title: MM468_GSKJ4_day91_H3K27me3 [scChIP-seq]

data_processing:
scChIP-seq: Each #Read 2 was first separated into two parts – a cell barcode part composed of the first 79 nucleotides and the last 22 nucleotides composed of genomic DNA.
scChIP-seq: Full #Read 1 and genomic DNA of #Read 2 were mapped in paired-end mode to hg38 whole genome using STAR v2.6.0c with parameters --alignEndsType EndToEnd --outFilterMultimapScoreRange 2 --winAnchorMultimapNmax 1000 --alignIntronMax 1 --peOverlapNbasesMin 10 --alignMatesGapMax 450 --limitGenomeGenerateRAM 25000000000 --outSAMunmapped Within
scChIP-seq: Barcodes were extracted from the 79bp of Reads #2 by retrieving the three 16-mer indices (respectively  located at positions 1-16, 21-36, 41-56 on Read #2). Each index was independently aligned on the 96 possibles indexes of it’s respective set of indices using Bowtie2 2.2.9  with options ‘-N 1 -L 10 --rdg 0,7 --rfg 0,7 --mp 7,7 --ignore-quals --score-min L,0,-1 -t --no-unal –no-hd’, allowing up to two mismatches / indels on the entire sequence. Full non redundant barcodes were then reconstructed for reads mapping all of the three indexes.
scChIP-seq: For each barcode, aligned reads were deduplicated by removing successively:  1. PCR duplicates, identified if #Read1 + #Read 2 mapped at the same position, 2. RT duplicates, identified if #Read 1 mapped at the same postion and  3. Window duplicates : all the reads falling in the same 50 bp window were stacked into one as reads possibly originating from PCR duplicates or from the same nucleosome. Then, reads were either counted on a ‘consensus peak annotation’  or onto 10kbp regions around Transcript Start Site (TSS) to generate a n x m coverage matrix with n barcodes and m genomic regions used in downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count for each cell genomic bins (scChIP-seq). Single-cell raw BED files can be easily generated from BAM files using the bash script at https://github.com/vallotlab/ChemoPersistance/blob/master/Scripts/scChIPseq/bam_to_single_cell_bed.sh

source_name: MDA-MB-468 cell line

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). HCC38 cell lines were cultured in RPMI 1640 (Gibco-BRL, Ref: 11875085), supplemented with 10% heat-inactivated fetal calf serum. All cell lines were cultured in a humidified 5% CO2 atmosphere at 37 °C, and were tested as mycoplasma negative.   For the PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used a xenograft model generated from a residual triple-negative breast cancer post-neoadjuvant chemotherapy (HBCx95) established previously at Institut Curie with informed consent from the patient51,52.

extract_protocol:
For MDA-MB-468 cell line, prior to scChIP-seq cells were  individualized and re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).  For the PDX model, prior scChIP-seq and scRNA-seq, PDX were digested at 37°C for 2h with a cocktail of Collagenase I (Roche, # 11088793001) and Hyaluronidase (Sigma, # H3506) as previously described (Petit et al, Lab Investigation 2013). Cells were further individualized at 37°C using a cocktail of 0.25% trypsin/Versen (ThermoFisher Scientific, #15040-033), Dispase II (Sigma, # D4693) and Dnase I (Roche, # 11284932001). Red Blood Cell lysis buffer (ThermoFisher Scientific, # 00-4333-57) was then added to degrade red blood cells. To increase the viability of the cell suspension, we removed dead cells using a Dead Cell Removal kit (Miltenyi Biotec). Cells were re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).  After immunoprecipitation targeting H3K4me3 or H3K27me3, scChIP-seq libraries were prepared as following: barcoded-nucleosomes were amplified by in vitro transcription using the T7 MegaScript kit (ThermoFisher Scientific). The resulting amplified RNA was purified using 1x RNAClean XP beads (Beckman) and reverse transcribed by random priming in cDNA. After RNA digestion, DNA was amplified by PCR using with Illumina Primers for 12 cycles and library fragments ranging from 300 to 600 bp (single-cell barcode plus nucleosomal sequence + PCR primer sequence) were size-selected on an agarose gel. Single-cell ChIP-seq libraries were sequenced on Illumina NextSeq 500 MidOutput 150 cycles
After immunoprecipitation targeting H3K27me3, scChIP-seq libraries were prepared as following: barcoded-nucleosomes were amplified by in vitro transcription using the T7 MegaScript kit (ThermoFisher Scientific). The resulting amplified RNA was purified using 1x RNAClean XP beads (Beckman) and reverse transcribed by random priming in cDNA. After RNA digestion, DNA was amplified by PCR using with Illumina Primers for 12 cycles and library fragments ranging from 300 to 600 bp (single-cell barcode plus nucleosomal sequence + PCR primer sequence) were size-selected on an agarose gel. Single-cell ChIP-seq libraries were sequenced on Illumina NextSeq 500 MidOutput 150 cycles

treatment_protocol: GSKJ4 (KDM6A/B inhibitor, Sigma, Ref: SML0701), GSKJ5 (GSK-J4 inactive isomer, Abcam, Ref: ab144397) and UNC1999 (EZH2 inhibitor, Abcam, Ref: ab146152) were used at indicated concentrations. Cells were treated with 5 μM of 5-FU (Sigma, Ref: F6627) alone or in combination with KDM6A/Bi or EZH2i for indicated days.   For the PDX model,  five mice were not treated and kept as controls and twenty-seven mice were treated orally with Capecitabine (Xeloda; Roche Laboratories) at a dose of 540 mg/kg, 5 d/week for 6 to 14 weeks. Relative tumor volumes (mm3) were measured as described previously22. Latency was defined as the number of days between the observation of a complete response (Tumor size < 10 mm3) after the first cycle of Capecitabine, and the detection of a recurrent tumor (Tumor size > 10 mm3). Eight mice were sacrificed after the first cycle of chemotherapy to study residual (2 mice) and persister (6 mice) human tumor cells. Seven mice with recurrent tumors (tumor volume between 200 and 600 mm3) were treated for a second round of Capecitabine.

value: Untreated

tag: day

value: H3K27me3 - Cell Signaling, Ref:9733


title: JK125_reg2_org_5_r1 [scRNA-seq]

status: Public on Feb 15 2022

type: SRA

city: Vancouver

first: Marco

middle: A

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

library_source: transcriptomic

data_processing:
Raw sequencing data were demultiplexed using the CellRanger software (10X Genomics; cellranger mkfastq with default parameters; v2.0.0 or v2.1.1)
Alignment, filtering, barcode counting, and UMI counting were done using the CellRanger software (cellranger count with default parameters except --expect-cells set to 1000; v2.1.1). The CellRanger GRCh38-1.2.0 reference was used for alignment.
Additional cell and gene filtering were performed in R on the filtered count matrices output by CellRanger using the scater package (v1.10.0). Outlier cells were identified as those with >3 median absolute deviations (MADs) below the median total UMI counts or total number of genes detected, or with >3 MADs above the median percent of counts from mitochondrial genes (per sample). Genes detected (UMI >0) in at least 10 cells with at least 20 UMIs were retained. Normalization was applied on remaining cells/genes using the scran package (v1.10.1). Putative doublets were identified using the doubletCells frunction from the scran package (k = 30) and cells with outlier doublet scores (>3 MADs above the sample median) were discarded. Gene filtering and normalization were performed again on the final dataset.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNAseq_all_cells_counts_matrix.mtx is a sparse matrix of raw UMI counts from all cells identified by the CellRanger pipeline. scRNAseq_all_cells_barcodes.tsv and scRNAseq_all_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_all_cells_metadata.csv contains associated cell metadata.
Supplementary_files_format_and_content: scRNAseq_filtered_cells_norm_counts_matrix.mtx is a sparse matrix of normalized UMI counts from QC-filtered cells. scRNAseq_filtered_cells_barcodes.tsv and scRNAseq_filtered_cells_genes.tsv contain associated barcode (column) and gene (row) names. scRNAseq_filtered_cells_metadata.csv contains associated cell metadata.

molecule: polyA RNA

organism: Homo sapiens

source_name: glioblastoma

growth_protocol: Small sections (~1mm3) of freshly resected tumour tissue were rinsed and placed into small Matrigel forms. Organoids were then cultured in neural stem cell media (NeuroCult) supplemented with EGF, FGF-2, and heparin sulfate.

extract_protocol: Single-cell 3’ RNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics) following the manufacturer’s protocol. Briefly, the provided targeted cell recovery table was used to determine the volume of cell suspension added to the Single Cell Master Mix prior to loading onto the Single Cell A chip (2,000 cells for tissue and PDO samples and 1,000 cells for BTIC lines). Following gel beads in emulsion (GEM) generation on the Chromium Controller, the GEM-RT reaction was performed, the GEMs were broken, and cDNA cleanup was performed using Dynabeads MyOne Silane beads. Samples that underwent evident clogs or wetting failures at the GEM generation step were not further processed. cDNA amplification was performed with 12 amplification cycles, and reaction cleanup was then performed using the SPRIselect reagent kit (Beckman Coulter). Total cDNA quantification was performed using the Agilent High Sensitivity DNA Kit. Enzymatic fragmentation, library construction, and additional SPRIselect clean-ups were then performed to generate the final indexed libraries. The number of sample index PCR cycles was determined based on the total cDNA yield and ranged from 10-14 cycles. Library quality was assessed using the Agilent High Sensitivity DNA kit and libraries were quantified using the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled (seven to eight libraries/pool) and sequenced on one lane of an Illumina HiSeq2500 flow cell (San Diego, CA, USA) using v3 or v4 chemistry and paired-end sequencing with single indexing following Illumina protocols and 10X sequencing parameters (26 bp read 1, 98 bp read 2, and 8 bp i7 index).

treatment_protocol: Cryopreserved tissues or PDOs were rapidly thawed in a 37oC water bath. Tissues were washed once in NeuroCult NS-A Basal Medium (human; STEMCELL Technologies), and PDOs were washed in the same media at room temperature for 15 min with rocking. Samples were resuspended in 0.2 mg/mL collagenase (Sigma-Aldrich) plus 0.5 mg/mL DNaseI (Worthington Biochemical Corp) and incubated at 37oC for 30 min with shaking every 10 min. Tissues were dissociated by tituration, incubated for another 10 min at 37oC, and filtered through a 40 μm mesh filter (BD Falcon) with added NeuroCultTM medium (STEMCELL Technologies) to remove larger pieces of debris and undissociated tissue. PDOs were dissociated by tituration and incubated for another 10 min at 37oC. Dissociated cells were then washed twice in Hank’s balanced salt solution (HBSS; Thermo Fisher Scientific) and resuspended in phosphate-buffered saline (PBS; Thermo Fisher Scientific) with 0.04% (w/v) bovine serum albumin (BSA; Thermo Fisher Scientific). Additional HBSS washes were performed in samples with high debris and/or Matrigel content (up to four washes). Single-cell suspensions were filtered through 40 μm FlowMi tip filters (Bel-Art SP Scienceware), and final cell concentrations were determined using the Countess automated cell counter (Thermo Fisher Scientific).

