title: CRISPR2_Input_EZH2

city: Montpellier

first: Emmanuel

last: Varlet

address: 141 rue de la Cardonille

country: France

institute: CNRS

data_processing:
Reads were mapped to the human reference genome using Bowtie2 (version 2.3.2)
Peak-calling was performed using MACS2 (version 2.1.2) with the significance cut-off q-value ≤ 0.05
Peak annotation and differential binding analyses of ChIP-seq peak data were performed using ChIPseeker and DiffBind R/bioconductor packages, respectively
bigWig files were generated using the genomicRanges R package. Score représents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings
Assembly: GRCh37
Supplementary files format and content: tab-deliminited text file includes raw counts for each Sample
Supplementary files format and content: bigWig , narrowPeak (except for Input sample)

source_name: Human Myeloma Cell Line

growth_protocol: XG7, CRISPR-1 and CRISPR-2 cell lines were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and 2ng/ml human recombinant interleukin-6 (hrIL-6) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cells were fixed with 4% formaldehyde for 8 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Plus sonication device (Diagénode)
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Human Myeloma Cell Line

value: Plasma cells

tag: chip antibody


title: mESC, naive pluripotency, QKO, rep3

status: Public on Aug 09 2024

type: SRA

city: San Francisco

first: Harold

last: Marin

state: CA

address: 555 Mission Bay Boulevard South

department: Smith Cardiovascular Institute

country: USA

institute: University of California San Francisco

description:
QKO_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

library_source: transcriptomic

data_processing:
Reads were mapped to the GENCODE primary assembly M30 release of the mouse genome (GRCm39) using STAR (version 2.7.10a): --runMode alignReads --readFilesCommand zcat --clip3pAdapterSeq CTGTCTCTTATA CTGTCTCTTATA --clip3pAdapterMMp 0.1 0.1 --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --twopassMode Basic. Bam files were indexed with SAMtools (version 1.10).
The subread featureCounts package (version 1.6.4) and GENCODE M30 primary annotation file was used to generate a read counts table for all conditions.
The subread featureCounts package was used for obtaining read counts on uniquely mapped transposable elements using a custom annotation file made by the Hammell lab.
For multimapping of RNA-seq reads, as recommended by the TEtranscripts authors, STAR parameters were changed from –outFilterMultimapNmax 1 to the following: –outFilterMultimapNmax 100 --winAnchorMultimapNmax 100. A read counts table was generated using the TEcount command from the TEtranscripts package (version 2.2.3) with the following parameters: --sortByPos --format BAM --mode multi. The GENCODE M30 primary annotation file was used for gene annotations and a custom annotation file from the Hammell lab for transposable elements were used to generate a read counts table.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in genes for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in transposable elements for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from multi-mapped reads in genes and transposable elements for each sample.

molecule: total RNA

organism: Mus musculus

source_name: mESC

growth_protocol: Cells were cultured at 5% CO2 and 37°C. mESCs were grown in serum- and feeder-free 2i + LIF medium: N2B27 basal medium supplemented with the following compounds at a final concentration of 3 μM CHIR-99021 (Selleckchem S1263), 1 μM PD0325901 (Selleckchem S1036), 103 U/mL LIF (MilliporeSigma™ ESG1107), 55 μM β-mercaptoethanol (Gibco™ 21985023), and 1X PenStrep (GenClone 25-512). N2B27 medium was made by mixing equal parts of DMEM:F12 (GenClone 25-503) and Neurobasal medium (Gibco™ 21103049) then adding 1X N-2 (Gibco™ 17502001), 1X B-27 (Gibco™ 17504001) and 2 mM Glutamax (Gibco™ 35050061). mESCs were seeded at 4.21 x 104 cells/cm2 on dishes pre-coated with 0.1% gelatin (MilliporeSigma ES-006-B).

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini Kit (QIAGEN 74136). RNA was treated with DNAse using the TURBO DNA-free kit (Invitrogen™ AM1907) prior to prepping libraries. RNA quality was assessed by electrophoresis on a 1% agarose gel and detecting 28S and 18S rRNA bands with ethidium bromide staining (0.6µg/mL).
A version of the Tecan Genomics’ Universal Plus mRNA prep kit (Tecan Genomics 0520B-A01) was modified for rRNA depletion by replacing the mRNA isolation in the first segment of the protocol with ribo depletion using FastSelect rRNA (Qiagen 334387) as follows: 200ng of total RNA in 10µL of water was mixed with 10µL of Universal Plus 2X Fragmentation Buffer and 1µL FastSelect. The solutions were fragmented and ribo depleted simultaneously per the FastSelect protocol. 20µL of the resulting fragmented/ribo depleted RNA were prepped per the Universal Plus protocol starting with First Strand Synthesis. The Universal Plus Unique Dual Index Set B was used, and the samples were quality checked using a MiniSeq benchtop sequencer (Illumina).

treatment_protocol: Treated cells got doxycycline at a final concentration of 1µg/mL. Cells were replenished with fresh 2i + LIF medium every day. WT, TKO and QKO mESCs were collected after 2 days. For day 4 doxycycline timepoints, mESCs were split at day 2, keeping the same seeding density.

tag: cell line

value: mESC

tag: cell type

tag: genotype

value: Lamins_and LBR_quadruple_knockout

tag: treatment

value: Untreated, Lamins and LBR quadruple knockout mESC


title: p300_ChIP_LPS6h_Rep2

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
BMDM_ChIP_p300_AllTFmerged.txt
BMDM_ChIP_p300_ATACmerged.txt

library_source: genomic

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
For p300, SREBP and LXR ChIP-seq experiments peaks were called with HOMER for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Only peaks with > 16 normalized tags (normalized to total tags of 1e7) were kept. Overlapping peak sets were determined using mergePeaks command. The pooled tag directory from two replicates was used for track visualization. To annotate p300 signal in ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 200 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential p300 signal > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For p65 and ATAC-Seq analysis of data from GSE79423 and GSE109965 respectively: Relevant raw FASTQ files were mapped to mm10 genome with Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010). For p65 peaks were called with HOMER findPeaks for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Peak files across various timepoints for vehicle and KLA treated timepoints were merged using HOMER mergePeaks. Merged peaks were annotated for H3K27ac and p300 signal as indicated. For ATAC-Seq, mm10 mapped, IDR defined peaks from GSE109965, for both vehicle and KLA treatment conditions, were used. Peaks were merged using HOMER mergePeaks, then merged peak file was used for further analysis as indicated in text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were either from random genome sequences or from peaks from the comparing condition indicated in the main text and in the figure legends.
Assembly: mm10
Supplementary files format and content: Processed files include peak text files (ChIP-Seq, ATAC, and H3K27Ac peak or region data, using default HOMER parameters). Peak or region files BMDM_ChIP_p300_AllTFmerged.txt and BMDM_ChIP_H3K27Ac_AllTFmerged.txt are summed transcription factor peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data as indicated. Peak files BMDM_ChIP_p300_ATACmerged.txt and BMDM_ChIP_H3K27Ac_ATACmerged.txt are summed ATAC-Seq peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data. Peak annotation, with p300 and H3K27Ac tag directories, was done using HOMER annotatePeaks command, with option -size 200 or -size 1000, respectively. All genomic coordinates are relative to mm10 mouse assembly.

molecule: genomic DNA

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For p300, LXR and SREBP ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for p300, LXR, and SREBP ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Cells were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 1-2 million cells  (for p300, SREBP ChIP), 20 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for p300, LXR, and SREBP ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), p300 (2 μg, Millipore, cat# 05-257,Diagenode, cat# C15200211), LXR (Santa Cruz Biotechnology: sc-1000X, sc- 133221X, sc-271064X) , and SREBP (2 μg, Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For p300, LXR and SREBP ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA). Bead complexes were resuspended in 25 μl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit with reaction volumes reduced by half, essentially as previously described (Heinz et al., 2018). Libraries were eluted and crosslinks reversed by adding to the 46.5 μl NEB reaction 20 μl water, 4 μl 10% SDS, 4.5 μl 5M NaCl, 3 μl 0.5 M EDTA, and 1 μl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 65C for 30 minutes to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 μl SpeedBeads 3 EDAC in 61 μl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 μl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 25 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 50 μl reaction volume using NEBNext Ultra II PCR master mix and 0.5 μM each Solexa 1GA and Solexa 1GB primers. Libraries were cleaned up with SpeedBeads as above using 36.5 μl 20% PEG 8000/1.5 M NaCl and 2 μl SpeedBeads. After ethanol washing and drying, PCR amplified libraries were eluted from the SpeedBeads using 20 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween- 20. Next, libraries were size selected 250-500 bp using gel extraction using 10% TBE acrylamide gels. Libraries were single-end sequenced using either a HiSeq 4000 or a NextSeq 500 to a depth of 10-20 million reads.

treatment_protocol: The following day after replating BMDMs, fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with or without 100 µg/ml 3'SL , with 10 ng/ml of LPS for 1 – 24 hours as indicated. For LXR and SREBP experiments cells were treated with 1uM GW3965.

value: Bone Marrow Derived Macrophages

value: LPS 6h


title: p300_ChIP_3SL2h_Rep2

value: 3'SL 2h


title: CRISPR1_Input_EZH2

organism: Homo sapiens


title: InputChIP_PBS6_Rep2

description:
BMDM_ChIP_H3K27Ac_AllTFmerged.txt
BMDM_ChIP_H3K27Ac_ATACmerged.txt
BMDM_ChIP_H3K27Ac_Merged.txt

value: PBS


title: Jejunum_M_GF_WT_14.1

type: RNA

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: 1601 SW Jefferson Way

institute: Oregon State University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalisation using Gene Expression software (GSGX v1.9.0, Illumina, San Diego, CA, USA)

label: biotin

source_name: Jejunum

label_protocol: Biotin labeled

extract_protocol: Tissue was homogenized using Tissue-Tearor (Biospec Products) and RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: Sex

value: M

value: GF

value: WT


title: Jejunum_F_GF_WT_17.1

value: F


title: Jejunum_F_GF_WT_13.1


title: Jejunum_M_GF_WT_15.1


title: Jejunum_F_GF_WT_16.1


title: CRISPR1_Input_H3K27me3


title: InputChIP_3SLLPS6_Rep2

value: 3'SL_LPS 6h


title: CRISPR2_Input_H3K27me3


title: Jejunum_M_GF_WT_10.1


title: R+Ctrl3

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
R+Ctrl
salmon_gene_counts_ras_early_late.csv
salmon_gene_counts_normalized_ras_early_late.csv

