title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_input_rep3

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

data_processing:
Raw ChIP-Seq reads were aligned to a combined reference of mm10 and dm6 genome assembly using BWA version 0.7.17 with default parameters. Afterwards, they were filtered using a cut-off of MAPQ < 3 using Samtools v.1.18.
Raw ATAC-Seq reads were trimmed and filtered for quality using Trimmomatic v0.39. Trimmed reads were mapped to the mm10 genome assembly using Bowtie2 v2.5.1, and non-uniquely mapping reads were removed. Afterwards, the reads were adjusted by shifting all positive-strand reads 4 bp downstream and all negative-strand reads 5 bp upstream to the center of the reads on the transposase binding event.
For H3K36me2 NSD1/2/3-SETD2-QKO and NSD1/2/3-SETD2-ASH1L-QuiKO replicates, samclip v.0.2 (samtools view -h in.bam | samclip --ref ref.fa | samtools sort > out.bam) was used to filter contaminated sequences prior to alignment.
ENCODE blacklisted regions were excluded from all analyses.
For ATAC-Seq samples, peak calling was performed on each replicate using MACS2 v2.2.6 with ‘-extsize 200 -shift -100 -nomodel’ parameters. To find a set of reproducible peaks across ATAC-Seq replicates, the irreproducible discovery rate (IDR) was calculated and peaks with an IDR greater than 0.05 across every pair of replicates were excluded.
bigWig files were generated using deepTools v3.5.3 bamCoverage with parameters '-b ${samp}.sorted.bam -o ${samp}.cpm.bw -p $nprocs --normalizeUsing CPM --centerReads -e 200'.
Replicates were merged using the deepTools v3.5.3 bigwigCompare tool. The initial merging step employed these parameters: '-b1 rep1 -b2 rep2 $outdir --operation mean -bs 200 -o $merged.step1.cpm.bw' while the final merging step utilized the following parameters: '-b1 $merged.step1.cpm.bw -b2 rep3 $outdir --operation mean -bs 200 -o $merged.final.cpm.bw.'
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax.

extract_protocol:
Approximately 20 million mMSC cells per cell line were used. Crosslinking was performed in 150 mm cell culture plates using 1% formaldehyde (Sigma) at room temperature with gentle rocking for 10 minutes. The crosslinking reaction was quenched using 1.25 M Glycine with gentle rocking at room temperature for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped, and then washed twice more with ice-cold PBS. Crosslinked pellets were resuspended in 500 μl cell lysis buffer (5 mM pH 8.5 PIPES, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Samples were centrifuged and pellets were resuspended in 500 μl of nuclei lysis buffer (50 mM pH 8.0 Tris-HCl, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Sonication of lysed nuclei was performed using the BioRuptor UCS-300 at maximum intensity for 75-90 cycles (10s on, 20s breaks). Sonication efficiency to achieve fragments between 150 - 500 bp was evaluated using gel electrophoresis on a reversed-crosslinked and purified aliquot from each sample. After sonication, chromatin was diluted to reduce SDS levels to 0.1% and concentrated using Nanosep 10K OMEGA (Pall) columns. Prior to the chromatin immunoprecipitation (ChIP) reaction, 2% sonicated Drosophila S2 cell chromatin was spiked into each sample for quantification of total levels of histone marks. The ChIP reactions were performed using the Diagenode SX-8G IP-Star Compact and Diagenode automated iDeal ChIP-seq Kit for Histones. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hrs, followed by a 20 min wash cycle using the provided wash buffers (Diagenode Immunoprecipitation Buffers, iDeal ChIP-seq Kit for Histones). Reverse cross-linking was then performed using 5M NaCl at 65℃ for 4 hrs. ChIP samples were then treated with 2 μl RNase Cocktail at 65℃ for 30 min followed by 2 μl Proteinase K at 65℃ for 30 min. Samples were then purified with QIAGEN MinElute PCR purification kit (QIAGEN) as per the manufacturer’s protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
ChIP-seq library preparation was performed using the Kapa Hyper Prep library preparation reagents following the manufacturer’s protocol (Kapa Hyper Prep Kit, Roche 07962363001). ChIP libraries were sequenced using the Illumina HiSeq 4000 at 50 bp single reads or NovaSeq 6000 at 100 bp single reads. ATAC-seq library preparation was performed according to the Omni-ATAC protocol. 50,000 C3H10T1/2 cultured cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 rcf for 5 min in a pre-chilled (4°C) fixed-angle centrifuge. After centrifugation, supernatant was aspirated and cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL and digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 rcf in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (2x TD Buffer, 100 nM final transposase, 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O ) (Illumina Tagment DNA Enzyme and Buffer Small Kit, 20034197). Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up with DNA Clean and Concentrator 5 columns (Zymo Research). Illumina Nextera DNA Unique Dual Indexes Set C (Illumina, 20027215) were added and amplified (12 cycles) using NEBNext 2x MasterMix. Sequencing of the ATAC-Seq libraries was performed on the Illumina NovaSeq 6000 system using 100-bp paired-end sequencing.

value: Mouse mesechymal stem cells

value: NSD1/2/3 SETD2 ASH1L quintuple knock-out


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_input_rep1

status: Public on Sep 25 2024

type: SRA

country: Canada

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: chip antibody

tag: cell line

tag: cell type

tag: genotype


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me3_rep3

value: H3K36me3 (Active Motif, 61101)


title: AF1183_P6

city: New York

first: ZHUXUAN

last: LI

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Bulk RNA-sequencing data from ex vivo transformation experiments of young and aged cells was compiled object and normalized using the size factor normalization function of DESeq2. Highly variable features were identified using a variance stabilizing transformation. Diffusion maps were generated in scanpy using the top principal components from normalized, log2-transformed count data. The pseudotime position of each sample was then calculated in scanpy in diffusion space using untransformed AT2 cells as root. To identify genes differentially expressed between young and aged ex vivo transformed cells independent of differentiation stage, gene expression models controlling for either passage or pseudotime were fitted in DESeq2 (version 1.26.0).
Assembly: GRCm38/mm10
Supplementary files format and content: txt file includes raw counts for each sample.

molecule: polyA RNA

source_name: 3D culture

growth_protocol: Cells were seeded the density of 3000 cell/matrigel plug with media change every three days. Recipe of the media: Advanved DMEM/F12, 2% heat-inactivated fetal bovine serum and pen/strep.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, #217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 9.0 to 9.7 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech,  #63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, #KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

tag: tissue

value: 3D culture

value: 3D fulture from primary mouse cells

value: Tumor


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me3_rep2


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me3_rep1


title: GH2 108_P0

value: Normal


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me2_rep2

value: H3K36me2 (Cell Signaling, 2901)


title: AF1183_P5


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me2_rep3


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me1_rep1

value: H3K36me1 (Cell Signaling, 14111)


title: AF1183_P4


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me1_rep3


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me2_rep1


title: AF1183_P2


title: AF1337_P4


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_H3K36me1_rep2


title: C3H10T1-2_NSD123_SETD2_QKO_input_rep3

value: NSD1/2/3 SETD2 quadruple knock-out


title: C3H10T1-2_NSD123_SETD2_QKO_input_rep1


title: C3H10T1-2_NSD123_SETD2_QKO_input_rep2


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me3_rep3


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me3_rep1


title: AF1181_P5


title: C3H10T1-2_NSD123_SETD2_ASH1L_QuiKO_input_rep2


title: AF1337_P2


title: AF1181_P4


title: AF1183_P3


title: A375 cells, TTC_2

city: luzhou

first: yi

last: peng

address: xianglinlu

country: China

institute: 西南医科大学

data_processing:
Raw sequencing data was processed through the following steps to obtain high-quality clean data:  Removal of adapter sequences and reads without inserts Trimming of low-quality bases (quality score < 20) at the 3' end, and removal of entire reads if any remaining base has a quality score < 10 Removal of reads with N ratio > 10% Removal of reads shorter than 20 bp Quality control was performed using fastp software (https://github.com/OpenGene/fastp)
Clean data was aligned to the reference genome to obtain mapped data for downstream analyses. Alignment was done using HiSat2 software (http://ccb.jhu.edu/software/hisat2/index.shtml), and quality assessment of the alignment results was conducted (sequencing saturation, gene coverage, read distribution, etc.).
RSEM software (http://deweylab.github.io/RSEM/) was used to quantify gene and transcript expression levels, generating Read Counts data.
For samples with biological replicates, differential expression analysis was performed using DESeq2 software (http://bioconductor.org/packages/stats/bioc/DESeq2/). For samples without replicates, DEGseq software (https://www.rdocumentation.org/packages/DEGseq/versions/1.26.0) was used. Differentially expressed genes were filtered using the criteria of FDR < 0.05 and |log2FC| ≥ 1.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

growth_protocol: A375 cells were maintained in  RPMI 1640 medium supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from C918 cells using the QIAzol Lysis Reagent. 1.5 μg of total RNA was used for subsequent library construction.
Libraries were constructed using the Illumina® Stranded mRNA Prep Ligation Kit according to the manufacturer's instructions.

treatment_protocol: For the treatment group, a 100 mM stock solution of TTC was prepared in PBS, and then diluted in the culture medium to a final concentration of 400 μM. For the control group, an equivalent volume of PBS was added to the culture medium. Cells were treated for 24 hours.

value: skin primary melanoma

value: WT

tag: treatment


title: AF1181_P3


title: A375 cells, TTC_3


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me2_rep2


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me2_rep1


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me2_rep3


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me1_rep3


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me1_rep2


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me3_rep2


title: AF1165_P5


title: AF1181_P6


title: C3H10T1-2_NSD123_SETD2_QKO_H3K36me1_rep1


title: AF1165_P4


title: A375 cells, Con_2

value: PBS


title: AF1165_P3


title: hepa16_shcontrol

city: Sacramento

first: yatian

last: yang

state: CA

institute: UC Davis

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 Sequencer. The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Briefly, sequence reads were aligned to the reference human genome assembly (hg19) with BWA and Bowtie software. Subsequently, the Cufflinks package was applied for transcript assembly and quantification gene expression.
To avoid spurious fold levels due to low expression values, only subsets of genes that have expression value of FPKM (fragments per kilobase of exon model per million mapped reads) above 1 for either the vehicle treated cell, or the compound treated cells are included.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

extract_protocol:
Total RNA was isolated from cells using TRIzol™ Reagent
RNA-seq libraries from 1μg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer

value: liver cancer

value: shctrl

tag: time

value: 48 hours


title: A375 cells, Con_1


title: hepa16_shNR1D1


title: C3H10T1-2_NSD12_SETD2_TKO_input_rep2

value: NSD1/2 SETD2 triple knock-out


title: AF1181_P2


title: AF1165_P2


title: hepa16_Veh

value: veh


title: GH2108_P6


title: hepa16_SR8278


title: AF1165_P6


title: A375 cells, TTC_1


title: C3H10T1-2_NSD12_SETD2_TKO_H3K36me3_rep2

value: Mouse mesechymal stem cells


title: Mixed three-species biofilms_biol rep2 (br2)

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description:
Gvaginae_Single vs Mixed biofilms_RPKM
Fvaginae_Single vs Mixed biofilms_RPKM
Pbivia_Single vs Mixed biofilms_RPKM

