title: esophageal squamous cell para-carcinoma, biol rep 6

city: Wuhan

first: Lijuan

last: Gao

address: Luojiashan

institute: Wuhan University

data_processing:
Use FastQC to control the base quality, GC content, adapter content, etc. of the data, and generate a sequencing quality report
Use Trimmomatic data filtering to re-evaluate the quality. Data filtering mainly filters low-quality reads that contain too many N
Align reads1 and reads2 with the reference genome using bismark to obtain bam files and summaries of methylation information
Use samtools to sort, index, view bam files in igv
Assembly: hg19
Supplementary files format and content: the methylation rate of the promoter CpG island for each Sample

organism: unidentified

source_name: esophageal squamous cell

extract_protocol:
Specifically, hippocampal tissues were incubated with tissue lysis buffer ( 10 mM Tris pH 8.0, 100 mM NaCl, 10 mM EDTA pH 8.0, 10% SDS) containing proteinase K at 56℃overnight, and DNA was extracted by phenol-chloroform and quantified by NanoDrop2000.
The genomic DNA was bisulfite converted using EZ DNA Methylation-Gold™ Kit (ZYMO) according to the manufacturer’s instruction. The bisulfite-converted DNA was amplified with primers specific for the NR2B gene promoter region.

value: esophageal squamous cell para-carcinoma

value: esophageal squamous cell


title: CowO10

status: Public on Jun 20 2025

type: SRA

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

country: USA

institute: Medical University of South Carolina

description: Bulk RNA-seq

library_source: transcriptomic

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Rat reference was used for gene annotation and counting (mRatBN7.2). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: mRatBN7.2
Supplementary files format and content: Input tables are included as tab separated files.

molecule: total RNA

organism: Rattus norvegicus

source_name: Sprague Dawley

extract_protocol:
Tissue was processed for RNA extraction using a modified manufacturer’s procedure (miRNA Easy Kit, Qiagen)
Tissue was processed for RNA extraction using a modified manufacturer’s procedure (miRNA Easy Kit, Qiagen). Frozen samples were sent to BGI Americas Cooperation (Cambridge, MA) and sequencing was performed using polyA mRNA directional RNA-seq library preparation using a DNBSEQTM platform.

tag: strain

value: Sprague Dawley

tag: treatment

value: Saline

tag: genotype

value: eGFP

tag: time

value: 13-15 weeks


title: HMLE-TWIST1_150nm-D2_1

city: Boston

first: Gracia

middle: M.

last: Bonilla

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Illumina software used for basecalling.
Reads were mapped using the STAR aligner (Dobin, Davis et al. 2013) and the hg19 assembly of the human genome.
Read counts for individual transcripts were obtained using HTSeq (Anders, Pyl et al. 2014) and the Ensembl GRCh37 release 75 gene annotation.
Analysis of differential expression was performed using only genes with normalized counts (CPM) >=1 in at least one sample
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with RPKM normalized counts for every gene and every sample

organism: Homo sapiens

growth_protocol: HMLE cells and HMLE-TWIST cells were cultured in 10 cm dish with mammary epithelial growth (MEGM) medium plus DMEM/F12 medium with 10% FCS and penicillin/streptomycin (P/S) (3:7).

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) following the manufacturer’s protocol and concentrated by ethanol precipitation. Column purification of 50µg of extracted RNA was performed using RNeasy Mini kits (Qiagen, 74106), with minor modifications to the manufacturer’s protocol, including an extension of on-column DNase treatment from 15 to 30 minutes. For each sample, 1µg of RNA was used to generate libraries using SMARTer Stranded Total RNA Sample Prep kits (Takara, 634876), with integrated RiboGone enzymatic rRNA depletion.
RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA Sample Prep kits (Takara, 634876) protocols

treatment_protocol: HMLE and HMLE-TWIST cells were treated in 3 ways; 1) Three replicates were treated with different doses of chaetocin (0, 100, 150, 200, 500nM) for 48h; 2) Three replicates were treated with 80 nM of chaetocin for 15 h and washed out, and then cells were incubated with fresh medium for additional 48h; 3) Three replicates were transfected with DsiRNA against SUV39H1/H2 genes for 48h, and then cells were incubated with fresh medium for additional 48h.

tag: cell line

tag: cell type

value: Mammary gland epithelial cells

tag: tissue

value: Breast

value: overexpressing TWIST1

value: 150 nm Chaetocin for 2 days


title: H3K9me3_HMLE_KD_3

description: Immunoprecipitated (IP) DNA

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome using BWA version 0.7.15
bigWig files were generated using the deepTools bamCompare command by comparing ChIP with Input, normalizing using CPM, and with bin size of 100, and smooth length of 300
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: HMLE

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were made from 5ng of ChIP DNA using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) or 1ng of ChIP DNA using Nextera XT DNA Library Prep kit (Illumina).

treatment_protocol: H3K9me3 ChIP-seq of HMLE and HMLE-TWIST1 cells  treated DMSO or 80nM chaetocin for two days, after which the cells were washed and incubated in chaetocin-free media for an additional two days (n=3). Also, H3K9me3 ChIP-seq of HMLE and HMLE-TWIST1 cells in which SUV39H1/H2 were knocked down using DsiRNAs for two after which the cells were incubated for an additional two days (n=3). Next generation high throughput sequencing libraries were then generated.

value: HMLE

value: Wild type

tag: chip antibody

value: H3K9me3 antibody (ab8898)

value: SUV39H1/H2 DsiRNA for 2 days


title: Cd4cre-3

city: Beijing

first: Ying

last: Liu

address: Tiantan street, Tiantan Xili 2rd

department: Institute of Medicinal Biotechnology

country: China

institute: Chinese Academy of Medical Sciences

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Mus musculus

source_name: spleen

extract_protocol:
CD8+ T cells were collected from spleen of Cd4cre or Cd4creGlut10fl/fl mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: primary

value: CD8 + T cell


title: Targeted DMS-MaPseq analysis of TXNL4A 5′ UTR, replicate 2

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description:
Library name: TXNL4A_targeted_rep2
Instrument: Illumina iSeq 100

data_processing:
Following sequencing, paired-end reads were clipped of sequencing adapters using Cutadapt (parameters: -A AGATCGGAAG -a AGATCGGAAG -m 75:75 -O 1), and merged using PEAR (parameters: -n 75 -q 20 -u 0 -e -y 10G -z). Merged reads were then combined with R1 and the reverse-complemented R2 for read pairs that could not be merged. Reads were then mapped to a reference containing the sole TXNL4A 5′ UTR+CDS using the rf-map tool of the RNA Framework and Bowtie2, after clipping terminal bases with Phred quality < 20, and discarding reads containing internal Ns (parameters: -b2 -cq5 20 -ctn -cmn 0 -mp "--very-sensitive-local" -bnr). Alignments in SAM format were sorted and converted to BAM format using Samtools. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage) and MM files (containing a map of mutated positions per read). Aligned reads spanning less than 100 nt, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1).
Supplementary files format and content: Wiggle files of DRACO-deconvolved normalized DMS-MaPseq mutation frequencies for the 2 conformations (c0 and c1).

molecule: cytoplasmic RNA

growth_protocol: Human HEK293 cells were cultured in high glucose DMEM medium (cat. L0104, Biowest), supplemented with 10% fetal bovine serum (FBS) (cat. H1138, Merck), 25 U/mL penicillin and 25 μg/mL streptomycin, at 37°C and 5% CO2.

extract_protocol:
Cell pellets were immediately lysed by direct addition of 1 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific). RNA was extracted as per manufacturer instructions. Residual gDNA was removed by digestion with TURBO DNase I (cat. AM2239, ThermoFisher Scientific) at 37°C for 30 min.
Targeted DMS-MaPseq analysis of CKS2 and TXNL4A 5′ UTRs was performed by using total RNA from HEK293 transfected for 24 h with the pEF6 vector carrying the wild type 5′ UTR sequences and probed with 150 mM DMS for 2 min at 37°C. Reverse transcription was carried out using gene-specific reverse transcription primers targeting the CDS of EGFP, harboring the reverse complemented Illumina 3′ adapter.  3 μg RNA were supplemented with 2 μl 10 μM gene-specific RT primer and 2 μl 10 mM dNTPs. RNA was incubated at 70°C for 5 min, and then snap-cooled on ice for 1 min. Samples were supplemented with 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, 200 U TGIRT™-III Enzyme, and incubated 10 min at 50°C, 1 h at 57°C and 1 h at 60°C. RT reactions were performed in a final volume of 20 μl. The TGIRT™-III-RNA-cDNA complex was destroyed by addition of 1 μl 10 M NaOH, followed by incubation at 95°C for 3 min. Reactions were cleaned up on Monarch® Spin RNA Cleanup columns, as per manufacturer instructions. Addition of the Illumina 5′ adapter and barcoding were performed simultaneously by PCR, using 0.5 μM of i5 and i7 multiplexing primers, 0.025 μM of gene-specific forward primer harboring the Illumina 5′ adapter, and the NEBNext® Ultra™ II Q5® Master Mix, as per manufacturer instructions.

treatment_protocol: Dimethyl sulfate (DMS; cat. D186309, Merck) from a fresh 1:4 dilution in ethanol (~2.64 M) was directly added to the cells at a final concentration of 150 mM. Probing was conducted for 2 min at 37°C. Reactions were then quenched by addition of 1 volume 1 M DTT, after which cells were collected by centrifugation at 5,000g for 1 min.


title: H3K9me3_HMLE_KD_2

description: Immunoprecipitated (IP) DNA


title: HMLE-TWIST1_200nm-D2_3

value: 200 nm Chaetocin for 2 days


title: esophageal squamous cell para-carcinoma, biol rep 4

tag: disease

value: esophageal squamous cell para-carcinoma

value: esophageal squamous cell


title: H3K9me3_HMLE_KD_1

description: Immunoprecipitated (IP) DNA


title: esophageal squamous cell para-carcinoma, biol rep 3


title: DMS-MaPseq of HEK293 total RNA, replicate 2

description:
Library name: DMS-MaP_HEK293_totalRNA_rep2
Instrument: Illumina NextSeq 1000

data_processing:
Following sequencing, reads were clipped of sequencing adapters using Cutadapt (parameters: -a AGATCGGAAG -m 75 -O 1). Clipped reads were then mapped to a reference composed of 18S and 28S rRNA sequences, using the rf-map tool of the RNA Framework and Bowtie2, after clipping terminal bases with Phred quality < 20, and discarding reads containing internal Ns (parameters: -b2 -cq5 20 -ctn -cmn 0 -mp "--very-sensitive-local" -bnr). Alignments in SAM format were sorted and converted to BAM format using Samtools. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage). Aligned reads spanning less than 100 nt, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1).
Supplementary files format and content: Wiggle files of bulk normalized DMS-MaPseq mutation frequencies

extract_protocol:
Cell pellets were immediately lysed by direct addition of 1 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific). RNA was extracted as per manufacturer instructions. Residual gDNA was removed by digestion with TURBO DNase I (cat. AM2239, ThermoFisher Scientific) at 37°C for 30 min.
To mimic the same conditions used for the 5′UTR-MaP library preparation, 100 ng total RNA per sample were fragmented in 4 mM MgCl2, for 5.5 min at 94°C, and then cleaned up on Monarch® Spin RNA Cleanup columns, as per manufacturer instructions. 2′-3′-cyclic phosphates generated by chemical fragmentation were removed by treatment with 1 U rSAP, in a final volume of 20 μl, at 37°C for 30 min, followed by heat inactivation of the enzyme at 70°C for 5 min. Reactions were then supplemented with 20 U T4 Polynucleotide Kinase (cat. M0201L, New England Biolabs), 1 mM ATP, 5 mM DTT, in a final volume of 50 μl, and incubated at 37°C for 1 h. 5′-phosphorylated RNA fragments were then cleaned up on Monarch® Spin RNA Cleanup columns, and then subjected to adapter ligation, reverse transcription and PCR as for 5UTR-MaP libraries.