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: hg38
Supplementary files format and content: comma-delimited csv file includes raw counts for each sample
Supplementary files format and content: comma-delimited csv file includes normalized counts for each sample

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D lentiviral vector rep3

extract_protocol:
RNAeasy kit (Qiagen)
PerkinElmer:NOVA-5138-08 NEXTflex Rapid Directional RNA-Seq Kit

tag: tissue

value: hematopoietic

value: Human iPSC N-2.12-D1-1

value: HSPC

value: NRAS G12D


title: Jejunum_M_GF_WT_11.1


title: mESC, naive pluripotency, QKO, rep2

description:
QKO_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: Jejunum_F_GF_WT_12.1


title: InputChIP_3SLLPS2_Rep2

value: 3'SL_LPS 2h


title: Jejunum_M_GF_KO_14

value: KO


title: mESC, naive pluripotency, TKO, rep4

description:
TKO_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: mESC

value: Untreated, Lamins triple knockout mESC, parental line of all cells harboring the tetracycline-inducible shRNA cassette


title: InputChIP_PBS2_Rep2

value: Bone Marrow Derived Macrophages


title: XG7_R2_Input_EZH2

value: Human Myeloma Cell Line

value: Plasma cells


title: mESC, naive pluripotency, TKO, rep2

description:
TKO_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, rep3

description:
TKO_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: p300_ChIP_3SL6h_Rep2

value: 3'SL 6h


title: Jejunum_M_GF_KO_10

value: M


title: XG7_R1_Input_EZH2


title: mESC, naive pluripotency, TKO, rep1

description:
TKO_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, QKO, rep1

description:
QKO_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: Lamins_and LBR_quadruple_knockout

value: Untreated, Lamins and LBR quadruple knockout mESC


title: Jejunum_M_GF_KO_15

value: GF


title: Jejunum_M_GF_KO_11


title: Jejunum_F_GF_KO_17

value: F


title: mESC, naive pluripotency, WT, rep4

description:
WT_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: wildtype

value: Untreated, wildtype littermate mESC


title: H3K27Ac_ChIP_PBS6_Rep2

value: PBS


title: D1, Sarco, 4

city: Portland

first: Thomas

middle: Dexter

last: Morse

state: ME

address: 154 New Island Ave

institute: MDIBL

description:
D4
Sarco2_gene_counts.txt

data_processing:
The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection.
Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. At the same time, Q20, Q30 and GC content were calculated
Paired-end clean reads were aligned to the reference genome GRCz11 (Danio rerio)  using Hisat2 v2.0.5 < hisat2 -x reference_genome -p 4 --dta -t --phred33  -1 sample_1.clean.fq.gz -2 sample_2.clean.fq.gz --un-conc-gz sample.unmap.fq.gz 2> sample_align.log >
Mapped reads of each sample were assembled by StringTie [3](v1.3.3b) in a reference-based approach < stringtie sample.bam -p 4 -G genome.gtf -o sample.gtf --rf >
FeatureCounts [4] v1.5.0-p3 was used to count the reads numbers mapped to each gene. < featureCounts -T 4 -F GTF -t exon -g gene_id -s 2 -Q 10 -C -B -p -a genome.gtf -o feature_count.xls sample.bam >
Differential Expression Analysis was performed with the MDIBL Bioinformatics Core’s DESeq2 R script R version 4.3.2 and DESeq2 version 1.42.1. (parameters are contained in the report file: ML233_Simple_Base_Pairwise.html )
PCA Clustering was resolved using the R package PCAtools version 2.14.0
Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler version 4.10.1
Assembly: GRCz11 (Danio rerio) reference genome obtained from Ensembl
Supplementary files format and content: csv, pdf, rmd, and html files containing raw and transformed/normalized expression data and analysis are described below.

organism: Danio rerio

source_name: whole embryo

growth_protocol: Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory, and all methods were performed in accordance with the relevant guidelines and regulations. To generate sarcopinia phenotype (Fbxo32 over-expressed) fish were treated for 24hrs with 4oht 10μm and wild type were treated for 24hr with DMSO 10μm.

extract_protocol:
Embryos were homogenized in Trizol solution (Invitrogen) and total RNA was purified using chloroform (Fischer) and then isopropanol (Fischer). RNA (1 μg) was reverse-transcribed using an oligo-dT primer and RevertAid kit (Thermo-Scientific). Total RNA samples for bulkRNAseq analysis were prepared with ~50 embryos/sample. Each experimental condition has been performed using biological quadruplicates to ensure reproducibility. Trizol (Invitrogen) was used to homogenize cellular extracts with the TissueLyzer (Qiagen). RNA purification was performed as described above.
RNA was quantified and sent to Novogene  for Illumina library preparation and paired-end sequencing.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNAsynthesis using dUTP.

value: whole embryo

value: Sarco

tag: developmental stage

value: 8 dpf embryo

tag: time

value: 4oht 10μm


title: XG7_R1_Input_H3K27me3


title: CRISPR2_EZH2

value: EZH2, 5246T, Cell Signaling Technologies


title: D1, Sarco, 3

description:
D3
Sarco2_gene_counts.txt


title: mESC, naive pluripotency, WT, rep3

description:
WT_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: mESC


title: D1, Sarco, 2

description:
D2
Sarco2_gene_counts.txt


title: mESC, naive pluripotency, WT, rep2

description:
WT_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: XG7_R2_Input_H3K27me3

value: Human Myeloma Cell Line


title: Jejunum_F_GF_KO_16

value: KO


title: CRISPR1_EZH2

value: Plasma cells


title: mESC, naive pluripotency, WT, rep1

description:
WT_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: XG7_R2_EZH2


title: D1, Sarco, 1

description:
D1
Sarco2_gene_counts.txt


title: CRISPR2_H3K27me3

value: H3K27me3, C15410195, Diagenode


title: XG7_R1_EZH2


title: C1, WT, 4

description:
C4
Sarco2_gene_counts.txt

value: WT

value: DMSO 10μm


title: Jejunum_F_GF_KO_12

value: GF


title: mESC, naive pluripotency, TKO, shLBR, day4, rep3

description:
LBRd4_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: Doxycycline treated for 4 days, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting mouse LBR


title: CRISPR1_H3K27me3


title: C1, WT, 3

description:
C3
Sarco2_gene_counts.txt


title: C1, WT, 2

description:
C2
Sarco2_gene_counts.txt


title: mESC, naive pluripotency, TKO, shLBR, day4, rep2

description:
LBRd4_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: XG7_R2_H3K27me3


title: Jejunum_F_GF_KO_13

value: F


title: Jejunum_M_SPF_WT_122

value: M

value: SPF


title: mESC, naive pluripotency, TKO, shLBR, day4, rep1

description:
LBRd4_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: C1, WT, 1

description:
C1
Sarco2_gene_counts.txt

value: whole embryo


title: Jejunum_M_SPF_WT_124


title: Jejunum_M_SPF_WT_123


title: mESC, naive pluripotency, TKO, shLBR, day4, rep4

description:
LBRd4_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: Jejunum_M_SPF_WT_113


title: Jejunum_M_SPF_WT_106


title: Jejunum_M_SPF_WT_103


title: mESC, naive pluripotency, TKO, shLBR, day2, rep4

description:
LBRd2_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: Doxycycline treated for 2 days, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting mouse LBR


title: mESC, naive pluripotency, TKO, shLBR, day2, rep3

description:
LBRd2_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: XG7_R1_H3K27me3


title: CRISPR-2

description:
count_normalized.txt
raw_count.txt

data_processing:
RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner.
All statistical analyses were performed with the statistics software R (version 4.1.0) and R packages developed by BioConductor project.
The expression level of each gene was summarized and normalized using DESeq2 R/Bioconductor package.
Assembly: GRCh37
Supplementary files format and content: tab-deliminited text file includes raw counts for each Sample
Supplementary files format and content: tab-deliminited text file includes RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 150ng of total RNA was used for the construction of sequencing librairies.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: MMSET-depleted


title: B1_SARCO1d_2

description:
B2
Sarco1_gene_counts.txt

value: Sarco

value: 6 dpf embryo

value: 4oht 10μm


title: B1_SARCO1d_3

description:
B3
Sarco1_gene_counts.txt


title: B1_SARCO1d_1

description:
B1
Sarco1_gene_counts.txt


title: CRISPR-1

description:
count_normalized.txt
raw_count.txt

value: Human Myeloma Cell Line


title: mESC, naive pluripotency, TKO, shLBR, day2, rep1

description:
LBRd2_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: mESC


title: Jejunum_F_SPF_WT_129


title: A1_CTRL_2

description:
A2
Sarco1_gene_counts.txt


title: Jejunum_F_SPF_WT_117


title: A1_CTRL_3

description:
A3
Sarco1_gene_counts.txt


title: Jejunum_F_SPF_WT_119


title: C5

city: Santa Clara

first: Marcos

last: Otero-Garcia

address: 2255 Martin Ave suite D

institute: Rebus Biosystems

data_processing:
Sequencing data quality check. Performed with Illumina SAV.
Demultiplexing. Performed with Illumina Bcl2fastq2 v 2.19 program.
Alignment and filtering. Performed with Dstools-v2.3, default parameters.
Barcode and UMI counting. Performed with Dstools-v2.3, default parameters.
Genome_build: Genome_build: GRCh38 Ensembl 97
Supplementary_files_format_and_content: rds file cointaining single cell gene expression matrix, generated with R::Seurat. Low quality cells and doublets were filtered out

