIP was performed using a modified native RNA immunoprecipitation procedure as previously described. In briefly, approximately 3x10^7 HKC cells were lysed with lysis buffer (100mM KCl, 5mM MgCl2, 10mM HEPES pH 7.0, 0.5% NP-40, 1mM DTT, supplemented with RNase inhibitor and EDTA-free Protease inhibitor before using). Incubate the cell lysate with protein-A/G magnetic beads that immobilized with corresponded antibodies for overnight at 4 °C. Wash the beads 6 times with NT-2 buffer (50mM Tirsh-HCl pH 7.4, 250mM NaCl, 1 mM MgCl2, 0.05% NP-40, 20mM EDTA, 1mM DTT, supplemented with RNase inhibitor before using). Input and co-immunoprecipitated RNAs were first digested with Proteinase K buffer (NT-2 buffer supplemented with 1% SDS and 1.2 mg/ml Proteinase K) at 55 °C for 30 min and then recovered by TRIzol according to the supplier’s instructions.
Immunoprecipitated RNA was extracted with RNeasy mini kit (Qiagen, 74106). cDNA library was prepared with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7775). Samples were subjected for qPCR analysis or sequenced on the Illumina NextSeq 500 NGS system as 75 bp pair-ended reads.

treatment_protocol: METTL3 and IGF2BP1 lentiviral shRNA constructs were purchased from Sigma-Aldrich. VHL, PIK3R3, HIF1a, HIF2a, ARNT, IGF2BP2, IGF2BP3, p85a and p85b sgRNAs were cloned into pLentiCRISPR V2 -Puromycin vector. siRNAs were purchased from Invitrogen. Target sequences of shRNA, sgRNA and siRNA are listed in supplementary tables in the manuscript.

value: HKC


title: I14


title: H3K27ac E14 wild-type 120hP, rep1


title: buccal DNA 69


title: I10


title: H3K27ac E14 wild-type 0hP, rep2


title: buccal DNA 68


title: I9


title: I7


title: HKC_sgVHL_sg2_RNA_Rep1

description: RNA-seq


title: I8


title: buccal DNA 67


title: buccal DNA 65


title: buccal DNA 66


title: HKC_sgVHL_sg1_RNA_Rep3

description: RNA-seq


title: HKC_sgVHL_sg1_RNA_Rep1

description: RNA-seq


title: H3K27ac E14 wild-type 0hP, rep1


title: buccal DNA 70


title: H3K27ac Tet1/2 DKO 96hR, rep1

value: Tet1/2 DKO


title: I5


title: HKC_sgVHL_sg1_RNA_Rep2

description: RNA-seq


title: buccal DNA 64


title: I6


title: I11


title: H3K27ac Tet1/2 DKO 72hR, rep2


title: H3K27ac Tet1/2 DKO 72hR, rep1


title: HKC_sgCtrl_RNA_Rep3

description: RNA-seq

value: sgCtrl


title: buccal DNA 63


title: I3

value: colonoscopic biopsy specimens


title: H3K27ac Tet1/2 DKO 72hP, rep2


title: HKC_sgCtrl_RNA_Rep2

description: RNA-seq


title: I4


title: HKC_sgVHL_sg2_RNA_Rep2

description: RNA-seq


title: H3K27ac Tet1/2 DKO 96hR, rep2


title: HKC_sgCtrl_RNA_Rep1

description: RNA-seq


title: buccal DNA 61

value: F


title: H3K27ac Tet1/2 DKO 72hP, rep1


title: HKC_sgVHL_sg2_MeRIP_input

description: MeRIP-seq


title: I2


title: HKC_sgVHL_sg1_MeRIP_input

description: MeRIP-seq


title: H3K27ac Tet1/2 DKO 6hR, rep1


title: I1


title: N14

source_name: Colon tissue samples from mucosa in healthy normal control

value: Normal mucosa


title: H3K27ac Tet1/2 DKO 48hR, rep1


title: N13


title: buccal DNA 59

value: M


title: HKC_sgVHL_sg2_MeRIP_Rep3

description: MeRIP-seq


title: HKC_sgCtrl_MeRIP_input

description: MeRIP-seq


title: HKC_sgVHL_sg2_MeRIP_Rep2

description: MeRIP-seq


title: N15


title: buccal DNA 62


title: buccal DNA 58


title: buccal DNA 57


title: H3K27ac Tet1/2 DKO 48hP, rep2

value: embryonic stem cell


title: H3K27ac Tet1/2 DKO 48hR, rep2

value: mTORi


title: N12


title: buccal DNA 56


title: N11


title: buccal DNA 55


title: HKC_sgVHL_sg1_MeRIP_Rep3

description: MeRIP-seq


title: HKC_sgVHL_sg2_MeRIP_Rep1

description: MeRIP-seq


title: H3K27ac Tet1/2 DKO 24hR, rep2


title: H3K27ac Tet1/2 DKO 48hP, rep1


title: H3K27ac Tet1/2 DKO 6hR, rep2


title: N10


title: buccal DNA 60


title: buccal DNA 54


title: H3K27ac Tet1/2 DKO 24hR, rep1


title: HKC_sgVHL_sg1_MeRIP_Rep2

description: MeRIP-seq


title: buccal DNA 53


title: HKC_sgVHL_sg1_MeRIP_Rep1

description: MeRIP-seq


title: N8


title: buccal DNA 52


title: HKC_sgCtrl_MeRIP_Rep3

description: MeRIP-seq


title: H3K27ac Tet1/2 DKO 24hP, rep1


title: buccal DNA 51


title: N7


title: N6


title: buccal DNA 50


title: N5


title: H3K27ac Tet1/2 DKO 144hR, rep2


title: HKC_sgCtrl_MeRIP_Rep1

description: MeRIP-seq


title: buccal DNA 48


title: PC3_input_rep1

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding input sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: PC-3 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

value: Bone Metastasis Prostate Cancer 3


title: H3K27ac Tet1/2 DKO 144hR, rep1


title: H3K27ac Tet1/2 DKO 12hR, rep2


title: N4


title: PC3_SIX2_rep2

value: SIX2 (Sigma-Aldrich, HP056958)


title: N9


title: buccal DNA 47

value: birth


title: H3K27ac Tet1/2 DKO 12hR, rep1


title: PC3_SIX2_rep1


title: H3K27ac Tet1/2 DKO 24hP, rep2


title: N3


title: HKC_sgCtrl_MeRIP_Rep2

description: MeRIP-seq


title: buccal DNA 45


title: N1


title: buccal DNA 44


title: buccal DNA 49


title: PC3 OE TP63 ab TP63

city: Moscow

first: Rinat

middle: I

last: Sultanov

address: Malaya Pirogovskaya, 1a

country: Russia

institute: FRCC of Physical Chemical Medicine of the FMBA of the Russian Federation

data_processing:
The following algorithm was used to analyze chromatin immunoprecipitation followed by sequencing: pre-processing of raw reads was performed by trimmomatic tool; then the reads were mapped onto human genome version hg19 using the bwa mem program with standard parameters. The *.bam files thus obtained were sorted and indexed with the samtools program. Reliably determined regions of TP63 or histone binding with determined modifications were found using the macs2 program. ChIP-seq data were visualized using the deepTools program.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: Cells were cultured in corresponding media in a 5% CO2 incubator at 37ºC as described

extract_protocol:
Chromatin immunoprecipitation was performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling) according to the manufacturer's manual.
Paired-end libraries were prepared according to the manufacturer's recommendations using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, USA). The libraries were indexed with NEBNext Multiplex Oligos kit for Illumina (96 Index Primers, New England Biolabs, USA). Size distribution for the libraries and their quality were assessed using a high-sensitivity DNA chip (Agilent Technologies). The libraries were subsequently quantified by Quant-iT DNA Assay Kit, High Sensitivity (Thermo Scientific, USA). DNA sequencing was performed on the HiSeq 2500 platform (Illumina, USA) according to the manufacturer's recommendations, using the following reagent kits: HiSeq Rapid PE Cluster Kit v2, HiSeq Rapid SBS Kit v2 (200 cycles), HiSeq Rapid PE FlowCell v2 and a 1% PhiX spike-in control.