title: HMLE-TWIST1_100nm-D2_2

value: 100 nm Chaetocin for 2 days


title: HMLE-TWIST1_100nm-D2_1


title: H3K9me3_HMLE-TWIST_scr_3

description: Immunoprecipitated (IP) DNA

value: scramble siRNA for 2 days


title: Targeted DMS-MaPseq analysis of CKS2 5′ UTR, replicate 2

description:
Library name: CKS2_targeted_rep2
Instrument: Illumina iSeq 100

data_processing:
Following sequencing, paired-end reads were clipped of sequencing adapters using Cutadapt (parameters: -A AGATCGGAAG -a AGATCGGAAG -m 75:75 -O 1), and merged using PEAR (parameters: -n 75 -q 20 -u 0 -e -y 10G -z). Merged reads were then combined with R1 and the reverse-complemented R2 for read pairs that could not be merged. Reads were then mapped to a reference containing the sole CKS2 5′ UTR+CDS using the rf-map tool of the RNA Framework and Bowtie2, after clipping terminal bases with Phred quality < 20, and discarding reads containing internal Ns (parameters: -b2 -cq5 20 -ctn -cmn 0 -mp "--very-sensitive-local" -bnr). Alignments in SAM format were sorted and converted to BAM format using Samtools. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage) and MM files (containing a map of mutated positions per read). Aligned reads spanning less than 100 nt, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1).
Supplementary files format and content: Wiggle files of DRACO-deconvolved normalized DMS-MaPseq mutation frequencies for the 2 conformations (c0 and c1).


title: CowO11

description: Bulk RNA-seq

value: Sprague Dawley

value: Saline

value: 13-15 weeks


title: esophageal squamous cell para-carcinoma, biol rep 2


title: Targeted DMS-MaPseq analysis of CKS2 5′ UTR, replicate 1

description:
Library name: CKS2_targeted_rep1
Instrument: Illumina iSeq 100


title: esophageal squamous cell para-carcinoma, biol rep 1


title: Posterior hindlimb, mZRS446T>AZIC-hZRS446T>A, H3K27ac, rep2

city: Irvine

first: Evgeny

last: Kvon

state: CA

address: 836 Health Sciences Road

institute: University of California, Irvine

description: Library name: Sample32

data_processing:
Paired-end reads were aligned to the mm10 reference genome using Bowtie2 with the following parameters: -end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 70.
Samtools, version 1.15.1 was used to generate, sort and index bam files, from which bigwig files were generated using deeptools, version 3.5.1.
Assembly: Wild-type samples = mm10 reference genome Wild-type + reporter samples = A custom mm10 genome (mm10 reference and an extra chromosome for the hZRS transgene reporter). Knock-in + reporter samples = A custom mm10 genome (mm10 with variant mouse ZRS allele replacing the wild type ZRS at chromosome 5 and an extra chrosome for the hZRS transgene reporter)
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: FVB

extract_protocol:
Hindlimb cells were dissected, dissociated, sorted, and then immobilized onto ConA-magnetic beads. Following the CUT&Tag-direct protocol (version 4), bead-bound cells were incubated with primary and secondary antibodies then Tn5 for transposition. DNA libraries were then barcoded and indexed before being sequenced.
cDNA library construction was performed by Novogene and pair-end sequenced to an average depth of 25M reads per sample.

value: FVB

tag: reporter

tag: batch


title: H3K9me3_HMLE-TWIST_scr_1

description: Immunoprecipitated (IP) DNA

value: Mammary gland epithelial cells

value: Breast

value: overexpressing TWIST1


title: HMLE-TWIST1_DMSO-D2_3

value: DMSO for 2 days


title: Posterior hindlimb, mZRS446T>AZIC-hZRS446T>A, H3K27ac, rep1

description: Library name: Sample31


title: H3K9me3_HMLE_scr_3

description: Immunoprecipitated (IP) DNA

value: HMLE

value: Wild type

value: H3K9me3 antibody (ab8898)


title: HMLE-TWIST1_DMSO-D2_2


title: esophageal squamous cell carcinoma, biol rep 5

value: esophageal squamous cell carcinoma


title: esophageal squamous cell para-carcinoma, biol rep 5


title: Central hindlimb, mZRS446T>AZIC-hZRS446T>A, H3K27ac, rep2

description: Library name: Sample30


title: HMLE-TWIST1_DMSO-D2_1


title: esophageal squamous cell carcinoma, biol rep 6


title: HMLE-TWIST1_100nm-D2_3


title: esophageal squamous cell carcinoma, biol rep 4


title: Central hindlimb, mZRS446T>AZIC-hZRS446T>A, H3K27ac, rep1

description: Library name: Sample29


title: HMLE_DMSO-D2_3


title: H3K9me3_HMLE_scr_2

description: Immunoprecipitated (IP) DNA


title: H3K9me3_HMLE_scr_1

description: Immunoprecipitated (IP) DNA


title: Targeted DMS-MaPseq analysis of TXNL4A 5′ UTR, replicate 1

description:
Library name: TXNL4A_targeted_rep1
Instrument: Illumina iSeq 100


title: HMLE_DMSO-D2_2


title: Anterior hindlimb, mZRS446T>AZIC-hZRS446T>A, H3K27ac, rep2

description: Library name: Sample28


title: H3K9me3_HMLE-TWIST_scr_2

description: Immunoprecipitated (IP) DNA


title: IP_OX_REP3

city: Padova

first: Ilaria

middle: Rebecca

last: Maurizio

address: Via Gabelli, 63

department: Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Raw reads were quality checked using FastQC on Galaxy platform. Trimmomatic was apllied to remove adaptor sequences and to cut reads at 70bp in length.
Bowtie2 (v. 2.5.0) was used to align reads to the reference Mtb genome (NC_000962.3). Bigwig were generated using bamcoverage ( v.3.5.4).
Rmdup (v.2.0.1) was performed on aligned file before peak calling using Epic2.
Assembly: NC_000962.3
Supplementary files format and content: BigWig

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis

growth_protocol: Mtb culture was grown to early exponential phase,

extract_protocol:
Bacteria were fixed fixed with 1% formaldehyde for 10 minutes at 37°C. Glycine was added to quench the reaction. Bacteria were resuspended in Immunoprecipitation buffer and sonicated.
ChIP-seq samples were prepared using NEBNext Ultra II Library Prep kit for Illumina. IP, MOCK and INPUT samples were PCR amplified according to the amount of starting material. Libraries' quality and size was checked on Bioanalyzer 2100 with Agilent DNA High Sensitivity Chips.

treatment_protocol: Mtb culture were either grown at exponential phase without any treatment or either subjected to 5 mM H2O2 for 40 minutes.

value: Mycobacterium tuberculosis

tag: antibody

value: oxidative stress


title: esophageal squamous cell carcinoma, biol rep 1

value: esophageal squamous cell


title: IP_OX_REP2


title: INPUT_OX


title: HMLE_DMSO-D2_1


title: Anterior hindlimb, mZRS446T>A-hZRS446T>A, H3K27ac, rep2

description: Library name: Sample24


title: Anterior hindlimb, mZRS446T>AZIC-hZRS446T>A, H3K27ac, rep1

description: Library name: Sample27


title: Anterior hindlimb, mZRS446T>A-hZRS446T>A, H3K27ac, rep1

description: Library name: Sample23


title: Input_HMLE-TWIST_chaetocin_rep2

description: genomic DNA (INPUT)

value: Input DNA before adding antibody

value: 80 nm of chaetocin for 15 hours, then the cells were washed and placed in chaetocin-free media for an additional 2 days


title: Central hindlimb, mZRS446T>A-hZRS446T>A, H3K27ac, rep2

description: Library name: Sample26


title: Input_HMLE-TWIST_chaetocin_rep3

description: genomic DNA (INPUT)


title: esophageal squamous cell carcinoma, biol rep 2


title: Anterior hindlimb, mZRS404G>A-hZRS404G>A, H3K4me1, rep2

description: Library name: Sample22


title: Central hindlimb, mZRS446T>A-hZRS446T>A, H3K27ac, rep1

description: Library name: Sample25


title: CYM 1

city: Miami

first: Matthew

last: Tolerico

state: FL

address: 1580 NW 10th Ave

institute: University of Miami

description: Library name: CYM 1

data_processing:
Total RNA was quantified and qualified using the Nugen Universal Plus mRNA-Seq (M01442 v2) to have an RNA integrity score (RIN) above 7.
The quality of the reads was determined with FASTQC software for per base sequence quality, duplication rates, and overrepresented k-mers
Illumina adapters were trimmed from the ends of the reads using Trim Galore! package.
Gene count quantification for total RNA was performed using the GeneCounts function within STAR against the GENCODE vM35 transcript file.Gene count data were input into edgeR software for differential expression analysis, and gene counts were normalized against total aligned reads for each sample to generate counts per million (cpm) expression value for each gene in each sample.
Assembly: mm39
Supplementary files format and content: xlxs format with fold change and p values and raw counts

source_name: Col4a3-/- podocytes

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 1.5ug of total RNA was used to construct the sequencing libraries.
Total RNA was prepared with the Nugen Universal Plus mRNA-Seq (M01442 v2) using 100ng via Qubit and 15 cycles PCR.

value: Col4a3-/- podocytes

value: CYM


title: IP_OX_REP1


title: Input_HMLE-TWIST_DMSO_rep2

description: genomic DNA (INPUT)

value: DMSO for 15 hours, then the cells were washed and placed in DMSO-free media for an additional 2 days


title: CYM 3

description: Library name: CYM 3


title: Input_HMLE-TWIST_chaetocin_rep1

description: genomic DNA (INPUT)


title: APOM 2

description: Library name: APOM 2

value: APOM


title: Input_HMLE-TWIST_DMSO_rep1

description: genomic DNA (INPUT)

value: Mammary gland epithelial cells


title: CYM 2

description: Library name: CYM 2


title: Anterior hindlimb, mZRS404G>A-hZRS404G>A, H3K27ac, rep2

description: Library name: Sample20

value: FVB


title: INPUT_STD

value: standard growth


title: IP_STD_REP3


title: Anterior hindlimb, mZRS404G>A-hZRS404G>A, H3K4me1,rep1

description: Library name: Sample21


title: esophageal squamous cell carcinoma, biol rep 3


title: IP_STD_REP2


title: IP_STD_REP1


title: Input_HMLE-TWIST_DMSO_rep3

description: genomic DNA (INPUT)

value: Breast

value: overexpressing TWIST1


title: Input_HMLE_DMSO_rep3

description: genomic DNA (INPUT)

value: HMLE

value: Wild type


title: APOM 3

description: Library name: APOM 3


title: APOM 1

description: Library name: APOM 1


title: IgG_OX_REP3

data_processing:
Raw data were uploaded on the Galaxy platoform and togheter with R studio (version ) were used to analyze sequencing data.
Reads quality was performed using FastQC. Reads underwent trimming with TrimGalore! (Galaxy Version 0.6.7) were aligned to Mtb reference genome (NC_000962.3) with Bowtie2 (Galaxy Version 2.5.0)17 with -I 10 and -X 700 and default paired-end options.
Peaks were called against the IgG negative control using MACS2 (Galaxy Version 2.2.7.1). Peak detection was based on q-value of 0.05.
BEDTools intersect was employed to retain high confidence peaks among biological replicates.
Peaks annotation was performed using the ChippeakAnno package on R studio.
Assembly: NC_000962.3
Supplementary files format and content: Bigwig
Library strategy: CUT&Tag

growth_protocol: M. tuberculosis H37Rv virulent strain was grown at 37°C in Middlebrook 7H9 supplemented with 10% albumin-dextrose-sodium chloride complex , 0.2% glycerol and 0.05% Tween 80 and harvested at an early-mid exponential phase.