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (v 2.17.1.14) starting from raw sequencing reads. The quality of individual sequences was evaluated using FastQC software after adapter trimming with cutadapt software (v 1.18).
Adapter trimmed data was further analysed by CLC Genomics Workbench v 21.99.
Sequence data were trimmed for low quality using CLC Genomics Workbench (parameter - quality limit: 0.05 and Maximum number of ambiguities allowed: 2).
Trimmed sequences read were mapped to either G. vaginalis NCTC 10287, F. vaginae FDAARGOS_934 or P. bivia DSM 20514 using CLC Genomics Workbench (parameters-Mismatch cost: 2, insertion cost; deletion cost: 3; length fraction 0.8, similarity fraction: 0.8 and maximum number of hits for a read: 10).
Differential expression analysis was performed using CLC Genomics Workbench, upon normalisation to RPKM. Baggerley statistical test was used to identify significant alterations in gene transcription. Only alterations with fold-changes > 2 and a false discovery rate (FDR)-adjusted P value < 0.05 were used for further bioinformatics analyses.
Assembly: G. vaginalis NCTC 10287 (NZ_LR134385.1), F. vaginae FDAARGOS_934 (CP065631.1) and P. bivia DSM 20514 (scaffolds NZ_JH660658.1; NZ_JH660659.1; NZ_JH660660.1)
Supplementary files format and content: The tab-delimited text file present RPKM values of either G.vaginalis, F. vaginae or P. bivia of the three replicas performed, for both single (S) and multispecies/mixed (M) biofilms.

organism:
Gardnerella vaginalis
Prevotella bivia
Fannyhessea vaginae

source_name: Gv + Fv + Pb

growth_protocol: Single and triple-species biofilms of G. vaginalis, F. vaginae and P. bivia were formed on 24-well culture plates (Orange Scientific). First, an inoculum of each species was prepared in NYCIII medium [0.24% (w/v) HEPES (VWR), 1.5% (w/v) proteose peptone (Liofilchem), 0.38% (w/v) yeast extract (Liofilchem), 0.5% (w/v) NaCl (VWR), 0.5% (w/v) glucose (Fisher Scientific), and 10% (v/v) of inactivated horse serum (Sigma)] and incubated at 37˚C under anaerobic conditions for 24 h. Bacterial concentration was then adjusted to 1x107 CFU/mL and 1 mL of suspension was dispensed into 24-well plates. The plates were incubated for 48 h at 37˚C under anaerobic conditions. After 48 h, the medium was removed, and the biofilms were washed once with 1x phosphate-buffered saline (PBS) solution (Fisher Scientific). Biofilms were then detached from the bottom of the plate in RNA Protect bacteria reagent (QIAGEN), which was diluted 2:1 in PBS; and 12 biofilms (i.e. biofilms from 12 wells) were combined to obtain samples with enough RNA for further analysis. Finally, samples were centrifuged at 5000 xg for 10 min at room temperature.

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (QIAGEN), according to the manufacturer's instructions with some brief modifications. First, cells were suspended in 600 μL of the lysis buffer RLT and the volume was transferred into a tube with 0.1 mm zirconium beads (Merck). Cells were lysed using the BeadBug 6 Microtube Homogenizer (Benchmark Scientific) at maximum speed for 35s. The cycle was repeated four times and the samples were kept on ice for 5 min between cycles. Then, the samples were centrifuged, and the supernatant was recovered into a new tube. Ethanol [70% (Thermo Fisher Scientific)] was added, in the same proportion (vol: vol), to the supernatant and the solution was transferred to an RNeasy Mini spin column. RNA was then eluted in RNase-free water (GRISP) and treated with Turbo DNase (Invitrogen) to degrade genomic DNA following the manufacturer's instructions for rigorous protocol. RNA quality was assessed using an Agilent 2100 Fragment Analyzer system (Agilent) and only samples with RNA quality indicators above 7 were used.
RNA-seq libraries were prepared by Lexogen (outsourced) using Lexogen’s CORALLTM Total RNA-seq kit with 100 ng of total RNA. Before RNA-seq, rRNA was removed using the RiboCop for Bacteria (Mixed Bacterial Samples META) rRNA Depletion kit (Lexogen). Sequencing libraries were evaluated for quality on a Fragment Analyzer System (Agilent) and quantified with QubitTM dsDNA HS Assay Kit (Invitrogen). Data were generated using Illumina NextSeq2000 Sequencing from single-end reads (SR100).

tag: strain

value: ATCC 14018; ATCC BAA-55; ATCC 29303


title: Mixed three-species biofilms_biol rep3 (br3)


title: A375 cells, Con_3


title: Mixed three-species biofilms_biol rep1 (br1)


title: Hepa16_input_Veh

data_processing:
Fastq files from ChIP-seq were processed by the pipeline of AQUAS Transcription Factor and Histone. Briefly, sequencing tags were mapped against the Homo sapiens (human) reference genome (hg19) using BWA 0.7.15. Uniquely mapped tags after filtering and deduping were used for peak calling by model-based analysis for ChIP-seq (MACS 2.1.0) to identify regions of enrichment over background.
Normalized genome-wide signal-coverage tracks from raw-read alignment files were built by MACS2, UCSC tools and bedTool.
Visualization of ChIP-seq signal at enriched genomic regions (avg profile and heatmap) was achieved by using deepTools.
Peak associated genes were identified using the annotatePeaks function of HOMER.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
samples were subject to crosslinking in 1% formaldehyde for 5 min followed by quenching with glycine for 5 min on ice. Cells were pelleted by centrifugation and resuspended in lysis buffer (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X100). The pellets were then resuspended in washing buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl), washed and resuspended in shearing buffer (0.1% SDS, 1mM EDTA, pH 8, 10mM Tris HCl, pH 8) before sonication using Covaris E220 following manufacturer’s instruction. Chromatin fragments were precipitated using specific antibodies and Protein G beads, washed and treated with Proteinase K and RNAse A.
The ChIP complexes were washed and eluted in 50 mM NaHCO3 and 1% SDS, followed by overnight reverse crosslinking. The recovered DNAs from ChIP and ChIP-reChIP were used for library generation. Libraries were quantified with the Bioanalyzer 2100.

value: Vehicle 24hr


title: C3H10T1-2_NSD12_SETD2_TKO_H3K36me3_rep1

value: H3K36me3 (Active Motif, 61101)


title: GH2108_P4

value: 3D culture

value: 3D fulture from primary mouse cells

value: Tumor


title: Prevotella bivia single biofilms_biol rep3 (br3)

description: Pbivia_Single vs Mixed biofilms_RPKM

organism: Prevotella bivia

source_name: Prevotella bivia (Pb)


title: GH2108_P5


title: Hepa16_input_SR8278


title: C3H10T1-2_NSD12_SETD2_TKO_input_rep3


title: GH2108_P3


title: Prevotella bivia single biofilms_biol rep2 (br2)

description: Pbivia_Single vs Mixed biofilms_RPKM


title: Hepa16_NR1D1_Veh

value: REV-ERBα (CST, #13418 and Proteintech, #14506-1-AP)


title: C3H10T1-2_NSD12_SETD2_TKO_H3K36me2_rep2

value: H3K36me2 (Cell Signaling, 2901)


title: GH2108_P2


title: C3H10T1-2_NSD12_SETD2_TKO_input_rep1


title: Prevotella bivia single biofilms_biol rep1 (br1)

description: Pbivia_Single vs Mixed biofilms_RPKM


title: GH1397_P6


title: Hepa16_NR1D1_SR8278


title: H37Rv whiB6 mutant complemented promoter WT - whiB6 T51P Rep3

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were mapped against the reference genome of M. tuberculosis H37Rv using BWA-MEM v0.7.17-r1188 (parameters: -M; -h 1000).
Uniquely-mapped reads were extracted from the alignment maps according to the XA tag using the Python wrapper pysam v0.20.0 of SAMtools.
Reads mapped on gene features were counted using featureCounts v2.0.4 (parameters: -s 2; --primary).
Read counts were normalized and transformed by regularized logarithm using DESeq2 v1.38.3.
Assembly: Mycobacterium tuberculosis H37Rv AL123456.3
Supplementary files format and content: Tab-delimited matrix file containing the raw read counts for each gene (rows) for all samples (columns) determined by featureCounts

organism: Mycobacterium tuberculosis H37Rv

growth_protocol: Bacterial strains were cultured in triplicate in Middlebrook 7H9 broth supplemented with 10% OADC (oleic acid, albumin, dextrose, and catalase, BD) and 0.05% Tween 80 at 37°C. Cultures were harvested when reaching the exponential phase of growth with a final OD at 600 nm between 0.4 and 0.8.

extract_protocol:
Bacterial strains were pelleted and bead beated in 1 mL of TRIzol (Life Technologies) with 0.1 mm silica beads (MP Biomedicals). After centrifugation, supernatants were extracted with chloroform, and RNA was precipitated with isopropanol and glycogen. RNA pellets were washed with 75% ethanol and dissolved in RNase-free water. Contaminant DNA was removed by incubation with DNase (TURBO DNA-free kit, Life Technologies). RNA cleanup was performed with the RNeasy Mini Kit (Qiagen). RNA integrity and quality were assessed with an Agilent Bioanalyzer device (Agilent Technologies).
RNA-seq libraries were prepared using the Stranded Total RNA Prep and Ligation with Ribo-Zero Plus kit (Illumina) and sequenced using a NextSeq 2000 device (Illumina).

value: {delta}whiB6::promoter WT - whiB6 T51P

tag: batch

tag: replicate

tag: growth medium


title: C3H10T1-2_NSD12_SETD2_TKO_H3K36me2_rep1


title: Hepa16_FOXA1_Veh

value: FOXA1(active motif, #39837 and abcam, #ab170933)


title: GH1397_P5


title: C3H10T1-2_NSD12_SETD2_TKO_H3K36me1_rep1

value: H3K36me1 (Cell Signaling, 14111)


title: C3H10T1-2_NSD12_SETD2_TKO_H3K36me1_rep2


title: Hepa16_FOXA1_SR8278

value: liver cancer


title: H37Rv whiB6 mutant complemented promoter WT - whiB6 T51P Rep1


title: H37Rv whiB6 mutant complemented promoter WT - whiB6 T51P Rep2


title: C3H10T1-2_NSD12_DKO_input_rep2

value: NSD1/2 double knock-out


title: C3H10T1-2_NSD12_DKO_input_rep1


title: C3H10T1-2_NSD12_SETD2_TKO_H3K36me2_rep3


title: H37Rv whiB6 mutant complemented promoter WT - whiB6 WT Rep3

value: {delta}whiB6::promoter WT - whiB6 WT


title: GH1397_P3


title: GH1397_P2


title: LR_051_from_right_to_left

city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

country: Japan

institute: Aoyama Gakuinn University

description:
DjTomo2-279
Lasy-Seq ver. 1.1
LR.csv

data_processing:
The BCL (base calls) binary is converted into FASTQ using illumina package bcl2fastq2-v2.20.0. The demultiplexing option (--barcode-mismatches) was set to default (value : 0).
Read 1 reads were processed with fastp (version 0.21.0) using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to a D. japonica reference sequences, using BWA mem (version 0.7.17-r1188) with the default parameters. The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0).
D. japonica reference transcriptome sequences deposited in http://www.planarian.jp/download.html

organism: Dugesia japonica

source_name: whole

extract_protocol: Lasy-Seq version 1.1 (Kashima et al., Frontiers in bioinformatics, 2021)

treatment_protocol: Direct-TRI (Ujibe et al., bio-protocol, 2021)

value: whole

value: AF


title: H37Rv whiB6 mutant complemented promoter WT - whiB6 WT Rep2


title: LR_049_from_right_to_left

description:
DjTomo2-277
Lasy-Seq ver. 1.1
LR.csv


title: GH1394_P6


title: LR_048_from_right_to_left

description:
DjTomo2-276
Lasy-Seq ver. 1.1
LR.csv


title: H37Rv whiB6 mutant complemented promoter WT - whiB6 WT Rep1


title: C3H10T1-2_NSD12_DKO_H3K36me3_rep2

value: Mouse mesechymal stem cells


title: C3H10T1-2_NSD12_DKO_H3K36me3_rep1


title: LR_047_from_right_to_left

description:
DjTomo2-275
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD12_DKO_H3K36me2_rep2


title: GH1397_P4


title: H37Rv whiB6 mutant Rep3


title: GH1394_P4


title: H37Rv whiB6 mutant Rep2


title: LR_050_from_right_to_left

description:
DjTomo2-278
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD12_DKO_H3K36me2_rep1


title: GH1394_P3


title: LR_046_from_right_to_left

description:
DjTomo2-274
Lasy-Seq ver. 1.1
LR.csv


title: LR_045_from_right_to_left

description:
DjTomo2-273
Lasy-Seq ver. 1.1
LR.csv


title: JJ012 _re1

type: RNA

city: Taichung

first: Ya

middle: Huey

last: Chen

address: No. 100號, Section 1, Jingmao Road, Beitun District, Taichung City, 406

department: Cancer Center

country: Taiwan

institute: China Medical University

description: Gene expression from cancer

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images were analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: chondrosarcoma cell line