value: TP63 overexpression

value: prostate cancer

value: TP63 (Cell Signaling #13109)


title: LNCaP_ATAC_CTRL_rep2

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >6-fold over local background. ENCODE hg38 blacklist peaks were filtered out from the peak list.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: LNCaP

growth_protocol: LNCaP cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) according to instructions.

treatment_protocol: LNCaP cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for 3 weeks before the start of nuclei extraction.

value: Lymph Node Carcinoma of the Prostate

value: LNCaP

tag: enz treatment


title: PC3 OE TP63 IgG

value: IgG


title: buccal DNA 42


title: H3K27ac Tet1/2 DKO 0hP, rep2

value: Tet1/2 DKO


title: RWPE-1 abTP63

value: prostate basal epithelium


title: LNCaP_ATAC_ENZ_rep2

value: 3 weeks


title: RWPE-1 IgG


title: buccal DNA 41


title: E14 DNMT3ABKO 144 hours, rep 2

data_processing:
RNAseq reads were pre-processed using cutadapt v2.4 to remove adapter and trim low quality bases.
Reads were subsequently aligned against the reference gnenome mm10 using STAR v2.7.3a (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie v2.0 was used for transcript quantification, e.g. calculation of strand-specific coverage, RPKMs and TPMs (reference: mm10 gencode gene annotation gtf). TPMs were normalized according to ERCC RNA Spike-In Mix (Thermo, 4456740) manufacturers information.
Assembly: mm10
Supplementary files format and content: tab delimited text file (.bed) <Reference> <Strand> <Start> <End> <Gene ID> <Gene Name> <TPM>

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74004). Samples were spiked-in using ERCC RNA Spike-In Mix (Thermo, 4456740) and 500ng RNA was used as input for library preparacion. Library preparation was performed using KAPA RNA HyperPrep Kit with RiboErase (Roche, 8098131702) following manufacturer's instructions.

treatment_protocol: Cells were cultured without (0h) or in presence of the mTOR inhibitor Ink128 (24h, 72h, 144h)

value: E14 DNMT3ABKO

value: mTOR inhibitor Ink128 144h


title: LNCaP_ATAC_ENZ_rep1


title: buccal DNA 43

value: M


title: buccal DNA 46

value: F


title: LNCaP_ATAC_CTRL_rep1


title: N2

value: Normal mucosa

value: colonoscopic biopsy specimens


title: E14 DNMT3ABKO 72 hours, rep 1

value: embryonic stem cell

value: mTOR inhibitor Ink128 72h


title: buccal DNA 40

value: birth


title: E14 DNMT3ABKO 0 hours, rep 2

value: control


title: E14 DNMT3ABKO144 hours, rep 1


title: H3K27ac Tet1/2 DKO 0hP, rep1

value: mTORi


title: PC3 TRIM29 overexpression rep2 [PC3_OE_TRIM29_2]

data_processing:
Pre-processing of raw readings was performed with trimmomatic. Then, the readings were mapped onto the genome version hg19 using STAR software. To quantify gene coverage, the featureCounts software with gencode v37 annotation was used. For differential analysis, the DESeq2 package was used. Genes were considered differentially expressed, if abs(logFC) > 0.5 and FDR < 0.05.
Assembly: hg19
Supplementary files format and content: comma-delimited text files include raw coverage for each Sample

growth_protocol: Cells were cultured in corresponding media in a 5% CO2 incubator at 37ºC

extract_protocol:
Isolation of RNA from cells was performed using the Lira reagent (Biolabmix, Russia) according to the manufacturer's protocol.
Library preparation was performed with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacturer’s protocol. The library underwent a final cleanup using the Agencourt AMPure XP system (Beckman Coulter) after which the libraries’ size distribution and quality were assessed using a high sensitivity DNA chip (Agilent Technologies). Libraries were subsequently quantified by Quant-iT DNA Assay Kit, High Sensitivity (ThermoFisher).

treatment_protocol:
TP63 and TRIM29 knockdown was performed using RNA interference. siRNA was transfected into RWPE-1 cells in a 24-well plate using HiPerFect Transfection Reagent (Qiagen, 301704).
Cells were transduced with virus particles containing TP63-FLAG or TRIM29-FLAG. After 24 h, cell medium was replaced. Two days after transfection, cells were trypsinized and TP63/TRIM29-infected cells were isolated on a FACS BD Aria III cell sorter.

value: prostate cancer

value: TRIM29 overexpression


title: PC3 TRIM29 overexpression rep1 [PC3_OE_TRIM29_1]


title: E14 DNMT3ABKO 72 hours, rep 2


title: E14 DNMT3ABKO 0 hours, rep 1


title: PC3 TP63 overexpression rep2 [PC3_OE_TP63_2]

value: TP63 overexpression


title: E14 KH 144 hours, rep 1

value: E14 KH


title: E14 KH 144 hours, rep 2


title: PC3 TP63 overexpression rep1 [PC3_OE_TP63_1]


title: E14 KH 72 hours, rep 2


title: buccal DNA 38

data_processing:
Data normalization and QC were performed using ChAMP: non-CpG probes, probes with a beadcount <3 in at least 5% of samples, probes annotated to SNPs, probes with a detection p-value > 0.01 in one or more samples, cross-hybridizing probes, and probes on X/Y chromosomes were removed and remaining probes (n=746,421) were normalized using via functional normalization.
functional normalized beta
Unmethylated and methylated signal intensities


title: buccal DNA 37


title: PC3 empty vector rep2 [PC3_OE_cntr_2]

value: empty vector


title: buccal DNA 36


title: buccal DNA 39


title: PC3 empty vector rep1 [PC3_OE_cntr_1]


title: E14 KH 72 hours, rep 1


title: buccal DNA 34


title: K 68

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

institute: UKE Hamburg-Eppendorf

description: Replicate 3

hyb_protocol: Raw data were obtained by standard array hybridization techniques

scan_protocol: GeneChip Scanner 3000

data_processing: Data was normalized via the Single Channel Array Normalization algorithm  mapping the probes to the custom chip definition file from the BrainArray resources in version  18.

source_name: Kif3aΔTub + PBS

label_protocol: RNA was analysed using Affymetrix Mouse Genome 430 2.0 gene chips.

growth_protocol: Intraperitoneal (IP) injection with 10mg/kg of sActRIIB-Fc every week, two times till week 6

extract_protocol: RNA extracted using QIAZOL lysis Reagent (QIAGEN) according to manufacturer instructions.

treatment_protocol: Snap-frozen muscle and kidney samples.