extract_protocol:
Bacteria were mildly fixed with 1% formaldehyde for 2 minutes at room temperature. Reaction was stopped by the addition of glycin. Fixed bacteria were washed with Wash buffer and subjected to CUT&Tag protocol
Library preparation was achived using pA-Tn5 adaptor complex.

treatment_protocol: Mtb colture have been treated for 40 minutes with 5 mM H2O2

value: IgG


title: Input_HMLE_DMSO_rep2

description: genomic DNA (INPUT)


title: IMAS 3

description: Library name: IMAS 3

value: Vehicle


title: IgG_OX_REP2

value: Mycobacterium tuberculosis

value: oxidative stress


title: IMAS 1

description: Library name: IMAS 1


title: Input_HMLE_DMSO_rep1

description: genomic DNA (INPUT)

value: Input DNA before adding antibody


title: IMAS 2

description: Library name: IMAS 2


title: Posterior hindlimb, ZIC2, rep2

description: Library name: Sample5

value: wild-type


title: H3K9me3_HMLE-TWIST_chaetocin_rep2

description: Immunoprecipitated (IP) DNA

value: H3K9me3 antibody (ab8898)

value: 80 nm of chaetocin for 15 hours, then the cells were washed and placed in chaetocin-free media for an additional 2 days


title: H3K9me3_HMLE-TWIST_chaetocin_rep3

description: Immunoprecipitated (IP) DNA


title: BG4_OX_REP3


title: Anterior hindlimb, mZRS404G>A-hZRS404G>A, H3K27ac, rep1

description: Library name: Sample19


title: Posterior hindlimb, ZIC2, rep3

description: Library name: Sample6


title: Posterior hindlimb, ZIC2, rep1

description: Library name: Sample4


title: BG4_OX_REP2


title: Heart, DOXO+anti-ACBP/DBI, replicate 2

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

description: Library name: D2

library_source: transcriptomic single cell

data_processing:
Data quality check with FastQC C57Bl/6J genome with HISAT2 (v. X.X.X).  The resulting SAM file was transformed into a count matrix with htseq-count, still using the GRCm38 reference genome.
Alignment with HISAT2 on GRCm38 genome.
Counts matrix generated with htseq-count.
Assembly: mm10
Supplementary files format and content: Barcodes and filtered barcodes in tsv files, which contain cellular barcodes present in dataset all or after filtering.
Supplementary files format and content: Features and filtered features in tsv files, which contain IDs of quantified genes before and after filtering. (Same complete features list for all samples, recorded as `LM72-All_mm10_features.tsv.gz` )
Supplementary files format and content: Count matrix in mtx file, where rows are associated with the aforementioned gene IDs and columns correspond to the cellular barcodes. Note that there are many zero values in this matrix.

molecule: nuclear RNA

source_name: Left ventricle

extract_protocol:
Chromium Nuclei Isolation with RNase Inhibitor Kit (10X Genomics; #1000494)
Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics; #1000269) following the Single cell 3' v. 3.1 Dual Index, revision E instruction booklet (10× Genomics, USA).

treatment_protocol: 8-week-old females, randomized to receive either anti- ACBP or the matching isotype control at 5 mg/kg i.p., and, on the next day, freshly dissolved doxorubicin (DOXO, 5 mg/kg i.p., Sigma #D1515) or saline vehicle, both once per week for 4 weeks. Animal were sacrificed one week after the last injection of DOXO.

value: Left ventricle

value: Doxorubicin 5 mg/kg (4 weeks, weekly i.p.) Anti-ACBP/DBI (4 weeks, weekly i.p.)


title: H3K9me3_HMLE-TWIST_chaetocin_rep1

description: Immunoprecipitated (IP) DNA

value: Mammary gland epithelial cells


title: Anterior hindlimb, ZIC2, rep3

description: Library name: Sample3

value: FVB


title: RNA_POL_OX_REP2

value: RNA polymerase


title: H3K9me3_HMLE-TWIST_DMSO_rep3

description: Immunoprecipitated (IP) DNA

value: Breast

value: DMSO for 15 hours, then the cells were washed and placed in DMSO-free media for an additional 2 days


title: RNA_POL_OX_REP3


title: IgG_OX_REP1


title: H3K9me3_HMLE-TWIST_DMSO_rep2

description: Immunoprecipitated (IP) DNA

value: overexpressing TWIST1


title: BG4_OX_REP1


title: Heart, DOXO, replicate 2

description: Library name: C2


title: Anterior hindlimb, ZIC2, rep2

description: Library name: Sample2


title: RNA_POL_OX_REP1


title: H3K9me3_HMLE-TWIST_DMSO_rep1

description: Immunoprecipitated (IP) DNA


title: IgG_STD_REP3

value: standard growth


title: Heart, DOXO, replicate 1

description: Library name: C1


title: H3K9me3_HMLE_DMSO_rep1

description: Immunoprecipitated (IP) DNA

value: HMLE

value: Wild type


title: Central hindlimb, mZRS446T>AZIC-hZRS446T>A, ATAC, rep2

description: Library name: Sample14

data_processing:
Paired-end reads were first trimmed using Fastp, version 0.23.2 and then mapped using Bowtie2, version 2.5.1 with the following parameters: --local --very-sensitive --no-mixed --no-discordant -I 25 -X 700.
Bam files were sorted and indexed using samtools, version 1.15.1, and converted to bigwig files for genome visualization using deeptools, version 3.5.1
Assembly: Wild-type + reporter samples = A custom mm10 genome (mm10 reference and an extra chromosome for the hZRS transgene reporter). Knock-in + reporter samples = A custom mm10 genome (mm10 with variant mouse ZRS allele replacing the wild type ZRS at chromosome 5 and an extra chrosome for the hZRS transgene reporter)
Supplementary files format and content: bigwig

extract_protocol:
Hindlimb cells were dissected, dissociated, sorted, and then lysed into nuclei. Nuclei were then incubated with Tn5 for the transposition reaction.
Transposased DNA was extracted and then indexed before being sequenced for 50M reads.


title: Anterior hindlimb, ZIC2, rep1

description: Library name: Sample1


title: Heart, anti-ACBP/DBI, replicate 2

description: Library name: B2

value: Vehicle (4 weeks, weekly i.p.) Mouse IgG2a 5 mg/kg (4 weeks, weekly i.p.)


title: Posterior hindlimb, mZRS446T>AZIC-hZRS446T>A, ATAC, rep1

description: Library name: Sample15


title: Heart, control, replicate 2

description: Library name: A2


title: Heart, DOXO+anti-ACBP/DBI, replicate 1

description: Library name: D1


title: BG4_STD_REP3

value: Mycobacterium tuberculosis


title: H3K9me3_HMLE_DMSO_rep2

description: Immunoprecipitated (IP) DNA


title: Central hindlimb, mZRS446T>AZIC-hZRS446T>A, ATAC, rep1

description: Library name: Sample13


title: RNA_POL_STD_REP3


title: Posterior hindlimb, mZRS446T>AZIC-hZRS446T>A, ATAC, rep2

description: Library name: Sample16


title: OX_REP 3

data_processing:
Reads were quaility checked using FastQC on Galaxy platform.
Aligment was performed using Hisat2 (v. 2.2.1) using paired-end option and Reverse strand information and --fr option for mate orientation.
Feature counts and gene length were obtained with FeatureCounts (v. 2.0.3) specifying reverse strand option.
Assembly: NC_000962.3
Supplementary files format and content: tab-delimited text file containing raw counts for each sample.

growth_protocol: Bacteria were grown at 37°C in Middlebrook 7H9 supplemented with 10% albumin- dextrose-sodium chloride complex (ADN), 0.2% glycerol and 0.05% Tween 80  and they were harvested at an early-mid exponential phase.

extract_protocol:
5mL of bacterial culture were samples were pelleted, resuspended in TRIzol® Reagent (InvitrogenTM), and transferred to 2-mL screw cap tubes containing Zirconia/Silica beads. To achieve cellular disruption three rounds of 35-second pulses in a Mini Bead Beater (BioSpec Products), with each pulse alternated with 35-second incubations on ice were performed. Samples were finally centrifuged at maximum speed for 15 minutes at 13200 rpm at 4°C and Direct-zol RNA MicroPrep kit was used for RNA extraction.
Qiagen QIAseq FastSelect – 5S/16S/23S was employed to perform rRNA depletion and stranded libraries were prepared using Illumina Stranded mRNA Prep.

treatment_protocol: Mtb cultures were exposed to 5 mM H2O2 for 40 min before being harvested.

value: oxidative stress


title: Anterior hindlimb, mZRS446T>AZIC-hZRS446T>A, ATAC, rep2

description: Library name: Sample12


title: Heart, control, replicate 1

description: Library name: A1


title: IgG_STD_REP2

value: IgG


title: Anterior hindlimb, mZRS446T>AZIC-hZRS446T>A, ATAC, rep1

description: Library name: Sample11


title: Heart, anti-ACBP/DBI, replicate 1

description: Library name: B1


title: Ppp6r3 cKO testis_rep2

city: Jinan

first: Qian

last: Fang

state: Shandong

address: 44 Wenhua West RD. Lixia District

institute: Shandong University

data_processing:
RNA-seq data were trimmed and aligned to mouse genome (mm10), then Hisat2 was used to mapping the reads with default parameters.
DEseq2 was used to calculate the significant different genes under the parameters: adjust of p value < 0.05 and log2 fold change > 1.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: testis

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbard, CA, USA). RNA quantity and quality were determined with 2100 Bioanalyzer (Agilent Technologies).
RNA-Seq libraries was prepared using the KAPA Stranded mRNA-Seq kit (KAPA Biosystems, Wilmington, MA, USA), following the manufacturer's protocol

value: testis

value: Ppp6r3 cKO


title: H3K9me3_HMLE_DMSO_rep3

description: Immunoprecipitated (IP) DNA

value: H3K9me3 antibody (ab8898)


title: OX_REP 2


title: BG4_STD_REP2


title: Ppp6r3 cKO testis_rep1


title: OX_REP 1


title: Central hindlimb, mZRS446T>A-hZRS446T>A, ATAC, rep2

description: Library name: Sample10


title: Central hindlimb, mZRS446T>A-hZRS446T>A, ATAC, rep1

description: Library name: Sample9


title: RNA_POL_STD_REP2


title: STD_REP 3


title: IgG_STD_REP1


title: Wild type testis_rep2


title: BG4_STD_REP1


title: STD_REP 2


title: Anterior hindlimb, mZRS446T>A-hZRS446T>A, ATAC, rep2

description: Library name: Sample8


title: STD_REP 1


title: Anterior hindlimb, mZRS446T>A-hZRS446T>A, ATAC, rep1

description: Library name: Sample7


title: Wild type testis_rep1


title: MT963_CHD3_KO_D10_CNCC_ATAC_rep1

status: Public on Jun 19 2025

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: MT963_CHD3_KO_D10_CNCC_ATAC_rep1
ATAC-seq

data_processing:
[ChIP data processing step] ChIP-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
[ATAC data processing step]  ATAC-seq data were aligned to hg19 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg19 (homo sapiens)
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq

source_name: BIONi010-A clone 2.12 (CHD3-KO 1)

growth_protocol: Human iPSCs were plated on Geltrex LDEV-Free hESC-qualified Reduced Growth Factoer Basement Membrane Matrix and maintained in feeder-free, serum-free mTeSR plus medium in small clusters

extract_protocol:
[ChIP-seq library construction protocol] Barcoded libraries were made with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) using NEBNext Multiplex Oligos Dual Index Primers for Illumina (NEB, E7600S), and sequenced on Illumina NextSeq2000, producing 60 bp paired-end reads
[ATAC-seq library construction protocol]  ATAC-seq was performed using 50,000 cells per sample. Libraries were prepared using the ATAC-seq Kit (Active Motif, 53150) and sequenced on either Illumina NextSeq2000, producing 60 bp paired-end reads or Illumina NovaSeq X Plus producing 150 bp paired-end reads.