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Human primary chondrocytes were maintained in Dulbecco’s modified Eagle’s medium (DMEM)/F12 media, 10% fetal bovine serum (FBS) and 50 μg/ml 2-phospho-L-ascorbic acid salts.

extract_protocol: Total RNA was isolated by using Trizol.

value: chondrosarcoma

tag: patient

value: Male, 39Y


title: N-P-chon_re1

description: Gene expression from normal chondrocyte

source_name: Normal osteoarthritis patient chondrocyte cells

value: chondrocyte

value: Male, 35Y


title: S-P-chon_re1

description: Gene expression from osteoarthritis chondrocyte

source_name: Severe osteoarthritis patient chondrocyte cells


title: GH1394_P2

value: 3D culture

value: 3D fulture from primary mouse cells


title: C3H10T1-2_NSD12_DKO_H3K36me1_rep2


title: head_young_btbr_embryo [h_y_b__2_1]

status: Public on Sep 26 2024

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

hyb_protocol: According to the manufacturer’s protocol.

scan_protocol: The acquisition and analysis of hybridization intensities were performed using an Agilent DNA Microarray Scanner G2505C. Data were extracted and the background subtracted using the standard procedures included in the Agilent Feature Extraction Software version 10.7.3.1.

data_processing: Statistical analysis of raw data was carried out using the default protocol of the Partek Genomics Suite. For each probe data were logged, normalized using quantile normalization, and annotated using the “GPL21163_noParents.an.txt” annotation file from the Gemma database (Lim et al., 2021). Results were adjusted for multiple comparisons using the FDR step-up method. Genes were considered to be differentially expressed if their absolute values of logged fold changes (base 2 logarithms) reached 1.5 and the adjusted p-value was lower than 0.05.

label_protocol: Genome-wide transcriptomic analysis was performed using SurePrint G3 Mouse GE v2 8x60K microarrays (GPL21163, Agilent Technologies, USA) and Agilent Technologies Reagent Set according to the manufacturer’s instructions. 100 ng of RNA of each sample (n=4 fetuses and placentas per maternal age group per tissue, only male offspring were selected for microarrays purposes) was labeled using Low Input QuickAmp Labeling Kit One-Color (Agilent Technologies, USA) and hybridized on the microarrays according to the manufacturer’s protocol.

extract_protocol: RNA for transcriptomic analyses was extracted from placentas and fetal heads following the manufacturers’ instructions. Total RNA extraction was conducted using the Universal RNA Purification Kit (Eurx, Poland), and included a DNase treatment (Eurx, Poland). The quantity and purity of isolated nucleic acids were validated using a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific, USA). RNA integrity of selected samples was additionally validated using a Bioanalyzer 2100 microcapillary electrophoresis device (Agilent, USA).

treatment_protocol: Fetuses with their placentas were collected from pregnant BTBR and B6 old (42-65 weeks old, AMA) and young (10-23 weeks old, YMA) females. Mice were ethically euthanized by cervical dislocation 12 days after plug detection. The uterus was isolated from the abdominal cavity followed by dissection of the conceptuses by separating the fetus from the placenta. Then, placentas and fetuses were gently dried with a paper towel and weighed, and the fetal head was separated from the rest of the body. All tissues were then immediately snap-frozen in liquid nitrogen and stored at -80°C until further analyses.

value: head

tag: age

value: young

value: btbr


title: H37Rv WT Rep3

value: wild type


title: LR_044_from_right_to_left

description:
DjTomo2-272
Lasy-Seq ver. 1.1
LR.csv


title: KW1401_P6

value: Tumor


title: LR_043_from_right_to_left

description:
DjTomo2-271
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD12_DKO_H3K36me1_rep1

value: H3K36me1 (Cell Signaling, 14111)


title: C3H10T1-2_H3K36M_OE_input

value: H3K36M overexpression


title: H37Rv WT Rep2


title: KW1401_P5


title: H37Rv WT Rep1


title: GH1394_P5


title: LR_042_from_right_to_left

description:
DjTomo2-270
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_H3K36M_OE_H3K36me3_rep2

value: H3K36me3 (Active Motif, 61101)


title: H37Rv kdpDE mutant complemented kdpDE delCA woK Rep3

growth_protocol: Bacterial strains were cultured in triplicate in Middlebrook 7H9 broth supplemented with 10% OADC (oleic acid, albumin, dextrose, and catalase, BD) and 0.05% Tween 80 containing either 7 mM or 0 mM K+ in which case KH2PO4 was replaced by NaH2PO4 at 37°C. Cultures were harvested when reaching the exponential phase of growth with a final OD at 600 nm between 0.4 and 0.8.

value: {delta}kdpDE::kdpDE {delta}CA

value: 7H9 with 0 mM K+


title: KW1401_P4


title: H37Rv whiB6 mutant Rep1


title: LR_041_from_right_to_left

description:
DjTomo2-269
Lasy-Seq ver. 1.1
LR.csv

value: whole

value: AF


title: C3H10T1-2_H3K36M_OE_H3K36me3_rep1

value: Mouse mesechymal stem cells


title: KW1401_P3


title: H37Rv kdpDE mutant complemented kdpDE delCA woK Rep1


title: LR_040_from_right_to_left

description:
DjTomo2-268
Lasy-Seq ver. 1.1
LR.csv


title: KW1401_P2


title: C3H10T1-2_H3K36M_OE_H3K36me2_rep2

value: H3K36me2 (Cell Signaling, 2901)


title: LR_039_from_right_to_left

description:
DjTomo2-267
Lasy-Seq ver. 1.1
LR.csv


title: LR_038_from_right_to_left

description:
DjTomo2-266
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_H3K36M_OE_H3K36me2_rep1


title: H37Rv kdpDE mutant complemented kdpDE delCA woK Rep2


title: GH1493_P8


title: C3H10T1-2_H3K36M_OE_H3K36me1_rep2


title: H37Rv kdpDE mutant woK Rep3

value: {delta}kdpDE


title: C3H10T1-2_H3K36M_OE_H3K36me1_rep1


title: H37Rv kdpDE mutant woK Rep2


title: GH1493_P6

value: 3D culture


title: H37Rv kdpDE mutant woK Rep1


title: LR_036_from_right_to_left

description:
DjTomo2-264
Lasy-Seq ver. 1.1
LR.csv


title: LR_037_from_right_to_left

description:
DjTomo2-265
Lasy-Seq ver. 1.1
LR.csv


title: GH1493_P5

value: 3D fulture from primary mouse cells


title: LR_035_from_right_to_left

description:
DjTomo2-263
Lasy-Seq ver. 1.1
LR.csv


title: H37Rv WT woK Rep3


title: C3H10T1-2_SETD2_KO_input_rep2

value: SETD2 knock-out


title: GH1493_P4


title: LR_034_from_right_to_left

description:
DjTomo2-262
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_SETD2_KO_input_rep1


title: H37Rv WT woK Rep2


title: GH1493_P3


title: H37Rv WT woK Rep1


title: H37Rv kdpDE mutant complemented kdpDE delCA wK Rep3

value: 7H9 with 7 mM K+


title: LR_033_from_right_to_left

description:
DjTomo2-261
Lasy-Seq ver. 1.1
LR.csv


title: GH1493_P2


title: C3H10T1-2_SETD2_KO_H3K36me3_rep3


title: C3H10T1-2_SETD2_KO_H3K36me3_rep2


title: GH1493_P7


title: LR_032_from_right_to_left

description:
DjTomo2-260
Lasy-Seq ver. 1.1
LR.csv


title: GH1493_P1


title: C3H10T1-2_SETD2_KO_input_rep3


title: LR_030_from_right_to_left

description:
DjTomo2-258
Lasy-Seq ver. 1.1
LR.csv


title: LR_031_from_right_to_left

description:
DjTomo2-259
Lasy-Seq ver. 1.1
LR.csv


title: H37Rv kdpDE mutant complemented kdpDE delCA wK Rep2


title: GH1493_Alv_Org

value: Normal


title: C3H10T1-2_SETD2_KO_H3K36me3_rep1


title: GH1493_AT2


title: C3H10T1-2_SETD2_KO_H3K36me2_rep3


title: LR_029_from_right_to_left

description:
DjTomo2-257
Lasy-Seq ver. 1.1
LR.csv


title: AF1338_P8


title: LR_028_from_right_to_left

description:
DjTomo2-256
Lasy-Seq ver. 1.1
LR.csv


title: H37Rv kdpDE mutant wK Rep2


title: C3H10T1-2_SETD2_KO_H3K36me2_rep2


title: H37Rv kdpDE mutant wK Rep3


title: C3H10T1-2_SETD2_KO_H3K36me2_rep1


title: H37Rv kdpDE mutant wK Rep1


title: LR_027_from_right_to_left

description:
DjTomo2-255
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_SETD2_KO_H3K36me1_rep3


title: AF1338_P6


title: H37Rv WT wK Rep3

value: wild type


title: AF1338_P5

value: Tumor


title: H37Rv kdpDE mutant complemented kdpDE delCA wK Rep1


title: LR_025_from_right_to_left

description:
DjTomo2-253
Lasy-Seq ver. 1.1
LR.csv


title: H37Rv WT wK Rep2


title: LR_026_from_right_to_left

description:
DjTomo2-254
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_SETD2_KO_H3K36me1_rep1

value: H3K36me1 (Cell Signaling, 14111)


title: AF1338_P4


title: H37Rv WT wK Rep1


title: AF1338_P3


title: C3H10T1-2_NSD3_KO_input_rep3

value: NSD3 knock-out


title: LR_024_from_right_to_left

description:
DjTomo2-252
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD3_KO_input_rep2


title: LR_023_from_right_to_left

description:
DjTomo2-251
Lasy-Seq ver. 1.1
LR.csv


title: BACL-CHIR99021 rep2

city: Chengdu

first: Yan

last: Li

state: Sichuan

address: 375#Panda Road,Northern Suburb

institute: Chengdu Research Base of Giant Panda Breeding

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto.
Assembly: CPB_AME_v1
Supplementary files format and content: tab-delimited text files include TPM and counts for each sample.

organism: Ailuropoda melanoleuca

source_name: primary fibroblast cells

extract_protocol:
Total RNA per sample was extracted using Rneasy mini plus kit (Qiagen). A total amount of 2 μg RNA per sample was used for the library construction.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library  Prep  Kit  for  Illumina following  the  manufacturer’s recommendations.