value: Kidney

value: PBS


title: K 40

description: Replicate 3

source_name: Kif3aΔTub + sActRIIB-Fc

value: sActRIIB-Fc


title: K 15

description: Replicate 4


title: E14 KH 0 hours, rep 2


title: PC3 TP63 and TRIM29 overexpression rep1 [PC3_OE_TP63_TRIM29_1]

value: TP63 and TRIM29 overexpression


title: E14 KH 0 hours, rep 1


title: K 65

description: Replicate 4


title: PC3 TP63 and TRIM29 overexpression rep2 [PC3_OE_TP63_TRIM29_2]


title: E7_embryo_female_WT_rep5

data_processing:
Reads were trimmed to remove base pairs with a Phred score less than 20 and any Illumina adapter sequence using cutadapt 4.1. Reads less than 36 base pairs after trimming were removed.
Reads were then aligned to the mm10 reference genome using STAR 2.7.7a. The following STAR options were used in alignment: --quantMode TranscriptomeSAM GeneCounts, --twopassMode Basic, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, --outFilterMultimapNmax 1. For the STAR option --sjdbGTFfile, a GTF file from GENCODE vM25 was provided.
Post-alignment gene quantification was conducted using Salmon 1.5.2 using the same GENCODE vM25 gene annotations.
Differential expression tests were performed on raw counts using DESeq2 1.34.0. Gene expression differences were considered significant at an adjusted p-value threshold of 0.05.
Assembly: mm10
Supplementary files format and content: The DESeq2 xlsx file contains the direct output from DESeq2 (columns A-F) for all genes as well as the VST-normalized expression for each gene and individual sample (columns G-R).

source_name: E7.0 embryo

growth_protocol: Eight-week-old male and female C57BL/6J mice were purchased from The Jackson Laboratory (Stock #000664) and housed in a temperature and humidity-controlled environment on a 12:12 light/dark cycle with ad libitum access to food (Prolab Isopro RMH 3000, LabDiet, St. Louis, MO) and water. Females were housed in same-treatment groups of up to 5 and males were housed singly in standard Techniplast cages with nesting material and shelter. After acclimating for at least one week, females weighing over 20g were mated two per male for 1 to 2 hours. The date a vaginal plug was detected was defined as embryonic day 0 (E0) and the female was weighed and separated into a new cage.

extract_protocol:
RNA was isolated from untreated male and female E7.0 embryos for whole transcriptome sequencing (n = 5 females, 7 males from 7 litters). No more than two embryos from each sex were used per litter.
Libraries were prepared using the SMARTer Ultra Low Input RNA and Nextera XT DNA kits by the UNC High Throughput Sequencing Facility.
Samples were pooled prior to sequencing and run paired-end (2x100) on a NovaSeq 6000 instrument using the S4 XP workflow.

value: E7.0 embryo

value: Female

tag: strain

value: WT

tag: litter


title: buccal DNA 33

source_name: buccal swab

extract_protocol: Buccal DNA was extracted using the Maxwell® 16 Instrument (Promega AS3000) and   Maxwell® 16 Blood DNA Extraction Kit (Promega AS1010). Proteinase K (Promega   20mg/ml) was added to 15ml conicals containing 4 swabs and ~1.6ml SLB. Tubes were   vortexed to collect SLB at bottom. Tubes were incubated in s 56°C water bath for 1 hr  and then vortexed. Lysate (800ul) was added to well #7 of the Maxwell® 16 Blood DNA  cartridge. The remaining lysate was stored for a second DNA extraction. Alcohol Wash  Buffer (2 parts Milli-Q water, 1 part 100% EtOH, 1 part 100% isopropanol) was added to  wells #4, #5 and #6. Cartridges were processed using the Buffy Coat Protocol on the  Maxwell® 16 Instrument and eluted in 400ul elution buffer. Purity was measured by  spectrophotometer and concentration measured with the Quant-iT PicoGreen dsDNA  Assay (Invitrogen® P7589).

value: M


title: buccal DNA 32

value: F


title: K 16

description: Replicate 3

source_name: WT + sActRIIB-Fc


title: K 28

description: Replicate 3

source_name: WT + PBS


title: RWPE-1 knockdown TP63 rep 2 [RWPE1_siTP63_2]

value: normal basal epithelium

value: knockdown TP63


title: E7_embryo_male_WT_rep7

value: Male


title: K 9

description: Replicate 4


title: RWPE-1 knockdown TP63 rep 1 [RWPE1_siTP63_1]


title: buccal DNA 31

value: birth


title: RWPE-1 knockdown TRIM29 rep 1 [RWPE1_siTRIM29_1]

value: knockdown TRIM29


title: buccal DNA 30


title: E7_embryo_female_WT_rep4


title: buccal DNA 35


title: RWPE-1 knockdown cntr rep 2 [RWPE1_LUC2]

value: knockdown cntr


title: E7_embryo_female_WT_rep3


title: K 26

description: Replicate 2


title: K 10

description: Replicate 2


title: K 25

description: Replicate 1


title: K 24

description: Replicate 1


title: E7_embryo_male_WT_rep6


title: RWPE-1 knockdown cntr rep 1 [RWPE1_LUC1]


title: buccal DNA 29


title: E7_embryo_male_WT_rep5


title: buccal DNA 28


title: cold eAT, epicardial fat 6

data_processing:
RNA-seq data were processed and analyzed using pseudo-mapping to the zebrafish transcriptome (GRCz11, Ensembl) and unique transcript counts were performed using Kallisto (v0.46.1).
Transcript level counts were summarized into gene counts using Tximport (v1.22.0), and genes with over 10 counts were maintained.
Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package (version 1.34.0)
Assembly: GRCz11
Supplementary files format and content: Tab-separated values of DESeq2 normalized counts for cold treated eAT  and control temperature epicardial adipocytes

organism: Danio rerio

extract_protocol:
Adipocytes were collected for RNA extraction. Total RNA was prepared using TRIzol (Life Technologies, 15596026)
Libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v3 (TaKaRa, 634487) following manufacturer's protocols.

value: adipose tissue

value: epicardial fat

value: female


title: buccal DNA 26


title: buccal DNA 27


title: K2

description: Replicate 1

value: Kidney


title: E7_embryo_male_WT_rep4


title: K 18

description: Replicate 2

value: sActRIIB-Fc


title: K 3

description: Replicate 1


title: cold eAT, epicardial fat 5


title: E7_embryo_female_WT_rep1


title: E7_embryo_female_WT_rep2


title: buccal DNA 24


title: control eAT, epicardial fat 3


title: buccal DNA 25


title: control eAT, epicardial fat 2


title: buccal DNA 23


title: M68

description: Replicate 3

value: Muscle

value: PBS


title: vAT, visceral fat 3

data_processing:
RNA-seq data were processed and analyzed using the PiGx-RNAseq pipeline (version 0.0.19)
The raw reads were mapped to the zebrafish genome using STAR aligner (version 2.7.3a)
Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package (version 1.32.0)
Assembly: GRCz11
Supplementary files format and content: Tab-separated values of DESeq2 normalized counts for eAT and vAT

tag: tissue subtype

value: Viscerlal fat


title: E7_embryo_male_WT_rep1

tag: tissue

value: E7.0 embryo

value: WT


title: E7_embryo_male_WT_rep3

tag: genotype


title: control eAT, epicardial fat 1


title: E7_embryo_male_WT_rep2


title: buccal DNA 21

value: M


title: sample_8699

first: Bastian

last: Opitz

address: Augustenburgerplatz 1

department: Department of Infectious Diseases, Respiratory Medicine and Critical Care

institute: Charité – Universitätsmedizin Berlin

data_processing:
sequence cleaning
screening and removal of host sequences
taxonomic profiling
diversity indices and plotting
Assembly: NCBI Genomes (complete)
Supplementary files format and content: large table with raw counts
Supplementary files format and content: large table with proportions