treatment_protocol: iPSCs were cultured with CNCC specification media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 5 μg/ml bovine insulin, 20 ng/ml EGF, and 20 ng/ml hFGF for 6 days. At day ~7 when early migratory CNCCs first appeared, the cells were transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, serum replacement grade, 20 ng/ml EGF, and 20 ng/ml hFGF for 7 days. After 14 full days of CNCC specification, the cells were maintained in an “early CNCC” state for up to 18 days for subsequent experiments, or immediately transitioned to CNCC late maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, 20 ng/ml EGF, 20 ng/ml hFGF, 3uM ChIRON 99021, and 50pg/mL BMP2.

value: BIONi010-A clone 2.12 (CHD3-KO 1)

value: day 10 cranial neural crest cell

value: cranial neural crest cell specification


title: MT966_CHD3_WT_D14_CHIP_MBD3_32

description:
Library name: MT966_CHD3_WT_D14_CHIP_MBD3_32
ChIP-seq

source_name: BIONi010-A clone 3.2 (CHD3-WT 1)

value: MBD3 Abcam AB157464

value: BIONi010-A clone 3.2 (CHD3-WT 1)

value: day 14 cranial neural crest cell


title: MT964_CHD3_KO_D10_CNCC_ATAC_rep2

description:
Library name: MT964_CHD3_KO_D10_CNCC_ATAC_rep2
ATAC-seq

source_name: BIONi010-A clone 3.5 (CHD3-KO 2)

value: BIONi010-A clone 3.5 (CHD3-KO 2)


title: Ppp6r3 cKO testis_rep3


title: MT967_CHD3_WT_D14_CHIP_MBD3_33

description:
Library name: MT967_CHD3_WT_D14_CHIP_MBD3_33
ChIP-seq

source_name: BIONi010-A clone 3.3 (CHD3-WT 2)

value: BIONi010-A clone 3.3 (CHD3-WT 2)


title: MT961_CHD3_WT_D10_CNCC_ATAC_rep1

description:
Library name: MT961_CHD3_WT_D10_CNCC_ATAC_rep1
ATAC-seq


title: Wild type testis_rep3


title: MT733_CHD3_KO_D0_CNCC_ATAC_rep2

description:
Library name: MT733_CHD3_KO_D0_CNCC_ATAC_rep2
ATAC-seq

value: induced pluripotent stem cell


title: MT957_CHD3_WT_D4_CNCC_ATAC_rep1

description:
Library name: MT957_CHD3_WT_D4_CNCC_ATAC_rep1
ATAC-seq

value: day 4 cranial neural crest cell


title: MT958_CHD3_WT_D4_CNCC_ATAC_rep2

description:
Library name: MT958_CHD3_WT_D4_CNCC_ATAC_rep2
ATAC-seq


title: MT959_CHD3_KO_D4_CNCC_ATAC_rep1

description:
Library name: MT959_CHD3_KO_D4_CNCC_ATAC_rep1
ATAC-seq


title: MT960_CHD3_KO_D4_CNCC_ATAC_rep2

description:
Library name: MT960_CHD3_KO_D4_CNCC_ATAC_rep2
ATAC-seq


title: MT729_CHD3_WT_D0_CNCC_ATAC_rep2

description:
Library name: MT729_CHD3_WT_D0_CNCC_ATAC_rep2
ATAC-seq


title: passage15 batch 3

city: Suwon-si

first: Youngho

last: Song

state: Gyeonggi-do

address: Room 25302, Engineering Building 2, 2066 Seobu-ro, Jangan-gu

department: School of Chemical Engineering

country: South Korea

institute: Sungkyunkwan University

description:
Library name: p15_3
Human dermal fibroblast, passage 15, replicate 3 (old group)

data_processing:
Sequence reads are trimmed for adapter sequence/low quality sequence (average Q20) using BBDuk).
Raw reads were aligned to the human reference genome(UCSC hg19) using Bowtie2.
Gene counts were calculated from aligned reads. Data were filtered to remove genes with zero or low counts and normalized using the TMM method in edgeR.
Differential gene expression was analyzed using the limma package in R. Genes with |log2 fold change| > 2 and p-value < 0.01 were considered significantly differentially expressed.
Assembly: UCSC hg19 (GRCh37)
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Skin

growth_protocol: hDFs were purchased from Lonza (Basel, Switzerland) and cultured in Dulbecco’s modified eagle's medium (DMEM; Gibco BRL) supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin/streptomycin at 37 °C with 5% CO₂. Culture media were changed every 2 days. Cells were harvested at passage 5 (p5) and passage 15 (p15) for RNA extraction.

extract_protocol:
Total RNA was extracted from cultured hDFs using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed with a Nanodrop 2000 (Thermo Fisher Scientific) and Agilent 4000 TapeStation. Only samples with RIN > 10 were used for sequencing.
RNA libraries were prepared using the QuantSeq 3’ mRNA-seq Library Prep Kit FWD for Illumina (Lexogen) following the manufacturer’s instructions. Sequencing was performed using the Illumina NextSeq 550 platform with single-end 75 bp reads.

treatment_protocol: No treatment was applied. Samples represent different cellular aging stages based on passage number.

value: Skin

value: human dermal fibroblast

tag: aging stage

value: passage 15 (p15)

value: Batch 3


title: MT965_CHD3_WT_D14_MBD3_CHIP_INPUT

description:
Library name: MT965_CHD3_WT_D14_MBD3_CHIP_INPUT
ChIP-seq input


title: passage5 batch 3

description:
Library name: p5_3
Human dermal fibroblast, passage 5, replicate 3 (young group)

value: passage 5 (p5)


title: RNA_POL_STD_REP1

value: Mycobacterium tuberculosis

value: RNA polymerase

value: standard growth


title: passage15 batch 1

description:
Library name: p15_1
Human dermal fibroblast, passage 15, replicate 1 (old group)

value: Batch 1


title: passage15 batch 4

description:
Library name: p15_4
Human dermal fibroblast, passage 15, replicate 4 (old group)

value: Batch 4


title: MT699_CHD3_WT_D0_CNCC_ATAC_rep1

description:
Library name: MT699_CHD3_WT_D0_CNCC_ATAC_rep1
ATAC-seq


title: MT703_CHD3_KO_D0_CNCC_ATAC_rep1

description:
Library name: MT703_CHD3_KO_D0_CNCC_ATAC_rep1
ATAC-seq

value: BIONi010-A clone 2.12 (CHD3-KO 1)


title: passage15 batch 2

description:
Library name: p15_2
Human dermal fibroblast, passage 15, replicate 2 (old group)

value: Batch 2


title: MT962_CHD3_WT_D10_CNCC_ATAC_rep2

description:
Library name: MT962_CHD3_WT_D10_CNCC_ATAC_rep2
ATAC-seq

value: day 10 cranial neural crest cell

value: cranial neural crest cell specification


title: hiPSC_7 cell line, dSMAD protocol, 28d differentiation, replicate 1

city: Ludwigshafen

first: Peter

last: Reinhardt

address: Knollstrasse

country: Germany

institute: AbbVie Deutschland GmbH & Co. KG

data_processing:
fastQC, multiQC
STAR alignment
FeatureCounts
retaining only genes expressed at >= 1 CPMs in at least 3 samples
GRCh38 (gencode v31)
Assembly: fastq files
Supplementary files format and content: raw counts

extract_protocol:
RNA was harvested using the RNeasy Plus Mini (Qiagen) Kit
Library preparation was performed with Illumina Stranded mRNA Prep, Ligation (20040534) and IDT for Illumina RNA UD Indexes Set A, B,C (20040553, 20040554, 20040555). The denaturation was carried out according to protocol A (Denature and Dilute Libraries Guide, Illumina).

tag: differentiation time

value: 28 days

tag: protocol

value: dSMAD


title: hiPSC_7 cell line, dSMAD protocol, 14d differentiation, replicate 3

value: 14 days


title: hiPSC_7 cell line, dSMAD protocol, 28d differentiation, replicate 4


title: hiPSC_7 cell line, dSMAD protocol, 28d differentiation, replicate 2


title: passage5 batch 2

description:
Library name: p5_2
Human dermal fibroblast, passage 5, replicate 2 (young group)

value: Skin


title: passage5 batch 1

description:
Library name: p5_1
Human dermal fibroblast, passage 5, replicate 1 (young group)

value: human dermal fibroblast


title: BMWi6D, snRNAseq

description: 10X Genomics

data_processing:
Demultiplexing, barcoded processing and gene counting were performed using CellRanger version 7.2
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: tab-separated values and matrix files

source_name: cell line

extract_protocol:
For single nuclei isolation, the cells were washed with cold DPBS (-/-). Each well was treated with 500 µL of lysis buffer (Table S5) on ice, and the samples were incubated for a duration of 15 min. The cells were scraped off and the resulting lysate was mixed with 1.4 mL washing buffer (Table S6). After the 10-minute centrifugation step at 4°C and 500 rcf, the cells were subjected to a second wash using 800 uL of washing buffer. Subsequently, the cells were resuspended in washing buffer containing 1:750 Sytox blue solution (Thermo Fisher). 65,000 nuclei (SytoxBlue+) were sorted on a BD FACSAria™ Fusion Flow Cytometer into 1.5 mL DNA LoBind tubes (Eppendorf) pre-coated with 20% BSA (Merck) in PBS pH 7.2 (ThermoFisher Scientific).
snRNAseq procedure were performed with the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x genomics) for generating Gel Beads-in-emulsion (GEMs), barcoding and cDNA amplification as well as the 3’ gene expression library according the manufacturer’s protocol for Chromium Next GEM Single Cell 3’ Dual Index Reagent Kits v3.1. The sorted nuclei suspensions were mixed with master mix (reverse transcriptase and template switch oligo) and loaded together with Next GEM Single Cell 3’ v3.1 Gel Beads and the Chromium Partitioning Oil in different wells of a Next GEM Chip G. After completion the GEM generation on the Chromium X instrument, GEMs were transferred and incubated in a SimpliAmp™ Thermal Cycler for generating cDNA. After a CleanUp with Recovery Agent and Dynabeads MyOne SILANE followed by a double washing step with final 80% ethanol (Merck) in nuclease-free water (ThermoScientific), cDNA was amplified with 13 PCR cycles and cleaned up with SPRIselect Reagent Kit (Beckman Coulter). cDNA QC and quantification were carried out with the High Sensitivity D5000 ScreenTape assay (Agilent) on a 4200 TapeStation. 25% of generated cDNA underwent enzymatic fragmentation, end repair and A-tailing, followed by double-sided size selection SPRIselect cleanup, before adapter ligation took place. After post ligation cleanup with SPRIselect, sample indexes are added by 13 PCR cycles and double-sided size selection purified final library for QC (average library fragment sizes) and quantification with D1000 ScreenTape assay (Agilent) on 4200 TapeStation. In addition, the library concentrations were measured with Qubit dsDNA High Sensitivity assay (ThermoFisher) on Qubit Flex Fluorometer to confirm the measured concentrations. Libraries were normalized first to 10 nM, then to 1 nM, pooled and denatured using 0.2 NaOH (Sigma-Aldrich) and 200 mM Tris-HCl (ThermoFisher). Finally, 1.8 pM of pooled and denatured library was sequenced on a NextSeq 550 (Illumina).