molecule: polyA RNA

source_name: Brain cortex BA9

extract_protocol:
Single nuclei isolation from post-mortem frozen human brain tissue  Protocol based on (Krishnaswami et al 2016). All steps and performed on ice, in RNase free conditions.    Frozen brain tissue blocks were stored at -80°C. The tissue is first attemperated at -12°C to enable dissection. Small pieces between (60-200 mg) of the region of interest are dissected encompassing an equal representation of all cortical layers. The tissue sample is chopped into small fragments using a chilled scalpel and immediately transferred to a Dounce grinder (7mL, clearance 0.020 to 0.056 mm) with 2.4 mL of homogenization buffer (Tris pH8 10 nm, MgCl2 5 mM, KCl 25 mM, Sucrose 250 mM, DTT 1 μM, Protease Inhibitor 0.5x [cOmplete, Roche #4693159001], RNase inhibitor 0.2 U/μl [NxGen, Lucigen #30281], Triton-x100 0.1% v/v). While one ice, the tissue is homogeinized with 30 firm grinder strokes. The homogenate is filtered through a 40 μm Corning cell strainer into two 1.5 mL Eppendorf tubes and its quality assessed on a hemocytometer. After centrifuging the homogenate at 1000g for 8 minutes at 4°C, the supernatant is aspirated and the pellets gently resuspended in 200 μl of cold homogenization buffer. The homogenate is pooled and the total volume measured (should be ~450 μl). An exactly equal volume (~450 μl) of 50% v/v iodixanol is added and gently mixed with a pipette, for a final 25% iodixanol concentration. The mixture is transferred to a new 2 mL Eppendorf tube containing 900 μl of cold iodixanol 29%, slowly layering it over. Then, the tubes are centrifuged at 13500g for 20 min at 4°C. The supernatant is removed and discarded without disrupting the pellet, and avoiding contamination from the top layer. The pellet containing the nuclei is detached with a small amount of immunostaining buffer (PBS pH 7.4, BSA 0.05%, MgCl2 5 mM, DNAse I 2U/mL, RNase inhibitor 0.2 U/μl), transferred to a new tube and gently resuspended in a total volume of 500 μl of immunostaining buffer. After 15 min incubation, the primary antibody is added (Mouse anti NeuN, 1:1000; Millipore #MAB377) and the suspension incubated for 40 min at 4°C with rotation. After incubation an equal volume (500 μl) of immunostaining buffer is added and the tube inverted several times, followed by centrifugation at 500g for 5 min at 4°C. The supernatant is carefully removed and the pellet resuspended in 500 μl of immunostaining buffer. After adding the secondary antibody (goat anti mouse, Alexa Fluor 647, 1:1000) and nuclear staining (Hoescht 33258, 5 μg/mL), the tube is incubated for 30 min at 4°C with rotation. Before bringing the sample for sorting, its quality is checked on a hemocytometer, expecting a yield between 1 and 5 million nuclei per milliliter.    Fluorescence Activated Cell Sorting (FACS) of neuronal and non-neuronal nuclei    Immunostained nuclei suspension is sorted using FACS to obtain a clean single-nuclei suspension enriched for the population of interest.    Nuclei were sorted with a BD SORP FACSAria II at the Janis V. Giorgi Flow Cytometry Core Laboratory at UCLA. The settings and calibrations are as follows: PBS was used as the sheath fluid, with a sheath pressure of 20 psi. A 100 μm nozzle tip was used, and the frequency of droplet generation was ~30kHz. The primary laser was a blue Trigon 488-nm, used in the generation of forward scatter (FSC) and side scatter (SSC). The secondary lasers were a UV Trigon 355-nm and red Trigon 640-nm, used for the excitation of Hoechst 33258 and Alexa Fluor 647, respectively. Sample events were acquired at <30% of droplet occupancy. Sort decision gates were based on a combination of regions drawn around target populations in several 2D plots: FSC height versus SSC height: SSC area versus FSC width: FSC area versus FSC width: Hoechst fluorescence (bandpass filter 450/50) versus Alexa Fluor 647 fluorescence (bandpass filter 670/30). Hoechst fluorescence was used to discriminate singles from nuclei aggregates and debris. Alexa Fluor 647 was used to discriminate neuronal nuclei (NeuN positive) from non-neuronal nuclei (NeuN negative). Two populations were collected serially, the first corresponding to neuronal nuclei and the second one corresponding to neuronal nuclei plus non-neuronal nuclei. For each population, 3.2*105 nuclei are collected in a 1.5 mL Eppendorf tube containing 200 μl of collection buffer (PBS pH 7.4, RNase inhibitor 1 U/μl). After collection, BSA 10% is added to the tube for a final concentration of 0.01% and the tube inverted several times.
Drop-Seq was performed largely as described previously (Macosko et al., 2015). Few modifications were made to the original protocol to accommodate single nuclei, which contain small amounts of RNA and are more resistant to surfactant-induced lysis. Reducing droplet size and increasing surfactant concentration in lysis buffer gave satisfactory results.    The sorted nuclei were kept in ice and processed for Drop-Seq between 1 h and 1.5 h after collection. Final nuclei concentration was 180 nuclei/μl, for a droplet occupancy of ~5%. Barcoded beads were diluted in lysis buffer containing 1% Sarkosyl (6% Ficoll PM-400, 1% Sarkosyl, 20mM EDTA, 0.2M Tris pH 7.5, 50 mM DTT) to a final concentration of 230 beads/μl, for a droplet occupancy of ~7%. Droplets were generated using the microfluidics device from Macosko et al., 2015 with flow rates of 3 mL/h for each aqueous suspension and 16 mL/h for the droplet generation oil (QX200 Oil for EvaGreen, Bio Rad). About 1 mL of each aqueous solution was flowed, generating droplets of 100-105 μm of diameter. Droplets suspension was incubated on ice for ~1h, then 5 min at 70°C and put back in ice. Emulsion was broken, beads washed and harvested and hybridized RNA was reverse transcribed as described in Macosko et al., 2015. For each sample, PCR amplification with 17 cycles was performed on populations of ~32000 beads (∼1600 STAMPs [single-cell transcriptomes attached to microparticles]) divided in ~4000 beads per well on eight-wells PCR strips. Size distribution and concentration were measured using Agilent Bioanalyzer (High Sensitivity 2100). Single-cell sequencing libraries were generated by tagmentation using Nextera XT (Illumina, Cat# FC-131-1024) and size distribution and concentration were measured again with Agilent Bioanalyzer (High Sensitivity 2100) and Qubit Fluorometric Quantitation respectively. Sequencing was performed on the Illumina NextSeq500 sequencer with a loading concentration of 1.55 pM, paired ends with 20 bp for read 1 and 50 bp for read 2.
Paired-end sequence reads were processed as described in Mackosko et al., 2015, with the Java tools provided. After de-multiplexing, bases 1-12 (barcode) and 13-20 (unique molecular identifier; UMI) from read 1 were used to identify the cell of origin and molecule (transcript) of origin, respectively. Low quality read pairs with a cell barcode or UMI base quality less than 10 were filtered out. Read 2 was trimmed at the 5’ end to remove the SMART adaptor sequence, and at the 3’ end to remove polyA tails. Sequences were then aligned to the human genome (GRCh38.88) using HISAT2 v2.1.0 (Kim D, Langmead B and Salzberg SL., Nature Methods 2015) with default settings.   Reads uniquely mapped to exonic regions of genes were recorded and grouped by cell barcode. Correction for barcode synthesis errors was performed as previously described (Shekhar et al., 2016). A digital expression matrix containing the number of UMIs in each gene within each cell was then assembled, with UMIs within an edit distance of 1 collapsed. Digital expression matrices were loaded in R::Seurat and doublets and cells with low number of UMIs were removed (Germain P (2021). scDblFinder: scDblFinder)

value: Brain cortex BA9

value: AD

value: IV

tag: amyloid

tag: age

tag: gender

tag: rin


title: mESC, naive pluripotency, TKO, shLBR, day1, rep4

description:
LBRd1_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: Doxycycline treated for 1 day, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting mouse LBR


title: mESC, naive pluripotency, TKO, shLBR, day1, rep3

description:
LBRd1_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: Jejunum_F_SPF_WT_110

value: WT


title: mESC, naive pluripotency, TKO, shLBR, day2, rep2

description:
LBRd2_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, shLBR, day1, rep2

description:
LBRd1_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: C4

value: III

value: DP (C0)


title: iPSC-cardiomyocytes, 1µM AS1842856 for 5days, Well 3

city: Cambridge

first: Nivedhitha

last: Velayutham

state: Massachusetts

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36.
Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome on ENSEMBL using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including TPM values for each sample

source_name: UCSD142i-86-1 iPSC line (female 116 donor, fibroblast-derived)

extract_protocol:
Total RNA was isolated for each sample from cells using the E.Z.N.A. Total RNA I extraction kit (Omega) according to manufacturer’s instructions. RNA samples were flash-frozen then shipped to Azenta Life Sciences for RNA sequencing services.
mRNA poly(A) selection library preparation was performed by Azenta Life Sciences utilizing their 'Standard & Strand-specific' RNA sequencing service package.