source_name: feces

extract_protocol:
ZymoBIOMICS DNA Miniprep Kit
Standard genomic library preparation of eurofins genomics

value: feces

tag: strain background

tag: phenotype

value: yes


title: buccal DNA 22

tag: Sex

value: F

tag: age days


title: cold eAT, epicardial fat 4


title: M40

description: Replicate 3


title: vAT, visceral fat 2


title: K 34

description: Replicate 2


title: buccal DNA 20

tag: dataset

value: birth

tag: smoking


title: vAT, visceral fat 1


title: buccal DNA 19


title: sample_8697


title: M16

description: Replicate 3

tag: treatment


title: sample_8696


title: buccal DNA 18


title: eAT, epicardial fat 3


title: M15

description: Replicate 4


title: M28

description: Replicate 3


title: M9

description: Replicate 4


title: eAT, epicardial fat 2


title: M34

description: Replicate 2


title: sample_8692


title: eAT, epicardial fat 1


title: buccal DNA 16


title: sample_8691


title: sample_8694


title: buccal DNA 15


title: sample_8622


title: Arabisopsis root cells - sc_136

city: Durham

first: Philip

middle: N.

last: Benfey

state: North Carolina

address: 130 Science Drive

department: Biology

institute: Duke University

description: 10X Genomics kit v3.1

library_source: transcriptomic single cell

data_processing:
Processed by COPILOT (https://github.com/ohlerlab/COPILOT)
Assembly: TAIR10
Supplementary files format and content: Seurat object

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis accession Columbia-0 (Col-0) was used as wild type. The following lines were previously described: bri1  GABI_134E10 (Jaillais et al., 2011); bri1-116brl1brl3 triple mutant (bri1-T) (Irani et al., 2012); pGL2:BRI1-GFP/bri1-T (Vragović et al., 2015); gtl1-1 (WiscDsLox413-416C9), df1-1 (SALK_106258), and gtl1-1 df1-1 (Shibata et al., 2018); JKD-Ypet recombineering line (Moreno-Risueno et al., 2015). Seeds were sterilized using 50% (v/v) bleach with 0.05% Tween-20 for 10-15 minutes, plated on 1/2 Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media, and stratified 2-4 days at 4°C in the dark. Plates were kept vertically in a Percival growth chamber set to 22°C, 16 hours light/8 hours dark and grown for 7 days unless otherwise indicated. Chemical treatments were conducted by cooling the growth media to approximately 60°C after autoclaving and adding DMSO (a mock solvent), 1μM Brassinazole (BRZ, SML1406,  Sigma) or 100nM Brassinolide (BL, 21594, Cayman Chemical).

extract_protocol: Chromium Single Cell 3ʹ GEM Kit v3 and v3.1

value: Root

tag: cell type

value: All cell types of root


title: Arabisopsis root cells - sc_132

description: 10X Genomics kit v3.1


title: sample_8621


title: buccal DNA 17


title: buccal DNA 13


title: M65

description: Replicate 4


title: buccal DNA 14


title: sample_8619


title: M25

description: Replicate 1


title: buccal DNA 11


title: buccal DNA 12


title: M26

description: Replicate 2


title: OCI-AML2-shADGRE2-1

city: Hangzhou

first: lu

last: huan

address: 866 Yuhangtang Road

institute: Zhejiang University medical center

data_processing:
For analysis, the raw data were checked by FastQC (version 0.11.5). Reads were trimmed by TrimGalore-0.6.5 with default parameters. Clean reads were aligned to reference genome of human hg38 by HISAT2 (v2.2.1). featureCounts (2.0.1) was used to calculate read counts of genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: peripheral blood

growth_protocol: OCI-AML2 cells were maintained in α-MEM medium supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using RNAiso Plus (Takara). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA library prep kit (New England BioLabs) following manufacturer’s protocols.

value: peripheral blood

tag: cell line

value: Human acute myeloid leukemia cells

value: ADGRE2 knockdown


title: sample_8618


title: OCI-AML2-shADGRE2-2


title: OCI-AML2-shADGRE2-3


title: M3

description: Replicate 1


title: sample_8620


title: buccal DNA 10


title: M18

description: Replicate 2


title: OCI-AML2-shCtrl-3


title: M10

description: Replicate 2


title: M2

description: Replicate 1


title: sample_8617


title: M24

description: Replicate 1


title: OCI-AML2-shCtrl-2


title: buccal DNA 9


title: sample_8615


title: OCI-AML2-shCtrl-1


title: buccal DNA 8


title: buccal DNA 7


title: sample_8613


title: 119202_TCCGCGAA-GCCTCTAT

city: SAN FRANCISCO

first: Hanrui

last: Zhang

state: California

address: 148 Locksley Ave Apt2

institute: University of Michigan

description:
65w-CB-a425-2
Sample_119202

data_processing:
The RNAseq data were processed as previously described. Briefly, reads were pseudo-aligned to the ENSEMBL 108 mouse reference cDNA sequences (June 2020, GRCm39) using Kallisto 0.45 and quantified transcripts aggregated by their gene were fed to Sleuth 0.30.1 for differential expression analysis.
Assembly: mm39
Supplementary files format and content: tar archives include abundance.h5, abundance.tsv, and run_info.json files.
Supplementary files format and content: Tab-delimited text files include est_counts and tpm values.

source_name: Cerebellum

growth_protocol: Homozygous YACMJD84.2Q-C57BL/6 transgenic mice (referred to in this study as “Q84 mice”) and wild type (WT) sex- and age-matched controls were used. Genotyping was completed via tail biopsy DNA isolation prior to weaning and confirmed postmortem.

extract_protocol:
RNA was extracted from PBS-perfused, flash-frozen BS/Dien, spinal cord, and cerebellum samples from the left hemisphere. Using the Next Advance Bullet Blender, samples were homogenized in radioimmunoprecipitation assay (RIPA, by Sigma, St. Louis, MO) buffer (750 µL for BS/Dien and 500 µL for cerebellum and spinal cord samples) with added proteinase inhibitor (BioRad, Hercules, CA). A 250 µL aliquot of this lysate was reserved for Western blot analysis and the remaining sample was used for RNA extraction.
RNA extraction was conducted using the QIAshredder (Qiagen Hilden, Germany), RNeasy Mini Kit (Qiagen, Hilden, Germany), and DNase I kit (Qiagen, Hilden, Germany), then eluted in RNase-free water, according to manufacturer’s instructions. RNA samples were assessed by nanodrop to determine concentration and sample purity.
For library preparation, 1 μg of total BS/Dien RNA was submitted to the University of Michigan Sequencing Core for Illumina HiSeq library preparation, quality control, and RNA sequencing. WT and Q84 RNA samples were chosen for RNA sequencing based on RIN number (>7 RIN) and, if applicable, CAG repeat expansion size (>average 72Q) as determined by Laragen, Inc. The University of Michigan Bioinformatics Core generated libraries (Illumina TruSeq) from purified brain RNA samples, completed quality control analysis, and ran 75x75 paired end sequencing on Illumina HiSeq 4000.