tag: sample type

value: organoid

tag: tumour type

value: primary

tag: patient id


title: Exe_Plasma sEV2

city: Xi 'an

first: Hang

last: Zhao

address: 127 Changle west road, Xi 'an  China

country: China

institute: Air force military medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: rawcounts

molecule: total RNA

organism: Mus musculus

source_name: plasma small extracellular vesicle

extract_protocol:
total miRNA was extracted from sEVs from different samples by using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 90 min twice per day, lasts for 4 weeks

tag: tissue

value: plasma

tag: strain

tag: exercise protocal

value: 90 min twice per day, lasts for 4 weeks

tag: molecule type

value: microRNA


title: Exe_Plasma sEV1


title: HeLa.+sncRNAU14.-AHT.A

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

description: small RNAseq

data_processing:
Reads that passed the chastity filter on the NextSeq 500 were subject to de-multiplexing and trimming of TriLink adapter residuals using Illumina’s bcl2fastq v2 software (v2.19.1). To refine the output, read quality was checked with FastQC software (v0.11.5) and reads shorter 10 bases or longer 25 bases or containing “N” as a base call, were discarded.
STAR_2.5.3a was used to map all reads against a combined index prepared for the human genome (Ensembl 90) and the HHV6A genome (genbank accession X83413). The following parameters were used: --alignIntronMax 1 --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16.
Reads were counted using Gedi 1.0.3.
Genome_build: hg38, X83413

source_name: Human cervical carcinoma cells carrying lentiviral backbone with sncRNA-U14

growth_protocol: Cells were grown in RPMI1640 media with 10% FCS without any antibiotics.

extract_protocol:
Cells were washed once with PBS and total cellular RNA was extracted using Qiagen RNeasy mini kit.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using both, Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts and were sequenced using NextSeq 500.

treatment_protocol: Cells were washed with PBS just before the treatment and then were replaced with freash media containing Ethanol/DMSO/Doxycycline/TSA.

tag: cell type

tag: time post induction

tag: treated with

value: DMSO (solvent control)


title: Exe_BAT sEV2

source_name: brown adipose tissue small extracellular vesicle

value: brown adipose tissue


title: patient_tumor_HBCx166_H3K27me3

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

library_source: genomic

data_processing:
Library strategy: Bulk CUT&Tag
CUT&TAG: Read #1 and Read #2 were aligned to hg38 Human genome reference using bowtie2 with options ‘-k 1 -N 1 –end-to-end’
CUT&TAG: After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.
CUT&TAG: Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCoverage function with options ‘--normalizeUsing CPM --binSize 50 --smoothLength 500 --extendReads 150 --ignoreForNormalization chrX’.
CUT&TAG: Reads were counted on 10kbp-region around TSS for both H3K27me3 and H3K4me3 (52138 TSS). The matrice was normalized with log2(RPKM). Each TSS with a normalized signal greater than the 85th percentile of the distribution of all TSS respectively in both H3K4me3 and H3K27me3 were considered bivalent’.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file of the normalized signal at TSS for each H3K27me3-H3K4me3 couple, indicating if the TSS is considered bivalent (‘Significant’ column).   Coverage files (.bw) for each histone mark.

molecule: genomic DNA

source_name: Patient Triple-negative breast tumor

growth_protocol: Patient samples used in this study (n=9) originated from patient treated at Institut Curie with residual triple-negative breast cancers post-neoadjuvant chemotherapy, who gave informed consent for the profiling.

extract_protocol: CUT&Tag on frozen tumor samples. CUT&Tag was performed as in Kaya-Okur et al. with minor modifications on 50,000 to 100,000 nuclei with 1:50 antibody (Cell Signaling Antibodies : Anti-H3K27me3, Ref: 9733- C36B11, Anti-H3K4me3, Ref: 9751- C42D8) (Kaya-Okur et al., Bartosovic et al.,). All washes were performed in a volume of 500µL and all centrifugations were done using a swinging bucket centrifuge at 1300g, 4min, at 4°C for nuclei preparation and  600g, 8min, 4°C for subsequent steps. Nuclei were extracted and permeabilized from 10-20mg frozen tumor tissues by incubating samples 10min on ice in 6mL ice-cold NE1 buffer (20mM HEPES pH7.2, KCl 10mM, spermidine 0.5mM, glycerol 20%, BSA 1%, NP-40 1%, digitonin 0.01%, proteases inhibitor 1x) after mechanical dissociation. Following antibody incubation and tagmentation, samples were incubated for 1h at 55°C with max speed agitation with 3uL SDS10% and 2,5uL 20mg/mL proteinase K. After DNA extraction (Qiagen, Ref: 139046 MaXtract High density), PCR amplification (with 17 cycles, 20s at 63°C combined annealing/extension step) of the sequencing libraries was performed and profiles were checked on the Agilent TapeStation using High-sensitivity D1000 reagents. CUT&Tag libraries were sequenced on a NovaSeq 6000 (Illumina) in PE50 mode.

value: Patient Triple-negative breast tumor

tag: treatment

value: Post-NAC

tag: experiment

value: H3K27me3 bulk Cut&Tag

value: FALSE


title: JK125_reg2_org_3_r1 [scRNA-seq]


title: HeLa.+sncRNAU14.+AHT.A

description: small RNAseq

value: Human cervical carcinoma cells carrying lentiviral backbone with sncRNA-U14

value: Doxycycline (1 ug/ml)


title: RIPseq-EZH2-rep1

city: Singapore

first: Chan-Shuo

last: Wu

address: 14 Medical Drive, #12-01

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

description: RIP-seq EZH2 Ab: Active Motif (#39875, lot: 06313005)

data_processing:
For ChIP-seq analysis, reads were mapped by bowtie2 against human reference genome GRCh38 (Langmead and Salzberg 2012).
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
The resulting bam files are converted to bigWig format by bedGraphToBigWig from bedGraph generated by bedtools.
For 4C-seq analysis, the long-range genomic interaction regions generated by the 4C-Seq experiment were analyzed by using the R package r3CSeq v1.30.0 on hg19.
Bam files are converted to read coverage by bedGraphToBigWig. The read coverage was normalized according to sequencing depth.
The resulting bedGraph files are converted to bigWig format.
The genome version of bigWig files was converted to hg38 by CrossMap.
For total RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation GENCODE 26.
PCR duplicates were removed in the paired-end alignments by samtools rmdup.
Alignments with mapping quality < 20 were removed.
Gene expression levels in FPKM were determined by cuffdiff in the Cufflinks package.
For fraction RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation.
The read count on each EZH2 peak region was generated by featureCount. The read count was normalized according to the sequencing depth.
For RIP-seq analysis, reads from the RIP data set and its control data set were mapped respectively by STAR against human reference genome GRCh38 with gene annotation.
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
Bam files was converted to bedGraph to represent read coverage by bedtools. The read coverage was normalized according to the size of transcriptome mapping.
The resulting bedGraph files are converted to bigWig format.
For NANOPOPRE-seq total polyA+ RNA, the reads were mapped to hg38 by Minimap2 with -ax splice -uf -k14.
The bam files were converted to bed12 by bamToBed and were converted to bigBed file by bedToBigBed. Only uniquely mapped reads were retained.
For NANOPORE-seq nuclear cDNA sequencing, the reads were mapped to hg38 by LAST with lastal -d90 -m50 -D10 and last-split -d2
The maf files were converted to psl file with maf-convert -j1e6 psl. The psl files were subsequently converted to bam file with psl2sam.pl and cigar_tweaker scripts within the SAMtools package.
The read alignments were then converted into bedGraph by BEDTools and into bigWig format by bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq.genes.fpkm.txt: Tab-delimited text file includes FPKM values.
Supplementary_files_format_and_content: *.ReadCount.txt: Tab-delimited text files include read counts.
Supplementary_files_format_and_content: *bw: bigWig format
Supplementary_files_format_and_content: *.bigBed: bigBed format

source_name: K562 leukemia cell line

growth_protocol: K562 cells and its derivatives were cultured with RPMI supplemented with 10% fetal bovine serum. The cells were passage every 3 to 4 days.

extract_protocol:
1) RIP-seq: Cells were fixed with 1% formaldehyde. RNA was sonicated to around 3000 and protein-RNA complexes were pulled down by antibodies. 2) RNA-seq: Fractionated RNA was harvested by Trizol followed by DNaseI treatment. 3) NANOPRE-seq: Fractionated RNA was harvested by Trizol followed by DNaseI treatment. Superscript IV was used for nuclear cDNA preparation. 4) ChIP-seq: Cells were fixed with 1% formaldehyde and insoluble chromatin fraction was isolated. Chromatin was sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antibodies. 5) 4C-seq: Cells were fixed with 2% formaldehyde. gDNA was digested first with DpnII and ligated. The ligated chromatin was digested again with NlaIII, MseI or MluCI and ligated.
1) ChIP-seq: Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 2) RIP-seq and RNA-seq: Libraries were prepared using Scriptseq V2 RNA-seq Library preparation kit (SSV21124) according to manufacturer's instruction.  Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 3) NANOPORE-seq:  Library for nuclear cDNA was constructed with 1D cDNA library kit (SQK-LSK108) according to manufacturer's instruction. RNA library for total polyA+ RNA was constructed with direct-RNA sequencing kit (SQK-RNA001) according to manufacturer's instruction. 4) 4C-seq: 4C library was constructed with customized primers with Illumina adaptor and barcodes and KAPA HiFi HotStart ReadyMix (KK2602).

treatment_protocol: LEVER knock out was achieved using CRISPR-Cas9 gene editing method. LEVER knock down was achieved using inducible CRISPR-dCas9 strategy.

tag: cell line

value: Leukemia cell line

tag: genotype/variation

value: Wild type

tag: passage

tag: antibody


title: JK125_reg1_org_3_r1 [scRNA-seq]


title: patient_tumor_HBCx147_H3K4me3

value: H3K4me3 bulk Cut&Tag


title: JK136_reg1_tis_1 [scRNA-seq]

value: tissue


title: JK125_reg1_org_2_r1 [scRNA-seq]

value: organoid


title: JK125_reg1_org_1 [scRNA-seq]

value: primary


title: 24hpf_H2AZ_Rep3

city: Rochester

first: Fanju

last: Meng

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics

country: USA

institute: University of Rochester Medical Center

data_processing:
Library strategy: CUT&Tag
Sequencing reads were trimmed using cutadapt, aligned to zebrafish genome (GRCz11) using Bowtie2, then unmapped reads were filtered using samtools and PCR duplicates were marked and removed using Picard
Peak calling was performed using MACS2 with the following parameters: -f BAMPE -g 1.5e9 --nomodel --broad using bam files of triplicates
Read count normalized genome browser tracks were generated using bamCoverage from merged bam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Genome_build: GRCz11
Supplementary_files_format_and_content: bigWig files and bed files

organism: Danio rerio

source_name: zebrafish embryos

growth_protocol: Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle

extract_protocol: Around 100,000 nuclei from 6hpf embryos and anterior portion of 24hpf embryos were used for CUT&Tag and library construction according to standard methods. Polyclonal H2A.Z antibody from Active Motif (Cat. 39113) was used.