title: AF1338_P7


title: BACL-CHIR99021 rep1


title: BACL control rep2

value: BACL control


title: AF1338_P1


title: AF1338_P2


title: C3H10T1-2_NSD3_KO_input_rep1


title: LR_022_from_right_to_left

description:
DjTomo2-250
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD3_KO_H3K36me3_rep3

value: H3K36me3 (Active Motif, 61101)


title: LR_021_from_right_to_left

description:
DjTomo2-249
Lasy-Seq ver. 1.1
LR.csv


title: BACL control rep1


title: AF1338_Alv_Org


title: LR_020_from_right_to_left

description:
DjTomo2-248
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD3_KO_H3K36me3_rep2


title: AF1338_AT2


title: C3H10T1-2_SETD2_KO_H3K36me1_rep2


title: BACL LB GPiPSCs rep2

value: BACL LB GPiPSCs


title: LR_019_from_right_to_left

description:
DjTomo2-247
Lasy-Seq ver. 1.1
LR.csv

value: whole


title: C3H10T1-2_NSD3_KO_H3K36me3_rep1


title: C3H10T1-2_NSD3_KO_H3K36me2_rep3


title: BACL LB GPiPSCs rep1


title: LR_018_from_right_to_left

description:
DjTomo2-246
Lasy-Seq ver. 1.1
LR.csv

value: AF


title: GFP+ cells carrying control shRNA (shRen) or shRNAs targeting Dnmt1, replication 3

library_source: transcriptomic single cell

data_processing:
FASTQ files of single-cell RNA-sequencing data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version 5.0.0). Reads were aligned to a custom GRCm38 / mm10 reference containing additional transgenes used in the study. The generated cell-gene count matrices were analyzed using a combination of published packages and custom scripts in either the scanpy (v 1.6.0) / AnnData (v. 0.7.5, Python) or Seurat (v 3.0.2, R) ecosystems.
Assembly: GRCm38/mm10
Supplementary files format and content: .txt matrix file

source_name: lung

growth_protocol: Cells were isolated from animals. No additional growth is involved.

extract_protocol:
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq 6000 platform (Illumina).
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq 6000 platform (Illumina).

treatment_protocol: Aged (> 2 years old) and young (12-16 weeks old) Rosa26-mTmG mice were infected by either control shRNA (Ren713) or shRNAs targeting DNMT1. Due to the Cre recombinase, cells bearing shRNAs were turned green (GFP positive). Eleven days post-infection,  lungs were harvested and GFP+ epithelial cells or other cells were collected for scRNA-Seq.

value: lung

value: Primary AT2 cells


title: Hashtag sequencing of replicate 3 data


title: A83-01 D16 rep2


title: Hashtag sequencing of replicate 2 data


title: C3H10T1-2_NSD3_KO_H3K36me2_rep2

value: H3K36me2 (Cell Signaling, 2901)

value: Mouse mesechymal stem cells


title: C3H10T1-2_NSD3_KO_H3K36me2_rep1


title: A83-01 D16 rep1


title: LR_017_from_right_to_left

description:
DjTomo2-245
Lasy-Seq ver. 1.1
LR.csv


title: GFP+ cells carrying control shRNA (shRen) or shRNAs targeting Dnmt1, replication 2


title: LR_016_from_right_to_left

description:
DjTomo2-244
Lasy-Seq ver. 1.1
LR.csv


title: control D16 rep2

value: control D16


title: C3H10T1-2_NSD3_KO_H3K36me1_rep3


title: LR_015_from_right_to_left

description:
DjTomo2-243
Lasy-Seq ver. 1.1
LR.csv


title: control D16 rep1


title: LR_014_from_right_to_left

description:
DjTomo2-242
Lasy-Seq ver. 1.1
LR.csv


title: Hashtag sequencing of replicate 1 data


title: XR GPiPSCs rep2

value: XR GPiPSCs


title: LR_013_from_right_to_left

description:
DjTomo2-241
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD3_KO_H3K36me1_rep1


title: XR GPiPSCs rep1


title: GFP+ cells carrying control shRNA (shRen) or shRNAs targeting Dnmt1, replication 1


title: C3H10T1-2_NSD3_KO_H3K36me1_rep2


title: LR_012_from_right_to_left

description:
DjTomo2-240
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD2_KO_input_rep3

value: NSD2 knock-out


title: Hashtag sequencing of replicate 3 data

treatment_protocol: Aged (> 2 years old) and young (12-16 weeks old) Rosa26-mTmG mice were infected by either control shRNA (Ren713) or shRNAs targeting Nupr1. Due to the Cre recombinase, cells bearing shRNAs were turned green (GFP positive). Five days post-infection, mice were exposed to hyperoxia-induced alveolar injury. Four weeks after injury (when lung injury healedin general), lungs were harvested and GFP+ epithelial cells or other cells were collected for scRNA-Seq.

value: Normal


title: GFP+ cells carrying control shRNA (shRen) or shRNAs targeting Nupr1), replication 3


title: stageⅡ D8rep2

value: stageⅡ D8


title: Hashtag sequencing of replicate 2 data


title: C3H10T1-2_NSD2_KO_input_rep2


title: LR_011_from_right_to_left

description:
DjTomo2-239
Lasy-Seq ver. 1.1
LR.csv


title: LR_010_from_right_to_left

description:
DjTomo2-238
Lasy-Seq ver. 1.1
LR.csv


title: stageⅡ D8rep1


title: C3H10T1-2_NSD2_KO_input_rep1


title: GFP+ cells carrying control shRNA (shRen) or shRNAs targeting Nupr1), replication 2


title: Hashtag sequencing of replicate 1 data


title: stageǀ D24rep2

value: stageǀ D24


title: stageǀ D24rep1


title: C3H10T1-2_NSD2_KO_H3K36me3_rep3


title: LR_008_from_right_to_left

description:
DjTomo2-236
Lasy-Seq ver. 1.1
LR.csv


title: GFP+ cells carrying control shRNA (shRen) or shRNAs targeting Nupr1), replication 1


title: LR_009_from_right_to_left

description:
DjTomo2-237
Lasy-Seq ver. 1.1
LR.csv


title: LR_006_from_right_to_left

description:
DjTomo2-234
Lasy-Seq ver. 1.1
LR.csv


title: stageǀ D8 rep2

value: stageǀ D8


title: LR_007_from_right_to_left

description:
DjTomo2-235
Lasy-Seq ver. 1.1
LR.csv


title: lung tissue transferred ALDHdim cells, rep5

city: Hiroshima-shi

first: Shugo

last: Inada

state: Hiroshima

address: 5-17-5 Midorii

institute: Hiroshima University

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCm38
Supplementary files format and content: DESeq2 normalized count

source_name: lung administered bleomycin

extract_protocol:
The lung tissues of bleomycin-induced pulmonary fibrosis were homogenized using 1 mL TRIzol reagent (Life Technologies) and total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: lung administered bleomycin

value: WT

value: injection with bone marrow cells with low ALDH activity (ALDHdim)


title: stageǀ D8 rep1


title: LR_005_from_right_to_left

description:
DjTomo2-233
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD2_KO_H3K36me2_rep3


title: lung tissue transferred ALDHdim cells, rep4


title: C3H10T1-2_NSD2_KO_H3K36me3_rep1

value: H3K36me3 (Active Motif, 61101)


title: C3H10T1-2_NSD2_KO_H3K36me2_rep2


title: XR PF rep1

value: XR PF


title: LR_004_from_right_to_left

description:
DjTomo2-232
Lasy-Seq ver. 1.1
LR.csv

value: whole

value: AF


title: C3H10T1-2_NSD2_KO_H3K36me2_rep1


title: lung tissue transferred ALDHdim cells, rep2


title: LB GPiPSCs rep3

value: LB GPiPSCs


title: LR_003_from_right_to_left

description:
DjTomo2-231
Lasy-Seq ver. 1.1
LR.csv


title: C3H10T1-2_NSD2_KO_H3K36me1_rep3

value: H3K36me1 (Cell Signaling, 14111)


title: lung tissue transferred ALDHdim cells, rep1


title: LB GPiPSCs rep2


title: C3H10T1-2_NSD2_KO_H3K36me3_rep2

value: Mouse mesechymal stem cells


title: C3H10T1-2_NSD2_KO_H3K36me1_rep2


title: LR_002_from_right_to_left

description:
DjTomo2-230
Lasy-Seq ver. 1.1
LR.csv


title: LB GPiPSCs rep1


title: C3H10T1-2_NSD2_KO_H3K36me1_rep1


title: XR PF rep2


title: lung tissue transferred ALDHbr cells, rep4

value: injection with bone marrow cells with high ALDH activity (ALDHbr)


title: DV_028_from_dorsal_to_ventral

description:
DjTomo2-228
Lasy-Seq ver. 1.1
DV.csv


title: lung tissue transferred ALDHdim cells, rep3


title: C3H10T1-2_NSD1_KO_input_rep3

value: NSD1 knock-out


title: lung tissue transferred ALDHbr cells, rep3


title: LB PF rep2

value: LB PF


title: lung tissue transferred ALDHbr cells, rep2


title: C3H10T1-2_NSD1_KO_input_rep1


title: DV_026_from_dorsal_to_ventral

description:
DjTomo2-226
Lasy-Seq ver. 1.1
DV.csv


title: DV_025_from_dorsal_to_ventral

description:
DjTomo2-225
Lasy-Seq ver. 1.1
DV.csv


title: male bone marrow cells with high ALDH activity, rep3

source_name: bone marrow cells obtained from male mice

extract_protocol:
The bone marrow cells obtained from male and female mice were suspended using 1 mL TRIzol reagent (Life Technologies) and total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.


title: C3H10T1-2_NSD1_KO_H3K36me3_rep3


title: HEK293T, (B9 clone + KRABY46A), nodox, H3K9ac, rep2

city: Stanford

first: Taihei

last: Fujimori

state: California

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

data_processing:
Make genome file with synthetic reporter integration
Align reads to genome with Bowtie 2 version 2.3.4.1 with command 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x {reference genome} -p 16 -1 {first mate of pair} -2 {second mate of pair} -S {output SAM file name}'
Convert SAM files to BAM files and subsequently sort and index BAM files with Samtools version 1.7
Quantify and mark duplicates with Picard version 11.0.7 with command 'java -jar {picard tool} MarkDuplicates -I {input sorted BAM file} -O {output deduplicated BAM file} -M {output metrics file} --REMOVE_DUPLICATES true'
Normalize by reads per million with bamCoverage version 3.3.1 with command 'bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file}  --outFileFormat bedgraph --extendReads --centerReads -p 12 --binSize 10 --normalizeUsing CPM'
Assembly: hg38
Supplementary files format and content: bedgraph files
Library strategy: CUT&RUN

growth_protocol: DMEM-GlutaMAX media (10566024, Gibco) supplemented with 1x Penicillin-Streptomycin-Glutamine (10378016, Gibco) and 10 % FBS (FB-15, Omega Scientific)

extract_protocol:
Cells were permeabilized by 0.025% digitonin followed by incubation with antibody and Mnase excision using CUTANA ChIC/CUT&RUN Kit (14-1048, EpiCypher)
Library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, New England Biolabs) for H3K9me3, H3K4me3 (positive control), IgG (negative control) or CUTANA™ CUT&RUN Library Prep Kit with Primer Set 1 (14-1001, EpiCypher) for other modifications. Library fragment sizes were checked with Agilent 2100 Bioanalyzer.