value: iPSC-derived cardiomyocyte suspension cultures

value: Wild type

value: Small molecule


title: A1_CTRL_1

description:
A1
Sarco1_gene_counts.txt

value: whole embryo

value: DMSO 10μm


title: iPSC-cardiomyocytes, 1µM AS1842856 for 5days, Well 2

value: UCSD142i-86-1 iPSC line (female 116 donor, fibroblast-derived)


title: mESC, naive pluripotency, TKO, shLBR, day1, rep1

description:
LBRd1_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: C3

value: PART

value: II

value: No

value: M


title: mESC, naive pluripotency, TKO, shLBR, day0, rep4

description:
LBRd0_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: mESC

value: Untreated, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting mouse LBR


title: XG7

description:
count_normalized.txt
raw_count.txt

value: Human Myeloma Cell Line

value: Plasma cells


title: iPSC-cardiomyocytes, 1µM AS1842856 for 5days, Well 1


title: C6

value: Brain cortex BA9


title: mESC, naive pluripotency, TKO, shLBR, day0, rep3

description:
LBRd0_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: Jejunum_M_SPF_KO_128

value: SPF

value: KO


title: Jejunum_M_SPF_KO_121


title: Jejunum_M_SPF_KO_114


title: mESC, naive pluripotency, TKO, shLBR, day0, rep2

description:
LBRd0_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: iPSC-cardiomyocytes, 0.2% DMSO for 5days, Well 2

value: iPSC-derived cardiomyocyte suspension cultures

value: Vehicle control


title: Jejunum_M_SPF_KO_105


title: Jejunum_M_SPF_KO_104


title: Jejunum_M_SPF_KO_126


title: C2

value: AD

value: IV


title: mESC, naive pluripotency, TKO, shLBR, day0, rep1

description:
LBRd0_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: iPSC-cardiomyocytes, 0.2% DMSO for 5days, Well 1

value: Wild type


title: C1

value: Control


title: 1659_WT

city: Houston

first: Khandan

last: Keyomarsi

state: TX

address: 6565 MD Anderson Blvd. Unit 1052

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

data_processing:
Paired-end reads were mapped to the mouse reference genome (GRCm38) using STAR 2.7.10a
Htseq-count was to extract gene counts from the bam files
EdgeR was used to get log-CPM values from the raw count data
Assembly: GRCm38
Supplementary files format and content: Matrix_RawCounts.tsv has raw count data
Supplementary files format and content: Matrix_CPM.tsv has log-CPM data

source_name: Mammary Tumor

growth_protocol: In vivo studies were tumors were transplanted into mice and treated.

extract_protocol:
Total RNA was isolated from tumor tissues using Trizol reagent (Ambion Life Technologies) according to manufacturer's protocol
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols

treatment_protocol: Mice were treated with vehicle control and PKMYT1 inhibitor (RP-6306) at 20mg/kg per day for different time periods and subjected to RNAseq analysis.

value: Mammary Tumor

value: FVB


title: 1636_WT


title: 2544_WT


title: lungs, PRDM3/16KO IgG, rep2

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Trimmomatic was used to remove adapter sequences and low quality base pairs
Reads were aligned with Bowtie2 to the mm10 reference genome using the --dovetail and --phred33 options
MACS2 was used to call peaks from bam files using -p 0.01 -B -f BAMPE --keep-dup all options and the appropriate IgG control
Peaks were annotated with in-house scripts and the RefSeq annotation database.
bedtools genomecov was used to convert bam files into bigwig files
Assembly: mm10
Supplementary files format and content: big wig files for visulization
Supplementary files format and content: tab delimited narrowPeak files
Library strategy: Cut&Run

source_name: lung

extract_protocol:
Lungs from E17.5 Wild Type C57Bl6 mice were harvested, minced, and incubated in RPMI media containing Liberase TM (Roche, 50ug/ml) and DNAse I (MilliporeSigma, 100ug/ml) at 37C for 30min. Tissues were dissociated with GentleMACS cell dissociator, then subjected to RBC lysis buffer for 2min on ice, followed by an incubation with FcR blocking reagent (Miltenyi: 130-092-575) on ice for 10min, followed by an incubation with CD326 anti-Mouse-EpCAM microbeads (Miltenyi: 130-105-958) at 4C for 15min. Cells were subjected to positive selection with an LS column and collected in MACS buffer (Miltenyi). Cells were quantified manually via hemacytometer with trypan blue.
100,000 EpCAM+ cells were bound to concanavalin A beads, then incubed with antibodies against H3K4me3. IgG controls with either a rabbit or sheep IgG were also generated. Cut&Run Assay Kit (Cell Signaling Technologies, 86652S) was used.
Cells were incubated with pAG-Mnase to facilitate anitbody-guided DNA digestion. The extracted DNA was purified by phenol-chloroform-isoamyl alcohol (Invitrogen: 15593-031) extraction and  Phasemaker tubes (Invitrogen: A33248)
DNA was quantified using a Qubit (ThermoFisher) and libraries were constructed using the Illumina DNA Library Prep Kit (Cell Signaling Technology, 56795S) and Multiplexoligos (47538S). Libraries were sequenced for at least 15mil reads.
Libraries sequenced by Genewiz

value: lung

tag: antibody

value: IgG Rabbit

tag: antibody catalog_info

value: Vector Labs, BA-1000

value: Epcam+ sorted Epithelial cells


title: 1633_WT


title: 2661_WT


title: mESC, naive pluripotency, TKO, shLUC, day4, rep4

description:
LUCd4_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: mESC

value: Doxycycline treated for 4 days, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting Renilla Luciferase


title: lungs, PRDM3/16KO, rep2

value: H3K4me3 Rabbit

value: Cell Signaling, 9751


title: mESC, naive pluripotency, TKO, shLUC, day4, rep3

description:
LUCd4_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, shLUC, day4, rep2

description:
LUCd4_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: Jejunum_F_SPF_KO_130

value: F

value: SPF

value: KO


title: lungs, PRDM3/16KO IgG, rep1


title: iPSC-cardiomyocytes, 0.2% DMSO for 5days, Well 3

value: UCSD142i-86-1 iPSC line (female 116 donor, fibroblast-derived)

value: iPSC-derived cardiomyocyte suspension cultures

value: Vehicle control


title: Jejunum_F_SPF_KO_118


title: Jejunum_F_SPF_KO_116


title: mESC, naive pluripotency, TKO, shLUC, day4, rep1

description:
LUCd4_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: SPON911


title: Jejunum_F_SPF_KO_109


title: lungs, PRDM3/16KO, rep1


title: mESC, naive pluripotency, TKO, shLUC, day2, rep4

description:
LUCd2_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: Doxycycline treated for 2 days, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting Renilla Luciferase


title: SPON441H

value: Mammary Tumor


title: SPON708

value: FVB


title: mESC, naive pluripotency, TKO, shLUC, day2, rep2

description:
LUCd2_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: SPON403


title: mESC, naive pluripotency, TKO, shLUC, day2, rep3

description:
LUCd2_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: lungs, Control IgG, rep1

value: lung

value: Control


title: B6: MAF2-mCherry_PLX

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R

source_name: Melanoma-associated fibroblast mono-cultures stimulated with PLX

label_protocol: Standard Illumina biotin labelling protocol

growth_protocol: Human primary melanoma-associated fibroblasts labeled with mCherry (MAF2-mCherry) were co-culture with 5555 mouse melanoma cells labeled with mEGFP (5555-mEGFP) in DMEM on plastic dishes

extract_protocol: RNA was extracted using a Qiagen RNA extraction kit. The RNA was amplified using an Ambion Illumina TotalPrep RNA Amplification Kit.

treatment_protocol: MAF2-mCherry and 5555-mEGFP co-cultures were treated with DMSO (0.1%) or PLX4720 (1 mM) for 24 hours. Cherry-positive fraction (MAF2-mCherry) were FACS-sorted.

value: melanoma-associated fibroblast (MAF2-mCherry) mono-cultured

value: PLX


title: mESC, naive pluripotency, TKO, shLUC, day1, rep4

description:
LUCd1_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: mESC

value: Doxycycline treated for 1 day, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting Renilla Luciferase


title: MYT968

value: RP-6306 20mg/kg/bid


title: lungs, Control, rep2

value: H3K4me3 Rabbit

value: Cell Signaling, 9751

value: Epcam+ sorted Epithelial cells


title: SPON648


title: B8: Co-cultured_MAF2-mCherry_PLX

source_name: Melanoma-associated fibroblast co-cultured with melanoma cells and stimulated with PLX

value: melanoma-associated fibroblast (MAF2-mCherry) co-cultured with melanoma cells (5555-mEGFP)


title: mESC, naive pluripotency, TKO, shLUC, day1, rep3

description:
LUCd1_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: MYT431


title: mESC, naive pluripotency, TKO, shLUC, day1, rep2

description:
LUCd1_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: CutRun_dKO_H3K27me3_3

first: Naitao

last: Wang

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq data were processed with STAR.
ChIPseq, ATACseq, and CutRun data were processed with bowtie2. Peaks were called using MACS3. Bigwig files were generated with deeptools.
Assembly: GRCm38 (mm10)
Supplementary files format and content: RNAseq: tab-delimited text files include raw gene counts. ATACseq, ChIPseq and CUTnRUN: bigWig files.
Supplementary files format and content: Raw reads for RNAseq, RPGC normalized BigWig files for ATACseq, ChIP-seq, and CutRun

source_name: Mouse bladder urothelial cells

growth_protocol: For ChIPseq, CutRun, and RNAseq, urothelial organoids were cultured in advanced DMEM/F12 (#12634010, Gibco) [supplemented with B27 (2% v/v, #17504044, Gibco), Noggin conditioned medium (10% v/v), R-spondin conditioned medium (10% v/v), EGF (50ng/ml, #AF-100-15, PeproTech), Y-27632 (10µM, #S1049, Selleckchem), A83-01 (0.5µM, #S7692, Selleckchem), N-Acetyl-L-cysteine (1.25mM, #A9165, Millipore Sigma), Primocin (1% v/v, #ant-pm-2, InvivoGen), Penicillin-Streptomycin (1% v/v, #15140122, Gibco), L-Glutamine (1% v/v, 25030081, Gibco), and GlutaMAX (1% v/v, #35050061, Gibco)].