value: AB/Tuebingen

tag: developmental stage

value: 24hour post fertilization

tag: target


title: Sed_Plasma_sEV1

value: plasma

value: 90 min twice per day, lasts for 4 weeks

value: microRNA


title: patient_tumor_HBCx144_H3K4me3

value: Patient Triple-negative breast tumor


title: patient_tumor_HBCx167_H3K4me3

value: Post-NAC


title: HepG2_KO_mRNA_Rep1

city: New Haven

first: Wendy

last: Gilbert

state: CT

address: 333 Cedar Street – Room C-129

department: MB&B

institute: Yale University

description: HepG2_prefs_newpkcall_v2_7reps_p1.0_l7.txt

data_processing:
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed for in vitro Pseudo-seq libraries using fastx_collapser
Reads were mapped to bowtie indices of the pool or GRCh37 for chromatin-associated RNA Pseudo-seq with tophat2. Reads from PUS1 knockout and wild type mRNA-seq were mapped to GRCh37 using STAR
Pseudouridylation was assessed using cutom python scripts (see text)
Differential mRNA level analysis of PUS1 knockout and wildtype mRNA-seq using DEseq2
Differential splicing analysis of PUS1 knockout and wildtype mRNA-seq using rMATS
Genome_build: GRCh37 for sequencing experiments from cellular RNA and Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)
Supplementary_files_format_and_content: rMATS output
Supplementary_files_format_and_content: DEseq2 output

growth_protocol: HepG2 cells were grown in high glucose DMEM (HyClone cat# SH30022.01) 10% FBS HyClone cat.# SH30070.03

extract_protocol:
HepG2 cells were biochemically fractionated and chromatin-associated RNA was isolated and Pseudo-seq was performed. Total RNA was isolated from PUS1 knockout and wildtype HepG2 cells with Qiazol and poly(A)+ mRNA-seq was perfomed with TruSeq Stranded mRNA kit.   Oligo pools (human, Twist Biosciences) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
Pseudo-seq samples were treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.

tag: source

value: poly(A)+ mRNA HepG2 PUS1 KO

tag: cmc use

tag: bowite fasta


title: HepG2_WT_mRNA_Rep1

value: poly(A)+ mRNA HepG2


title: patient_tumor_HBCx95_H3K27me3

tag: tissue

value: H3K27me3 bulk Cut&Tag

value: TRUE


title: 24hpf_H2AZ_Rep2

tag: strain


title: JK125_reg2_tis_1 [scRNA-seq]

tag: sample type

tag: tumour type

tag: patient id


title: JK125_reg1_tis_1.2 [scRNA-seq]


title: JK136_reg1_org_1 [scRNA-seq]


title: HepG2_KO_mRNA_Rep2


title: patient_tumor_HBCx147_H3K27me3

value: FALSE


title: Sed_BAT sEV3

value: brown adipose tissue

tag: exercise protocal

tag: molecule type


title: 24hpf_H2AZ_Rep1


title: patient_tumor_HBCx144_H3K27me3

tag: treatment

tag: experiment


title: patient_tumor_HBCx166_H3K4me3

value: H3K4me3 bulk Cut&Tag


title: patient_tumor_HBCx130_H3K4me3


title: JK125_reg1_btic_1 [scRNA-seq]

growth_protocol: Organoid cells that escaped the Matrigel and created neurospheres were collected and propagated in 25cm flasks in neural stem cell media (NeuroCult) supplemented with EGF, FGF-2, and heparin suflate.

value: neurosphere line


title: patient_tumor_HBCx130_H3K27me3


title: 12 month old mCat Tg whole medulla, biological rep2

type: RNA

city: San Antonio

first: Ann

last: Griffith

address: 7703 Floyd Curl Drive

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

description: Gene expression data from microdissected whole medullary tissue from 12 month old mCat Tg mouse thymus

hyb_protocol: Fragmentaion/hybridization to MOE430v2.0 arrays (Affymetric) were performed according to Affymetrix protocol. Imagingwas performed on an Affymetrix GeneChip Scanner 3000 per manufacturer's instructions.

data_processing: Raw .cel files were processed with the mas5 function and present calls were generated using the mas5calls function, both from the R package affy (Gautier et al., 2004).  The samples were quantile normalized using the normalizequantiles function from R package preprocessCore (https://github.com/bmbolstad/preprocessCore).

label: biotin

source_name: microdissected whole medulla

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.2-1.0 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Thymi were collected from 12 month old mCat Tg mice and snap frozen in OCT.

extract_protocol: RNA was isolated using RNAqueous Micro kits (Ambion) according to manufacturer's instructions. Each independent RNA pool included tissue from multiple sections and mice.

treatment_protocol: Transverse 20 μm sections were cut from the middle third of the tissue and mounted on PEN membrane slides (Leica). Sections selected for microdissection were chosen to have cortical regions 400-600um deep, medullary regions at least 200μm deep, and symmetrical cortical/medullary borders. Tissue was fixed in cold acetone:ethanol (3:1 v/v), rehydrated through graded ethanol, stained with hematoxylin:ethanol (1:1), and dehydrated through graded ethanol. Slides were dried at room temperature and immediately used for microdissection on a Leica AS LMD system. RNA was isolated using RNAqueous Micro kits (Ambion). Each independent RNA pool included tissue from multiple sections and mice.

value: thymus

tag: genotype

value: mCat Tg

tag: age

value: 12 months old


title: patient_tumor_HBCx106_H3K4me3


title: JK124_reg2_org_12mix [scRNA-seq]

value: organoid

value: primary


title: JK124_reg2_tis_2 [scRNA-seq]

value: tissue


title: 6hpf_H2AZ_Rep3

value: AB/Tuebingen

value: 6hour post fertilization


title: 12 month old mCat Tg whole medulla, biological rep3

scan_protocol: Imagingwas performed on an Affymetrix GeneChip Scanner 3000 per manufacturer's instructions.


title: Sed_BAT sEV2

value: 90 min twice per day, lasts for 4 weeks

value: microRNA


title: Sed_BAT sEV1


title: patient_tumor_HBCx106_H3K27me3

value: Patient Triple-negative breast tumor

value: Post-NAC


title: 12 month old mCat Tg whole medulla, biological rep1


title: HepG2_WT_mRNA_Rep2

value: poly(A)+ mRNA HepG2


title: JK124_reg1_org_2.1 [scRNA-seq]


title: JK124_reg1_org_1 [scRNA-seq]


title: JK125_reg1_tis_1.1 [scRNA-seq]


title: 6hpf_H2AZ_Rep2


title: JK124_reg1_tis_1 [scRNA-seq]


title: TCR Sequences Lane 1

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

data_processing:
Raw read processing was performed as in Macosko et al.
Briefly, sequencing reads were aligned to the mm10 reference genome, collapsed by unique molecular identifier (UMI) and aggregated by cell barcode to obtain a gene expression matrix of cells versus genes
Barcodes with under 300 unique genes detected were then excluded from analysis.
Genome_build: mm10

source_name: CD8+ TIL

growth_protocol: B16F10 cells were cultured in Dulbecco’s Modified Eagle’s Medium (ATCC) supplemented with 10% fetal bovine serum (FBS, R&D Systems), 100 U/mL penicillin (Thermo), and 100 μg/mL streptomycin (Thermo).

extract_protocol:
On day 26, mice were euthanized. Single cell suspensions were generated from tumors and spleens. Pan-T cell isolations were performed using an EasySep mouse T cell isolation kit (Stem Cell), and then T cells from three tumors were pooled and stained with Zombie Aqua, Fc block, 5 nM p15E-tetramer (produced in-house), CD3, and CD8. Splenocytes were used as controls for sorting.
Seq-Well

treatment_protocol: Female C57BL/6 mice from Taconic were inoculated with 106 B16F10 cells subcutaneously on the right flank. At day 8, mice received AIP therapy, followed by ICB every three days thereafter. On day 26, mice were euthanized.

tag: celltype

value: CD8+ T Cell


title: MM468_reChIP_H3K4me3_IgG

data_processing:
Library strategy: Sequential ChIP-Seq
ChIP-seq: Read #1 was aligned to hg38 Human genome reference using bowtie with options ‘-S -k 1 -m 1’
ChIP-seq: After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.
ChIP-seq: Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCoverage function with options ‘--normalizeUsing CPM --binSize 50 --smoothLength 500 --extendReads 150 --ignoreForNormalization chrX’.
ChIP-seq: Comparison Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCompare function with options ‘--binSize 30 --smoothLength 200 --extendReads 150 --ignoreForNormalization chrX --operation log2 --pseudocount 1 –skipNonCoveredRegions’ and re-smoothed using a custom R script.
For the H3K4me3 -> H3K27me3 reChIP datasets, peaks were first called on primary ChIP using MACS2 without control with parameters ‘--call-summits -p 0.01 --nomodel --extsize 300’. The number of reads in the region 2.5kbp upstream and downstream of each peak were counted in the primary and secondary ChIP. Reads were normalized by total library size. First, the ratio between secondary and primary ChIP were calculated for each peak and then the odd-ratio between each TSS and it’s 60 closest neighbours were calculated from the ratios. In order for a TSS to be considered bivalent, the odd ratio of a given peak compared to the 60 closest neighbour peaks must be greater than 4. Then, A Fisher exact test was performed on the contingency table to reject the null hypothesis that the number of reads in secondary compared to reads in primary ChIP is greater in the given peak than in it’s 60 neighbor peaks. P-values were adjusted for multiple testing using the Benjamini-Hochberg procedure50. In order to choose adequate thresholds for adjusted p-value and “peak”/“locus”, we calculated the number of false positives for p-values ranging from 0.001 to 1e-30, using H3K4me3/IgG ChIP and ChIP-reChIP as a negative control. Adjusted p-value thresholds were always lower than 0.001 and were defined so that we obtained the greatest number of bivalent peaks in the H3K4me3/H3K27me3 experiment compared to the H3K4me3/IgG negative control.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig binary file of coverage and compared coverage

growth_protocol:
MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). HCC38 cell lines were cultured in RPMI 1640 (Gibco-BRL, Ref: 11875085), supplemented with 10% heat-inactivated fetal calf serum.
Patient samples and PDX models.We used three xenograft models generated from three different residual triple-negative breast cancers post-neoadjuvant chemotherapy (HBCx95 called PDX_95, HBCx39 called PDX_39 and HBCx172 called PDX_172 in the manuscript) established previously at Curie Institute with informed consent from the patient. Female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02).   Before downstream analysis (scChIP-seq, scRNA-seq or sequential ChIP-seq), control and treated tumors were digested for 2h at 37°C with a cocktail of Collagenase I (Roche, Ref: 11088793001) and Hyaluronidase (Sigma-Aldrich, Ref: H3506). Cells were then individualized at 37°C using a cocktail of 0.25% Trypsin-Versen (Thermo Fisher Scientific, Ref: 15040-033), Dispase II (Sigma-Aldrich, Ref: D4693) and DNase I (Roche, Ref: 11284932001) as described previously43. Then, eBioscience red blood cell lysis buffer (Thermo Fisher Scientific, Ref: 00-4333-57) was added to the cell suspension to remove red blood cells. To increase the viability of the final cell suspension, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, Ref:130-090-101)