value: cell line

value: MAPTTM

value: hiPSCs, 6 days differentiation with BMP, MEK and WNT inhibition


title: BMWi, snRNAseq

description: 10X Genomics

value: final BMWi neurons, 14 days after replating


title: hiPSC_7 cell line, dSMAD protocol, 28d differentiation, replicate 3


title: hiPSC, snRNAseq

description: 10X Genomics

value: hiPSCs


title: iNGN2, snRNAseq

description: 10X Genomics

value: final iNGN2 neurons, 14 days after replating


title: hiPSC_7 cell line, dSMAD protocol, 14d differentiation, replicate 2


title: hiPSC_3 cell line, dSMAD protocol, 28d differentiation, replicate 4


title: hiPSC_3 cell line, dSMAD protocol, 28d differentiation, replicate 2


title: hiPSC_3 cell line, dSMAD protocol, 28d differentiation, replicate 3


title: hiPSC_7 cell line, dSMAD protocol, 14d differentiation, replicate 1


title: hiPSC_3 cell line, dSMAD protocol, 28d differentiation, replicate 1


title: hiPSC_3 cell line, dSMAD protocol, 14d differentiation, replicate 2


title: hiPSC_3 cell line, dSMAD protocol, 14d differentiation, replicate 3


title: hiPSC_3 cell line, dSMAD protocol, 14d differentiation, replicate 4


title: hiPSC_3 cell line, BMWi protocol, 28d differentiation, replicate 2

value: BMWi


title: hiPSC_3 cell line, BMWi protocol, 28d differentiation, replicate 3


title: passage5 batch 4

description:
Library name: p5_4
Human dermal fibroblast, passage 5, replicate 4 (young group)

value: passage 5 (p5)

value: Batch 4


title: hiPSC_3 cell line, dSMAD protocol, 14d differentiation, replicate 1


title: hiPSC_3 cell line, BMWi protocol, 21d differentiation, replicate 3

value: 21 days


title: hiPSC_3 cell line, BMWi protocol, 21d differentiation, replicate 2


title: hiPSC_3 cell line, BMWi protocol, 28d differentiation, replicate 1


title: hiPSC_3 cell line, BMWi protocol, 14d differentiation, replicate 4


title: hiPSC_7 cell line, dSMAD protocol, 14d differentiation, replicate 4


title: hiPSC_3 cell line, BMWi protocol, 21d differentiation, replicate 1


title: hiPSC_5 cell line, dSMAD protocol, 14d differentiation, replicate 1


title: hiPSC_5 cell line, dSMAD protocol, 14d differentiation, replicate 2


title: hiPSC_5 cell line, dSMAD protocol, 14d differentiation, replicate 4


title: hiPSC_3 cell line, BMWi protocol, 14d differentiation, replicate 3


title: hiPSC_5 cell line, dSMAD protocol, 14d differentiation, replicate 3


title: hiPSC_5 cell line, dSMAD protocol, 28d differentiation, replicate 4


title: hiPSC_3 cell line, BMWi protocol, 14d differentiation, replicate 2


title: hiPSC_5 cell line, BMWi protocol, 28d differentiation, replicate 3


title: hiPSC_5 cell line, dSMAD protocol, 28d differentiation, replicate 3


title: hiPSC_5 cell line, dSMAD protocol, 28d differentiation, replicate 1


title: hiPSC_5 cell line, BMWi protocol, 21d differentiation, replicate 2


title: hiPSC_5 cell line, BMWi protocol, 28d differentiation, replicate 1


title: hiPSC_5 cell line, BMWi protocol, 14d differentiation, replicate 3


title: hiPSC_5 cell line, BMWi protocol, 21d differentiation, replicate 1


title: hiPSC_5 cell line, BMWi protocol, 14d differentiation, replicate 4


title: hiPSC_5 cell line, BMWi protocol, 21d differentiation, replicate 3


title: hiPSC_5 cell line, dSMAD protocol, 28d differentiation, replicate 2


title: hiPSC_5 cell line, BMWi protocol, 14d differentiation, replicate 1


title: hiPSC_1 cell line, dSMAD protocol, 28d differentiation, replicate 3


title: hiPSC_5 cell line, BMWi protocol, 14d differentiation, replicate 2


title: hiPSC_1 cell line, dSMAD protocol, 28d differentiation, replicate 2


title: hiPSC_1 cell line, dSMAD protocol, 14d differentiation, replicate 3


title: hiPSC_5 cell line, BMWi protocol, 28d differentiation, replicate 2


title: hiPSC_1 cell line, dSMAD protocol, 14d differentiation, replicate 2


title: hiPSC_1 cell line, dSMAD protocol, 28d differentiation, replicate 1


title: hiPSC_1 cell line, dSMAD protocol, 14d differentiation, replicate 4


title: hiPSC_1 cell line, dSMAD protocol, 28d differentiation, replicate 4


title: hiPSC_1 cell line, dSMAD protocol, 14d differentiation, replicate 1


title: hiPSC_1 cell line, BMWi protocol, 28d differentiation, replicate 3


title: hiPSC_1 cell line, BMWi protocol, 28d differentiation, replicate 2


title: hiPSC_1 cell line, BMWi protocol, 28d differentiation, replicate 1


title: hiPSC_1 cell line, BMWi protocol, 21d differentiation, replicate 3


title: hiPSC_1 cell line, BMWi protocol, 21d differentiation, replicate 1


title: hiPSC_1 cell line, BMWi protocol, 14d differentiation, replicate 3


title: hiPSC_1 cell line, BMWi protocol, 14d differentiation, replicate 2


title: hiPSC_1 cell line, BMWi protocol, 14d differentiation, replicate 4


title: hiPSC_1 cell line, BMWi protocol, 21d differentiation, replicate 2


title: hiPSC_5_2_BMWi_frozen_NPC_final

data_processing:
fastQC, multiQC
STAR alignment
FeatureCounts
retaining only genes expressed at >= 1 CPMs in at least 3 samples
Assembly: GRCh38 (gencode v31)
Supplementary files format and content: raw counts

source_name: iPSC

value: iPSC

value: frozen


title: hiPSC_1 cell line, BMWi protocol, 14d differentiation, replicate 1


title: hiPSC_5_1_BMWi_frozen_NPC_final


title: hiPSC_5_4_BMWi_frozen_NPC_final


title: hiPSC_3_3_BMWi_frozen_NPC_final


title: hiPSC_5_3_BMWi_frozen_NPC_final


title: hiPSC_2_4_BMWi_frozen_NPC_final


title: hiPSC_3_1_BMWi_frozen_NPC_final


title: hiPSC_2_3_BMWi_frozen_NPC_final


title: hiPSC_3_2_BMWi_frozen_NPC_final


title: hiPSC_2_2_BMWi_frozen_NPC_final


title: hiPSC_2_1_BMWi_frozen_NPC_final


title: hiPSC_5_4_BMWi_final

value: fresh


title: hiPSC_3_4_BMWi_frozen_NPC_final


title: hiPSC_3_2_BMWi_final


title: hiPSC_5_3_BMWi_final


title: hiPSC_3_4_BMWi_final


title: hiPSC_3_3_BMWi_final


title: hiPSC_5_1_BMWi_final


title: hiPSC_5_2_BMWi_final


title: hiPSC_3_1_BMWi_final


title: hiPSC_2_3_BMWi_final


title: hiPSC_2_4_BMWi_final


title: iPSC_hiPSC_3_3

tag: medium


title: iPSC_hiPSC_3_1


title: hiPSC_2_1_BMWi_final


title: iPSC_hiPSC_1_2


title: hiPSC_2_2_BMWi_final


title: iPSC_hiPSC_2_3


title: iPSC_hiPSC_2_1


title: iPSC_hiPSC_1_3


title: iPSC_hiPSC_2_2


title: iNGN2_D2_hiPSC_2_1


title: iNGN2_D2_hiPSC_3_2


title: iNGN2_D2_hiPSC_1_1


title: iNGN2_D2_hiPSC_1_3


title: iNGN2_D2_hiPSC_3_1


title: iNGN2_NMMpls_final_hiPSC_2_2

value: final

value: NMM pls


title: iNGN2_NMMpls_final_hiPSC_2_3


title: iNGN2_NMMpls_final_hiPSC_1_1


title: iNGN2_NMMpls_final_hiPSC_3_2


title: iNGN2_NMMpls_final_hiPSC_2_1


title: iNGN2_D2_hiPSC_3_3


title: iNGN2_NMMpls_final_hiPSC_1_3


title: iNGN2_NMMmin_final_hiPSC_3_4

value: NMM min


title: iNGN2_NMMmin_final_hiPSC_3_3


title: iNGN2_NMMpls_final_hiPSC_3_1


title: iNGN2_NMMpls_final_hiPSC_1_2


title: iPSC_hiPSC_3_2


title: iNGN2_NMMmin_final_hiPSC_3_2


title: iPSC_hiPSC_1_1


title: iNGN2_NMMmin_final_hiPSC_2_1


title: iNGN2_NMMmin_final_hiPSC_3_1


title: iNGN2_NMMmin_final_hiPSC_1_1


title: BMWi_D8_hiPSC_2_1


title: iNGN2_D2_hiPSC_1_2


title: iNGN2_NMMmin_final_hiPSC_1_2


title: BMWi_D8_hiPSC_3_3


title: BMWi_D6_hiPSC_3_3


title: iNGN2_NMMmin_final_hiPSC_1_3


title: iNGN2_NMMpls_final_hiPSC_3_3


title: BMWi_D8_hiPSC_1_1


title: BMWi_D6_hiPSC_2_1


title: BMWi_D6_hiPSC_1_3


title: BMWi_D8_hiPSC_3_2


title: BMWi_NMMplsmin_final_hiPSC_1_1

value: NMM plsmin


title: BMWi_D6_hiPSC_3_1


title: BMWi_D6_hiPSC_1_2


title: BMWi_D6_hiPSC_1_1


title: BMWi_NMMplsmin_final_hiPSC_3_2


title: iNGN2_NMMmin_final_hiPSC_2_3


title: iNGN2_NMMmin_final_hiPSC_2_2


title: BMWi_NMMplsmin_final_hiPSC_3_1


title: BMWi_NMMmin_final_hiPSC_2_3


title: BMWi_NMMplsmin_final_hiPSC_1_2


title: BMWi_D6_hiPSC_3_2


title: BMWi_NMMmin_final_hiPSC_2_1


title: BMWi_NMMmin_final_hiPSC_2_2


title: BMWi_NMMmin_final_hiPSC_3_5


title: BMWi_NMMmin_final_hiPSC_3_3


title: BMWi_D8_hiPSC_3_1


title: BMWi_NMMmin_final_hiPSC_3_4


title: BMWi_NMMmin_final_hiPSC_3_2


title: BMWi_NMMmin_final_hiPSC_1_1


title: BMWi_D4_hiPSC_2_3


title: BMWi_NMMmin_final_hiPSC_1_3


title: BMWi_NMMmin_final_hiPSC_2_4


title: BMWi_D4_hiPSC_2_1


title: BMWi_D4_hiPSC_3_3


title: BMWi_D4_hiPSC_3_2


title: BMWi_D4_hiPSC_2_2


title: SAT, Pooled Patients, Obese, Rep6

first: William

middle: Robert

last: Scott

address: Hammersmith Hospital, Du Cane Road

department: Institute of Clinical Sciences

description:
Library name: Pool_16
10x Genomics

data_processing:
Raw sequencing data was de-multiplexed and analysed using CellRanger v5.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest) and bcl2fastq v2.20.0. Libraries were de-multiplexed with CellRanger mkfastq based on the sample indices (allowing 1 mismatch) and the CellRanger count pipeline was used to perform alignment against human genome GRCh38 (using STAR), filtering and counting UMIs (including introns).
Assembly: Human GRCh38-2020-A
Supplementary files format and content: Tab separated files containing genes and barcodes
Supplementary files format and content: matrix file containing counts