treatment_protocol:
4-6 mice (equal numbers of males and females) per genotype were collected for tissue analysis at 4, 12, or 16 weeks of age. Left hemisphere brain tissue was macrodissected into brainstem and diencephalon tissue (BS/Dien - includes whole of brainstem, striatum, and thalamus), cerebellum, and cervical spinal cord for biochemical analysis.
Premanifest mice used in this study received a post-natal day 0 injection of either ASO-5 or PBS into both lateral ventricles. Pups were placed on ice for cryo-anesthetization before performing a bilateral intracerebroventricular (ICV) injection of either ASO-5 or PBS (2 µL per hemisphere, 5 µg/µL ASO-5). Immediately following injection, pups were placed on a heating pad before returning to their cage. Pups were monitored and weighed weekly following treatment. Brain and peripheral tissue were collected from mice at 4 weeks of age for biochemical and histological assessment. Symptomatic ASO treatment was completed as previously described,9,18,53 with 700 µg of ASO-5 injected in a total volume of 10 µL at 8 weeks of age. Post-operative care was performed for at least 7 days following treatment.

value: Cerebellum

tag: time

value: 65 weeks


title: 119200_CGGCTATG-GTCAGTAC

description:
65w-CB-a463-1
Sample_119200


title: 90-Air-PBS-5 US84403582_252800519480_S01_GE1_107_Sep09_2_4

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

institute: Japanese Science and Technology Agency

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with mouse arrays (Agilent Microarray Design Identification Number 028005) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using the LIMMA package in R.

source_name: lung

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: Total RNA was extracted from lung samples by using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Seven-week-old female C57BL/6j mice were purchased from Charles River Japan Inc. Mice were exposed to cigarette smoke (Peace®, 28 mg of tar, 2.3 mg of nicotine/cigarette, Japan Tobacco Inc., Tokyo, Japan) or to air (as a control) for 20‒30 min per time by using a mainstream smoke-generating apparatus for period of 30, 90, or 180 days. Following smoke exposure, mice were intranasally inoculated with A(H7N9) virus (refered to as the Anhiu strain). For controls, mice were mock-infected with sterile PBS-solution. Lungs were harvested at days 2 or 5 post infection.

tag: animal #

value: female

tag: exposure days

tag: smoking or air

value: Air

tag: day

value: C57BL/6j mouse


title: 90-Smoking-Anhui-5 US84403582_252800519480_S01_GE1_107_Sep09_2_2

value: Smoking

tag: strain

value: Anhui


title: 30-Smoking-Anhui-5 US84403582_252800519480_S01_GE1_107_Sep09_1_4


title: 90-Smoking-PBS-5 US84403582_252800519480_S01_GE1_107_Sep09_2_3

value: PBS


title: 90-Smoking-Anhui-2 US84403582_252800519480_S01_GE1_107_Sep09_2_1


title: sample_8474

tag: tissue

value: feces


title: sample_8612

value: yes

tag: genotype

value: WT


title: buccal DNA 4

first: Lyndsey

last: Shorey-Kendrick

address: 505 NW 185th Ave

institute: Oregon Health and Science University

value: F

value: birth


title: 119201_TCCGCGAA-AGGCTATA

description:
65w-CB-a488-2
Sample_119201


title: buccal DNA 6

value: M


title: 119197_CGGCTATG-CTTCGCCT

description:
65w-CB-a463-4
Sample_119197


title: sample_8472

tag: strain background


title: sample_8471

tag: phenotype


title: 30-Smoking-Anhui-5 US84403582_252800519480_S01_GE1_107_Sep09_1_3

tag: Sex


title: buccal DNA 1

tag: age days


title: 30-Smoking-Anhui-2 US84403582_252800519480_S01_GE1_107_Sep09_1_1


title: sample_8611


title: 180-Air-PBS-5 US84403582_252800518903_S01_GE1_107_Sep09_2_4


title: buccal DNA 5

tag: dataset


title: 30-Smoking-Anhui-5 US84403582_252800519480_S01_GE1_107_Sep09_1_2


title: 119199_CGGCTATG-ACGTCCTG

description:
65w-CB-a500-1
Sample_119199


title: sample_8473


title: 119198_CGGCTATG-TAAGATTA

description:
65w-CB-a490-6
Sample_119198


title: 119195_CGGCTATG-AGGATAGG

description:
65w-CB-a427-0
Sample_119195


title: buccal DNA 3

tag: smoking


title: sample_8462

value: no


title: 119193_CGGCTATG-AGGCTATA

description:
65w-CB-a421-0
Sample_119193


title: 180-Air-Anhui-5 US84403582_252800518902_S01_GE1_107_Sep09_2_3


title: sample_8461


title: sample_8459


title: 119194_CGGCTATG-GCCTCTAT

description:
65w-CB-a424-4
Sample_119194


title: 119196_CGGCTATG-TCAGAGCC

description:
65w-CB-a424-5
Sample_119196


title: sample_8470


title: 119190_TAATGCGC-TAAGATTA

description:
16w-CB-a580-5
Sample_119190

value: 16 weeks

tag: treatment


title: buccal DNA 2


title: 119189_TAATGCGC-CTTCGCCT

description:
16w-CB-a556-2
Sample_119189


title: 119192_TAATGCGC-GTCAGTAC

description:
65w-CB-a423-4
Sample_119192


title: sample_8469


title: 180-Air-PBS-5 US84403582_252800518901_S01_GE1_107_Sep09_2_4


title: 119191_TAATGCGC-ACGTCCTG

description:
65w-CB-a425-1-3
Sample_119191


title: ovary, L8

city: Changchun

first: Yutao

last: Li

address: Jingyue Street

institute: Northeast Normal University

data_processing:
Raw sequencing data format was shown as “.fastq” and the joint sequence (adapter) was removed from the original tags using CUTADAPT 1.9. Low quality and repetitive sequences were filtered to obtain clean data. De novo splicing in TRINITY tool (Version 2.4.0) was selected to assemble the clean reads and then the software was used to perform the transcript clustering based on shared sequences contents. The longest transcript in each cluster was regarded as one Unigene. All obtained Unigenes were annotated based on known databases. Quantitative assessment for transcripts per million (TPM) of each Unigene was executed with the SALMON package.
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Huso dauricus x Acipenser schrenckii

source_name: ovary

extract_protocol:
Commercial RNA simple extraction kit (DP419, TIANGEN, China) was selected to extract the total RNA in ovary tissues. 60 mg fresh tissue was ground by high-speed homogenizer (DHFSTPRP-32D, LAWSON, China) with 1 mL lysis buffer RZ to obtain homogenate and then trichloromethane was added. After staying at room temperature for 4 min, the mixture was centrifuged at 12000 rpm to obtain the aqueous phase that was mixed with absolute ethyl alcohol. RD solution was used to remove residual protein impurity in RNA samples and the purified total RNA was stored at RNase-free tubes after repeated centrifugation.
When RNA integrity number > 7.0 and A260/280 > 1.8, messenger RNA (mRNA) with poly A was caught using oligo(dT) dynabeads (25-61005, THERMO FISHER, USA) and then broken into fragmentation with the specific kit (E6150S, NEBNEST, USA). Double-strands complementary DNA was synthesized based on the reverse transcriptase and E. coli DNA polymerase I that were provided by LIANCHUAN BIO TECHNOLOGIES Co., LTD (Hangzhou, China). Paired-ends of the complementary DNA were added with a “A” base, which could combine with the adapter sequence. After the second strand was digested, the sequencing library (300±50 bp) was established by amplifying the target sequences.