extract_protocol:
Sequential ChIP-seq:The first ChIP experiments were performed as described previously (Grosselin et al.,  2018) on 30e6 cells using anti-H3K4me3 (Cell signaling, Ref: #9733) or anti-H3 (Cell signaling, Ref: #4620) antibodies. After the washes, samples were eluted twice at 37°C for 15 min under agitation in the first ChIP elution buffer (50mM Tris-Hcl pH8, 5mM EDTA, 20mM DTT, 1%SDS)(Desvoyes et al., 2018). Samples were diluted 10 times to reduce SDS and DTT concentration. 10% of the eluted chromatin were kept as primary ChIP. The second ChIP was performed overnight on the rest of the chromatin using anti-H3K27me3 or anti-IgG (Cell signaling, Ref: #3900) antibodies. After the washes, samples were eluted twice at 65°C for 15 min under agitation in the ReChIP elution buffer (0,1M NaHCO3 and 1% SDS)(Desvoyes et al., 2018). As a negative control, we first immunoprecipitated H3K4me3 followed by IgG immunoprecipitation.
Sequential ChIP-seq : After reverse crosslinking and DNA clean-up, 3 to 15ng of immunoprecipated DNA were used to prepare the sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to theLibraries were sequenced on a NovaSeq 6000 (Illumina) in SE100 mode.

treatment_protocol: All cell lines were cultured in a humidified 5% CO2 atmosphere at 37 °C, and were tested as mycoplasma negative. GSKJ4 (KDM6A/B inhibitor, Sigma, Ref: SML0701), GSKJ5 (GSK-J4 inactive isomer, Abcam, Ref: ab144397) and UNC1999 (EZH2 inhibitor, Abcam, Ref: ab146152) were used at indicated concentrations. Cells were treated with 5 μM of 5-FU (Sigma, Ref: F6627) alone or in combination with KDM6A/Bi or EZH2i for indicated days.

value: MDA-MB-468 cell line


title: TCR Sequences Lane 2


title: 6hpf_H2AZ_Rep1

tag: developmental stage


title: Myeloid Cells - Blood (Tumor) 10x SCC002

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

data_processing:
Samples 1-8 (10x) samples were processed using CellRanger pipline version 2.1.1 or 3.0.2
Sample 9 aligned RNA reads using 1342_Fred_Hutch_suppt2_amplicons.fasta
Sample 10 aligned RNA reads using 1342_Fred_Hutch_suppt2_amplicons.fasta and aligned protein reasd using AbSeq_Prlic_NEW_v2.fasta
FASTQ files were processed with BD Rhapsody Analysis Pipeline hosted by SevenBridges Genomics
FASTQ files were processed with CellRanger software v2.1.1 or v3.0.1 and corresponding sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: Peripheral Blood Myloid Cells (SCC)

extract_protocol:
RNA was extracted using BD Rhapsody or 10x genomics protocols
RNA was constructed using BD Rhapsody or 10x genomics protocols

treatment_protocol: T  cells were stimulated for 2 hour with PMA/ Ionomycin or IL-12, IL-15, IL-18

tag: phenotype

tag: donors

value: Peripheral Blood


title: BT20_primary_H3K4me3_IgG

source_name: BT20 cell line

value: BT20 cell line


title: P18 xenos2 Lgr5 neg (1336-2016)

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

source_name: P18 xenos2 Lgr5 neg

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: P18T organoids grown in Utrech organoid medium and injected in 50% BME-HBSS into Swiss-Nude mice.

extract_protocol: RNA was isolated using magnetic beads from 1000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 23 cycles.

treatment_protocol: Xenografts dissagregation with Collagenase IV, treated with amonium chloride, and stained for Epcam and Lgr5 (Fab072)

value: P18T organoids

tag: condition

value: xenograft 2, Fab072-

tag: cell type

value: Fab072- epithelial cells

tag: replicate


title: JK124_reg2_tis_1 [scRNA-seq]


title: P18 xenos2 Lgr5 pos (1335-2016)

source_name: P18 xenos2 Lgr5 pos

tag: tissue

value: xenograft 2, Fab072+

value: Fab072+ epithelial cells


title: JK124_reg1_org_2.2 [scRNA-seq]

tag: sample type

value: organoid

value: primary


title: Day14_WT_rep2

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: skin wound, wild-type group (WT) on Day14, replicate 2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Mouse Genome microarry 4x44K Ver. 2.0 (G2519F, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026655_D_F_20121126) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was exluded. After filtering, control probes were excluded, and log scale values were transformed into normal scale.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from whole-wound homogenate using the Purelink RNA mini kit (ThermoFisher Scientific) according to the manufacturer's instructions.

treatment_protocol: Mice were euthanized by an overdose of isoflurane on days 7 and 14 after wounding. The wound and surrounding intact skin were harvested and frozen in liquid nitrogen and stored at - 80℃ before RNA isolation.

value: skin wound

tag: disease state

value: wild-type group (WT)

value: no treatment

tag: time


title: Day14_estrogen_rep1

description: skin wound, a topical estrogen wound treatment diabetic group (db/db+E) on Day14, replicate 1

value: diabetic group

value: topical estrogen


title: P18 xenos1 Lgr5 pos (1333-2016)

source_name: P18 xenos1 Lgr5 pos

value: xenograft 1, Fab072+


title: Day14_WT_rep1

description: skin wound, wild-type group (WT) on Day14, replicate 1


title: BT20_reChIP_H3K4me3_IgG


title: MM468_primary_H3K4me3_IgG


title: P18 xenos1 Lgr5 neg (1334-2016)

source_name: P18 xenos1 Lgr5 neg

value: xenograft 1, Fab072-


title: Tetramer Negative CD8+ rep1

value: CD8+ T Cell

tag: sort fraction

value: Tetramer Negative

tag: strain


title: Day14_estrogen_rep2

description: skin wound, a topical estrogen wound treatment diabetic group (db/db+E) on Day14, replicate 2

tag: treatment


title: Day14_dbdb_rep2

description: skin wound, diabetic group on Day14, replicate 2

source_name: skin wound, diabetic group on Day14


title: BT20_reChIP_H3K4me3_H3K27me3

value: BT20 cell line

tag: experiment


title: T cells - SCC 10x SCC002

source_name: SCC-derived T cells

value: Squamous Cell Carcinoma


title: Tetramer Positive CD8+ rep1

value: Tetramer Positive


title: HCC38_reChIP_H3K4me3_IgG

source_name: HCC38 cell line

value: HCC38 cell line


title: JK124_reg1_tis_2 [scRNA-seq]

source_name: glioblastoma

value: tissue

tag: tumour type

tag: patient id


title: HCC38_reChIP_H3K4me3_H3K27me3


title: Tetramer Negative CD8+ rep2

tag: celltype


title: Day7_vehicle_rep2

description: skin wound, vehicle wound treatment diabetic group (db/db+vehicle) on Day7, replicate 2

value: vehicle


title: Day14_vehicle_rep2

description: skin wound, vehicle wound treatment diabetic group (db/db+vehicle) on Day14, replicate 2


title: HCC38_primary_H3K4me3_IgG


title: injured SP-C mutant lung tissue

city: Salt Lake City

first: Alessandro

last: Venosa

state: UT

department: Pharmacology and Toxicology

institute: University of Utah

data_processing:
Mouse lung tissue GRCm38 FASTA and GTF files were downloaded from Ensembl release 98.  The reference database was created using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0.
Counts were filtered to remove features with zero counts or less than 5 reads
PCA analysis and differential gene expression analysis was performed using hciR package, using DESeq2 (version 1.28.1).
Genome_build: mm10, M_musculus_Dec_2011, GRCm38
Supplementary_files_format_and_content: txt file with counts

source_name: lung primary cells

growth_protocol: all animals were eutanized according to IACUC protocol. Lungs were lavaged with ice cold saline solution. This was followed by  perfusion through the heart with saline. Lungs were then incubated in collagenase D for 30 min (37C, 5%CO2), followed by single cell suspension through a 70um strainer.Red blood cells were lyzed, cell counted and submitted for library preparation and sequencing.

extract_protocol:
Total RNA was extracted from fresh frozen cell pellets using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
Libraries were prepped according to the 10X Genomics Single Cell 3’ Gene expression Library prep protocol V3, then analyzed using Agilent D1000 ScreenTape on an Agilent Technology 2200 TapeStation system

treatment_protocol: Single oral gavage treatment with tamoxifen (175mg/kg, in corn oil) excises neomycin cassette and boosts mutant SPC mutant expression. Corn oil gavage was used for

value: whole lung digest

tag: genotype

value: SP-CI73T mutant

value: untreated


title: Myeloid Cells - Blood (Oral) 10x OM121

source_name: Peripheral Blood Myloid Cells (OM)

tag: phenotype

value: Peripheral Blood


title: Jak1KO_IgG1_5

city: Atlanta

first: Gabriel

last: Kwong

state: Georgia

address: 345 Ferst Dr NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

data_processing:
Raw FASTQ reads passing quality control (FastQC v0.11.2) were aligned on the mm10 reference genome using STAR aligner (v2.5.2a) with default parameters.
Aligned fragments were then counted and annotated using Rsamtools (v3.2) and Cufflinks (v.2.2.1) after a ‘dedup’ step using BamUtils (v1.0.11).
Differential expression was performed using the edgeR package (v3.24.3) in R using the exactTest method with tagwise dispersion.
TMM normalization considering mice in all treatment groups was performed to remove library size effect through the calcNormFactors function.
Differential expression was performed on Ensembl IDs before mapping to gene names. Then the identified differentially expressed genes were filtered by a list of extracellular and transmembrane endopeptidases queried from UniProt.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt files with read counts for each sample
Supplementary_files_format_and_content: matrix table .csv file with read counts for every gene and every sample

source_name: MC38 tumour

growth_protocol: 1x10^6 MC38 tumour cells were subcutaneously injected into C57BL/6 mice.

extract_protocol:
On 14 days post-inoculation, approximately 50 mg of tumours were dissected and rapidly frozen with dry ice and IPA. Frozen tumour samples were homogenized in MACS M Tubes (Miltenyi) using the MACS Dissociator (Miltenyi). Total RNA was isolated from the homogenate using the RNeasy Plus Mini Kit (Qiagen).
Library preparation with TruSeq RNA Library Prep Kit (Illumina) and mRNA NGS sequencing (40x106 paired end read) were performed by Admera Health (South Plainfield, NJ).

treatment_protocol: 100 ug of aPD1 antibody or IgG1 control was intravenously injected 7, 10, and 13 days post-inoculation.