value: Human embryonic kidney


title: HEK293T, (B9 clone + KRAB), dox1day, H3K9me3, rep1


title: male bone marrow cells with high ALDH activity, rep2

value: bone marrow cells obtained from male mice


title: C3H10T1-2_NSD1_KO_H3K36me3_rep2


title: DV_024_from_dorsal_to_ventral

description:
DjTomo2-224
Lasy-Seq ver. 1.1
DV.csv


title: lung tissue transferred ALDHbr cells, rep5


title: HEK293T, (B9 clone + KRABY46A), nodox, H3K9ac, rep1


title: LR_001_from_right_to_left

description:
DjTomo2-229
Lasy-Seq ver. 1.1
LR.csv


title: DV_023_from_dorsal_to_ventral

description:
DjTomo2-223
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRAB), dox1day, H3K9me3, rep2


title: C3H10T1-2_NSD1_KO_H3K36me3_rep1


title: DV_027_from_dorsal_to_ventral

description:
DjTomo2-227
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRABY46A), dox5days, H3K9ac, rep2


title: male bone marrow cells with high ALDH activity, rep1


title: DV_022_from_dorsal_to_ventral

description:
DjTomo2-222
Lasy-Seq ver. 1.1
DV.csv


title: LB PF rep1


title: C3H10T1-2_NSD1_KO_H3K36me2_rep3

value: H3K36me2 (Cell Signaling, 2901)


title: C3H10T1-2_NSD1_KO_input_rep2


title: female bone marrow cells with high ALDH activity, rep2

source_name: bone marrow cells obtained from female mice


title: DV_021_from_dorsal_to_ventral

description:
DjTomo2-221
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRABY46A), dox5days, H3K9ac, rep1


title: DV_020_from_dorsal_to_ventral

description:
DjTomo2-220
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRABY46A), dox1day, H3K9me3, rep2


title: C3H10T1-2_NSD1_KO_H3K36me2_rep2


title: female bone marrow cells with high ALDH activity, rep1

value: bone marrow cells obtained from female mice


title: HEK293T, (B9 clone + KRABY46A), dox1day, H3K9me3, rep1


title: C3H10T1-2_NSD1_KO_H3K36me1_rep3


title: HEK293T, (B9 clone + KRABY46A), dox1day, H3K9ac, rep1


title: female bone marrow cells with high ALDH activity, rep3


title: DV_017_from_dorsal_to_ventral

description:
DjTomo2-217
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRABY46A), dox1day, H3K9ac, rep2


title: C3H10T1-2_NSD1_KO_H3K36me1_rep1


title: CKO H3K27ac CUT&Tag Rep2

city: shanghai

first: bao

last: wang

address: jin zun road

institute: shanghai jiao tong university school of medicine

data_processing:
For CUT&Tag data analysis, raw sequenced fastq data were trimmed using TrimGalore (version 0.6.6) with the default parameters. Trimmed sequence reads were then aligned to the mouse reference genome (mm10) using bowtie261 (https://github.com/BenLangmead/bowtie2) with the parameters --very-sensitive -X 2000. Duplicates of mapped reads were removed using sambamba62 (version 0.8.1). The mapped reads were subsequently shifted before peak calling using the alignmentSieve --ATACshift function from the deepTools package 39 (version 3.3.1). For each CUT&Tag library, we generated the bigwig files at 10bp bin size using the bamCoverage function from DeepTools and normalized by RPKM. Peak calling for CUT&Tag data was performed using SEACR (https://github.com/FredHutch/SEACR) under the stringent mode with default parameters.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: spleen

growth_protocol: T cells were cultured in RPMI-1640 medium, supplemented with 10% FBS, 1% β-mercaptoethanol and 1% penicillin-streptomycin. DynabeadTM mouse activator CD3/CD28 (Thermofisher, 11453D) was added to the isolated cells, and the cells were activated for 24 hours.

extract_protocol:
DNA was extracted by DNA clean beads
CUT&Tag sample preparation and experiments were performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD901-01) as described before (Kaya-Okur et al., 2019) with minimal changes. Briefly, cells were immobilized using ConA beads. Then, cells were permeabilized and incubated with different primary antibodies (anti-H3K27ac, Abcam 177178) overnight for 4°C and then treated with secondary antibodies (Goat anti-Rabbit IgG) for 1 h at room temperature. Afterward, cells were incubated with pG-Tn5 transposase for 1 h and then cells were washed twice and incubated at 37 °C for 1 h. DNA of each sample was extracted using phenol-chloroform-isoamyl alcohol and amplified by PCR. All CUT&Tag libraries were sequenced on the Illumina Nova Seq 6000 platform at PE150 mode.

value: spleen

value: T cell


title: CON H3K27ac CUT&Tag Rep2


title: CKO H3K27ac CUT&Tag Rep1


title: DV_016_from_dorsal_to_ventral

description:
DjTomo2-216
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRAB), dox5days-release5days, H3K9me3, rep2


title: C3H10T1-2_ASH1L_KO_input_rep3

value: ASH1L knock-out


title: HEK293T, (B9 clone + KRAB), dox5days-release5days, H3K9me3, rep1


title: DV_015_from_dorsal_to_ventral

description:
DjTomo2-215
Lasy-Seq ver. 1.1
DV.csv


title: C3H10T1-2_ASH1L_KO_input_rep2


title: CON H3K27ac CUT&Tag Rep1


title: Hsd-3_A

city: Hong Kong

first: CHUANXIN

last: ZHONG

state: Hong Kong

address: ACC205, Hong Kong Baptist University, 15 Baptist University Road Kowloon Tong

institute: HONG KONG BAPTIST UNIVERSITY

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using bowtie2 (v2.11.1)
Significant peak regions of each sample were identified using MACS2 (v2.1.2) with parameters "-q 0.05 --nomodel --shift -100 --extsize 200"
Assembly: mm10
Supplementary files format and content: diffATAC peaks
Supplementary files format and content: diffATAC

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
Chromatin DNA was isolated from cells for library construction using EpiTM ATAC-seq kit(Epibiotek, cat. no EPI20180202)

value: pre-osteoblastic cells

value: Hsd11b3 overexpression

value: 11-DHC incubation


title: C3H10T1-2_ASH1L_KO_input_rep1

extract_protocol:
Approximately 20 million mMSC cells per cell line were used. Crosslinking was performed in 150 mm cell culture plates using 1% formaldehyde (Sigma) at room temperature with gentle rocking for 10 minutes. The crosslinking reaction was quenched using 1.25 M Glycine with gentle rocking at room temperature for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped, and then washed twice more with ice-cold PBS. Crosslinked pellets were resuspended in 500 μl cell lysis buffer (5 mM pH 8.5 PIPES, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Samples were centrifuged and pellets were resuspended in 500 μl of nuclei lysis buffer (50 mM pH 8.0 Tris-HCl, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Sonication of lysed nuclei was performed using the BioRuptor UCS-300 at maximum intensity for 75-90 cycles (10s on, 20s breaks). Sonication efficiency to achieve fragments between 150 - 500 bp was evaluated using gel electrophoresis on a reversed-crosslinked and purified aliquot from each sample. After sonication, chromatin was diluted to reduce SDS levels to 0.1% and concentrated using Nanosep 10K OMEGA (Pall) columns. Prior to the chromatin immunoprecipitation (ChIP) reaction, 2% sonicated Drosophila S2 cell chromatin was spiked into each sample for quantification of total levels of histone marks. The ChIP reactions were performed using the Diagenode SX-8G IP-Star Compact and Diagenode automated iDeal ChIP-seq Kit for Histones. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hrs, followed by a 20 min wash cycle using the provided wash buffers (Diagenode Immunoprecipitation Buffers, iDeal ChIP-seq Kit for Histones). Reverse cross-linking was then performed using 5M NaCl at 65℃ for 4 hrs. ChIP samples were then treated with 2 μl RNase Cocktail at 65℃ for 30 min followed by 2 μl Proteinase K at 65℃ for 30 min. Samples were then purified with QIAGEN MinElute PCR purification kit (QIAGEN) as per the manufacturer’s protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
ChIP-seq library preparation was performed using the Kapa Hyper Prep library preparation reagents following the manufacturer’s protocol (Kapa Hyper Prep Kit, Roche 07962363001). ChIP libraries were sequenced using the Illumina HiSeq 4000 at 50 bp single reads or NovaSeq 6000 at 100 bp single reads. ATAC-seq library preparation was performed according to the Omni-ATAC protocol. 50,000 C3H10T1/2 cultured cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 rcf for 5 min in a pre-chilled (4°C) fixed-angle centrifuge. After centrifugation, supernatant was aspirated and cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL and digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 rcf in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (2x TD Buffer, 100 nM final transposase, 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O ) (Illumina Tagment DNA Enzyme and Buffer Small Kit, 20034197). Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up with DNA Clean and Concentrator 5 columns (Zymo Research). Illumina Nextera DNA Unique Dual Indexes Set C (Illumina, 20027215) were added and amplified (12 cycles) using NEBNext 2x MasterMix. Sequencing of the ATAC-Seq libraries was performed on the Illumina NovaSeq 6000 system using 100-bp paired-end sequencing.


title: Hsd-2_A

value: Hsd11b2 overexpression


title: DV_019_from_dorsal_to_ventral

description:
DjTomo2-219
Lasy-Seq ver. 1.1
DV.csv

value: whole

value: AF


title: DV_014_from_dorsal_to_ventral

description:
DjTomo2-214
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRAB), dox5days-release2days, H3K9me3, rep1


title: C3H10T1-2_NSD1_KO_H3K36me2_rep1

value: Mouse mesechymal stem cells


title: C3H10T1-2_ASH1L_KO_H3K36me3_rep3

value: H3K36me3 (Active Motif, 61101)


title: HEK293T, (B9 clone + KRAB), dox5days-release2days, H3K9me3, rep2


title: C3H10T1-2_NSD1_KO_H3K36me1_rep2

value: H3K36me1 (Cell Signaling, 14111)

value: NSD1 knock-out


title: DV_018_from_dorsal_to_ventral

description:
DjTomo2-218
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRAB), dox5days-release10days, H3K9me3, rep2

value: Human embryonic kidney


title: DV_012_from_dorsal_to_ventral

description:
DjTomo2-212
Lasy-Seq ver. 1.1
DV.csv


title: C3H10T1-2_ASH1L_KO_H3K36me3_rep2


title: GFP-3_A

value: WT


title: C3H10T1-2_ASH1L_KO_H3K36me3_rep1


title: HEK293T, (B9 clone + KRAB), dox5days-release10days, H3K9me3, rep1


title: GFP-2_A


title: DV_013_from_dorsal_to_ventral

description:
DjTomo2-213
Lasy-Seq ver. 1.1
DV.csv


title: DV_010_from_dorsal_to_ventral

description:
DjTomo2-210
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + KRAB), dox1day, H3K9ac, rep2


title: C3H10T1-2_ASH1L_KO_H3K36me2_rep3

value: H3K36me2 (Cell Signaling, 2901)


title: HEK293T, (B9 clone + KRAB), dox1day, H3K9ac, rep1


title: C3H10T1-2_ASH1L_KO_H3K36me2_rep1


title: Hsd-3_m

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: All.fpkm.anno
Supplementary files format and content: Differential genes

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction.

value: Hsd11b1 overexpression


title: Hsd-1_m


title: DV_008_from_dorsal_to_ventral

description:
DjTomo2-208
Lasy-Seq ver. 1.1
DV.csv


title: DV_007_from_dorsal_to_ventral

description:
DjTomo2-207
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + HDAC4), dox1day, H3K9ac, rep1


title: Hsd-2_m


title: Hsd-1_A


title: DV_009_from_dorsal_to_ventral

description:
DjTomo2-209
Lasy-Seq ver. 1.1
DV.csv


title: C3H10T1-2_ASH1L_KO_H3K36me1_rep2

data_processing:
Raw ChIP-Seq reads were aligned to a combined reference of mm10 and dm6 genome assembly using BWA version 0.7.17 with default parameters. Afterwards, they were filtered using a cut-off of MAPQ < 3 using Samtools v.1.18.
Raw ATAC-Seq reads were trimmed and filtered for quality using Trimmomatic v0.39. Trimmed reads were mapped to the mm10 genome assembly using Bowtie2 v2.5.1, and non-uniquely mapping reads were removed. Afterwards, the reads were adjusted by shifting all positive-strand reads 4 bp downstream and all negative-strand reads 5 bp upstream to the center of the reads on the transposase binding event.
For H3K36me2 NSD1/2/3-SETD2-QKO and NSD1/2/3-SETD2-ASH1L-QuiKO replicates, samclip v.0.2 (samtools view -h in.bam | samclip --ref ref.fa | samtools sort > out.bam) was used to filter contaminated sequences prior to alignment.
ENCODE blacklisted regions were excluded from all analyses.
For ATAC-Seq samples, peak calling was performed on each replicate using MACS2 v2.2.6 with ‘-extsize 200 -shift -100 -nomodel’ parameters. To find a set of reproducible peaks across ATAC-Seq replicates, the irreproducible discovery rate (IDR) was calculated and peaks with an IDR greater than 0.05 across every pair of replicates were excluded.
bigWig files were generated using deepTools v3.5.3 bamCoverage with parameters '-b ${samp}.sorted.bam -o ${samp}.cpm.bw -p $nprocs --normalizeUsing CPM --centerReads -e 200'.
Replicates were merged using the deepTools v3.5.3 bigwigCompare tool. The initial merging step employed these parameters: '-b1 rep1 -b2 rep2 $outdir --operation mean -bs 200 -o $merged.step1.cpm.bw' while the final merging step utilized the following parameters: '-b1 $merged.step1.cpm.bw -b2 rep3 $outdir --operation mean -bs 200 -o $merged.final.cpm.bw.'
Assembly: mm10
Supplementary files format and content: bigWig