source_name: Periumbilical Adipose Tissue

extract_protocol:
AT nuclei from individual participants were pooled for library preparation and sequencing to increase efficiency, cohort diversity and study power. Pooled samples were separated by condition to avoid cross-over (4-5 samples/pool; total of 6 pools/group). Sample pools for each experimental group were processed through to sequencing in lean-obese-weight loss trios to minimise between group batch effects. For each participant sample, nuclei extraction was carried out as follows. Frozen human AT (~100mg) was cut into <0.2cm pieces and homogenised with 1ml of ice-cold lysis buffer (Tris-HCL 10mM (Invitrogen, 15567-027), NaCl 10mM (Invitrogen, AM9760G), MgCl2 3mM (Invitrogen, AM9530G), 0.1% NP40 (BioBasic, NDB0385), 0.2U/µl RNase inhibitor (Roche, 03335402001)) in a glass dounce homogeniser (Merck, T2690/P0485/P1110, 15 strokes, loose then tight pestles) on ice. Following homogenisation, samples were transferred through a 100µM cell strainer (Greiner Bio-One, 542000) into a pre-chilled tube using ART wide-bore tips (Thermo Scientific, 2079G). The filtered homogenate was then transferred to 1.5ml low DNA-bind tubes (Sarstedt, 72.706.700) and centrifuged at 500g and 4C for 5mins. After lipid/supernatant removal, the nuclei pellet was resuspended in 1ml wash buffer (PBS with 0.5% BSA (Invitrogen, AM2616) and 0.2U/µl RNase inhibitor), transferred to new 1.5ml low DNA-bind tubes and re-centrifuged at 500g and 4C for 5mins. After repeat lipid/supernatant removal, the nuclei pellet was resuspended in 300µl wash buffer containing DAPI (Thermo Scientific, 62248) at 0.1µg/ml to stain nuclei, and filtered through a 35µM cell strainer into a FACS tube (Falcon, 352235) on ice. Isolated nuclei from 4-5 samples from the same experimental group were pooled prior to sorting by flow cytometry. FACS was used to clean up residual debris and lipid from isolated nuclei, and to remove doublets. Pooled nuclei were sorted on a BD FACS Aria SORP. The sheath tank was bleach cleaned prior to each run and nuclease-Free PBS (1X) (Invitrogen, AM9625) was used for sheath fluid. The 405nm laser was used to excite DAPI and emission was collected using a 450/50nm bandpass filter. Single nuclei were selected by gating on the first DAPI positive band on the DAPI vs FSC plot and then subsequently gating on SSC vs FSC and FSC A vs FSC H to ensure better debris and doublet removal. All sorts were performed using the 85-micron nozzle. The sorted nuclei were collected into a BSA and RNase inhibitor-rich collection buffer (70µl of PBS with 1.375% BSA and 2.15U/µl RNase inhibitor) in low DNA-bind tubes kept at 4C. After sorting, nuclei were centrifuged at 500g for 5mins at 4C to pellet. Supernatant was removed to leave ~40µl, which was used to resuspend pellet with a wide bore pipette tip.
Pooled single nuclei suspensions were used to generate barcoded single nucleus libraries for next generation sequencing: For each pool, 5,000 to 10,000 nuclei were co-encapsulated with 10X barcoded gel beads to generate Gel beads in Emulsion (GEMs) using the 10X Chromium Controller and the 10X Genomics Single Cell 3' v3.1 kit according to manufacturer’s instructions. After GEM-RT and clean-up, the quantity and fragment size distribution of amplified cDNAs derived from barcoded single-cell RNAs were assessed using the Agilent 2100 Bioanalyzer High Sensitivity DNA assay. From this cDNA, snRNAseq libraries were constructed and sequenced (Illumina NextSeq2000) in 3 batches, containing equal numbers of obese, lean and control library pools, to minimize between-group batch effects. Each unique library was sequenced to a minimum depth of >20,000 paired-end reads per nucleus (Read1 28bp + Read2 90bp, with unique dual 10bp indexes).

tag: disease state

value: Obese

tag: Sex

value: Female

value: Periumbilical Adipose Tissue


title: BMWi_D4_hiPSC_3_1


title: SAT, Pooled Patients, Lean, Rep5

description:
Library name: Pool_14
10x Genomics

value: Lean


title: SAT, Pooled Patients, Weight Loss, Rep4

description:
Library name: Pool_12
10x Genomics

value: Weight Loss

value: Pooled Male and Female


title: SAT, Pooled Patients, Lean, Rep4

description:
Library name: Pool_11
10x Genomics


title: SAT, Pooled Patients, Weight Loss, Rep5

description:
Library name: Pool_15
10x Genomics


title: SAT, Pooled Patients, Obese, Rep5

description:
Library name: Pool_13
10x Genomics


title: SAT, Pooled Patients, Weight Loss, Rep6

description:
Library name: Pool_18
10x Genomics


title: SAT, Pooled Patients, Lean, Rep3

description:
Library name: Pool_8
10x Genomics


title: SAT, Pooled Patients, Lean, Rep2

description:
Library name: Pool_5
10x Genomics


title: SAT, Pooled Patients, Weight Loss, Rep2

description:
Library name: Pool_6
10x Genomics


title: BMWi_NMMmin_final_hiPSC_3_1


title: SAT, Pooled Patients, Obese, Rep3

description:
Library name: Pool_7
10x Genomics


title: SAT, Pooled Patients, Weight Loss, Rep3

description:
Library name: Pool_9
10x Genomics


title: SAT, Pooled Patients, Weight Loss, Rep1

description:
Library name: Pool_3
10x Genomics


title: SAT, Pooled Patients, Obese, Rep2

description:
Library name: Pool_4
10x Genomics


title: BMWi_NMMmin_final_hiPSC_1_2


title: SAT, Pooled Patients, Lean, Rep1

description:
Library name: Pool_2
10x Genomics


title: SAT, Pooled Patients, Lean, Rep6

description:
Library name: Pool_17
10x Genomics


title: H4K16ac XO

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

institute: Erasmus MC

description: Library name: XO

data_processing:
The ChIP-seq samples were analyzed allele-specifically. The reads were trimmed using Trim Galore and mapped to the N-masked reference genome using Bowtie2 (Langmead and Salzberg 2012) (v2.5.0). The allele-specific ChIP-seq bam files were normalized using the ‘callpeak’ and ‘bdgcmp’ functions of MACS2 (Zhang et al. 2008) (v2.2.7). We called broad peaks (-f BAMPE --broad --bdg) and used the Poisson P-value as the method for normalizing the tracks.
Assembly: mm10
Supplementary files format and content: Bigwig files with CPM-normalized ChIP-seq tracks for reads mapping to 129/Sv, Cast/Ei and composite genomes.

source_name: mESCs

growth_protocol: Mouse embryonic fibroblasts (MEFs) were cultured in MEF medium [DMEM (Gibco, 10829-018) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10500-064), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140122), 1% (v/v) Glutamax (Gibco, 35050038), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140035), and 0.008% (v/v) beta-mercaptoethanol (Gibco, 31350010)]. Mouse embryonic stem cells and mouse induced pluripotent stem cells were cultured in mESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS (Gibco, 10500-064), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140122), 1% (v/v) Glutamax (Gibco, 35050038), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140035), 0.008% (v/v) beta-mercaptoethanol (Gibco, 31350010), and mouse LIF (1000U/mL, home-made).

extract_protocol:
mESCs were depleted of MEFs 16 hours before the harvest by pre-plating dissociated cells for 45 minutes at 37°C in non-gelatinized plates. In total, 1 × 10^8 cells were crosslinked by the addition of 1% formaldehyde (Sigma-Aldrich, F1635-25ML) to the dish and incubated at room temperature for 10 minutes on a rocking platform. Formaldehyde was quenched by adding 125 mM glycine for 5 minutes. Subsequently, cells were washed once with 1 × PBS before scraping in 1 × PBS supplemented with 1× protease inhibitors (Roche, 11836170001). Cells were pelleted, resuspended and incubated for 10 minutes at 4 °C in 1 × LB1 ( 50 mM HEPES pH 8.0, 140 mM NaCL, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors), in 1 × LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA,1× protease inhibitors) and in 1× LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-laurolylsarcosine, 1× protease inhibitors). DNA was sonicated to an average fragment length of 100-300 bp using a Bioruptor Pico (Diagenode, B01060001) for 10 cycles of 30 sec on and 30 sec off. 1/20th volume of 20% Triton X-100 was added to the sonicated chromatin, and incubated for 10 minutes at 4°C before centrifugation for 10 min at 4500 × g 10 at 4°C to remove debris. 10 µl chromatin was used to measure the chromatin concentration by nanodrop and check the sonication efficiency. Sheared chromatin was flash frozen in liquid nitrogen and stored at -80°C until further use. For H4K16ac ChIPs, 30 µg of chromatin was diluted to 500 µl in ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS, 1× protease inhibitors) and incubated while rotating overnight at 4°C d with 2 µg H4K16ac antibody (Sigma-Aldrich, 07-329) or IgG (Sigma-Aldrich, 12-370). 30 µl of Magnetic beads (Life Technologies, 10004D) were washed once in ChIP dilution buffer, added to each sample and incubated while rotating for 4 hours at 4°C. Beads were washed 3× in Low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 1× protease inhibitors), 1× in High salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 1× protease inhibitors), 1× in LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% Sodium Deoxycholate, 1× protease inhibitors) and rinsed once in TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA), 10 min rotating at 4°C each wash. Chromatin was eluted in 200 µL Elution Buffer (1% SDS, 0.1 M NaHCO3) with 5 µL protease K (10 mg mL−1) and 2 µL RNAse A (10 mg mL−1) while shaking at 1,000 rpm on an orbital thermal-mixer for 2 h at 37°C followed by 65°C overnight. DNA was purified using the Zymo ChIP DNA clean concentrator kit (Zymo Research, D5202) according to the manufacturer's instructions and eluted in 15 µL H2O. 0.1 µL DNA was used per qPCR to validate ChIP enrichment.
The ChIP-seq sequencing libraries were prepared with the ChIPThruPLEX method (Takara Bio, R400675).
These libraries were subsequently sequenced on an Illumina NextSeq2000 sequencer. Paired-end clusters were generated of 50 bases in length.

value: mESCs

tag: strain

value: 129/Sv x Cast/Ei

value: XO


title: Input XX

description: Library name: XX input

tag: genotype

value: IgG (Sigma-Aldrich, 12-370)


title: H4K16ac XX

description: Library name: XX

value: H4K16ac antibody (Sigma-Aldrich, 07-329)


title: SAT, Pooled Patients, Obese, Rep4

description:
Library name: Pool_10
10x Genomics


title: XO X129OCast.2

description: Library name: I23-1325-04

data_processing:
The SNPs in the 129/Sv and Cast/Ei lines were downloaded from the Sanger Institute (v.5 SNP142) (Sherry et al. 2001). These were used as input for SNPsplit (Krueger and Andrews 2016) (v0.3.4), to construct an N-masked reference genome based on mm10 in which all SNPs between 129/Sv and Cast/Ei are masked. The reads were trimmed and aligned to the N-masked reference genome using TrimGalore (Krueger et al. 2021) (v0.6.7) and HISAT2(Kim et al. 2019) (v2.2.1), respectively.
SNPsplit was then used to assign the reads to either the 129/Sv or Cast/Ei BAM file based on the best alignment or to an unassigned BAM file if mapping to a region without allele-specific SNPs (--paired for the paired-end samples). The allele-specific and unassigned BAM files were merged into a composite BAM file using Samtools (Li et al. 2009) (v1.10). The number of mapped reads per gene was counted for both alleles separately and for the composite BAM file using HTSeq (Anders et al. 2015) (v0.12.4) based on the gene annotation from Ensembl v98 (--stranded="reverse").
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with raw counts for each gene mapping to 129/Sv, Cast/Ei and composite genomes.