extract_protocol:
In RNAseq, total RNA was extracted with Trizol reagent following the manufacture's instruction. ChIPseq was performed using standard ChIP protocol (Shipra Shukla, et al. Cancer Cell, 16 November, 2017). Ten million cells were used for each antibody. CutRun was performed using standard protocol (Peter J Skene, et al. Nature Protocols, 12 April, 2018). For each WT and Kmt2c/d KO group, 250K cells were used in each reaction. ATACseq was performed using standard protocol (Jason D Buenrostro, et al. Natur Methods, 06 October, 2013). For each control and Kmt2c/d KO group, 50K cells were proceessed for transposase treatment.
RNAseq libraries were prepared using standard Illumina polyA library preparation protocol (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102, 8 cycles of PCR). ChIPseq, ATACseq, and CutRun libraries were prepared using KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions.
RNAseq:poly (A) capture; CurRun, ATACseq, and ChIPseq: epigenetic library.

treatment_protocol: In bulk RNAseq, urothelial cells were treated with DMSO or MI-503 (1µM, 4 days). The remianing samples were prepared under normal culture conditions.

value: Mouse bladder urothelial cells

value: Urothelial cells


title: B4: Co-cultured_MAF2-mCherry_DMSO

source_name: Melanoma-associated fibroblast co-cultured with melanoma cells and stimulated with DMSO

value: DMSO


title: MYT427


title: hypothalamus tissue, postpuberty, replicate3

city: Alar

first: Rong

last: Xuan

state: XinJiang

address: No. 1487, Tarim Avenue East, Alar City, Xinjiang

department: Tarim University

country: China

institute: College of Animal Science and Technology

data_processing:
In the present study, transcript libraries from Dolang sheep at the developmental stages of prepuberty, puberty, and postpuberty were constructed and assayed by high-throughput RNA-seq.
Clean reads were obtained using the program Trimmomatic v0.32 by removing reads containing adapters, reads containing poly-N, and low-quality raw reads.
Clean reads were then aligned and mapped to the sheep genome using HISAT2.
The matched reads were assembled and gene or transcript expression was calculated using StringTie.
Assembly: GCF_016772045.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

organism: Ovis aries

source_name: the hypothalamic tissue

growth_protocol: Hypothalamic tissue was collected from prepubertal, pubertal, and postpubertal sheep.

extract_protocol:
The total RNA content from the hypothalami was extracted using TRIzol reagent.
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions.

treatment_protocol: The hypothalamic tissue was placed in RNase-free cryotubes and frozen in liquid nitrogen.

value: the hypothalamic tissue

tag: group

value: postpuberty


title: CutRun_dKO_H3K27me3_2


title: mESC, naive pluripotency, TKO, shLUC, day1, rep1

description:
LUCd1_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: hypothalamus tissue, postpuberty, replicate2


title: CutRun_dKO_H3K27me3_1


title: mESC, naive pluripotency, TKO, shLUC, day0, rep4

description:
LUCd0_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: Untreated, clonal cell line with stable integration of a tetracycline-inducible shRNA cassette targeting Renilla Luciferase


title: CutRun_dKO_H3K4me2_3


title: MYT450

value: Mammary Tumor

value: FVB


title: lungs, Control, rep1

value: lung

value: Control


title: CutRun_dKO_H3K4me2_2


title: hypothalamus tissue, postpuberty, replicate1


title: mESC, naive pluripotency, TKO, shLUC, day0, rep2

description:
LUCd0_2
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

value: mESC


title: A4: Co-cultured_MAF2-mCherry_DMSO


title: CutRun_dKO_H3K4me2_1


title: A8: Co-cultured_MAF2-mCherry_PLX

value: PLX


title: lungs, Control IgG, rep2

value: IgG Rabbit

value: Vector Labs, BA-1000


title: A2: MAF2-mCherry_DMSO

source_name: Melanoma-associated fibroblast mono-cultures stimulated with DMSO

value: melanoma-associated fibroblast (MAF2-mCherry) mono-cultured


title: B2: MAF2-mCherry_DMSO


title: mESC, naive pluripotency, TKO, shLUC, day0, rep1

description:
LUCd0_1
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: mESC, naive pluripotency, TKO, shLUC, day0, rep3

description:
LUCd0_3
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt


title: CutRun_dKO_H3K4me1_3


title: MYT2639

value: RP-6306 20mg/kg/bid


title: A6: MAF2-mCherry_PLX


title: hypothalamus tissue, prepuberty, replicate3

value: prepuberty


title: hypothalamus tissue, puberty, replicate3

value: puberty


title: MYT2641


title: MYT2645


title: hypothalamus tissue, puberty, replicate1


title: MYT2706


title: LT34_LG1233-OVA_sgUHRF1_4 (biol rep 4)

city: Durham

first: Liuyang

state: NC

address: 213 Research Drive

institute: Duke University

description: TCR beta chain

data_processing:
TCRseq data was assembled and aligned to reference V, D, J, and C genes of T-cell receptors using MiXCR v2.19 and built-in reference database. Specifically, a two-round assembly, including a first-round partial assembly and a second-round full assembly, was conducted to capture more clonotypes, referred to a specific CDR3 sequence. High-quality reads were firstly assembled into core clonotypes, which were then extended based on unique V and J genes against germline sequences. The final assembly was performed with error correction algorithms to merge similar clonotypes and their abundance.
Assembly: MiXCR v2.19 built-in V/D/J/C database
Supplementary files format and content: all processed file are in text format
Library strategy: TCR-seq

growth_protocol: For LLC-OVA model, 2×105 shNT or shUhrf1 LLC-OVA cells were inoculated into male C57BL/6 mice and subsequently treated with either 30 µg IgG or CTLA4 antibodies on days 7, 10 and 14. Tumors were collected on day 17 for TCRb-seq. For LG1233-OVA model, 1 million sgNT or sgUHRF1 LG1233-OVA cells were subcutaneously injected into female C57BL/6 mice. Tumor tissues were collected on day 27 for TCRb-seq.

extract_protocol:
Total RNA was extracted from the bulk tumor tissues for TCR beta chain library construction using the Direct-zol RNA MiniPrep kit.
1 μg or lower amounts of RNA were converted into cDNA using a cDNA Synthesis Kit (Quantabio) with a constant region-specific primer. A multiplex PCR system was introduced to amplify the CDR3 region of rearranged TCRB loci. A set of forward primers, each specific to one or a set of functional TCR Vb segments, and a reverse primer specific to the constant region of TCRB, were used to generate amplicons covering the entire CDR3 region. PCR products were loaded onto 2.5% agarose gels, and bands centered at 250–400 bp were excised and purified using a QIAquick Gel Extraction kit (QIAGEN).

treatment_protocol: shRNAs were used to generate knockdown cell lines in LLC-OVA and CRISPR/Cas9 technology was used to generate UHRF1 knockout stable cell lines in LG1233-OVA.

value: murine lung cancer

value: UHRF1 Knockout

value: Knockout


title: hypothalamus tissue, puberty, replicate2

value: the hypothalamic tissue


title: CutRun_dKO_H3K4me1_1

value: Mouse bladder urothelial cells

value: Urothelial cells


title: CutRun_dKO_H3K4me1_2


title: MYT2642

value: Mammary Tumor

value: FVB


title: CutRUn_H3K27me3_WT_3

value: WT


title: MYT428


title: LT33_LG1233-OVA_sgUHRF1_3 (biol rep 3)

description: TCR beta chain


title: hypothalamus tissue, prepuberty, replicate2


title: LT32_LG1233-OVA_sgUHRF1_2 (biol rep 2)

description: TCR beta chain


title: MYT410


title: hypothalamus tissue, prepuberty, replicate1


title: CutRUn_H3K27me3_WT_2


title: VEH2860


title: ctrl-2

city: Shanghai

first: Hailong

last: Ma

address: Zhizaoju Rd

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

data_processing:
CUT&Tag reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: hg38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag analysis was performed using the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) as described by the manufacturers with some modifications. Briefly, nuclei were extracted from the 10,000 fresh cells, and added the ConA beads incubating at room temperature for 10 min. The mixed complexes were the incubated with antibodies with IgG antibody as a control, and the next day, followed by the secondary antibody. A diluted pA-Tn5 adapter complex was then added to the above system and incubated at room temperature for 1 h. After extensive washing, system were subsequently sheared by adding 5 × TTBL. Subsequent proteinase K and DNA extract beads were used for obtaining eluted DNA.
Finally, the sequencing libraries were established after 12 cycles of PCR amplification and sequenced using Illumina Novaseq 6000 with paired-end 2x150 as the sequencing mode.

value: Human oral squamous cell carcinoma cells

value: STR

value: hypoxia culturing condition


title: LT36_LG1233-OVA_sgUHRF1_5 (biol rep 5)

description: TCR beta chain


title: CutRUn_H3K27me3_WT_1


title: LT31_LG1233-OVA_sgUHRF1_1 (biol rep 1)

description: TCR beta chain


title: CutRun_H3K4me2_WT_3


title: VEH2855

value: Vehicle


title: ctrl-1


title: hypo-2

value: without treatment


title: VEH2857


title: CutRun_H3K4me2_WT_2


title: LT28_LG1233-OVA_sgNT_4 (biol rep 4)

description: TCR beta chain

value: Control


title: hypo-1


title: LT27_LG1233-OVA_sgNT_3 (biol rep 3)

description: TCR beta chain


title: VEH2140


title: HN30-Lac-2

value: lactic acid stimulation


title: CutRun_H3K4me2_WT_1


title: CutRun_H3K4me1_WT_3


title: HN30-Lac-1


title: 3436M20_7

value: RP-6306 20mg/kg/bid


title: LT25_LG1233-OVA_sgNT_1 (biol rep 1)

description: TCR beta chain

value: murine lung cancer


title: CutRun_H3K4me1_WT_2


title: HN30-ctrl-2


title: CutRun_H3K4me1_WT_1


title: LT26_LG1233-OVA_sgNT_2 (biol rep 2)

description: TCR beta chain


title: HN30-ctrl-1


title: LT23_LLC-OVA_shUHRF1_anti-CTLA4_5  (biol rep 5)

description: TCR beta chain

source_name: LLC-OVA

value: LLC-OVA

value: UHRF1 Knockdown

value: UHRF1 Knockdown plus anti-CTLA4


title: LT29_LG1233-OVA_sgNT_5 (biol rep 5)