title: GFP-3_m


title: HEK293T, (B9 clone + DNMT3B), nodox, H3K9me3, rep2


title: HEK293T, (B9 clone + DNMT3B), nodox, H3K9me3, rep1


title: C3H10T1-2_ASH1L_KO_H3K36me1_rep3


title: DV_006_from_dorsal_to_ventral

description:
DjTomo2-206
Lasy-Seq ver. 1.1
DV.csv


title: DV_011_from_dorsal_to_ventral

description:
DjTomo2-211
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + DNMT3B), nodox, H3K9ac, rep2


title: C3H10T1-2_ASH1L_KO_H3K36me1_rep1


title: DV_005_from_dorsal_to_ventral

description:
DjTomo2-205
Lasy-Seq ver. 1.1
DV.csv


title: C3H10T1-2_ASH1L_KO_H3K36me2_rep2


title: GFP-1_A


title: GFP-2_m


title: C3H10T1-2_Parental_input_rep3

value: Parental


title: DV_003_from_dorsal_to_ventral

description:
DjTomo2-203
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + DNMT3B), irreversible, H3K9me3, rep2


title: C3H10T1-2_Parental_input_rep2


title: GFP-1_m


title: lung tissue, fibrotic, treated with targeted anti-fibrotic antibody against integrin AMB2, replicate3

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
mapped to mm39 reference with STAR
quantified expression with featureCounts
Assembly: mm39
Supplementary files format and content: tab-delimited text of gene expression counts

source_name: lungs

growth_protocol: healthy mouse lungs were insulted with bleomycin, allowed to develop fibrosis, and treated with our experimental antibody and siRNA anti-fibrotics

extract_protocol:
FFPE-mounted lungs were sectioned and processed to isolate RNA.
poly-a enrichment followed by cDNA conversion

treatment_protocol: mice were treated with anti-fibrotic antibodies and siRNA that target the cell adhesion and stiffness-sensing proteins, in an effort to reverse existing fibrosis in the lungs and kidneys

value: lungs

tag: disease state

value: fibrotic


title: DV_002_from_dorsal_to_ventral

description:
DjTomo2-202
Lasy-Seq ver. 1.1
DV.csv


title: lung tissue, fibrotic, treated with targeted anti-fibrotic antibody against integrin AMB2, replicate2


title: DV_001_from_dorsal_to_ventral

description:
DjTomo2-201
Lasy-Seq ver. 1.1
DV.csv


title: lung tissue, fibrotic, treated with targeted anti-fibrotic antibody against integrin AMB2, replicate1


title: HEK293T, (B9 clone + DNMT3B), irreversible, H3K9ac, rep1


title: AP_078_from_anterior_to_posterior

description:
DjTomoAP80-78
Lasy-Seq ver. 1.1
AP80.csv


title: C3H10T1-2_Parental_input_rep1


title: HEK293T, (B9 clone + DNMT3B), irreversible, H3K9ac, rep2


title: C3H10T1-2_Parental_H3K36me3_rep1


title: lung tissue, fibrotic, treated with targeted anti-fibrotic antibody against integrin A3, replicate 2


title: HEK293T, (B9 clone + KRAB), reactivated, HP1a, rep2


title: C3H10T1-2_Parental_H3K36me3_rep3


title: DV_004_from_dorsal_to_ventral

description:
DjTomo2-204
Lasy-Seq ver. 1.1
DV.csv


title: HEK293T, (B9 clone + DNMT3B), nodox, H3K9ac, rep1


title: HEK293T, (B9 clone + DNMT3B), irreversible, H3K9me3, rep1


title: HEK293T, (B9 clone + KRAB), reactivated, HP1a, rep1


title: C3H10T1-2_Parental_H3K36me3_rep2


title: AP_076_from_anterior_to_posterior

description:
DjTomoAP80-76
Lasy-Seq ver. 1.1
AP80.csv


title: C3H10T1-2_Parental_H3K36me2_rep3


title: lung tissue, fibrotic, treated with targeted anti-fibrotic antibody against integrin A3, replicate 1


title: AP_077_from_anterior_to_posterior

description:
DjTomoAP80-77
Lasy-Seq ver. 1.1
AP80.csv


title: AP_075_from_anterior_to_posterior

description:
DjTomoAP80-75
Lasy-Seq ver. 1.1
AP80.csv


title: C3H10T1-2_Parental_H3K36me2_rep2


title: lung tissue, fibrotic, replicate 3


title: AP_074_from_anterior_to_posterior

description:
DjTomoAP80-74
Lasy-Seq ver. 1.1
AP80.csv


title: HEK293T, (B9 clone + KRAB), nodox, HP1a, rep1


title: lung tissue, fibrotic, treated with targeted anti-fibrotic antibody against integrin A3, replicate 3


title: C3H10T1-2_Parental_H3K36me2_rep1


title: lung tissue, fibrotic, replicate 2


title: C3H10T1-2_Parental_H3K36me1_rep3


title: AP_073_from_anterior_to_posterior

description:
DjTomoAP80-73
Lasy-Seq ver. 1.1
AP80.csv


title: lung tissue, fibrotic, replicate 1


title: AP_072_from_anterior_to_posterior

description:
DjTomoAP80-72
Lasy-Seq ver. 1.1
AP80.csv


title: C3H10T1-2_Parental_H3K36me1_rep2


title: HEK293T, (B9 clone + KRAB), dox5days, HP1a, rep2


title: AP_071_from_anterior_to_posterior

description:
DjTomoAP80-71
Lasy-Seq ver. 1.1
AP80.csv


title: lung tissue, healthy, replicate 3

value: healthy


title: C3H10T1-2_Parental_H3K36me1_rep1


title: HEK293T, (B9 clone + KRAB), nodox, HP1a, rep2


title: HEK293T, (B9 clone + KRAB), dox5days, HP1a, rep1


title: HEK293T, (B9 clone + HDAC4), nodox, H3K9me3, rep2


title: AP_070_from_anterior_to_posterior

description:
DjTomoAP80-70
Lasy-Seq ver. 1.1
AP80.csv


title: HEK293T, (B9 clone + HDAC4), nodox, H3K9me3, rep1


title: ACSTR59_4xLPS_3

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

institute: University of British Columbia

description: 3' Quant seq with UMI tags

data_processing:
Raw sequencing reads were assessed for quality control using FastQC and multiqc umi indexes were added using umi2index (Lexogen) and then trimmed to remove adapter contamination, polyA read through and low-quality reads using BBDuk.
All samples were then re-assessed for quality using FastQC and multiqc.
Samples were aligned to the mouse genome (mm10) using STAR
Aligned bam files were then filtered for only unique UMIs using collapse_UMI_bam (Lexogen).
Filtered bam files were sorted and indexed using samtools.
Reads per gene were then counted using feature counts at the gene id levels with -s 1 desginated for stranded RNAseq.
Counts were then read into R for statistical analysis using EdgeR and LimmaVoom.
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts counts table in .txt

source_name: striatum tissue

extract_protocol:
On the fourth day, all animals were immediately euthanized 3 hours post-injection. Mice were then transcardially perfused with PBS (1 mL/g of body weight). RNA was extracted from whole tissue from hippocampus, striatum and front cortex using the RNA/DNA Miniprep Plus Zymo Kit (Cat D7003) with on column DNase digestion as described in the kit manual. RNA quality was assessed by bioanalyzer and all samples had RNA Integrity Numbers >7.
QuantSeq 3’mRNA sequencing FWD (RNAseq) libraries (Lexogen, Cat No 015) were prepared as stated in the Lexogen manual using 75ng of total input RNA per sample and 17 cycles of PCR amplification. All samples were prepared with incorporation of Unique Molecular Identifiers as part of the second strand synthesis step (Lexogen, Cat No 081) and sample unique, dual index barcodes. All samples were then pooled, exonuclease VII treated and sequenced across two lanes of a HiSeq4000 to generate Single End 100 base pair reads.
Pooled samples were exonuclease VII treated and sequenced on the HiSeq4000 to generate Single End 100 base pair reads.

treatment_protocol: 10 week old male mice were injected intraperitoneally with low-dose lipopolysaccharide (LPS, Sigma) at a daily dose of 500 ug/kg bodyweight or an equal volume of vehicle PBS. Each mouse was given a total of four injections spaced 24 hours apart. Animals received either four LPS injections on four consecutive days (4xLPS), a single vehicle injection followed by three LPS injections on the following three days (3xLPS), two vehicle injections on two consecutive days followed by two LPS injections on the following two days (2xLPS), three vehicle injections on three consecutive days followed by a single LPS injection on the fourth day (1xLPS), or four vehicle injections (PBS control).

value: striatum

tag: hemisphere

value: left

tag: Sex

value: M

tag: age in weeks


title: ACSTR60_4xLPS_4

description: 3' Quant seq with UMI tags

value: right


title: AP_069_from_anterior_to_posterior

description:
DjTomoAP80-69
Lasy-Seq ver. 1.1
AP80.csv

value: whole

value: AF


title: 5MOA, TxA23, male, scRNAseq

city: St. Louis

first: Richard

last: DiPaolo

state: MO

address: 1100 S Grand Ave

institute: Saint Louis Univeristy

description: 10x Genomics

data_processing:
Raw data were processed using cellranger-6. Conditional repeats were combined using cellranger aggr. Analysis was conducted in R using Seurat. Each dataset was filtered to exclude cells with low gene expression (<500/cell), high gene counts (outliers), and high percent mitochondrial transcript load (>25%/cell). Per species, datasets were merged, normalized, scaled, and dimensionally reduced. Layers were joined and clusters were generated using a resolution of 0.8 for mouse and 1.2 for human datasets. Cluster identities were established by attaining global distinguishing genes per cluster and relating them to known profiles for gastric epithelial cells.
Signature scores were calculated using AddModuleScore. Scores were generated for each cell based on overall average gene expression across signature transcripts. Signature scores were normalized by subtracting average expression of randomly selected control genes, resulting in a relative per-cell signature score. Signatures were either extracted from the Molecular Signatures Database or generated from known metaplasia- and cancer-associated transcripts (Supplementals Tables 2 and 3) or from cluster defining transcripts within the original dataset (Supplemental Tables 4 and 5). Epithelial cell label transfers were created by transferring cluster labels from the Hp tumor biopsies onto the metaplastic subclusters using the Satija Lab reference-mapping approach.
See full code for reproducing figures on our GitHub repository: github.com/hoftsg/Hoft_et_al_2024.git.
Assembly: Mus musculus - mm10-2020-A, Homo sapiens - GRCh38-2020-A
Supplementary files format and content: All samples include files processed on cellranger 6. Replicates were aggregated together prior to processing. Each sample includes a filtered feature, barcode, and matrix file.