value: ovary

value: Huso dauricus (female) x Acipenser schrenckii (male)

value: normal breeding conditions(with low caviar yield)


title: sample_8460


title: ovary, L5


title: 119188_TAATGCGC-TCAGAGCC

description:
16w-CB-a532-3
Sample_119188

value: Cerebellum


title: 180-Air-PBS-5 US84403582_252800518902_S01_GE1_107_Sep09_2_4

value: female

value: Air


title: 180-Air-Anhui-5 US84403582_252800518903_S01_GE1_107_Sep09_2_3

value: C57BL/6j mouse


title: 180-Air-Anhui-5 US84403582_252800518901_S01_GE1_107_Sep09_2_3

value: Anhui


title: sample_8448


title: ovary, L7


title: sample_8451


title: ovary, L3


title: ovary, L6


title: sample_8319


title: sample_8450


title: 180-Smoking-PBS-5 US84403582_252800518903_S01_GE1_107_Sep09_2_2

value: Smoking

value: PBS


title: 180-Smoking-Anhui-5 US84403582_252800518902_S01_GE1_107_Sep09_2_1


title: 180-Smoking-PBS-5 US84403582_252800518901_S01_GE1_107_Sep09_2_2


title: 119187_TAATGCGC-AGGATAGG

description:
16w-CB-a580-3
Sample_119187


title: ovary, L2


title: 180-Smoking-PBS-5 US84403582_252800518902_S01_GE1_107_Sep09_2_2


title: 180-Smoking-Anhui-5 US84403582_252800518903_S01_GE1_107_Sep09_2_1


title: ovary, L4


title: 180-Air-PBS-2 US84403582_252800518903_S01_GE1_107_Sep09_1_4


title: 180-Smoking-Anhui-5 US84403582_252800518901_S01_GE1_107_Sep09_2_1


title: 119186_TAATGCGC-GCCTCTAT

description:
16w-CB-a579-0
Sample_119186


title: sample_8449

value: feces


title: 119185_TAATGCGC-AGGCTATA

description:
16w-CB-a580-6
Sample_119185


title: ovary, H8

value: normal breeding conditions(with high caviar yield)


title: sample_8318


title: 119184_CTGAAGCT-GTCAGTAC

description:
16w-CB-a503-1
Sample_119184


title: ovary, L1


title: sample_8317


title: 119183_CTGAAGCT-ACGTCCTG

description:
16w-CB-a579-3
Sample_119183


title: 119181_CTGAAGCT-CTTCGCCT

description:
16w-CB-a556-3
Sample_119181

value: WT

value: WT-Veh


title: ovary, H6


title: 180-Air-PBS-2 US84403582_252800518902_S01_GE1_107_Sep09_1_4


title: sample_8316


title: sample_8313


title: ovary, H5


title: 119180_CTGAAGCT-TCAGAGCC

description:
16w-CB-a557-4
Sample_119180


title: 119182_CTGAAGCT-TAAGATTA

description:
16w-CB-a577-0
Sample_119182


title: PC3 OE TP63 rep2 [methylation]

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

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

data_processing: To process the data, RnBeads (Assenov et al. 2014) program was used with the following setup parameters: ENmix (Xu et al. 2016) + BMIQ (Teschendorff et al. 2013); limma algorithm for differential analysis (Ritchie et al. 2015).

label: Cy5 and Cy3

source_name: PC3 overexpresion TP63

label_protocol: Standard Illumina Protocol

extract_protocol: Cells (~10^6) were resuspended in lysis buffer (10mM Tris pH=8.0, NaCl 100mM, 10mM EDTA pH=8.0, 0.5% SDS ) and incubated with Proteinase K overnight. For DNA purification the phenol chloroform extraction method was used.

value: overexpresion TP63

tag: gender

value: Male

tag: sample type

value: prostate cancer

tag: disease state

value: tumor


title: ovary, H7

value: ovary

value: Huso dauricus (female) x Acipenser schrenckii (male)


title: sample_8314

value: no


title: 119179_CTGAAGCT-AGGATAGG

description:
16w-CB-a562-0
Sample_119179

value: Cerebellum

tag: time

value: 16 weeks


title: 180-Air-Anhui-2 US84403582_252800518902_S01_GE1_107_Sep09_1_3

tag: animal #

value: female

tag: exposure days

value: Air

value: C57BL/6j mouse


title: 180-Air-PBS-2 US84403582_252800518901_S01_GE1_107_Sep09_1_4

tag: smoking or air

value: PBS

tag: day


title: sample_8312

tag: tissue

value: feces


title: ovary, H4

tag: genotype

value: normal breeding conditions(with high caviar yield)


title: 180-Air-Anhui-2 US84403582_252800518903_S01_GE1_107_Sep09_1_3

tag: strain

value: Anhui


title: PC3 OE TP63 rep1 [methylation]

tag: cell line


title: 180-Air-Anhui-2 US84403582_252800518901_S01_GE1_107_Sep09_1_3

tag: Sex


title: sample_7929

tag: strain background

tag: phenotype

value: yes


title: ovary, H3


title: sample_7927


title: ovary, H1


title: ovary, H2


title: 119176_GAATTCGT-GTCAGTAC

description:
8w-CB-a591-3
Sample_119176

value: 8 weeks


title: 119177_CTGAAGCT-AGGCTATA

description:
8w-CB-a588-3
Sample_119177


title: 119175_GAATTCGT-ACGTCCTG

description:
8w-CB-a594-2
Sample_119175


title: HUVEC,mycBirA, MOI15,rep4

city: Helsinki

first: Juuso

last: Taskinen

address: Tukholmankatu 8

institute: Minerva Foundation Institue for Medical Research

data_processing:
NovaSeq Control Software v1.7
Illumina bcl2fastq program version 2.20
Assembly: GRCh38
Supplementary files format and content: .TSV files contain tab separated count data for features

source_name: vascular

extract_protocol:
Used Qiagen RNAeasy min kit and DNAse 1 digestion
NEB Next Ultra RNA Library Prep Kit

treatment_protocol: ORP7 inhibitor CpdG 10 uM or DMSO 1:1000 24h. Overexpression constructs were transfected with lentiviruses at aporx MOI of 15 and grown to passage 6.

value: vascular

tag: cell type

value: HUVEC

value: oexmycBirA

value: mycBirA


title: 180-Smoking-PBS-2 US84403582_252800518902_S01_GE1_107_Sep09_1_2

value: Smoking


title: HUVEC,mycBirA, MOI15,rep3

tag: treatment


title: 119178_CTGAAGCT-GCCTCTAT

description:
16w-CB-a559-4
Sample_119178

value: WT

value: WT-Veh


title: 180-Smoking-PBS-2 US84403582_252800518903_S01_GE1_107_Sep09_1_2


title: sample_7921


title: 119174_GAATTCGT-TAAGATTA

description:
8w-CB-a592-1
Sample_119174

value: Cerebellum


title: 119173_GAATTCGT-CTTCGCCT

description:
8w-CB-a593-0
Sample_119173


title: sample_7925


title: HUVEC,mycBirA, MOI15,rep2


title: sample_7919


title: sample_7924


title: PC3 OE GFP rep2 [methylation]

source_name: PC3 overexpresion GFP

value: overexpresion GFP

tag: gender

value: Male

value: prostate cancer

value: tumor


title: 180-Smoking-PBS-2 US84403582_252800518901_S01_GE1_107_Sep09_1_2

value: female

value: PBS

value: C57BL/6j mouse


title: 119172_GAATTCGT-TCAGAGCC

description:
8w-CB-a591-7
Sample_119172


title: sample_7923

value: feces

value: yes


title: 180-Smoking-Anhui-2 US84403582_252800518903_S01_GE1_107_Sep09_1_1

value: Anhui


title: HUVEC,mycBirA, MOI15,rep1

value: vascular

value: HUVEC


title: sample_7776


title: 180-Smoking-Anhui-2 US84403582_252800518901_S01_GE1_107_Sep09_1_1


title: HUVEC,ORP7-mycBirA, MOI15,rep4


title: 90-Air-PBS-5 US84403582_252800518877_S01_GE1_107_Sep09_2_4

value: Air


title: sample_7775


title: 180-Smoking-Anhui-2 US84403582_252800518902_S01_GE1_107_Sep09_1_1

value: Smoking


title: 90-Air-PBS-5 US84403582_252800518876_S01_GE1_107_Sep09_2_4


title: 119171_GAATTCGT-AGGATAGG

description:
8w-CB-a590-0
Sample_119171

value: 8 weeks

value: WT


title: PC3 OE GFP rep1 [methylation]