tag: Sex

value: female

value: MC38 Jak1KO tumour


title: Myeloid Cells - Blood (Oral) 10x OM125

tag: donors


title: Tetramer Positive CD8+ rep2


title: MM468_primary_H3K4me3_H3K27me3

source_name: MDA-MB-468 cell line

value: MDA-MB-468 cell line


title: Day14_vehicle_rep1

description: skin wound, vehicle wound treatment diabetic group (db/db+vehicle) on Day14, replicate 1

value: skin wound

value: diabetic group


title: MM468_reChIP_H3K4me3_H3K27me3


title: T cells - Blood (Tumor) 10x SCC002

source_name: Peripheral Blood T Cells (SCC)


title: Jak1KO_IgG1_2


title: HCC38_primary_H3K4me3_H3K27me3


title: Day7_vehicle_rep1

description: skin wound, vehicle wound treatment diabetic group (db/db+vehicle) on Day7, replicate 1


title: Day7_dbdb_rep2

description: skin wound, diabetic group on Day7, replicate 2

source_name: skin wound, diabetic group on Day7

value: no treatment


title: Jak1KO_IgG1_1


title: HBCx95_primary_H3K4me3_IgG

value: patient derived xenograft


title: Jak1KO_IgG1_3


title: HBCx95_primary_H3K4me3_H3K27me3


title: Day7_estrogen_rep2

description: skin wound, a topical estrogen wound treatment diabetic group (db/db+E) on Day7, replicate 2

value: topical estrogen


title: T cells - Blood (Oral) 10x OM125

source_name: Peripheral Blood T Cells (OM)


title: Day7_estrogen_rep1

description: skin wound, a topical estrogen wound treatment diabetic group (db/db+E) on Day7, replicate 1


title: Day7_WT_rep1

description: skin wound, wild-type group (WT) on Day7, replicate 1

value: wild-type group (WT)


title: Day14_dbdb_rep1

description: skin wound, diabetic group on Day14, replicate 1


title: Myeloid Cells - SCC 10x SCC002

source_name: SCC-derived Myloid Cells

value: Squamous Cell Carcinoma


title: Jak1KO_aPD1_3


title: RNA-Seq HEK293 2B induced rep1

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
build tRNA+-7nt bowtie index
RNA-Seq: kallisto mapping to ensembl 89 ncRNA and cDNA
RNA-Seq: DESeq2 differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, Chr-Seq for + and - strands

source_name: HEK293 2B

growth_protocol: All cells were grown in DMEM.

extract_protocol:
RNA-Seq:  standard phenol chloroform extraction and ethanol precipitation
RNA-Seq: TruSeq Stranded Total RNA Sample Preparation Protocol.

treatment_protocol: RNA-Seq: HEK293 2B cells with Dicer shRNA and HEK293T cells were cultured, induced with 3ug/ml of doxycyclin and maintained for 7 days before lysis. RNA was purified using the Qiagen miRNEasy kit and 1.5 million cells were lysed for protein. 15ug of RNA from each sample was DNase treated (Thermo ENO521) at 37ºC for 30mins, phenol chloroform extracted and ethanol precipitated.

tag: cell line

value: HEK293 2B

tag: genotype/variation

value: Dicer knockdown

tag: molecule subtype

value: polyA RNA


title: T cells - Blood (Oral) 10x OM121

tag: tissue


title: Jak1KO_IgG1_4


title: RNA-Seq HEK293T induced rep3

value: wild type


title: HBCx39_primary_H3K4me3_IgG


title: HBCx95_reChIP_H3K4me3_H3K27me3


title: Myeloid Cells - Blood (Oral) 10x OM122


title: HBCx172_reChIP_H3K4me3_IgG


title: Myeloid Cells - Oral Mucosa 10x OM 122

source_name: Mucosa-derived Myloid cells

value: Oral Mucosa


title: Day7_WT_rep2

description: skin wound, wild-type group (WT) on Day7, replicate 2

tag: disease state


title: Myeloid Cells - Oral Mucosa 10x OM121


title: Jak1KO_aPD1_5


title: sRNA Dicer KD rep3

data_processing:
build tRNA+-7nt bowtie index
sRNA: bowtie mapping to tRNA genes
No abundance data generated for sRNA
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, Chr-Seq for + and - strands

extract_protocol:
sRNA: miRVana kit
sRNA: NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: sRNA: Dicer shRNA and scrambled shRNA cells were induced by incubation with doxycyclin (3ug/ml) for 7 days.  Cells were trypsinised, transferred to a fresh tube, pelleted and washed with PBS once.

value: sRNA


title: B2mKO_IgG1_5

value: MC38 B2mKO tumour


title: Myeloid Cells - Oral Mucosa 10x OM125


title: control SP-C mutant lung tissue

value: whole lung digest

value: SP-CI73T mutant

value: tamoxifen treated


title: T cells - Oral Mucosa 10x OM122

source_name: Mucosa-derived T cells


title: HBCx39_reChIP_H3K4me3_IgG


title: HBCx172_primary_H3K4me3_IgG


title: T cells - Oral Mucosa 10x OM121


title: RNA-Seq HEK293 2B induced rep2


title: HBCx95_reChIP_H3K4me3_IgG


title: IV_HepG2_NE_-CMC

data_processing:
Library strategy: Pseduo-seq
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed for in vitro Pseudo-seq libraries using fastx_collapser
Reads were mapped to bowtie indices of the pool or GRCh37 for chromatin-associated RNA Pseudo-seq with tophat2. Reads from PUS1 knockout and wild type mRNA-seq were mapped to GRCh37 using STAR
Pseudouridylation was assessed using cutom python scripts (see text)
Differential mRNA level analysis of PUS1 knockout and wildtype mRNA-seq using DEseq2
Differential splicing analysis of PUS1 knockout and wildtype mRNA-seq using rMATS
Genome_build: GRCh37 for sequencing experiments from cellular RNA and Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)
Supplementary_files_format_and_content: rMATS output
Supplementary_files_format_and_content: DEseq2 output

source_name: Pool

tag: source

value: Nuclear extract (NE) from HepG2 cells

tag: cmc use

tag: bowite fasta


title: Jak1KO_aPD1_4

tag: strain

value: female

value: MC38 Jak1KO tumour

tag: treatment


title: Day7_dbdb_rep1

description: skin wound, diabetic group on Day7, replicate 1

value: skin wound

value: diabetic group

value: no treatment

tag: time


title: T cells - Blood (Oral) 10x OM122

value: Peripheral Blood


title: HBCx39_reChIP_H3K4me3_H3K27me3

value: patient derived xenograft

tag: experiment


title: HBCx172_primary_H3K4me3_H3K27me3


title: sRNA Dicer KD rep1

value: Dicer knockdown


title: IV_RPUSD4_+CMC

value: Recombinant Full Length hRPUSD4

value: 0.4M CMC


title: B2mKO_IgG1_2


title: RNA-Seq HEK293 2B induced rep3

value: HEK293 2B

value: polyA RNA


title: HBCx172_persister [scRNA-seq]

data_processing:
The scRNA-seq sequencing files were preprocessed using the cellRanger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/3-0).   For the MDA-MB-468 human cell line, sequences were aligned against the hg38 genome only.   For the PDX samples, sequences were aligned against the files were aligned against hg19 and mm10 genomes and only cells with a majority of human reads were retained for the analysis.  The BAM files correspond to the « possorted_genome_bam.bam » in the cellRanger output.
Genome_build: hg19
Supplementary_files_format_and_content: Sparse-matrix in 10X format, corresponding to the ‘*barcodes.tsv’  files containing the cell barcode sequence ; the ‘*features.tsv’ files containing the features (transcripts) and the ‘*matrix.mtx’ files containing the matrix non-zeroes values and row and column indexes.  For the PDX model the matrices are counted on the hg19 genome.

source_name: HBCx172 PDX

growth_protocol: For PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used a xenograft model generated from a residual triple-negative breast cancer post-neoadjuvant chemotherapy (HBCx95) established previously at Institut Curie with informed consent from the patient51,52.

extract_protocol:
For PDX model, before downstream analysis, control and Capecitabine treated tumors were digested for 2 h at 37 °C with a cocktail of Collagenase I (Roche, Ref: 11088793001) and Hyaluronidase (Sigma-Aldrich, Ref: H3506). Cells were then individualized at 37°C using a cocktail of 0.25% Trypsin-Versen (Thermo Fisher Scientific, Ref: 15040-033), Dispase II (Sigma-Aldrich, Ref: D4693) and DNase I (Roche, Ref: 11284932001) as described previously53. Then, eBioscience red blood cell lysis buffer (Thermo Fisher Scientific, Ref: 00-4333-57) was added to the cell suspension to remove red blood cells. To increase the viability of the final cell suspension, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, Ref:130-090-101).
Libraries were sequenced on a NovaSeq 6000 (Illumina) in PE8-8-91 with a coverage of 50,000 reads/cell.

treatment_protocol: For PDX model,  five mice were not treated and kept as controls and twenty-seven mice were treated orally with Capecitabine (Xeloda; Roche Laboratories) at a dose of 540 mg/kg, 5 d/week for 6 to 14 weeks. Relative tumor volumes (mm3) were measured as described previously22. Latency was defined as the number of days between the observation of a complete response (Tumor size < 10 mm3) after the first cycle of Capecitabine, and the detection of a recurrent tumor (Tumor size > 10 mm3). Eight mice were sacrificed after the first cycle of chemotherapy to study residual (2 mice) and persister (6 mice) human tumor cells. Seven mice with recurrent tumors (tumor volume between 200 and 600 mm3) were treated for a second round of Capecitabine.