description: TCR beta chain


title: 3439M20_7


title: 3437M20_7


title: LT22_LLC-OVA_shUHRF1_anti-CTLA4_4  (biol rep 4)

description: TCR beta chain


title: cal27-Lac-2


title: LT21_LLC-OVA_shUHRF1_anti-CTLA4_3  (biol rep 3)

description: TCR beta chain


title: CutRun_Kmt2a_dKO_3

value: Mouse bladder urothelial cells


title: CutRun_Kmt2a_dKO_2

value: Urothelial cells


title: cal27-Lac-1


title: VEH302

value: Mammary Tumor


title: LT20_LLC-OVA_shUHRF1_anti-CTLA4_2  (biol rep 2)

description: TCR beta chain


title: 3443VEH_7

value: FVB


title: cal27-ctrl-2


title: 3440VEH_7


title: LT19_LLC-OVA_shUHRF1_anti-CTLA4_1  (biol rep 1)

description: TCR beta chain


title: CutRun_Kmt2a_dKO_1


title: cal27-ctrl-1


title: 3438VEH_7


title: CutRun_Kmt2a_WT_3

value: WT


title: LT18_LLC-OVA_shUHRF1_IgG_6  (biol rep 6)

description: TCR beta chain

value: UHRF1 Knockdown plus IgG


title: CutRun_Kmt2a_WT_2


title: EIPA06_P7GMP_0_G

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced fastq files were aligned, filtered, barcoded and UMI counted using Cell Ranger Chromium Single Cell RNA-seq version 5.0.1, by 10X Genomics with Cell Ranger, GRCh38database (version2020-A) as the human genome reference.
Each dataset was filtered to retain cells with ≥1000 UMIs, ≥1000 genes expressed, and <15% of the reads mapping to the mitochondrial genome. UMI counts were then normalized so that each cell had a total of 10,000 UMIs across all genes and these normalized counts were log-transformed with a pseudocount of 1 using the “LogNormalize” function in the Seurat package. The top 2000 most highly variable genes were identified using the “vst” selection method of “FindVariableFeatures” function and counts were scaled using the “ScaleData” function. Datasets were processed using the Seurat package
Principal component analysis was performed using the top 2000 highly variable features (“RunPCA” function) and the top 30 principal components were used in the downstream analysis.  Datasets for each patient were integrated separately by using the “RunHarmony” function in the harmony package (version 0.1.0). K-Nearest Neighbor graphs were obtained by using the “FindNeighbors” function whereas the UMAPs were obtained by the “RunUMAP” function (Korsunsky et. al., 2019). The Louvain algorithm was used to cluster cells based on expression similarity. The resolution was set at 0.4 for the AML-4 integrated dataset  for optimal clustering.
Harmony integrated seurat objects samples were save as RDS files using the "saveRDS" function for R (v4.0.3)
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, seurat object

source_name: hematopoietic

extract_protocol:
NA
Chromium 10x Genomics 3’ protocol (v3.0)

value: HSPC

value: hematopoietic


title: Kmt2c_Kmt2d_dKO_CUTnRUN, H3K36me3

data_processing:
RNA-seq data were processed with STAR.
ChIPseq and CURnRUN data were processed with bowtie2. Peaks were called using MACS3. Bigwig files were generated with bamcoverage.
In Kmt2d ChIP-seq, Sicer2 (sicer_df) was used to call differential peaks between WT and dKO conditions;
PRO-cap data were processed with STAR. Peaks were called with PINTS (pints_caller). Bigwig files of plus and minus strand alignments were generated with PINTS (pints_visualizer).
Assembly: GRCm38 (mm10)
Supplementary files format and content: RNAseq: tab-delimited text files include raw gene counts. PROcap, ChIPseq and CUTnRUN: bigWig files.
Library strategy: CUTnRUN

growth_protocol: For ChIPseq, CUTnRUN, RNAseq and PROcap, urothelial organoids were cultured in advanced DMEM/F12 (#12634010, Gibco) [supplemented with B27 (2% v/v, #17504044, Gibco), Noggin conditioned medium (10% v/v), R-spondin conditioned medium (10% v/v), EGF (50ng/ml, #AF-100-15, PeproTech), Y-27632 (10µM, #S1049, Selleckchem), A83-01 (0.5µM, #S7692, Selleckchem), N-Acetyl-L-cysteine (1.25mM, #A9165, Millipore Sigma), Primocin (1% v/v, #ant-pm-2, InvivoGen), Penicillin-Streptomycin (1% v/v, #15140122, Gibco), L-Glutamine (1% v/v, 25030081, Gibco), and GlutaMAX (1% v/v, #35050061, Gibco)].

extract_protocol:
In RNAseq, total RNA was extracted with Trizol reagent following the manufacture's instruction. ChIPseq was performed using standard ChIP protocol (Shipra Shukla, et al. Cancer Cell, 16 November, 2017). Ten million cells were used for each antibody. Cut_n_Run was performed using standard protocol (Peter J Skene, et al. Nature Protocols, 12 April, 2018). For each WT and Kmt2c/d KO group, 250K cells were used in each reaction. Precision nuclear run-on followed by cap-selection sequencing (PRO-cap) was performed as previously described (Dig Bijay Mahat, et al. Nature Protocols, 2016). Ten million WT or dKO urothelial cells were used for each reaction.
RNAseq libraries were prepared using standard Illumina polyA library preparation protocol. ChIPseq and CUTnRUN libraries were prepared using standard Illumina epigenetic library preparation protocol. PROcap library was prepared as previously described (Dig Bijay Mahat, et al. Nature Protocols, 2016).

treatment_protocol: In bulk RNAseq and CUTnRUN (H3K4me3, Menin), urothelial cells were treated with DMSO or MI-503 (1µM, 4 days). The remianing samples were prepared under normal culture conditions.


title: LT17_LLC-OVA_shUHRF1_IgG_5  (biol rep 5)

description: TCR beta chain


title: CutRun_Kmt2a_WT_1


title: ChIPseq_H3K27ac_dKO_3


title: WT_CUTnRUN, H3K36me3


title: 3435M20_7


title: LT15_LLC-OVA_shUHRF1_IgG_3  (biol rep 3)

description: TCR beta chain


title: EIPA06_P6CMP_0_G

description: 10x Genomics


title: EIPA06_SAR_0_G_S1

description: 10x Genomics

value: CB HSPC


title: Kmt2c_Kmt2d_dKO_CUTnRUN, H3K9me3


title: LT16_LLC-OVA_shUHRF1_IgG_4  (biol rep 4)

description: TCR beta chain


title: WT_CUTnRUN, H3K9me3


title: EIPA06_SA_R_0_G_S1

description: 10x Genomics


title: ChIPseq_H3K27ac_dKO_2


title: ChIPseq_H3K27ac_dKO_1


title: Kmt2c_Kmt2d_dKO_CUTnRUN_Rep2, Set1a


title: EIPA06_SA_noR_0_G_S1

description: 10x Genomics


title: LT13_LLC-OVA_shUHRF1_IgG_1  (biol rep 1)

description: TCR beta chain


title: ChIPseq_dKO_Input


title: EIPA06_R_SA_0_G_S1

description: 10x Genomics


title: LT14_LLC-OVA_shUHRF1_IgG_2  (biol rep 2)

description: TCR beta chain


title: WT_CUTnRUN_Rep2, Set1a


title: LT12_LLC-OVA_shNT_anti-CTLA4_6  (biol rep 6)

description: TCR beta chain

value: Control plus anti-CTLA4


title: LT11_LLC-OVA_shNT_anti-CTLA4_5  (biol rep 5)

description: TCR beta chain


title: ChIPseq_H3K27ac_WT_2


title: EIPA06_R_0_G_S1

description: 10x Genomics


title: ChIPseq_H3K27ac_WT_1


title: EIPA06_mCherry_GFP_0_G_S1

description: 10x Genomics


title: LT10_LLC-OVA_shNT_anti-CTLA4_4  (biol rep 4)

description: TCR beta chain


title: WT_CUTnRUN_Rep1, Set1a


title: Kmt2c_Kmt2d_dKO_CUTnRUN_Rep2, Cxxc1


title: ChIPseq_WT_Input


title: LT8_LLC-OVA_shNT_anti-CTLA4_2  (biol rep 2)

description: TCR beta chain


title: WT_CUTnRUN_Rep2, Cxxc1


title: H_NC_input

city: Guangzhou

first: Yutong

last: Zou

address: No.58, Zhongshan Rd.2

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
The fastqc was used for quality control.
Clean data aligned to reference genome using STAR.
Samtools was used to organize and sort sequences.
Peak and motif annotation results were generated by deeptools.
Assembly: GRCh38
Supplementary files format and content: read count

source_name: HOS

extract_protocol:
RNA was extracted using TRIzol and mRNA was enriched with Poly(A)Purist™ MAG Kitaccording to the manufacturer’s instructions. Then mRNA was fragmented using NEBNext Magnesium RNA Fragmentation buffer. Fragment mRNA was incubated anti-ac4C antibody coupled Dynabeads Protein G (Invitrogen). Then, RNA was extracted using phenol/chloroform extraction method.
The library was constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: HOS

value: Osteosarcoma

value: NC

tag: rip antibody

value: none (input)


title: H_sgNAT10_acRIP


title: ATACseq_dKO_3


title: LT7_LLC-OVA_shNT_anti-CTLA4_1  (biol rep 1)

description: TCR beta chain

value: LLC-OVA

value: murine lung cancer


title: H_sgNAT10_input


title: H_NC_acRIP


title: ATACseq_dKO_2


title: Kmt2c_Kmt2d_dKO_CUTnRUN_Rep1, Set1a


title: LT6_LLC-OVA_shNT_IgG_6 (biol rep 6)