source_name: Corpus

extract_protocol:
Corpus tissues were obtained from 2-7 mice per group and 3 AIG patients. Tissues were rinsed in PBS and placed in a 50mL conical with 10mL gland digest buffer: Advanced DMEM (Thermo Fisher), 20mM HEPES (Thermo Fisher), 0.2% BSA (MilliporeSigma, Burlington, MA), 50μg/mL gentamicin (MilliporeSigma), 1% penicillin/streptomycin (MilliporeSigma), DNaseI (100U/mL; MilliporeSigma). 1mg/mL collagenase 1A (MilliporeSigma) was added to each tube prior to 37C incubation with constant shaking for 20-45 minutes. Samples were then checked for presence of gastric glands, rinsed, and spun down (50RCF for 10 minutes). Samples were resuspended in 1mL/stomach prewarmed Trypsin-EDTA (MilliporeSigma) and incubated for ~25 minutes at 37C, agitating every 5-10 minutes. Digestion was considered complete when single cells were observed. Cells were then washed twice with DMEM plus 10% fetal bovine serum. Cells were filtered twice, counted, and resuspended to a final cell concentration of ~1,000 cells/uL. Viability of each sample was confirmed to be greater than 70% by trypan blue staining (Thermo Fisher).
Library construction of mouse tissues was performed at Saint Louis University and construction of AIG human libraries was performed at the Washington University in Saint Louis Genome Technology Access Center. To generate libraries, the Chromium Controller (10X Genomics, Pleasanton, CA) was used following manufacturer protocols. Libraries were prepared using the Chromium Next GEM Single Cell 5' Kit v2 (1000263, 10X Genomics). Each library was generated to have a maximum recovery of 10,000 cells. PCR reactions were conducted in the T100 Thermal Cycler (BioRad, Hercules, CA). Final quality control was performed on the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA) and libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, CA).

value: Corpus


title: HEK293T, (B9 clone + KRAB), irreversible, HP1a, rep1


title: HEK293T, (B9 clone + HDAC4), nodox, H3K9ac, rep2


title: ACSTR58_4xLPS_2

description: 3' Quant seq with UMI tags


title: HEK293T, (B9 clone + KRAB), irreversible, HP1a, rep2


title: AP_067_from_anterior_to_posterior

description:
DjTomoAP80-67
Lasy-Seq ver. 1.1
AP80.csv


title: AP_068_from_anterior_to_posterior

description:
DjTomoAP80-68
Lasy-Seq ver. 1.1
AP80.csv


title: 5MOA, TxA23, female, scRNAseq

description: 10x Genomics


title: lung tissue, healthy, replicate 2


title: HEK293T, (B9 clone + HDAC4), nodox, H3K9ac, rep1


title: AP_066_from_anterior_to_posterior

description:
DjTomoAP80-66
Lasy-Seq ver. 1.1
AP80.csv


title: lung tissue, healthy, replicate 1


title: lung tissue transferred ALDHbr cells, rep1

value: lung administered bleomycin

value: injection with bone marrow cells with high ALDH activity (ALDHbr)


title: ACSTR55_3xLPS_3

description: 3' Quant seq with UMI tags


title: AP_065_from_anterior_to_posterior

description:
DjTomoAP80-65
Lasy-Seq ver. 1.1
AP80.csv


title: HEK293T, (B9 clone + HDAC4), nodox, H3K27me3, rep1

value: Human embryonic kidney


title: Pancreas, Caerulein treated 5H, 18 months of age, mouse 3

city: Copenhagen

first: Luis

last: Arnes

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre

description:
recommended 20 million read pair per sample
A_5HvsY_5H_deg.tsv
A_5HvsA_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
A_5H_3

data_processing:
Mapping to the mouse genome was performed using hisat2 software 2.0.5
Reads with adapter contamination were removed. Reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) were removed. Reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read were removed.
Quantifications perfomed using Featurecounts 1.5.0-p3
Assembly: mm10
Supplementary files format and content: Tab-delimited tsv file includes raw counts for each sample
Supplementary files format and content: Tab-delimited tsv file includes fpkm values for each sample

source_name: Pancreas

growth_protocol: All animal experiments described were approved by the University of Copenhagen’s ethical committee. All animal experiments were performed in accordance with the Danish Animal Welfare Act and FELASA. Attention has been paid to the ARRIVE guidelines, recommendations, and policy. C57BL/6JRj mice used in this project were purchased from Janvier Labs (Le Genest-Saint-Isle, France), and animals were fed a laboratory chow diet and had free access to water. Mice were genotyped at weaning.

extract_protocol:
Based on the commercial protocol, the pancreatic tissue’s RNA was extracted using RNeasy Mini Kit (Qiagen #74106). Pancreatic tissue is added to 2 mL of RLT buffer (with 2-Mercaptoethanol, 1:100) and homogenised using a homogeniser (IKA, T10 basic). Homogenizer was washed between the samples with MilliQ water and 70% ethanol to avoid cross-contamination. After tissues were homogenised, 1 volume (2 mL) of 70% ethanol was added. Next, RNeasy Spin columns were loaded with 700μL of the sample and centrifuged for 30 seconds at maximum speed (>13.000rpm). All collected flow-through was discarded. This step was repeated several times. From here, the instructors´ protocol was followed.  The extracted RNA’s concentration and sample quality were measured using a spectrophotometer (DeNovix, DS-11).
For RNA library preparation the mRNA is enriched by poly(A) capture. RNA is then fragmented by enzyme digestion (or Covaris). cDNA reverse transcription is followed by RNA library preparation. After a library quality control, sequencing is performed using the Illumina NovaSeq 6000 platform, pair-end 150 bp sequencing strategy (short-reads), with a depth of the recommended 20 million read pair per sample. Following data quality control, bioinformatic analysis is performed. Gene set enrichment analysis was performed using the open source GSEA software46

treatment_protocol: To induce tissue injury in the pancreas, the cholecystokinin analogue caerulein (C9026; Sigma-Aldrich) was administered through intraperitoneal injections every hour for 4 hours at a concentration of 125ug/kg body weight.

value: Pancreas

value: Caerulein 5H


title: ACSTR56_3xLPS_4

description: 3' Quant seq with UMI tags


title: 13MOI, HP, female, scRNAseq

description: 10x Genomics

value: 13MOI Helicobacter pylori PMSS1


title: ACSTR57_4xLPS_1

description: 3' Quant seq with UMI tags


title: HEK293T, (B9 clone + HDAC4), dox5days, H3K9me3, rep2


title: ACSTR54_3xLPS_2

description: 3' Quant seq with UMI tags


title: Pancreas, Caerulein treated 5H, 18 months of age, mouse 2

description:
recommended 20 million read pair per sample
A_5HvsY_5H_deg.tsv
A_5HvsA_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
A_5H_2


title: AP_063_from_anterior_to_posterior

description:
DjTomoAP80-63
Lasy-Seq ver. 1.1
AP80.csv


title: Pancreas, Caerulein treated 5H, 18 months of age, mouse 1

description:
recommended 20 million read pair per sample
A_5HvsY_5H_deg.tsv
A_5HvsA_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
A_5H_1


title: ACSTR53_3xLPS_1

description: 3' Quant seq with UMI tags


title: 6MOI, HP, male, scRNAseq

description: 10x Genomics

value: 6MOI Helicobacter pylori PMSS1


title: AP_062_from_anterior_to_posterior

description:
DjTomoAP80-62
Lasy-Seq ver. 1.1
AP80.csv


title: HEK293T, (B9 clone + HDAC4), dox5days, H3K9me3, rep1


title: HEK293T, (B9 clone + HDAC4), nodox, H3K27me3, rep2


title: AP_064_from_anterior_to_posterior

description:
DjTomoAP80-64
Lasy-Seq ver. 1.1
AP80.csv


title: Pancreas, Caerulein treated 5H, 7w of age, mouse 3

description:
recommended 20 million read pair per sample
A_5HvsY_5H_deg.tsv
Y_5HvsY_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
Y_5H_3


title: HEK293T, (B9 clone + HDAC4), dox5days, H3K9ac, rep2


title: HEK293T, (B9 clone + HDAC4), dox5days, H3K9ac, rep1


title: AP_061_from_anterior_to_posterior

description:
DjTomoAP80-61
Lasy-Seq ver. 1.1
AP80.csv


title: ACSTR51_2xLPS_3

description: 3' Quant seq with UMI tags


title: Pancreas, Caerulein treated 5H, 7w of age, mouse 1

description:
recommended 20 million read pair per sample
A_5HvsY_5H_deg.tsv
Y_5HvsY_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
Y_5H_1


title: AP_060_from_anterior_to_posterior

description:
DjTomoAP80-60
Lasy-Seq ver. 1.1
AP80.csv


title: ACSTR50_2xLPS_2

description: 3' Quant seq with UMI tags


title: AP_059_from_anterior_to_posterior

description:
DjTomoAP80-59
Lasy-Seq ver. 1.1
AP80.csv


title: HEK293T, (B9 clone + HDAC4), dox5days, H3K27me3, rep2


title: ACSTR49_2xLPS_1

description: 3' Quant seq with UMI tags


title: HEK293T, (B9 clone + HDAC4), dox5days, H3K27me3, rep1


title: Pancreas, not treated, 18 months of age, mouse 3

description:
recommended 20 million read pair per sample
A_controlvsY_control_deg.tsv
A_5HvsA_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
A_control_3


title: ACSTR48_1xLPS_4

description: 3' Quant seq with UMI tags


title: Pancreas, not treated, 18 months of age, mouse 2

description:
recommended 20 million read pair per sample
A_controlvsY_control_deg.tsv
A_5HvsA_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
A_control_2


title: ACSTR52_2xLPS_4

description: 3' Quant seq with UMI tags


title: AP_058_from_anterior_to_posterior

description:
DjTomoAP80-58
Lasy-Seq ver. 1.1
AP80.csv


title: HEK293T, (B9 clone + HDAC4), dox1day, H3K9ac, rep2


title: Pancreas, not treated, 7w of age, mouse 3

description:
recommended 20 million read pair per sample
A_controlvsY_control_deg.tsv
Y_5HvsY_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
Y_control_3


title: AP_057_from_anterior_to_posterior

description:
DjTomoAP80-57
Lasy-Seq ver. 1.1
AP80.csv


title: USP39 iCLIP2 high Replicate 3

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

data_processing:
Quality control: FastQC (v0.11.9)
Barcode and adapter trimming: Flexbar (v3.5.0) with non-default parameters: flexbar --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta
Mapping: STAR (v2.7.3a) with non-default parameters: STAR --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 76 --runThreadN 1 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.10), bedtools (v2.29.2): samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0) || ($3>=$7)) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.1.2) with non-default parameters: umi_tools dedup -I SAMPLE.bam -S SAMPLE.duprm.bam --method unique --random-seed=100
BAM to BED shifting one base upstream: bedtools (v2.29.2): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.29.2): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v385)
Assembly: GRCh38.p12 (Gencode release 31)
Supplementary files format and content: BW files containing the genomic coordinates and counts of uniquely mapped X-links for each replicate separated by strand.
Supplementary files format and content: Bed files containing the genomic coordinates and counts of reproducible binding sites from merged replicates over all conditions.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and penicilin/streptomycin antibiotics at 37˚C with 5% CO2 and 21% oxygen.

extract_protocol:
Cells were lysed and treated with RNase I. USP39 was immunoprecipitated with Gamma binding beads coupled to anti-USP39 antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. Two different membrane regions above the expected size of the protein (Low and High) were cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer and a second adapter containing a barcode was ligated to the cDNAs. The cDNA was pre-amplified for 6 cycles using short Solexa P3 and P7 primers. After a size selection on beads a second PCR amplification was performed with the normal P3 and P7 primers to generate the final iCLIP2 libraries.
iCLIP2