value: Capecitabine (5-FU)

tag: day

tag: genome build


title: sRNA control rep3

value: wild type

value: sRNA


title: B2mKO_IgG1_1

value: MC38 B2mKO tumour


title: Jak1KO_aPD1_2


title: HBCx39_primary_H3K4me3_H3K27me3


title: T cells - Oral Mucosa 10x OM125

tag: phenotype

value: Oral Mucosa


title: sRNA control rep2


title: B2mKO_aPD1_5

tag: Sex

value: female


title: RNA-Seq HEK293T induced rep1


title: RNA-Seq HEK293T induced rep2


title: Jak1KO_aPD1_1

value: MC38 Jak1KO tumour


title: HBCx172_reChIP_H3K4me3_H3K27me3


title: B2mKO_aPD1_4


title: IV_PUS10_-CMC

value: Recombinant Full Length hPUS10


title: IV_PUS10_+CMC


title: B2mKO_aPD1_3


title: IV_HepG2_NE_+CMC

value: Nuclear extract (NE) from HepG2 cells


title: IV_RPUSD2_+CMC

value: Recombinant Full Length hRPUSD2


title: chr_HepG2_-CMC_11

description: HepG2_prefs_newpkcall_v2_7reps_p1.0_l7.txt

value: chromatin-associated RNA HepG2 cells


title: B2mKO_aPD1_2


title: IV_RPUSD2_-CMC


title: HBCx39_chemonaive [scRNA-seq]

source_name: HBCx39 PDX


title: B2mKO_aPD1_1


title: sRNA Dicer KD rep2


title: FT282 CCNE1 clone 4 rep1

city: Toronto

first: David

middle: WILLIAM

last: Gallo

state: ON

address: 600 University Ave

institute: Lunenfeld-Tanenbaum research instituite

data_processing:
Illumina CASAVA software was used for base calling
Sequenced reads were aligned to the hg38 primary assembly of the human genome and quantified using Salmon v1.4.0 with the command line flags “--validateMappings” and “--gcBias" to obtain read counts
Raw counts were processed using the bioconductor package edgeR v3.30.3 in R. Genes expressed with counts per million (CPM) > 0.1 in at least two samples were considered and normalized using trimmed mean of M-values (TMM) to remove the library-specific artefacts.
voomY transformation was applied to RNA-seq count data to obtain normalized expression values on the log2 scale.
Genome_build: hg38
Supplementary_files_format_and_content: matrix tabel contains log2 normalized gene expression values for every gene and every sample

source_name: Fallopian tube secretory epithelial cells

growth_protocol: FT282-hTERT p53-R175H WT (empty vector) and CCNE1 overexpressing cell lines were  cultured in DMEM: F-12(1:1) with 5% FBS, 1% UltroserG (Pall life sciences #15950-017) and 1% Pen/Strep

extract_protocol:
Pellets of FT282-hTERT p53R175H WT, CCNE1 C3 and C4 were flash frozen and RNA was harvested using Trizol reagent. Sequencing libraries were constructed using Illumina TruSeq RNA Sample Prep Kit with 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Fallopian tube secretory epithelial

tag: genotype

value: hTERT p53-R175H

value: CCNE1-overexpressing clone 4


title: B2mKO_IgG1_3


title: WT_IgG1_5

value: MC38 WT tumour


title: IV_noPUS_B_-CMC


title: B2mKO_IgG1_4


title: FT282 CCNE1 clone 3 rep3

value: CCNE1-overexpressing clone 3

tag: cell line


title: chr_HepG2_+CMC_9

value: 0.4M CMC


title: IV_TRUB2_+CMC

value: Recombinant Full Length hTRUB2


title: chr_HepG2_-CMC_9


title: FT282 CCNE1 clone 3 rep2


title: IV_RPUSD4_-CMC

value: Recombinant Full Length hRPUSD4


title: HBCx172_chemonaive [scRNA-seq]


title: HBCx39_persister [scRNA-seq]

value: Capecitabine (5-FU)


title: sRNA control rep1

tag: genotype/variation

value: wild type

tag: molecule subtype

value: sRNA


title: WT_IgG1_2

value: female

tag: tissue


title: IV_noPUS_A_+CMC

tag: source


title: FT282 WT rep3


title: chr_HepG2_-CMC_8

tag: cmc use


title: WT_IgG1_1


title: chr_HepG2_+CMC_11

tag: bowite fasta


title: IV_noPUS_A_-CMC


title: FT282 CCNE1 clone 4 rep3


title: 706

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

data_processing:
Evaluating quality of samples with FastQC ver  0.11.9
Remove adapters and unpaired reads using Trimmomatic ver 0.39
Mapping to the geonome by HISAT 2.2.0 release 2/6/2020
Making sorted bam files using SAMtools ver 1.11
Counting number of reads by Stringtie v2.1.2
Finding diffrenetinally expressed genes applying Deseq2 ver 1.28.1
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include log2 FPKM values for each Sample

organism: Rattus norvegicus

source_name: Medial preoptic area brain tissue

extract_protocol:
MPOA was dissected and flash frozen on dry ice. RNA was extracted using trizol reagent followed by the Qiagen micro RNAeasy kit
Library preps were created using the NEBNext Ultra library prep kit for illumina

tag: strain

value: Long evans

value: Female

value: Control


title: WT_aPD1_5

tag: treatment


title: chr_HepG2_+CMC_7


title: FT282 WT rep1


title: chr_HepG2_-CMC_7


title: FT282 CCNE1 clone 4 rep2


title: WT_aPD1_4


title: chr_HepG2_+CMC_10


title: WT_aPD1_3


title: chr_HepG2_+CMC_6


title: chr_HepG2_-CMC_10


title: IV_noPUS_B_+CMC


title: 733

value: LBN


title: WT_aPD1_1


title: chr_HepG2_+CMC_5

value: chromatin-associated RNA HepG2 cells


title: 598


title: chr_HepG2_-CMC_5


title: SilicaCCR2KO1

city: Noda

first: Tatsuro

last: Ogawa

address: 2641, Yamasaki

institute: Tokyo University of Science

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) were processed as follows. Adapter trimming of sequencing data was performed using cutadapt 2.10. Filtered reads were chunked into 16 parts for parallel processing by using Seqkit 0.14.0. Filtered cell barcode reads were annotated by Python script provided by BD Biosciences with minor modification for compatibility to Python 3.7. Reference RNA sequences were built by concatenating cDNA and ncRNA fasta files of the Ensembl database (build GRCm38 release-101). Associated cDNA reads were mapped to reference RNA using bowtie2-2.4.2 by the following parameters: -p 2 --very-sensitive-local -N 1 -norc -seed 656565 -reorder. Then, cell barcode information of each read was added to the bowtie2-mapped BAM files by the python script and pysam 0.15.4 (https://github.com/pysam-developers/pysam), and read counts of each gene in each cell barcode were counted using mawk. Resultant count data was converted to a single-cell gene-expression matrix file by using R-3.6.3. The inflection point of the knee-plot (total read count versus the rank of the read count) was detected using DropletUtils package in R-3.6.3. Cells of which total read count was over inflection point were considered as valid cells.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

source_name: lung

extract_protocol:
Murine lungs were isolated from silica-administrated WT or CCR2-/- mice. Lungs were minced into 0.5 mm2 with a razor blade and digested with Liberase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS (MP Bio Japan), 10 mM HEPES pH7.2-7.4 (Cytiva (Global Life Sciences Technologies Japan)), 0.25 mg/ml Liberase TM (Roche), and 2 kU/mL DNase I (Merck)] at 37 ºC for 60 minutes. Cell suspensions were washed and resuspended with 25% Percoll PLUS (Cytiva). After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were washed and resuspended with 1000 μL of preparation medium [RPMI-1640 supplemented with 5% FBS and 10 mM HEPES]. Each single-cell suspension cell concentration was counted using Flow-count fluorospheres (Beckman Coulter, Brea, CA, USA) and a Gallios flow cytometer (Beckman Coulter). Cells were stained with 2.5 μg/ml of Totalseq anti-mouse Hashtag-A antibodies (BioLegend) at 4ºC for 30 minutes and washed thrice with Cell Staining Buffer (BioLegend) and pooled.
Pooled single-cell suspensions were subjected to a BD Rhapsody system with BD Rhapsody Targeted & Abseq Reagent kit (BD Biosciences) following the manufacture’s instructions. 20000 cells were subjected to the BD Rhapsody workflow. After reverse transcription, Exonuclease I treatment of the resultant BD Rhapsody beads was performed at 37ºC for 60 minutes with 1,200 rpm on a Thermomixer C with Thermotop. Resultant beads were immediately chilled on ice; the supernatant was removed and washed with 1 mL of WTA wash buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA, and 0.05% Tween-20], 200 μL of BD Rhapsody lysis buffer (for inactivation of enzyme), once with 1 ml of WTA wash buffer, twice with 500 μL of WTA wash buffer, resuspended with 200 μL of Beads resuspension buffer. During the washing step, beads-containing DNA LoBind tubes (Eppendorf Japan) were replaced twice. Exonuclease I-treated BD Rhapsody beads were subjected to TAS- Seq workflow for cDNA and/or hashtag library amplification (Shichino S., bioRxiv, 2021). 150 ng of amplified cDNA libraries was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina. Ligated products were purified by AmPure XP beads and 9 cycles of Barcoding PCR were performed. Resultant products were purified twice by double size selection with 0.5× → 0.3× (final 0.8×) AmPure XP beads and eluted with 30 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system with appropriate dilutions. Resultant libraries and barcoded hashtag libraries were quantified using the KAPA Library Quantification Kit. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer.

treatment_protocol: WT or CCR2-/- mice were intratracheally administered with silica (400 mg/kg) and harvested lungs at day 3, 7, and 21.

value: lung

value: Silica

tag: date

value: Day 3, 7, and 21


title: IV_TRUB2_-CMC


title: WT_IgG1_3

value: MC38 WT tumour


title: chr_HepG2_+CMC_8


title: chr_HepG2_-CMC_4


title: S203AKI_1670_DSS

city: San Diego

last: Huang

state: CA

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: 10x scRNAseq

data_processing:
Cellranger v3.1.0 to align reads to mouse reference genome (mm10-3.0.0)
Used Seurat v4.0.1 to filter by mitochondrial counts >5% and <0.2%
Filtered these cells to remove cells with Cd4 expression < 0.4 based on gene expression
Filtered cells were scaled and log-normalized using ScaleData() and NormalizeData() functions from Seurat
Top 3000 genes selected for PCA analysis from RunPCA() function
Used PCA dimensions for non-linear dimensional reduction RunTSNE() and RunUMAP()
Identified clusters using function FindClusters()
Genome_build: mm10
Supplementary_files_format_and_content: UMI

source_name: Colonic lamina propria

growth_protocol: All mice were raised in Specific Pathogen Free (SPF) facility on normal diet. 10-12 week old animals were used for experiments.

extract_protocol:
Colons were harvest and cut into small pieces and washed, followed with digestion of the tissue using collagenase, DNase and dispase, the resulting cells are purified using Percoll gradient. Lamina propria cells from DSS or non-DSS treated mice were collected and subjected to mouse CD4+ T cell Isolation Kit (Miltenyi)
Enriched CD4+ cells (~10,000) were prepared for single cell libraries using Chromium Single Cell 3' Reagent Kits (10xGenomics) following the instructions. Briefly, GEM generation to get single cell resoution and barcoding, followed with clean and cDNA amplification and 3' gene expression library construction (inlcuding Fragmentation and end repair & A-tailing, adaptor ligation and double size selection)
The pooled libraries of each sample (20,000 reads/cell) ran on one lane of NovaSeq S4 following manufacturer’s recommendations.

treatment_protocol: Treated wildtype and RORgtS182 mutant mice were administered with 2% DSS in drinking water for 7 days and returned to regular water for 3 days. Untreated control mice remained on regular drinking water for 10 days. Both untreated and treated mice were harvested on day 10.