description: TCR beta chain

value: Control plus IgG


title: ChIPseq_H3K27ac_WT_3

value: Mouse bladder urothelial cells


title: WT_CUTnRUN_Rep1, Cxxc1

value: Urothelial cells


title: ATACseq_dKO_1


title: Kmt2c_Kmt2d_dKO_MI503_CUTnRUN, Menin


title: LT5_LLC-OVA_shNT_IgG_5 (biol rep 5)

description: TCR beta chain


title: ATACseq_WT_3


title: B_sgNAT10_acRIP


title: WT_MI503_CUTnRUN, Menin


title: LT4_LLC-OVA_shNT_IgG_4 (biol rep 4)

description: TCR beta chain


title: B_NC_input


title: ATACseq_WT_1


title: Kmt2c_Kmt2d_dKO_DMSO_CUTnRUN, Menin


title: LT9_LLC-OVA_shNT_anti-CTLA4_3  (biol rep 3)

description: TCR beta chain


title: Kmt2c_Kmt2d_dKO_CUTnRUN_Rep1, Cxxc1


title: WT_DMSO_CUTnRUN, Menin


title: LT2_LLC-OVA_shNT_IgG_2 (biol rep 2)

description: TCR beta chain


title: LT3_LLC-OVA_shNT_IgG_3 (biol rep 3)

description: TCR beta chain


title: Kmt2c_Kmt2d_dKO_MI503_CUTnRUN, H3K4me3


title: LT1_LLC-OVA_shNT_IgG_1 (biol rep 1)

description: TCR beta chain


title: B_sgNAT10_input


title: RNAseq_dKO_MI503_3


title: ATACseq_WT_2


title: AML-4-24-PDX

description: 10x Genomics

data_processing:
Sequenced fastq files were aligned, filtered, barcoded and UMI counted using Cell Ranger Chromium Single Cell RNA-seq version 7.1.0, by 10X Genomics with Cell Ranger, GRCh38database (version2020-A) as the human genome reference.
Each dataset was filtered to retain cells with ≥1000 UMIs, ≥1000 genes expressed, and <15% of the reads mapping to the mitochondrial genome. UMI counts were then normalized so that each cell had a total of 10,000 UMIs across all genes and these normalized counts were log-transformed with a pseudocount of 1 using the “LogNormalize” function in the Seurat package. The top 2000 most highly variable genes were identified using the “vst” selection method of “FindVariableFeatures” function and counts were scaled using the “ScaleData” function. Datasets were processed using the Seurat package
Principal component analysis was performed using the top 2000 highly variable features (“RunPCA” function) and the top 30 principal components were used in the downstream analysis.  Datasets for each patient were integrated separately by using the “RunHarmony” function in the harmony package (version 0.1.0). K-Nearest Neighbor graphs were obtained by using the “FindNeighbors” function whereas the UMAPs were obtained by the “RunUMAP” function (Korsunsky et. al., 2019). The Louvain algorithm was used to cluster cells based on expression similarity. The resolution was set at 0.4 for the AML-4 integrated dataset  for optimal clustering.
Harmony integrated seurat objects samples were save as RDS files using the "saveRDS" function for R (v4.1.0)
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, seurat object

source_name: AML-4-24 comes from a clone with WT KRAS

extract_protocol:
isolated from mouse xenografts and hCD45-sorted
Chromium 10x Genomics 3’ protocol (v3.0)

value: hCD45+ cells

value: AML-iPSC-derived xenograft


title: RNAseq_dKO_MI503_1


title: Kmt2c_Kmt2d_dKO_DMSO_CUTnRUN, H3K4me3


title: WT_MI503_CUTnRUN, H3K4me3

value: WT


title: F4B(rep2)

city: Beijing

first: Yuqing

address: NO.11 Xizhimen South St, Xicheng district, Beijing

department: Institute of Hematology

institute: Peking University People’s Hospital

description: Treatment with 4 μM FTY720 for 24 h

data_processing:
Clean reads were obtained by removing adaptor sequence/low-quality sequence from raw reads.
Index of the reference genome was built using Bowtie v2.0.6.
Paired-end clean reads were aligned to the reference genome of Homo sapiens GRCh38 using Hisat2 v2.1.0.
FPKM values were obtained using HTSeq v0.6.0.
Assembly: GRCh38
Supplementary files format and content: Excel files include FPKM values for each sample.

source_name: KG1 cell line

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (cat# 74104, Qiagen) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina

value: KG1 cell line

value: AML cell line

value: 4 uM FTY720


title: RNAseq_dKO_MI503_2


title: AML-4-10-PDX

description: 10x Genomics

source_name: AML-4-10 comes from a clone with MUT KRAS G12D


title: M_WT_PBS_3 [557_M_WT_PBS_S14]

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

data_processing:
trimming with cutadapt 0.17.4
alignment and counting with STAR 2.7.9a
workflow with snakemake 6.12.13
Assembly: GRCm39 with annotation Mus_musculus.GRCm39.108.gtf
Supplementary files format and content: tab delimited file including raw counts for each sample

source_name: CD11b enrichment of cells from whole brain

growth_protocol: Primary microglia were isolated and collected in RLT buffer. Subsequently RNA was extracted, so no culturing of these cells took place.

extract_protocol:
RNA extraction was done using the Qiagen RNA isolation kit following the manufacturer’s instructions (RNeasy® Mini Kit, 74104, Qiagen). A DNase treatment followed by a clean-up has been added using the RNA Clean & Concentrator™-5 kit (Zymo Research) following the manufacturer’s instructions. Quantification of total RNA was performed using a N60 Nanophotometer® (Implen GmbH) and a Qubit 2.0 Fluorometer® (Thermo Fisher Scientific) with the Qubit RNA HS Assay Kit. The quality was assessed using a Fragment Analyzer System (Agilent Technologies) using an RNA Pico Chip (Agilent Technologies) (only samples with RQN≥7 were further analysed).
The Illumina® stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit Library preparation has been used to process libraries for RNA-sequencing according to Illumina’s Reference Guide # 1000000124514 v00 June 2020, starting with 25 ng of total RNA. All libraries have been quantified using a Qubit HS dsDNA kit (Thermo Fisher Scientific) and the library quality check has been performed using a High Sensitivity NGS Fragment Analysis Kit on the Fragment Analyzer System (Agilent Technologies).

treatment_protocol: Male 3-4 months old DJ-1 KO and WT littermates were treated with 4ug/g body weight of LPS (Sigma, E.Coli O55:B5, L6529-1MG)  i.p. or saline vehicle for 6h before anesthesia followed by cardiac perfusion and sacrifice.

value: Primary Microglia

value: PBS


title: RNAseq_dKO_DMSO_3

value: DMSO


title: WT_DMSO_CUTnRUN, H3K4me3


title: M_WT_PBS_4 [600_M_WT_PBS_S25]

value: CD11b enrichment of cells from whole brain


title: F4A(rep1)

description: Treatment with 4 μM FTY720 for 24 h


title: B_NC_acRIP

value: Osteosarcoma

value: NC


title: F3B(rep2)

description: Treatment with 3 μM FTY720 for 24 h

value: 3 uM FTY720


title: M_WT_PBS_1 [534_M_WT_PBS_S13]


title: RNAseq_dKO_DMSO_1


title: Kmt2c_Kmt2d_dKO_RNAseq_Rep1, MI503, 4d

data_processing:
RNA-seq data were processed with STAR.
ChIPseq and CURnRUN data were processed with bowtie2. Peaks were called using MACS3. Bigwig files were generated with bamcoverage.
In Kmt2d ChIP-seq, Sicer2 (sicer_df) was used to call differential peaks between WT and dKO conditions;
PRO-cap data were processed with STAR. Peaks were called with PINTS (pints_caller). Bigwig files of plus and minus strand alignments were generated with PINTS (pints_visualizer).
Assembly: GRCm38 (mm10)
Supplementary files format and content: RNAseq: tab-delimited text files include raw gene counts. PROcap, ChIPseq and CUTnRUN: bigWig files.


title: F3A(rep1)

description: Treatment with 3 μM FTY720 for 24 h


title: RNAseq_WT_MI503_3


title: M_WT_LPS_5 [634_M_WT_LPS_S30]

value: LPS


title: F0B(rep2)

description: Sham group without FTY720

value: Sham group without FTY720


title: WT_RNAseq_Rep2, MI503, 4d

value: Mouse bladder urothelial cells


title: RNAseq_WT_MI503_2

value: Urothelial cells


title: F0A(rep1)

description: Sham group without FTY720


title: D2_neg_B(rep2)

description: Samples from healthy donor #2

source_name: Bone marrow

value: Bone marrow

value: CD34+S1PR1- bone marrow mononuclear cells


title: M_WT_LPS_2 [551_M_WT_LPS_S15]

value: WT


title: M_WT_PBS_2 [553_M_WT_PBS_S17]


title: D2_neg_A(rep1)

description: Samples from healthy donor #2


title: RNAseq_dKO_DMSO_2


title: Kmt2c_Kmt2d_dKO_RNAseq_Rep2, DMSO, 4d


title: RNAseq_WT_DMSO_3


title: M_WT_LPS_1 [531_M_WT_LPS_S12]


title: D2_pos_B(rep2)

description: Samples from healthy donor #2

value: CD34+S1PR1+ bone marrow mononuclear cells


title: Kmt2c_Kmt2d_dKO_RNAseq_Rep1, DMSO, 4d


title: RNAseq_WT_DMSO_2


title: M_KO_PBS_5 [644_M_KO_PBS_S28]

value: KO


title: Kmt2c_Kmt2d_dKO_RNAseq_Rep2, MI503, 4d


title: D2_pos_A(rep1)

description: Samples from healthy donor #2


title: WT_RNAseq_Rep2, DMSO, 4d


title: WT_RNAseq_Rep1, DMSO, 4d


title: M_KO_PBS_4 [579_M_KO_PBS_S27]


title: D1_neg_B(rep2)

description: Samples from healthy donor #1


title: WT_RNAseq_Rep1, MI503, 4d


title: Str R3

city: Barcelona

first: Montserrat

last: Corominas

state: Catalonia

address: Diagonal 643

department: Genètica, Microbiologia i estadística

country: Spain

institute: University of Barcelona

data_processing:
grape-nf (available at https://github.com/guigolab/grape-nf; revision: 5fb9c88236 [v0.2.1]); NEXTFLOW version 19.07.0
Sequence reads were mapped using STAR 2.4.0j (Max mismatches: 4, Max multimaps: 10, Sequencing platform: ILLUMINA, Sequencing center: CRG, Genome assembly: dm6, FlyBase genome annotation: dm6.r6.36)
Quantification was performed using RSEM 1.2.21
Assembly: dm6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were grown in Schneider's medium (Sigma) supplemented with 10% FBS (Gibco), 100 mg/ml of streptomycin and 100 mg/ml of penicillin at 25ºC.