extract_protocol:
Cells were cultured at least two passages before harvesting. mESCs were depleted of MEFs by pre-plating dissociated cells for 45 minutes at 37°C in  non-gelatinized plates. The supernatant containing the mESCs was spun down for 5 min at 300 × g. Cell pellets were lysed and RNA was extracted using the ReliaPrep™ RNA Miniprep kit (Promega, Z6012) with increased DNase treatment (25 min at room temperature). MEF depletion was validated on the gDNA of part of the cell pellet using PCRs targeting genotype-specific length polymorphisms and SNPs.
Sequencing libraries were prepared using the Truseq stranded mRNA library preparation method from Illumina.
The libraries of the XO cells were subsequently sequenced on an Illumina NextSeq2000 sequencer resulting in single read clusters of 50 bases in length. The libraries of all other cell lines were sequenced on a HiSeq2500 sequencer resulting in paired-end clusters of 50 bases.

tag: replicate


title: XO X129OCast.1

description: Library name: I23-1325-03

tag: cell line


title: XO XCastO129.1

description: Library name: I23-1325-01


title: Deletion K.2

description: Library name: I21-1615-20

value: Rnf12 +/-, Deletion K +/-


title: Deletion J.2

description: Library name: I21-1615-18

value: Rnf12 +/-, Deletion J +/-


title: XO XCastO129.2

description: Library name: I23-1325-02


title: Deletion J.1

description: Library name: I21-1615-17


title: Deletion I-TEL.2

description: Library name: I21-1615-22

value: Rnf12 +/-, Deletion I-TEL +/-


title: Deletion I-TEL.1

description: Library name: I21-1615-21


title: Deletion K.1

description: Library name: I21-1615-19


title: Deletion I.1

description: Library name: I21-1615-15

value: Rnf12 +/-, Deletion I +/-


title: SAT, Pooled Patients, Obese, Rep1

description:
Library name: Pool_1
10x Genomics


title: Deletion F.2

description: Library name: I21-1615-10

value: Rnf12 +/-, Deletion F +/-


title: Input XO

description: Library name: XO input


title: Deletion F.1

description: Library name: I21-1615-09


title: Deletion E.2

description: Library name: I21-1529-23

value: Rnf12 +/-, Deletion E +/-


title: Deletion E.1

description: Library name: I21-1529-21


title: Deletion D.1

description: Library name: I21-1615-07

value: Rnf12 +/-, Deletion D +/-


title: Deletion H.2

description: Library name: I21-1615-14

value: Rnf12 +/-, Deletion H +/-

value: Female


title: H3K9me3 sample of control ESCs for dFN

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

description:
Library name: control H3K9me3 for dFN (ChIP-seq)
sample 2

data_processing:
Terminal
Sequence reads were trimmed for adaptor sequence/low-quality sequence using sickle (parameter- -q 20 -l 20 ), Trimmed sequence reads were mapped to mm10 using bowtie2 and samtools, BigWig files were created using bamCompare
Assembly: mm10
Supplementary files format and content: BigWig files show H3K9me3 intensity for each sample

source_name: embryonic stem cell

growth_protocol: Wildtype and ATF7IPdeltaFNIII ESCs cultured under conventional ES culture condition with LIF.

extract_protocol:
Chromatins for ChIP-sequence were prepared from ESCs by following standardized method of fixation, cell lysis and fragmentation.
DNA libraries for ChIP-seq were prepared according to Illumina’s instructions using New England Biolab’s Next ChIP-seq Library Set (#E6200) and their quantity and average size were estimated using a KAPA Quantification Kit (Millipore) and Bioanalyzer (Agilent Technology).

tag: cell type

value: embryonic stem cell

value: wildtype

tag: treatment


title: H3K9me3 sample of Atf7ipdeltaFN ESCs

description:
Library name: dFN H3K9me3 (ChIP-seq)
sample 4

value: deltaFNIII


title: Input sample of Atf7ipdeltaFN ESCs

description:
Library name: dFN Input (ChIP-seq)
sample 3

value: reference to Sample 4


title: Deletion D.2

description: Library name: I21-1615-08

value: mESCs

value: 129/Sv x Cast/Ei


title: Input sample of control ESCs for dFN

description:
Library name: control Input for dFN (ChIP-seq)
sample 1

value: reference to Sample 2


title: Deletion C-G

description: Library name: I21-1615-23

value: Rnf12 +/-, Deletion C-G +/-


title: GRO t240

type: RNA

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: GRO labelling for 240 min sample. Replicates 1-3

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing:
Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.
Value in the GRO and cDNA processed data is the result of the Median Absolute Desviation normalization of each triplicate of the raw data.

organism: Saccharomyces cerevisiae

source_name: wild type

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For cDNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Yeast cells were cultured overnight at 24°C in YEPD medium (1% yeast extract, 2% peptone, and 2% glucose) until an optical density of 0.8–1 at 600 nm was reached. The culture was then refreshed in YEPD to an optical density of 0.1 at 600 nm and grown for 2.5 hours. After this period, a sublethal concentration of Congo Red (30 µg/ml; Merck KGaA, Darmstadt, Germany) was added, with a sample taken at time 0 for reference. Cells were collected at 30, 60, 120, 180, and 240 minutes following Congo Red treatment. The volume collected at each time point was adjusted based on cell size.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.


title: GRO t180

description: GRO labelling for 180 min sample. Replicates 1-3


title: GRO t120

description: GRO labelling for 120 min sample. Replicates 1-3


title: Deletion C.1

description: Library name: I21-1615-05

value: Rnf12 +/-, Deletion C +/-


title: GRO t60

description: GRO labelling for 60 min sample. Replicates 1-3


title: Deletion I.2

description: Library name: I21-1615-16


title: GRO t0

description: GRO labelling for start sample. Replicates 1-3


title: XX Rnf12.2

description: Library name: I21-1529-06


title: GRO t30

description: GRO labelling for 30 min sample. Replicates 1-3


title: XX Rnf12.1

description: Library name: I21-1529-05


title: cDNA t180

description: cDNA labelling for 180 min sample. Replicates 1-3


title: Deletion H.1

description: Library name: I21-1615-13


title: Deletion C.2

description: Library name: I21-1615-06


title: XX Wildtype.2

description: Library name: I21-1529-02

value: Wildtype


title: cDNA t30

description: cDNA labelling for 30 min sample. Replicates 1-3


title: Deletion A

description: Library name: I21-1615-02

value: Rnf12 +/-, Deletion A +/-


title: cDNA t0

description: cDNA labelling for start sample. Replicates 1-3


title: P10-TP

city: Seoul

first: Nam Sukl

last: Sim

address: Sinchon

institute: Yonsei University, College of Medicine

data_processing:
The Cell Ranger pipeline (version 3.0.2) was applied for pre-processing, including demultiplexing of sequencing results, barcode processing, read alignment, filtering of estimated droplets, and the generation of gene/barcode matrices.
Reads were aligned to the GRCh38 human reference genome (version GRCh38-1.2.0), and the UMI matrix of cell barcodes according to genes was generated for each sample.
Cell-free mRNA contamination was estimated and removed using SoupX (version 1.4.5) with default parameters.
Assembly: GRCh38 human reference genome (version GRCh38-1.2.0).
Supplementary files format and content: OSCC_UMI_count_matrix.txt.gz is a tab-delimited text file which includes UMI counts for all cells. Tab-delimited text files which include UMI counts were generated for each sample.

source_name: Tumor periphery from P10

extract_protocol:
Single-cell libraries were prepared using the Single Cell 3' Reagent Kit v3 (10× Genomics, Pleasanton, CA, United States) following the Chromium Single Cell 3' Reagent Kit v3 protocol (Document # CG000183)
Libraries underwent paired-end sequencing on the HiSeq X sequencer (Illumina, San Diego, CA, USA) according to the standard Illumina protocols.

tag: patient id

tag: tissue

value: Tumor periphery of OSCC


title: Deletion B

description: Library name: I21-1615-03

value: Rnf12 +/-, Deletion B +/-


title: P10-TC

source_name: Tumor core from P10

value: Tumor core of OSCC


title: XX Wildtype.1

description: Library name: I21-1529-01


title: P10-NT

source_name: Adjacent non-tumor tissue from P10

value: Adjacent non-tumor tissue of OSCC


title: cDNA t120

description: cDNA labelling for 120 min sample. Replicates 1-3


title: cDNA t60

description: cDNA labelling for 60 min sample. Replicates 1-3


title: DFO12A

city: Hangzhou

first: Fei

last: Li

address: 866 Yuhangtang Road

department: Department of Medicine

institute: Zhejiang University

data_processing:
Reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1.For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: mm10
Supplementary files format and content: TXT files includes raw counts and FPKM and matrix files for each sample

source_name: cell

growth_protocol: Bone marrow cells were harvested from femurs and tibias of WT mice. After removing RBCs and adhesion culture for 2 hours, unattached cell was resuspended to a density of 2 × 106/mL in Iscove’s Modified Dulbecco’s Medium (Gibco) supplemented with 20% FBS (Vistech), 2 mM L-glutamine (GlutaMAX™, Gibco), 5 × 105 M β-ME (Sigma-Aldrich), MEM Non-Essential Amino Acids (11140050, Gibco), 1 mM sodium pyruvate (11360070, Gibco), and 100 U/mL penicillin/streptomycin. The cytokines murine SCF (100 ng/mL) and murine FLT3-Ligand (100 ng/mL) were supplemented to the culture for 4 days. On day 4, cells were washed and treated in the presence of IL-5 (10 ng/mL, R&D systems) for the duration of the culture. FAC, DFO was treatment on days 4. RNAseq were analysis on Day 7.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

treatment_protocol: DFO:5 μM, FAC；10 μM

value: cell

value: Bone marrow-derived eosinophils

value: eosinophils

value: WT

value: DFO


title: DFO11A


title: Deletion AB

description: Library name: I21-1615-04

value: Rnf12 +/-, Deletion AB +/-

value: Female


title: cDNA t240

description: cDNA labelling for 240 min sample. Replicates 1-3


title: DFO9A


title: P09-mLN

source_name: Lymph node metastasis from P09

value: Lymph node metastasis of OSCC


title: P09-TC

source_name: Tumor core from P09


title: P09-TP

source_name: Tumor periphery from P09


title: FAC7A

value: FAC


title: FAC8A


title: FAC6A


title: P08-mLN

source_name: Lymph node metastasis from P08


title: P09-NT

source_name: Adjacent non-tumor tissue from P09


title: FAC5A


title: P10-mLN

source_name: Lymph node metastasis from P10


title: P08-TC

source_name: Tumor core from P08


title: CON2A

value: untreated


title: P08-TP

source_name: Tumor periphery from P08


title: CON1A


title: P07-mLN

source_name: Lymph node metastasis from P07


title: P08-NT

source_name: Adjacent non-tumor tissue from P08


title: GMP3

value: Bone marrow granulocyte-macrophage progenitors

value: GMPs


title: GMP2


title: P07-TC

source_name: Tumor core from P07


title: Eos3

value: Bone marrow eosinophils


title: P06-mLN

source_name: Lymph node metastasis from P06


title: P07-NT

source_name: Adjacent non-tumor tissue from P07


title: P06-TP

source_name: Tumor periphery from P06

value: Tumor periphery of OSCC


title: Eos1


title: GMP1


title: Eos2


title: P06-TC

source_name: Tumor core from P06


title: P05-mLN

source_name: Lymph node metastasis from P05


title: P05-TP

source_name: Tumor periphery from P05


title: P04-mLN

source_name: Lymph node metastasis from P04


title: P05-TC

source_name: Tumor core from P05


title: Prf1-/- SnMP MMTV-PyMT tumor 3; sample 12

first: Dominika

last: Sosnowska

state: Please select...