value: CD4+ T cell enriched

value: 2% DSS in drinking water for 7 days, harvested on day 10


title: HBCx95_persister [scRNA-seq]

data_processing:
The scRNA-seq sequencing files were preprocessed using the cellRanger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/3-0).   For the PDX samples, sequences were aligned against the files were aligned against hg19 and mm10 genomes and only cells with a majority of human reads were retained for the analysis.  The BAM files correspond to the « possorted_genome_bam.bam » in the cellRanger output.
Genome_build: hg38, hg19
Supplementary_files_format_and_content: Sparse-matrix in 10X format, corresponding to the ‘*barcodes.tsv’  files containing the cell barcode sequence ; the ‘*features.tsv’ files containing the features (transcripts) and the ‘*matrix.mtx’ files containing the matrix non-zeroes values and row and column indexes.  For MDA-MB-468 cell line, the matrices are counted on the hg38 transcripts, for the PDX model the matrices are counted on the hg19 genome.

source_name: HBCx95 PDX

growth_protocol: For PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used a xenograft model generated from a residual triple-negative breast cancer post-neoadjuvant chemotherapy (HBCx95) established previously at Institut Curie.

extract_protocol:
For PDX model, before downstream analysis (scChIP-seq, scRNA-seq and bulk ChIP-seq), control and Capecitabine treated tumors were digested for 2 h at 37 °C with a cocktail of Collagenase I (Roche, Ref: 11088793001) and Hyaluronidase (Sigma-Aldrich, Ref: H3506). Cells were then individualized at 37°C using a cocktail of 0.25% Trypsin-Versen (Thermo Fisher Scientific, Ref: 15040-033), Dispase II (Sigma-Aldrich, Ref: D4693) and DNase I (Roche, Ref: 11284932001) as described previously53. Then, eBioscience red blood cell lysis buffer (Thermo Fisher Scientific, Ref: 00-4333-57) was added to the cell suspension to remove red blood cells. To increase the viability of the final cell suspension, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, Ref:130-090-101). Approximately 3,000 cells were loaded on a Chromium Single Cell Controller Instrument (Chromium Single Cell 3ʹv3, 10X Genomics, Ref: PN-1000075) according to the manufacturer’s instructions. Samples and libraries were prepared according to the manufacturer's instructions.
Libraries were sequenced on a NovaSeq 6000 (Illumina) in PE 28-8-91.

treatment_protocol: For PDX model,  five mice were not treated and kept as controls and twenty-seven mice were treated orally with Capecitabine (Xeloda; Roche Laboratories) at a dose of 540 mg/kg, 5 d/week for 6 to 14 weeks. Eight mice were sacrificed after the first cycle of chemotherapy to study residual (2 mice) and persister (6 mice) human tumor cells. Seven mice with recurrent tumors (tumor volume between 200 and 600 mm3) were treated for a second round of Capecitabine.


title: MM468_chemonaive [scRNA-seq]

data_processing:
The scRNA-seq sequencing files were preprocessed using the cellRanger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/3-0).   For the MDA-MB-468 human cell line, sequences were aligned against the hg38 genome only.   For the PDX samples, sequences were aligned against the files were aligned against hg19 and mm10 genomes and only cells with a majority of human reads were retained for the analysis.  The BAM files correspond to the « possorted_genome_bam.bam » in the cellRanger output.
Genome_build: hg38, hg19
Supplementary_files_format_and_content: Sparse-matrix in 10X format, corresponding to the ‘*barcodes.tsv’  files containing the cell barcode sequence ; the ‘*features.tsv’ files containing the features (transcripts) and the ‘*matrix.mtx’ files containing the matrix non-zeroes values and row and column indexes.  For MDA-MB-468 cell line, the matrices are counted on the hg38 transcripts, for the PDX model the matrices are counted on the hg19 genome.

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106).

extract_protocol: For MDA-MB-468 cell line, for each single cell suspension, approximately 3,000 cells were loaded on a Chromium Single Cell Controller Instrument (Chromium Single Cell 3ʹv3, 10X Genomics, Ref: PN-1000075) according to the manufacturer’s instructions. Samples and libraries were prepared according to the manufacturer's instructions. Libraries were sequenced on a Illumina NovaSeq 6000 in PE 28-8-91.

value: DMSO


title: 556


title: WT_IgG1_4

source_name: MC38 tumour


title: FT282 CCNE1 clone 3 rep1

value: Fallopian tube secretory epithelial

value: hTERT p53-R175H

value: CCNE1-overexpressing clone 3


title: chr_HepG2_-CMC_3

extract_protocol:
HepG2 cells were biochemically fractionated and chromatin-associated RNA was isolated and Pseudo-seq was performed. Total RNA was isolated from PUS1 knockout and wildtype HepG2 cells with Qiazol and poly(A)+ mRNA-seq was perfomed with TruSeq Stranded mRNA kit.   Oligo pools (human, Twist Biosciences) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
Pseudo-seq samples were treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.


title: MM468_5FU1_UNC_day33 [scRNA-seq]

source_name: MDA-MB-468 cell line


title: FT282 WT rep2

value: wild type


title: 732


title: MM468_5FU1_day33 [scRNA-seq]


title: 546


title: 524


title: HBCx95_resistant [scRNA-seq]

value: Capecitabine (5-FU)


title: 557

value: Long evans


title: WT_1653_DSS

description: 10x scRNAseq


title: chr_HepG2_-CMC_2


title: MM468_5FU1_day214 [scRNA-seq]


title: 718

value: Female


title: chr_HepG2_-CMC_6


title: HBCx95_recurrent [scRNA-seq]


title: 669

value: Control


title: HBCx95_chemonaive [scRNA-seq]

extract_protocol:
For PDX model, before downstream analysis (scChIP-seq, scRNA-seq and bulk ChIP-seq), control and Capecitabine treated tumors were digested for 2 h at 37 °C with a cocktail of Collagenase I (Roche, Ref: 11088793001) and Hyaluronidase (Sigma-Aldrich, Ref: H3506). Cells were then individualized at 37°C using a cocktail of 0.25% Trypsin-Versen (Thermo Fisher Scientific, Ref: 15040-033), Dispase II (Sigma-Aldrich, Ref: D4693) and DNase I (Roche, Ref: 11284932001) as described previously53. Then, eBioscience red blood cell lysis buffer (Thermo Fisher Scientific, Ref: 00-4333-57) was added to the cell suspension to remove red blood cells. To increase the viability of the final cell suspension, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, Ref:130-090-101). Approximately 3,000 cells were loaded on a Chromium Single Cell Controller Instrument (Chromium Single Cell 3ʹv3, 10X Genomics, Ref: PN-1000075) according to the manufacturer’s instructions.
Libraries were sequenced on a NovaSeq 6000 (Illumina) in PE8-8-91 with a coverage of 50,000 reads/cell.


title: HBCx95_residual [scRNA-seq]


title: chr_HepG2_+CMC_4

value: 0.4M CMC


title: SilicaWT1

value: WT


title: MM468_5FU2_day67 [scRNA-seq]


title: 725

value: Male

value: LBN


title: MM468_5FU2_day171 [scRNA-seq]


title: WT_aPD1_2

value: female


title: 584


title: MM468_UNC_day33 [scRNA-seq]

value: UNC


title: S203AKI_1652_DSS

description: 10x scRNAseq

value: CD4+ T cell enriched


title: MM468_5FU3_day50 [scRNA-seq]


title: WT_1669_DSS

description: 10x scRNAseq

value: 2% DSS in drinking water for 7 days, harvested on day 10


title: chr_HepG2_+CMC_2

value: chromatin-associated RNA HepG2 cells


title: MM468_5FU3_day202 [scRNA-seq]


title: chr_HepG2_+CMC_3


title: IV_PUS7_+CMC

value: Recombinant Full Length hPUS7


title: WT_1813

description: 10x scRNAseq

value: untreated


title: IV_PUS7_-CMC


title: S203AKI_1810

description: 10x scRNAseq


title: chr_HepG2_+CMC_1


title: IV_PUS7L_+CMC

value: Recombinant Full Length hPUS7L


title: IV_PUS1_+CMC

value: Recombinant Full Length hTRUB1


title: J774.1 cells, GATA3-KO_DMSO rep2

city: Tokushima

first: kohta

last: ohnishi

address: Kuramoto-cho 3-18-15

institute: Tokushima University

data_processing:
Illumina Casava1.7 software used for basecalling.
The clean data were obtained by filtering of raw data as follows: (1) discard reads containing adapters, (2) discard reads containing undetermined base > 10%, and (3) discard reads containing low quality base> 50%.
The clean data were aligned to GRCm38 genome and calculated the gene expression values in the normalized form of transcripts Per Million (TPM) using CLC Genomics Workbench version 20.0.4
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel files include TPM values for each Sample and fold-change

source_name: J774.1 mouse macrophage-like cell line

extract_protocol:
Total RNA was isolated from J774.1 cells using RNeasy Plus Mini Kit (74134; Quiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: J774.1 cells were treated with isorhamnetin (10µM) or DMSO for 6h.

value: BALB/c

value: J774.1 cells

value: DMSO


title: 523

value: Long evans

value: Female


title: S203AKI_0110

description: 10x scRNAseq


title: MM468_UNC_5FU_day33_C02_H3K27me3

city: Paris

last: Vallot

institute: Institut Curie

data_processing: Chromatin indexing sequencing files were first demultiplexed by matching the first 8 bases of #Read 2 without any mismatches to the 8-bp long index of each sample from a pool of 5 samples. The same demultiplexing was done for the corresponding inputs. Read #1 was aligned to hg38 Human genome reference using bowtie with options ‘-S -k 1 -m 1’. After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.

extract_protocol:
Chromatin Indexing : Chromatin isolation, indexing, immunoprecipitation and library preparation was adapted from48. Briefly, 50,000 MDA-MB-468 were lysed and digested with MNase for 20min at 37°C in the following buffer: 46mM Tris-HCl pH 7.4, 0.154M NaCl, 0.1% Triton, 0.1% NaDoc, 4.65mM CaCl2, 0.47x Protease Inhibitor Cocktail (Roche, Ref: 11873580001) and 0.09u/uL MNase (Thermo Scientific, Ref: EN0181). Fragmented nucleosomes were then ligated for at least 24h at 16°C to double-stranded barcoded adapters containing 8bp barcodes to combine samples:  Pac1-T7-Read2-8bpBarcode-linker-Pac1 (Supplementary Table 1). Next, 5 indexed chromatin samples (DMSO, 5-FU, UNC, 5-FU + UNC, GSK-J4) were pooled, each containing a different 8-bp barcode, to perform anti-H3K27me3 ChIP (Cell Signaling, Ref: 9733 - C36B11) on 250,000 cells in total in each pool.
Sequential ChIP-seq : After reverse crosslinking and DNA clean-up, 3 to 15ng of immunoprecipated DNA were used to prepare the sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to theLibraries were sequenced on a NovaSeq 6000 (Illumina) in SE100 mode.  Bulk ChIP-seq : Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to the manufacturer’s instructions.  Libraries were sequenced on a NovaSeq 6000 (Illumina) in SE50 mode.  Chromatin Indexing : ChIP and DNA amplification was carried out as for scChIP-seq and a sequencing library was produced for both IP and input pools, sequenced on NovaSeq 6000 (Illumina) in PE100 mode.