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

tag: membrane region

value: high

value: WT

tag: rip antibody

value: anti-USP39 antibody

tag: barcode sequence

value: NNNNNATTGGCNNNN

tag: fraction

value: USP39-bound RNA


title: ACSTR46_1xLPS_2

description: 3' Quant seq with UMI tags

tag: tissue

value: striatum

value: M


title: Pancreas, Caerulein treated 5H, 7w of age, mouse 2

description:
recommended 20 million read pair per sample
A_5HvsY_5H_deg.tsv
Y_5HvsY_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
Y_5H_2

tag: cell line

tag: treatment


title: ACSTR47_1xLPS_3

description: 3' Quant seq with UMI tags

value: left

tag: strain


title: AP_055_from_anterior_to_posterior

description:
DjTomoAP80-55
Lasy-Seq ver. 1.1
AP80.csv

extract_protocol: Lasy-Seq version 1.1 (Kashima et al., Frontiers in bioinformatics, 2021)

value: whole

value: AF


title: AP_056_from_anterior_to_posterior

description:
DjTomoAP80-56
Lasy-Seq ver. 1.1
AP80.csv


title: ACSTR45_1xLPS_1

description: 3' Quant seq with UMI tags


title: Pancreas, not treated, 7w of age, mouse 1

description:
recommended 20 million read pair per sample
A_controlvsY_control_deg.tsv
Y_5HvsY_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
Y_control_1


title: USP39 iCLIP2 high Replicate 1

tag: genotype

value: NNNNNATCAGTNNNN


title: AP_054_from_anterior_to_posterior

description:
DjTomoAP80-54
Lasy-Seq ver. 1.1
AP80.csv


title: ACSTR44_PBS_4

description: 3' Quant seq with UMI tags

value: right

value: PBS


title: USP39 iCLIP2 high Replicate 2

value: NNNNNTGGTCANNNN


title: USP39 iCLIP2 low Replicate 3

value: low

value: NNNNNTTTCACNNNN


title: AP_052_from_anterior_to_posterior

description:
DjTomoAP80-52
Lasy-Seq ver. 1.1
AP80.csv


title: AP_053_from_anterior_to_posterior

description:
DjTomoAP80-53
Lasy-Seq ver. 1.1
AP80.csv


title: USP39 iCLIP2 low Replicate 2

value: NNNNNTGACATNNNN


title: ACSTR43_PBS_3

description: 3' Quant seq with UMI tags


title: ACSTR41_PBS_1

description: 3' Quant seq with UMI tags


title: USP39 iCLIP2 low Replicate 1

value: NNNNNTTGACTNNNN


title: AP_050_from_anterior_to_posterior

description:
DjTomoAP80-50
Lasy-Seq ver. 1.1
AP80.csv


title: AP_051_from_anterior_to_posterior

description:
DjTomoAP80-51
Lasy-Seq ver. 1.1
AP80.csv


title: ACPFC9_2xLPS_1

description: 3' Quant seq with UMI tags

source_name: frontal cortex tissue

value: frontal cortex


title: Pancreas, not treated, 7w of age, mouse 2

description:
recommended 20 million read pair per sample
A_controlvsY_control_deg.tsv
Y_5HvsY_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
Y_control_2

value: Pancreas


title: ACPFC6_1xLPS_2

description: 3' Quant seq with UMI tags


title: AP_049_from_anterior_to_posterior

description:
DjTomoAP80-49
Lasy-Seq ver. 1.1
AP80.csv


title: AP_046_from_anterior_to_posterior

description:
DjTomoAP80-46
Lasy-Seq ver. 1.1
AP80.csv


title: LPS-treated, Fth1-High, Replicate 2

city: Pittsburgh

first: Rachel

last: Gottschalk

state: PA

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

data_processing:
Sequencing data was demultiplexed by the on-board Illumina DRAGEN FASTQ Generation software (v3.10.12).
Rsubread was used to align and obtain raw read counts with the mm10 reference genome.
DESeq2 was used for read normalization and differential gene expression calculation.
Assembly: mm10
Supplementary files format and content: comma-separated values file with raw read count for each sample

source_name: Lung

extract_protocol:
Samples were lysed in TRIzol LS (Ambion) and RNA was isolated with the Direct-zol RNA MicroPrep Kit (Zymo Research). RNA concentration was quantified on a Qubit FLEX fluorometer. 25 ng of input RNA was used for each sample.
Libraries were generated with the Illumina Stranded mRNA Library Prep kit according to the manufacturer’s instructions. Following adapter ligation, 15 cycles of indexing PCR were completed, using IDT for Illumina RNA UD Indexes. Libraries were normalized and pooled to 2 nM by calculating the concentration based off the fragment size (base pairs) and the concentration (ng/l) of the libraries. Sequencing was performed on an Illumina NextSeq 2000, using a P3 200 flow cell. The pooled library was loaded at 750 pM and sequencing was carried out with read lengths of 2x58 bp, with a target of 25 million reads per sample.

value: Lung

tag: cell type

value: Myeloid

value: LPS


title: LPS-treated, Fth1-Low, Replicate 1


title: ACPFC7_1xLPS_3

description: 3' Quant seq with UMI tags

value: M


title: ACPFC5_1xLPS_1

description: 3' Quant seq with UMI tags

value: left


title: AP_047_from_anterior_to_posterior

description:
DjTomoAP80-47
Lasy-Seq ver. 1.1
AP80.csv

data_processing:
The BCL (base calls) binary is converted into FASTQ using illumina package bcl2fastq2-v2.20.0. The demultiplexing option (--barcode-mismatches) was set to default (value : 0).
Read 1 reads were processed with fastp (version 0.21.0) using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to a D. japonica reference sequences, using BWA mem (version 0.7.17-r1188) with the default parameters. The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0).
D. japonica reference transcriptome sequences deposited in http://www.planarian.jp/download.html

value: whole


title: LPS-treated, Fth1-High, Replicate 1


title: AP_044_from_anterior_to_posterior

description:
DjTomoAP80-44
Lasy-Seq ver. 1.1
AP80.csv

value: AF


title: AP_045_from_anterior_to_posterior

description:
DjTomoAP80-45
Lasy-Seq ver. 1.1
AP80.csv


title: LPS-treated, Fth1-High, Replicate 3


title: ACPFC4_PBS_4

description: 3' Quant seq with UMI tags


title: Non-treated, Fth1-Low, Replicate 2


title: Non-treated, Fth1-Low, Replicate 1


title: ACPFC3_PBS_3

description: 3' Quant seq with UMI tags


title: LPS-treated, Fth1-Low, Replicate 2


title: AP_043_from_anterior_to_posterior

description:
DjTomoAP80-43
Lasy-Seq ver. 1.1
AP80.csv


title: C2C12 cells, sCBD 6

city: Liverpool

first: Daniel

middle: John

last: Owens

address: Byrom Street

department: Research Institute for Sport and Exercise Science

country: United Kingdom

institute: Liverpool John Moores University

data_processing:
Partek® Flow® Genomic Analysis Software
Pre-alignment QA/QC was performed on all reads prior to read trimming. STAR alignment 4.4.1d was used to align trimmed reads to the Mus musculus genome
Aligned reads were then quantified to the Ensembl transcriptome annotation model associated with Mus musculus mm39 genome.
Filtered raw counts were used for normalisation and differential analysis with DESeq2
Assembly: Mus musculus mm39 genome
Supplementary files format and content: Matrix table, raw counts (quantification)
Supplementary files format and content: Matrix table, normalized counts (normalization)

growth_protocol: C2C12 murine myoblasts were cultured on gelatin (0.2%) coated 6-well culture plates in humidified 5% CO2 at 37°C in growth media comprising DMEM, 10% FBS, 10% NBCS and 1% of a pen-strep solution. Upon reaching ~80% confluence, monolayers were washed twice with pre-warmed PBS and switched to low serum differentiation media (DM), DMEM, 2% HS and 1% pen-strep. Every 48h thereafter, DM was removed from monolayers via aspiration and was replaced with fresh media. Cells were terminally differentiated by day-8 of low serum DM exposure

extract_protocol:
Following a 24-hour treatment with CBD/sCBD/vehicle control, terminally differentiated C2C12 monolayers were lysed with buffer RLT from the Qiagen RNeasy kit (Qiagen Ltd). RNA was then extracted from cell lysates using the RNeasy kit with proteinase K digestion, as per the manufacturer’s guidelines. Eluted RNA was stored at -80oC until required for determination of total RNA and library processing.
Libraries were constructed from 100 ng of total RNA with Poly-A tail enrichment of mRNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® with Agencourt AMPureXP Sample Purification Beads (Beckman Coulter. Wycombe, UK) as per manufacturers guidelines, by Bart's and the London Genome Centre at Queen Mary, University of London.

treatment_protocol: We terminally differentiated C2C12 myotubes as described above. On day 8 of differentiation, DM was removed and swapped with DM containing vehicle (DMSO), CBD (10 µM) and sCBD (10 µM). Myotubes were then cultured in the respective treatments for 24 hours before being harvested for RNA extraction. Duplicate wells for each treatment were used and the experiment repeated three times to generate an n=6 samples per treatment.

value: Myotube

value: WT

value: sCBD 10 uM


title: ACSTR42_PBS_2

description: 3' Quant seq with UMI tags

value: striatum

value: right

value: PBS


title: ACPFC8_1xLPS_4

description: 3' Quant seq with UMI tags


title: AP_042_from_anterior_to_posterior

description:
DjTomoAP80-42
Lasy-Seq ver. 1.1
AP80.csv


title: ACPFC20_4xLPS_4

description: 3' Quant seq with UMI tags


title: C2C12 cells, sCBD 4


title: ACPFC2_PBS_2

description: 3' Quant seq with UMI tags


title: AP_041_from_anterior_to_posterior

description:
DjTomoAP80-41
Lasy-Seq ver. 1.1
AP80.csv


title: AP_048_from_anterior_to_posterior

description:
DjTomoAP80-48
Lasy-Seq ver. 1.1
AP80.csv


title: C2C12 cells, sCBD 5


title: C2C12 cells, sCBD 3


title: ACPFC19_4xLPS_3

description: 3' Quant seq with UMI tags


title: AP_040_from_anterior_to_posterior

description:
DjTomoAP80-40
Lasy-Seq ver. 1.1
AP80.csv


title: ACPFC18_4xLPS_2

description: 3' Quant seq with UMI tags


title: C2C12 cells, sCBD 2


title: AP_039_from_anterior_to_posterior

description:
DjTomoAP80-39
Lasy-Seq ver. 1.1
AP80.csv


title: C2C12 cells, sCBD 1


title: ACPFC17_4xLPS_1

description: 3' Quant seq with UMI tags


title: ACPFC16_3xLPS_4

description: 3' Quant seq with UMI tags


title: AP_038_from_anterior_to_posterior

description:
DjTomoAP80-38
Lasy-Seq ver. 1.1
AP80.csv


title: C2C12 cells, CBD 6

value: CBD 10 uM


title: AP_037_from_anterior_to_posterior

description:
DjTomoAP80-37
Lasy-Seq ver. 1.1
AP80.csv


title: ACPFC15_3xLPS_3

description: 3' Quant seq with UMI tags


title: C2C12 cells, CBD 4


title: AP_036_from_anterior_to_posterior

description:
DjTomoAP80-36
Lasy-Seq ver. 1.1
AP80.csv


title: ACPFC14_3xLPS_2

description: 3' Quant seq with UMI tags


title: AP_035_from_anterior_to_posterior

description:
DjTomoAP80-35
Lasy-Seq ver. 1.1
AP80.csv


title: C2C12 cells, CBD 3


title: C2C12 cells, CBD 5


title: ACPFC12_2xLPS_4

description: 3' Quant seq with UMI tags


title: ACPFC13_3xLPS_1

description: 3' Quant seq with UMI tags


title: AP_034_from_anterior_to_posterior

description:
DjTomoAP80-34
Lasy-Seq ver. 1.1
AP80.csv


title: AP_033_from_anterior_to_posterior

description:
DjTomoAP80-33
Lasy-Seq ver. 1.1
AP80.csv


title: C2C12 cells, CBD 1


title: AP_032_from_anterior_to_posterior

description:
DjTomoAP80-32
Lasy-Seq ver. 1.1
AP80.csv


title: C2C12 cells, Control 6

value: Control (vehicle DMSO)