tag: sample type


title: HUVEC,ORP7-mycBirA, MOI15,rep3


title: 119170_GAATTCGT-GCCTCTAT

description:
8w-CB-a587-9
Sample_119170

value: Cerebellum


title: 90-Air-PBS-5 US84403582_252800518875_S01_GE1_107_Sep09_2_4


title: sample_7773


title: sample_7768


title: HUVEC,ORP7-mycBirA, MOI15,rep2


title: 119168_ATTCAGAA-GTCAGTAC

description:
8w-CB-a588-2
Sample_119168


title: sample_7767


title: 119169_GAATTCGT-AGGCTATA

description:
8w-CB-a594-3
Sample_119169


title: HUVEC,DMSO 1:1000, 24h,rep4

value: Wild type


title: HUVEC,ORP7-mycBirA, MOI15,rep1


title: sample_7766


title: 119166_ATTCAGAA-TAAGATTA

description:
65w-BS-a425-3
Sample_119166

source_name: Brain Stem

value: Brain Stem

value: 65 weeks


title: 119167_ATTCAGAA-ACGTCCTG

description:
8w-CB-a588-0
Sample_119167


title: HUVEC,DMSO 1:1000, 24h,rep3


title: sample_7765


title: 90-Air-Anhui-5 US84403582_252800518877_S01_GE1_107_Sep09_2_3


title: 119165_ATTCAGAA-CTTCGCCT

description:
65w-BS-a425-2
Sample_119165


title: sample_4473


title: HUVEC,DMSO 1:1000, 24h,rep1


title: HUVEC,DMSO 1:1000, 24h,rep2


title: sample_4472


title: 90-Air-Anhui-5 US84403582_252800518876_S01_GE1_107_Sep09_2_3


title: sample_4470


title: 119164_ATTCAGAA-TCAGAGCC

description:
65w-BS-a499-2-3
Sample_119164


title: HUVEC,CpdG 10 uM, 24h,rep3

value: CpdG 10 uM


title: HUVEC,CpdG 10 uM, 24h,rep4


title: 119163_ATTCAGAA-AGGATAGG

description:
65w-BS-a500-1
Sample_119163


title: 119161_ATTCAGAA-AGGCTATA

description:
65w-BS-a463-4
Sample_119161


title: 90-Air-Anhui-5 US84403582_252800518875_S01_GE1_107_Sep09_2_3

value: female


title: 119162_ATTCAGAA-GCCTCTAT

description:
65w-BS-a468-2
Sample_119162


title: sample_4471


title: 90-Smoking-PBS-5 US84403582_252800518876_S01_GE1_107_Sep09_2_2

value: PBS


title: sample_4469

value: no


title: 119160_GAGATTCC-GTCAGTAC

description:
65w-BS-a421-4
Sample_119160


title: 90-Smoking-PBS-5 US84403582_252800518875_S01_GE1_107_Sep09_2_2

value: C57BL/6j mouse


title: 90-Smoking-PBS-5 US84403582_252800518877_S01_GE1_107_Sep09_2_2


title: HUVEC,CpdG 10 uM, 24h,rep1


title: sample_4262

value: feces


title: 119159_GAGATTCC-ACGTCCTG

description:
65w-BS-a427-0
Sample_119159


title: HUVEC,CpdG 10 uM, 24h,rep2


title: 90-Smoking-Anhui-5 US84403582_252800518875_S01_GE1_107_Sep09_2_1

value: Anhui


title: 119158_GAGATTCC-TAAGATTA

description:
65w-BS-a424-5
Sample_119158


title: 90-Smoking-Anhui-5 US84403582_252800518877_S01_GE1_107_Sep09_2_1


title: 90-Air-PBS-2 US84403582_252800518877_S01_GE1_107_Sep09_1_4


title: HIO Mut Ile 35d Rep 2

city: Cincinnati

first: Jim

middle: M

last: Wells

state: Ohio

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Childrens Hospital

data_processing:
RNA-seq data was analyzed using Computational Suite for Bioinformaticians and Biologists (CSBB – v3.0.0) using the Process-RNASeq_PairedEnd and Generate-TPM_Counts_Matrix modules (https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists).
Assembly: hg38
Supplementary files format and content: tab-delimited text files including TPM per sample

source_name: hPSC-derived intestinal organoid

extract_protocol:
RNA was extracted using RNA NucleoSpin kit (Macherey-Nagel) according to manufacturer's instructions. >300 ng/sample of RNA used to make RNA library.
Library construction was performed by CCHMC DNA sequencing core using standard Illumina mRNA Stranded Library Preperation protocol.

value: hPSC-derived intestinal organoid

value: Pooled organoids epithelium and mesenchyme

tag: age

value: 35 days post-hPSC

value: No Treatment


title: 90-Air-PBS-2 US84403582_252800518876_S01_GE1_107_Sep09_1_4

value: Air


title: 90-Smoking-Anhui-5 US84403582_252800518876_S01_GE1_107_Sep09_2_1

value: Smoking


title: sample_4087

city: Berlin


title: 119157_GAGATTCC-CTTCGCCT

description:
65w-BS-a423-4
Sample_119157

tag: time

value: WT


title: sample_4260


title: HIO Mut Duo 35d Rep 3


title: sample_4085


title: HIO Mut Duo 35d Rep 2


title: sample_4086


title: 90-Air-PBS-2 US84403582_252800518875_S01_GE1_107_Sep09_1_4

tag: animal #


title: 119156_GAGATTCC-TCAGAGCC

description:
65w-BS-a420-0
Sample_119156


title: HIO Mut Ile 35d Rep 3


title: sample_4261


title: 119154_GAGATTCC-GCCTCTAT

description:
16w-BS-a557-6
Sample_119154

value: 16 weeks


title: 119155_GAGATTCC-AGGATAGG

description:
65w-BS-a421-1
Sample_119155

value: Brain Stem


title: HIO Mut Duo 35d Rep 1


title: sample_4084


title: HIO WT Ile 35d Rep 3


title: 119153_GAGATTCC-AGGCTATA

description:
16w-BS-a580-5
Sample_119153


title: sample_4083


title: HIO WT Ile 35d Rep 2


title: sample_4082


title: 119152_CGCTCATT-GTCAGTAC

description:
16w-BS-a556-2
Sample_119152


title: HIO Mut Ile 35d Rep 1


title: 119151_CGCTCATT-ACGTCCTG

description:
16w-BS-a579-0
Sample_119151


title: Il33-/- Spn. 60hpi (abx 30h+)

data_processing:
cellranger pipeline
seurat matrix files
integration
clustering
seurat pipeline (script attached)
Assembly: mm10
Supplementary files format and content: matrix files to analyse in seurat or other packages

extract_protocol:
10x extract protocol
10x library construction protocol

value: lung

value: Spn. 60hpi (abx 30h+)