value: UNC 5FU

tag: antibody

value: H3K27me3 - Cell Signaling, Ref:9733


title: MM468_UNC_day33_A02_H3K27me3

tag: day


title: chr_HepG2_-CMC_1


title: J774.1 cells, rictor-KO_IR rep2

value: rictor-KO

value: IR


title: MM468_5FU_day33_F02_H3K27me3


title: 724

value: Male

value: LBN


title: 710

value: Control


title: WT_0112

description: 10x scRNAseq

value: CD4+ T cell enriched


title: 591


title: MM468_DMSO_day33_E02_H3K27me3


title: MM468_5FU3_day77 [scRNA-seq]

tag: genome build


title: 590


title: IV_PUS7L_-CMC


title: 709


title: J774.1 cells, GATA3-KO_IR rep2


title: 230


title: J774.1 cells, GATA3-KO_IR rep1


title: J774.1 cells, rictor-KO_DMSO rep1


title: J774.1 cells, GATA3-KO_DMSO rep1


title: IV_noPUS_C_-CMC


title: 95


title: 583


title: IV_TRUB1_+CMC

value: 0.4M CMC


title: IV_PUS1_-CMC


title: 582


title: IV_TRUB1_-CMC


title: MM468_GSKJ4_day33_D02_H3K27me3

data_processing:
ChIP-seq: Read #1 was aligned to hg38 Human genome reference using bowtie with options ‘-S -k 1 -m 1’
ChIP-seq: After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.
Chromatin indexing sequencing files were first demultiplexed by matching the first 8 bases of #Read 2 without any mismatches to the 8-bp long index of each sample from a pool of 5 samples. The same demultiplexing was done for the corresponding inputs. Read #1 was aligned to hg38 Human genome reference using bowtie with options ‘-S -k 1 -m 1’. After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.

extract_protocol:
Chromatin Indexing : Chromatin isolation, indexing, immunoprecipitation and library preparation was adapted from48. Briefly, 50,000 MDA-MB-468 were lysed and digested with MNase for 20min at 37°C in the following buffer: 46mM Tris-HCl pH 7.4, 0.154M NaCl, 0.1% Triton, 0.1% NaDoc, 4.65mM CaCl2, 0.47x Protease Inhibitor Cocktail (Roche, Ref: 11873580001) and 0.09u/uL MNase (Thermo Scientific, Ref: EN0181). Fragmented nucleosomes were then ligated for at least 24h at 16°C to double-stranded barcoded adapters containing 8bp barcodes to combine samples:  Pac1-T7-Read2-8bpBarcode-linker-Pac1 (Supplementary Table 1). Next, 5 indexed chromatin samples (DMSO, 5-FU, UNC, 5-FU + UNC, GSK-J4) were pooled, each containing a different 8-bp barcode, to perform anti-H3K27me3 ChIP (Cell Signaling, Ref: 9733 - C36B11) on 250,000 cells in total in each pool.
Sequential ChIP-seq : After reverse crosslinking and DNA clean-up, 3 to 15ng of immunoprecipated DNA were used to prepare the sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to theLibraries were sequenced on a NovaSeq 6000 (Illumina) in SE100 mode.  Bulk ChIP-seq : Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to the manufacturer’s instructions.  Libraries were sequenced on a NovaSeq 6000 (Illumina) in SE50 mode.  Chromatin Indexing : ChIP and DNA amplification was carried out as for scChIP-seq19 and a sequencing library was produced for both IP and input pools, sequenced on NovaSeq 6000 (Illumina) in PE100 mode.


title: 11


title: J774.1 cells, rictor-KO_DMSO rep2


title: J774.1 cells, rictor-KO_IR rep1


title: MM468_DMSO2_day67_H3K27me3 [bulk ChIP-seq]

data_processing:
ChIP-seq: Read #1 was aligned to hg38 Human genome reference using bowtie with options ‘-S -k 1 -m 1’
ChIP-seq: After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.
ChIP-seq: Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCoverage function with options ‘--normalizeUsing CPM --binSize 50 --smoothLength 500 --extendReads 150 --ignoreForNormalization chrX’.
ChIP-seq: Comparison Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCompare function with options ‘--binSize 50 --smoothLength 1000 --extendReads 150 --ignoreForNormalization chrX --operation log2 --pseudocount 1 –skipNonCoveredRegions’.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig binary file of coverage and compared coverage

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). HCC38 cell lines were cultured in RPMI 1640 (Gibco-BRL, Ref: 11875085), supplemented with 10% heat-inactivated fetal calf serum.

extract_protocol: ChIP experiments were performed as previously described (Grosselin et al., 2019) on 3x10 457 6 MDA-MB-468 cells using an anti-H3K27me3 antibody (Cell Signaling Technology, Ref: 9733 - C36B11). Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to the manufacturer’s instructions. Libraries were sequenced on a NovaSeq 6000 (Illumina) in SE50 mode.


title: IV_noPUS_C_+CMC


title: MM468_5FU2_day67_H3K27me3 [bulk ChIP-seq]


title: J774.1 cells, WT_DMSO rep2

value: WT


title: J774.1 cells, WT_IR rep2


title: MM468_DMSO4_day113_b_H3K27me3 [bulk ChIP-seq]


title: 552


title: MM468_5FU3_day77_H3K27me3 [bulk ChIP-seq]


title: btl-GAL4::UAS-GFP – rep 3

city: Duluth

first: Matthew

last: Slattery

state: MN

address: 1035 University Drive, SMed 255

department: Biomedical Sciences

institute: University of Minnesota Medical School

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
50 bp single-end sequencing reads were trimmed for adapter sequence and low-quality ends were removed
For the samples with 2 replicates, remaining downstream processing was done using the ENCODE ChIP-seq-pipeline2 v1.8.0 (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default settings, including macs2 peak-calling and IDR peak threshold of 0.1.  Mapping – bowtie2 v2.3.4.3, map quality filtering > 30 – SAMtools v1.9, duplicate read removal – Picard MarkDuplicates v2.20.7, peak calling – macs2 v2.2.4.  For the final, independent btl-GAL4::UAS-rib-GFP replicate, the same parameters and filtering were used (mapping with bowtie v2.3.4.1 to dm6, map quality filtering > 30 with SAMtools v 1.7, duplicate removal with Picard MarkDuplicates v2.9.0), except no IDR thresholding was used and macs2 (v2.2.4) peaks were called with the following parameters: -q 0.05 -B --SMPR --keep-dup all --call-summits.
The final Tracheal Rib high confidence peak set was obtained by using the bedtools intersect command with the following sets of peaks: 1) the IDR peaks from btl-GAL4::UAS-GFP replicate experiment VERSUS the IDR peaks from the trh-GAL4::UAS-GFP replicate experiment --> 2) the set of intersecting IDR regions from btl- and trh-GAL4::UAS-GFP  (from previous step, 1) VERSUS the third, independent set of btl-GAL4::UAS-GFP peaks.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited genomic interval file of peak locations
Supplementary_files_format_and_content: tab-delimited genomic intervals for peaks (BED)
Supplementary_files_format_and_content: tab-delimited genomic intervals for peaks (narrowPeaks)

organism: Drosophila melanogaster

source_name: Drosophila melanogaster embryo

growth_protocol: Flies were raised at 25°C on a standard yeast/molasses medium (1212.5 mL water, 14.7 mL agar, 20.4 g yeast, 81.8 g cornmeal, 109.1 mL molasses, 10.9 mL Tegosept, 3.4 mL propionic acid, 0.4 mL phosphoric acid). All experiments were conducted on embryos collected at 25°C.

extract_protocol:
Chromatin from multiple independent collections of stage 11 – 16 btl-GAL4::UAS-rib-GFP and trh-GAL4::UAS-rib-GFP embryos were cross-linked at room temperature in 1.8% formaldehyde in 2 ml of homogenization buffer (60 mM KCl, 15 mM NaCl, 15 mM HEPES {pH7.6}, 4 mM MgCl2, 0.5 mM DTT, 0.5% Triton X-100 and cOmplete™ protease inhibitor cocktail [1 tablet per 50 ml buffer]). The cross-linked material was resuspended in 0.1% SDS and 0.5% N-lauroylsarcosine in lysis buffer (140mM NaCl, 15mM HEPES [pH 7.6], 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 1% Triton X-100, 0.5mM DTT and cOmplete™ protease inhibitor cocktail [1 tablet per 50 ml buffer]). Chromatin was sonicated three times at 4°C using the Sonic Dismembrator Model 100 (Fisher Scientific) under the following conditions: power setting 3, 20s ON, 20s OFF. Immediately after sonication, the chromatin extract was stored at −80°C prior to immunoprecipitation. Immunoprecipitations were performed, as described in (Negre et al., 2006), using a polyclonal goat anti-GFP antibody.
DNA libraries were prepared using the NuGen Ovation Ultralow Library System (btl-GAL4::UAS-rib-GFP and trh-GAL4::UAS-rib-GFP experimental replicates 1 & 2 and corresponding input control), or the KAPA DNA HyperPrep Library Prep Kit (independent replicate of btl-GAL4::UAS-rib-GFP).  Illumina sequencing was performed according to the manufacturers specifications at the University of Minnesota Genomics Center (btl-GAL4::UAS-rib-GFP and trh-GAL4::UAS-rib-GFP experimental replicates 1 & 2 and corresponding input control) or at th UCLA Technology Center for Genomics & Bioinformatics (independent replicate of btl-GAL4::UAS-rib-GFP) as 50 bp single-end reads.

value: whole embryo

value: goat anti-GFP immunoprecipitation

tag: age

value: stage 11-15

tag: replicate


title: MM468_DMSO3_day77_H3K27me3 [bulk ChIP-seq]

first: Céline

address: 26 Rue D'Ulm


title: WT3

city: Beijing

first: Xiaolong

last: Qi

state: Beijing

address: No. 2, Yuanmingyuan west Road

institute: China Agricultural University

data_processing:
Bowtie2 v2.2.3 was used for building the  genome index, and Clean Data was then aligned to the reference genome using HISAT2  v2.1.0.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the  Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM  (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the  expression level of genes in each sample.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/current/plants/fasta/zea_mays/dna_index/Zea_mays.AGPv4.dna.toplevel.fa.gz

organism: Zea mays

source_name: anther

extract_protocol:
Anthers were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
A total amount of 2 μg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA  Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.

value: anther

value: mature anther

tag: line

value: wild type


title: WT1

tag: genotype


title: WT2


title: J774.1 cells, WT_IR rep1

value: BALB/c

tag: cell line

value: J774.1 cells


title: J774.1 cells, WT_DMSO rep1

value: DMSO


title: btl-GAL4::UAS-GFP – input (3)

value: input (untreated)


title: trh-GAL4::UAS-GFP – input (1&2)


title: MT3


title: MM468_DMSO4_day113_a_H3K27me3 [bulk ChIP-seq]


title: trh-GAL4::UAS-GFP – rep 2

description: trh-rib-GFP_A_IDR0.1-peaks.narrowPeak.gz


title: MT2


title: MM468_5FU4_day113_b_H3K27me3 [bulk ChIP-seq]


title: MT1