address: King's College London Guy's Campus, New Hunt's House, Newcomen St

department: Comprehensive Cancer Centre

institute: King's College London

description:
Multiplex gene expression analysis (nCounter PanCancer Immune Profiling Panel) of 770 genes was performed on total RNA extracted from MMTV-PyMT mouse tumors
nCounter PanCancer Immune Profiling Panel [Mouse]

data_processing: The raw NanoString data was normalized to housekeeping genes using the remove unwanted variation (RUV) pipeline using the RUVSeq package in R. The subsequent differential expression analysis of the NanoString data was performed with DESeq2 package in R. Benjamini- Enriched pathways were identified based on differentially expressed genes using gProfiler (http://www.biit.cs.ut.ee/gprofiler/). We used pathways gene sets from the ‘biological processes’ (GO:BP) of Gene Ontology (http://www.geneontology.org/). Hochberg correction was applied to the p-values to adjust for multiple hypothesis testing. Genes with adjusted p-values lower than 0.05 were considered significant.

source_name: primary mouse MMTV-PyMT mammary tumor

label_protocol: A multiplex analysis of the expression of 770 genes including 40 housekeeping genes was performed using the nCounter® Pan-Cancer Immune Profiling Panel and the nCounter platform, loading 80 ng of total RNA for each sample according to themanufacturers’ recommendations (NanoString Technologies).

growth_protocol: Transgenic mice (knockout; KO) used in the study included homozygous Prf1-/- (C57BL/6-Prf1tm1Sdz/J) were on a C57BL/6 background and MMTV-PyMT mice were on FVB/N background; both obtained from The Jackson Laboratory. All mice used for experiments were female and randomly assigned to treatment groups. Mice were approximately 21-26 g when tumors became palpable.

extract_protocol: Excised MMTV-PyMT tumor tissue samples were placed in RNAlater Stabilisation Solution (Thermo Fisher Scientific) at 4 °C for 24 h, and subsequently transferred to and stored at -80 °C until used for RNA extraction. RNA from MMTV-PyMT tumors was isolated using Trizol (Thermo Fisher Scientific) according to the manufacturers’ protocol. Isolated RNA was quantified with the NanoDrop2000 spectrophotometer (Thermo Fisher Scientific) or using the Qubit RNA HS Assay Kit as per the manufacturers’ recommendations (Thermo Fisher Scientific). RNA samples were analyzed using the RNA 6000 Nano Kit (Agilent Technologies) and the RNA integrity was assessed based on the RNA integrity number (RIN) determined using the Agilent 2100 Bioanalyzer.

treatment_protocol: Drugs were freshly prepared on the day of injection and administered by intraperitoneal (i.p.) injection using a 26 G needle. Tin (IV) mesoporphyrin IX dichloride (SnMP; Frontier Scientific) was dissolved and administered at a dose of 25 µMol/kg/day.

value: Prf1-/- MMTV-PyMT

value: SnMP

value: C57BL/6 x FVB/N

value: tumor


title: Prf1-/- SnMP MMTV-PyMT tumor 1; sample 10


title: P07-TP

source_name: Tumor periphery from P07


title: P04-TP

source_name: Tumor periphery from P04


title: P04-TC

source_name: Tumor core from P04

value: Tumor core of OSCC


title: Prf1-/- vehicle MMTV-PyMT tumor 3; sample 6

value: Vehicle


title: Prf1+/+ SnMP MMTV-PyMT tumor 1; sample 7

value: Prf1+/+ MMTV-PyMT


title: Prf1+/+ SnMP MMTV-PyMT tumor 2; sample 8


title: P03-mLN

source_name: Lymph node metastasis from P03


title: P04-NT

source_name: Adjacent non-tumor tissue from P04

value: Adjacent non-tumor tissue of OSCC


title: Prf1-/- vehicle MMTV-PyMT tumor 1; sample 4


title: Prf1-/- vehicle MMTV-PyMT tumor 2; sample 5


title: P02-mLN

source_name: Lymph node metastasis from P02


title: Raw LPS-PjELNs rep3

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

institute: The University of Tokyo

data_processing:
BAM-formatted map files were generated using STAR version 2.7.10a with default parameters.
The gene-level expression values (counts and TPM) were estimated by RSEM version 1.3.1 with default paramters.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw read counts per gene
Supplementary files format and content: tab-delimited text files include transcripts per kilobase million (TPM)

source_name: Macrophage

growth_protocol: Raw-Blue (InvivoGen) mouse macrophage cells were cultured in DMEM supplemented with 10% FBS, 100 μg/ml Normocin (InvivoGen), 200 μg/ml Zeocin (InvivoGen), and Pen-Strep (100 U/ml) at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using RNA Clean & Concentrator (ZYMO RESEARCH) according to the manufacturer’s instructions.
Library construction, and sequencing (PE100) were performed by Beijing Genomic Institution (BGI, https://www.bgi.com/jp/home). The Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke software (BGI).

treatment_protocol: The cells were cultured in regular medium for an additional 24 hours. To assess the effect of ELNs, they were added to the medium at a final concentration of 1x10^10 particles/ml, and the cells were incubated for 16 hours. The cells were then stimulated with LPS (Wako) at a final concentration of 1 μg/ml for 24 hours to induce an inflammatory response.

value: Macrophage

value: RAW-Blue

value: cultured cell

value: LPS-PjELNs


title: P03-TC

source_name: Tumor core from P03


title: Prf1+/+ vehicle MMTV-PyMT tumor 3; sample 3

value: Female


title: P03-TP

source_name: Tumor periphery from P03


title: Prf1+/+ vehicle MMTV-PyMT  tumor 2; sample 2


title: P02-TP

source_name: Tumor periphery from P02


title: Raw LPS rep3

value: LPS


title: P06-NT

source_name: Adjacent non-tumor tissue from P06


title: Prf1+/+ vehicle MMTV-PyMT tumor 1; sample 1


title: Raw LPS-PjELNs rep1


title: Prf1+/+ SnMP MMTV-PyMT tumor 3; sample 9


title: Prf1-/- SnMP MMTV-PyMT tumor 2; sample 11


title: P02-TC

source_name: Tumor core from P02


title: P01-mLN

source_name: Lymph node metastasis from P01

value: Lymph node metastasis of OSCC


title: P01-TC

source_name: Tumor core from P01


title: P01-NT

source_name: Adjacent non-tumor tissue from P01


title: Raw LPS rep1


title: Raw None rep3


title: 9120G_liver_Control

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

data_processing:
FastQC (version 11.5) software was used for quality check.
Sequencing adapter sequences and low-quality bases were trimmed using Trimmomatic v0.36
On average, 98.18% of the remaining high0quality reads were mapped to the cattle reference genome (GenBank: GCA_002263795.2) by Tophat-2.1.1
Gene reads counts were performed in three software packages, Cufflinks-2.2.1, Bedtools -2.30.0, and HT-seq
DESeq2 packages in R were used to perform normalization and detect significant differentially expressed genes (DEGs) [23; 24], at an FDR (False Discovery Rate) cutoff of 0.05. The log2 fold change (LogFC) was determined for each gene. In addition, a volcano plot was generated using VolcaNoseR tool
Assembly: Cattle reference genome (GenBank: GCA_002263795.2)
Supplementary files format and content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene in all samples

organism: Bos taurus

source_name: Bos taurus liver biopsy

extract_protocol:
The total RNA of liver samples was extracted using the ZYMO Quick DNA/RNA Miniprep Plus Kit (Zymo Research, CA). For homogenization, tissue samples with DNA/RNA Shield were mechanically homogenized by Qiagen TissueRuptor II (Qiagen, MD). RNA concentrations were measured by Qubit fluorometer 3.0 (Thermo Fisher Scientific, MA) with Qubit RNA BR Assay Kit.
RNA sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA), with a 1500 ng total RNA input. The concentrations and the size distribution of the libraries were checked by the LabChip GX Touch HT machine using the HT DNA NGS 3K Assay (Perkin Elmer, MA). The fragment size of final libraries ranged from 343 to 409 bp. The libraries were individually barcoded and pooled. The libraries were sequenced on an Illumina NovaSeq 6000 sequencing machine to generate 150-bp paired-end reads

treatment_protocol: The diet offered was ad libitum Bermudagrass hay combined with a nutritional supplement composed of 1.61 kg of endophyte-free tall fescue seeds, and 1.61 kg of pellets composed of 46.5% ground corn, 46.5% soybean meal, 5% wheat middlings, and 2% soybean oil; and 0.1 kg of molasses per animal per day. Rumen-protected niacin was only administered for the treatment group,

tag: breed

value: Angus x Simmental

value: liver

tag: agent

value: Control


title: Raw None rep1


title: 9044G_liver_Niacin

value: Niacin


title: 9056G_liver_Control


title: HepG2 siKIAA1429-2

city: CHONG QING

first: HUA

middle: MEI

last: SHAN

address: 30 Gaotanyan, Shapingba

institute: Army Medical University

data_processing:
The sequencing data was filtered with SOAPnuke by  Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include read count values for each Sample

extract_protocol:
This procedure is suitable for Total RNA extraction of animal tissues, cells and other samples to provide high quality RNA for library preparation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs

value: tumor cell

value: KIAA1429 knockdown


title: Raw LPS-PjELNs rep2


title: 9028G_liver_Niacin


title: HepG2 siNC-1

value: WT


title: HepG2 siNC-2


title: 9036G_liver_Control


title: HepG2 siKIAA1429-1


title: C3_dTAG24h_Dox24h_m6AIP

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

description:
Library name: C3_dTAG24h_Dox24h_m6AIP
RNA type: m6A-containing RNA

library_source: other

data_processing:
rm6A-seq and input raw fastq files were mapped to mm10 by STAR (v2.5.2b).
Sequencing reads were split into positive and negative strands, and bigwig files were generated accordingly. Ten million mapped reads / library was used to perform normalization in conventional MeRIP-seq analysis.
Assembly: mm10
Supplementary files format and content: Bigwig, normalised, strand-spefici

molecule: other

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

growth_protocol: ES cells were grown in DMEM media supplemented with 10% Fetal Calf Serum (ThermoFisher), 0.1mM non-essential amino acids, 2mM L-glutamine, 50μM β-mercaptoethanol, 100 U/ml Penicillin/100 μg/ml Streptomycin (all from Life Technologies) and 1000U/mL Leukemia Inhibitory Factor (LIF) (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2. Differentiating cells were grown in DMEM media supplemented with 10% Fetal Calf Serum (ThermoFisher), 0.1mM non-essential amino acids, 2mM L-glutamine, 50μM β-mercaptoethanol, 100 U/ml Penicillin/100 μg/ml Streptomycin (all from Life Technologies) and 1μg/ml doxycycline (Sigma). Differentiating cells were grown without feeders on gelatinised plates at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated, and m⁶A-containing RNA was immunoprecipitated using an anti-m⁶A antibody.
Approximal 100 - 500 ng of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by Qubit. The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500/550.

treatment_protocol: Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 µg/mL of doxycycline for 24 hours. Cells were either treated with dTAG-13 for 24 hours or not (control).

tag: strain background

value: Cast x 129S

value: mESC

tag: xist type

value: Endogenous Xist

value: dTAG-13 24hous + dTAGDox24h


title: C3_dTAG24h_Dox24h_input

description:
Library name: C3_dTAG24h_Dox24h_input
RNA type: rRNA-depleted total RNA

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: C3_Dox24h_input

description:
Library name: C3_Dox24h_input
RNA type: rRNA-depleted total RNA