title: 119149_CGCTCATT-CTTCGCCT

description:
16w-BS-a576-2
Sample_119149


title: 90-Air-Anhui-2 US84403582_252800518877_S01_GE1_107_Sep09_1_3

value: female

tag: exposure days


title: HIO WT Duo 35d Rep 3


title: Il33-/- Spn. 36hpi

value: Spn. 36hpi


title: wt Spn. 60hpi (abx 30h+)


title: HIO WT Duo 35d Rep 2


title: 90-Smoking-PBS-2 US84403582_252800518875_S01_GE1_107_Sep09_1_2

tag: smoking or air

value: PBS


title: 90-Smoking-PBS-2 US84403582_252800518876_S01_GE1_107_Sep09_1_2

tag: day

value: C57BL/6j mouse


title: 119148_CGCTCATT-TCAGAGCC

description:
16w-BS-a580-6
Sample_119148

tag: tissue


title: 90-Air-Anhui-2 US84403582_252800518876_S01_GE1_107_Sep09_1_3


title: 90-Smoking-Anhui-2 US84403582_252800518877_S01_GE1_107_Sep09_1_1


title: HIO WT Duo 35d Rep 1


title: 90-Smoking-PBS-2 US84403582_252800518877_S01_GE1_107_Sep09_1_2


title: 119147_CGCTCATT-AGGATAGG

description:
16w-BS-a579-3
Sample_119147

tag: genotype


title: 90-Air-Anhui-2 US84403582_252800518875_S01_GE1_107_Sep09_1_3

tag: strain


title: HIO WT Ile 35d Rep 1

tag: cell line


title: 119146_CGCTCATT-GCCTCTAT

description:
16w-BS-a577-0
Sample_119146


title: 119150_CGCTCATT-TAAGATTA

description:
16w-BS-a580-3
Sample_119150


title: keloid, k3

city: Nagoya

first: Mayumi

last: Oishi

address: Tsurumaicho 65

department: Plastic and Reconstructive Surgery

institute: Nagoya University Graduate School of Medicine

data_processing:
RNA-seq Analysis Portal 2.0 powered by QIAGEN CLC Genomics Workbench
Demultiplex of QIAseq UPX 3' reads was performed using CLC Genomics Workbench Biomedical Plugin. (parameter- Allow mismatches: No)
Quantification was performed using RNA-seq Analysis Portal 2.0 (Analysis workflow versions v1.1)
Assembly: hg38
Supplementary files format and content: comma-separated text files include RPKM and TPM values for each sample

source_name: keloid

extract_protocol:
Frozen sections of immature scars and keloids were stained with TAGLN. TAGLN-positive areas were collected from serial sections by manual dissection. The total RNA from the obtained tissue was extracted by ReliaPrep RNA Tissue Miniprep System (Promega, Madison, WI, USA). 10ng of total RNA was used for the construction of sequencing libraries.
Libraries were constructed using the QIAseq UPX 3' Transcriptome Kit (QIAGEN, Hilden, Germany) following the manufacturer’s protocols.

value: keloid


title: 90-Smoking-Anhui-2 US84403582_252800518876_S01_GE1_107_Sep09_1_1

tag: Sex

value: Anhui


title: Il33-/- Spn. 12hpi

tag: strain background

value: Spn. 12hpi


title: wt Spn. 12hpi


title: 119145_CGCTCATT-AGGCTATA

description:
16w-BS-a558-0
Sample_119145

value: WT-Veh


title: 30-Air-PBS-5 US84403582_252800518909_S01_GE1_107_Sep09_2_4


title: 90-Smoking-Anhui-2 US84403582_252800518875_S01_GE1_107_Sep09_1_1


title: immature scar, s2

source_name: immature scar

value: immature scar


title: Il33-/- + pbs

value: pbs


title: 30-Air-PBS-5 US84403582_252800518907_S01_GE1_107_Sep09_2_4

value: Air


title: 119144_TCCGGAGA-GTCAGTAC

description:
16w-BS-a557-4
Sample_119144


title: 30-Air-PBS-5 US84403582_252800518908_S01_GE1_107_Sep09_2_4


title: 119143_TCCGGAGA-ACGTCCTG

description:
16w-BS-a556-3
Sample_119143


title: KO4 [10C]

data_processing:
cellranger pipeline
Seurat integration
Assembly: mm10
Supplementary files format and content: matrix files to analyse in seurat or other packages

extract_protocol:
Direct-zol RNA Microprep
Library preparation, Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input

value: KO


title: wt + pbs

value: WT


title: 30-Air-Anhui-5 US84403582_252800518908_S01_GE1_107_Sep09_2_3


title: keloid, k1


title: HIO Mut-Dox In vivo TXP Rep 3

data_processing:
RNA-seq data was analyzed using Computational Suite for Bioinformaticians and Biologists (CSBB – v3.0.0) using the Process-RNASeq_PairedEnd and Generate-TPM_Counts_Matrix modules (https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists).
Assembly: hg38 iPSC RNA-seq
Supplementary files format and content: tab-delimited text files including TPM per sample

value: hPSC-derived intestinal organoid

value: Pooled organoids epithelium and mesenchyme

value: 35 days post-hPSC + 10wk transplant

value: Doxycycline in vivo


title: HIO Mut-Dox In vivo TXP Rep 2


title: 30-Air-Anhui-5 US84403582_252800518909_S01_GE1_107_Sep09_2_3

value: female


title: 119141_TCCGGAGA-CTTCGCCT

description:
16w-BS-a559-4
Sample_119141

value: Brain Stem

value: 16 weeks


title: KO2 [8C]

value: lung


title: 119142_TCCGGAGA-TAAGATTA

description:
16w-BS-a562-0
Sample_119142


title: keloid, k2

value: keloid


title: 119140_TCCGGAGA-TCAGAGCC

description:
8w-BS-a594-2
Sample_119140

value: 8 weeks


title: wt Spn. 36hpi

value: Spn. 36hpi


title: HIO Mut-Dox In vivo TXP Rep 1


title: 119139_TCCGGAGA-AGGATAGG

description:
8w-BS-a593-0
Sample_119139


title: KO3 [9C]


title: immature scar, s1


title: 30-Air-Anhui-5 US84403582_252800518907_S01_GE1_107_Sep09_2_3

value: Anhui

value: C57BL/6j mouse


title: HIO Mut-Dox In vitro TXP Rep 3

value: Doxycycline in vitro


title: WT3 [5C]


title: KO1 [7C]


title: 119138_TCCGGAGA-GCCTCTAT

description:
8w-BS-a588-3
Sample_119138


title: WT2 [3C]


title: HIO Mut-Dox In vitro TXP Rep 2


title: 30-Smoking-PBS-5 US84403582_252800518907_S01_GE1_107_Sep09_2_2

value: Smoking

value: PBS


title: 119137_TCCGGAGA-AGGCTATA

description:
8w-BS-a592-1
Sample_119137


title: 30-Smoking-PBS-5 US84403582_252800518909_S01_GE1_107_Sep09_2_2


title: 30-Smoking-Anhui-5 US84403582_252800518909_S01_GE1_107_Sep09_2_1


title: 30-Smoking-PBS-5 US84403582_252800518908_S01_GE1_107_Sep09_2_2


title: HIO Mut-Dox In vitro TXP Rep 1


title: 119136_ATTACTCG-GTCAGTAC

description:
8w-BS-a591-3
Sample_119136


title: WT1 [2C]

value: WT


title: 119135_ATTACTCG-ACGTCCTG

description:
8w-BS-a591-1
Sample_119135


title: HIO Mut-No Dox TXP Rep 2

value: hPSC-derived intestinal organoid

value: No Treatment