extract_protocol:
Total RNA was isolated using Trizol (Ambion) and the RNA Clean and Concentrator kit (Zymo Research). For reverse transcription of poly(A) mRNA, 500-1000 ng were used.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina), following the manufacturer’s instructions.

treatment_protocol: Cells were incubated for 30 min at 25ºC with 10 mM of H2O2. The same volume of Schneider’s medium was added to control cells.

value: wild type

value: Cells were treated with 10mM H2O2 for 30min.


title: Kmt2c_Kmt2d_dKO_Rep2, Input


title: M_WT_LPS_3 [552_M_WT_LPS_S16]

value: Primary Microglia


title: M_KO_PBS_3 [561_M_KO_PBS_S21]

value: PBS


title: RNAseq_WT_DMSO_1

value: DMSO


title: RNAseq_WT_MI503_1


title: Str R2


title: M_WT_LPS_4 [581_M_WT_LPS_S26]

value: CD11b enrichment of cells from whole brain


title: Kmt2c_Kmt2d_dKO_Rep1, Input


title: Str R1


title: WT_Rep2, Input


title: D1_pos_B(rep2)

description: Samples from healthy donor #1


title: M_KO_PBS_2 [559_M_KO_PBS_S20]


title: Ctr R3

value: No treatment


title: Ctr R2


title: M_KO_PBS_1 [556_M_KO_PBS_S19]


title: M_KO_LPS_4 [586_M_KO_LPS_S24]


title: Kmt2c_Kmt2d_dKO_Rep2, Kmt2d ChIP


title: D1_pos_A(rep1)

description: Samples from healthy donor #1


title: Kmt2c_Kmt2d_dKO_Rep1, Kmt2d ChIP


title: M_KO_LPS_5 [645_M_KO_LPS_S29]


title: D1_neg_A(rep1)

description: Samples from healthy donor #1


title: WT_Rep1, Input


title: P10_neg_A(rep1)

description: Samples from patient #10


title: Str IP P-p38 R1

data_processing:
Data was processed using chip-nf pipeline (available at https://github.com/guigolab/chip-nf; revision: 47c471b6f4 [v0.2.3]); NEXTFLOW version 19.07.0
Reads were continuously mapped to the fly genome (dm6) using GEM mapper
Duplicated reads were removed using Picard (http://broadinstitute.github.io/picard/)
Fragment length was set to 200
Peak calling was performed using MACS2. Input was sequenced in two lanes. BAM files of input were merged before peak calling. Peak scores were rescaled to conform to the format supported by the UCSC genome browser (score must be <1000).
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin was immunoprecipitated with αP-p38 antibody. Finally DNA was purified by standard phenol extraction.
2-3 ng of DNA was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 10 cycles was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).


title: P10_pos_B(rep2)

description: Samples from patient #10


title: Ctr R1


title: Str input R2


title: M_KO_LPS_3 [568_M_KO_LPS_S23]


title: Str IP P-p38 R2


title: WT_Rep1, Kmt2d ChIP


title: M_KO_LPS_2 [562_M_KO_LPS_S22]


title: WT_Rep2, Kmt2d ChIP


title: M_KO_LPS_1 [554_M_KO_LPS_S18]


title: P10_pos_A(rep1)

description: Samples from patient #10


title: Kmt2c_Kmt2d_dKO_PROcap_Rep1

data_processing:
RNA-seq data were processed with STAR.
ChIPseq and CURnRUN data were processed with bowtie2. Peaks were called using MACS3. Bigwig files were generated with bamcoverage.
In Kmt2d ChIP-seq, Sicer2 (sicer_df) was used to call differential peaks between WT and dKO conditions;
PRO-cap data were processed with STAR. Peaks were called with PINTS (pints_caller). Bigwig files of plus and minus strand alignments were generated with PINTS (pints_visualizer).
Assembly: GRCm38 (mm10)
Supplementary files format and content: RNAseq: tab-delimited text files include raw gene counts. PROcap, ChIPseq and CUTnRUN: bigWig files.
Library strategy: PRO-cap

molecule: nuclear RNA


title: Str input R1


title: P28 cortical microglia rep5

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

data_processing:
Bases with quality scores less than 30 and adapters were trimmed from raw sequencing reads by Trim Galore (v 0.6.4). After trimming, only reads with lengths greater than 30bp were mapped to mm10 by STAR (v 2.7.1a) with average mapping efficiency of 81.5%.
Raw counts and normalized counts for each gene were outputted by RSEM (v1.2.28). The raw counts were used to identify differentially expressed genes (DEG) by DESeq2 (v 1.36.0). Only genes with adjusted p-value less than 0.05 and at least two-fold change were considered as differentially expressed genes.
Exon usage difference was performed using DEXseq (v 1.44.0). Exons with an average count greater than 10 in a single cell population, adjusted p-value less than 0.05, and fold change greater than or equal to two were considered as differentially expressed exons.
Assembly: mm10
Supplementary files format and content: comma-separated values file include TPM values for each Sample

source_name: cortex

extract_protocol:
RNA was isolated from cells with Direct-zol RNA Microprep kit (Zymo Research, #R2060) following the manufacturer’s instructions
Library preparation and RNA sequencing were performed by Novogene Co. Total RNA was reverse transcribed into the first-strand cDNA. Then the double-strand cDNA was synthesized by LD-PCR amplification, followed by the purification with AMPure XP beads and quantification with Qubit. PolyA enrichment was conducted to enrich all the coding RNA. The cDNA samples were then fragmented, end-repaired, A-tailed, and ligated with adaptors. After size selection and PCR enrichment, the RNA library was ready for sequencing. Sequencing was performed on a NovaSeq instrument. Paired-end reads 2 x 150 bp sequencing runs were performed with an average of 30 million reads per sample.

value: cortex

value: microglia


title: P9_neg_B(rep2)

description: Samples from patient #9


title: Ctr IP P-p38 R2


title: P9_neg_A(rep1)

description: Samples from patient #9


title: Ctr IP P-p38 R1


title: Kmt2c_Kmt2d_dKO_PROcap_Rep2


title: P28 cortical microglia rep4


title: P10_neg_B(rep2)

description: Samples from patient #10


title: P28 cortical microglia rep2


title: P9_pos_B(rep2)

description: Samples from patient #9


title: WT_PROcap_Rep2


title: P9_pos_A(rep1)

description: Samples from patient #9


title: L3_nonLSC_rep2

description: Samples from patient #L3

value: CD34+CD38-CD58+, CD34+CD38+CD58-, and CD34+CD38+CD58+ bone marrow mononuclear cells


title: Ctr input R1


title: Ctr input R2


title: Peripheral blood_EoE_003

city: cincinnati

first: Marc

last: Rothenberg

state: OHIO

address: 3333 burnet avenue

institute: cincinnati children's hospital mc

description: Hive CLX gravity-based scRNA-seq

data_processing:
*library strategy: Hive CLX gravity-based scRNA-seq
raw sequencing data from the peripheral blood samples were aligned to the GRCh38 reference genome using BeeNet v1.1 software to produce feature-barcode matrices for each dataset and was analyzed using the Seurat (version 4.4.0) package in R (version 4.1.3).
Sequences were trimmed for the adaptor/low-quality reads using default parameters and aligned to HG38 human genome
low-quality cells were removed from all datasets by applying the following quality control filtering thresholds: minimum of 300 genes per cell and a maximum of 20% of reads mapped to mitochondrial genes. Additionally, doublets were identified and excluded using the scDblFinder package.
Assembly: HG38
Supplementary files format and content: Filtered feature-barcode matrices in MEX format

source_name: Peripheral blood

extract_protocol:
Single-cell suspensions were prepared from blood samples following red blood cell lysis using EasySep™ RBC Depletion Reagent. The cells were subject to a commercial Seq-Well platform, the Hive CLX gravity-based scRNA-seq
15,000 cells were loaded into the HIVE according to the capture protocol by centrifugation at 30 relative centrifugal fields (RCF) for 3 minutes. HIVEs were frozen at -20C until processing according to the updated HIVE scRNA-seq Processing Kit revA. Each cell was uniquely barcoded during the 3’ cDNA library generation.

tag: batch

tag: subject status

value: patients with eosinophilic esophagitis

value: Peripheral blood


title: P28 cortical microglia rep1

tag: cell type


title: Control_scRNAseq_Rep4

data_processing:
RNAseq sequence data were processed and mapped to the mouse genome (mm10) using STAR v2.3 (Alexander Dobin, et al. Bioinformatics, 1 January, 2013)
Single cell RNAseq reads obtained from the 10x Genomics scRNAseq platform were demultiplexed and mapped to mouse genome (mm10) using the Cell Ranger package (10X Genomics).
ATACseq reads were quality and adapter trimmed using Trim Galore before aligning to mouse genome (mm10) with Bowtie2 with the default parameters.
ChIPseq and CUT_n_RUN reads were quality and adapter trimmed using Trim Galore before aligning to mouse genome assembly mm10 with Bowtie2 using the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited text files include raw gene counts. ATACseq, ChIPseq and CUT_n_RUN: bigWig files. Sinlge cell RNAseq: barcodes, features, and matrix raw files.

growth_protocol: For ChIPseq, CUT_n_RUN, RNAseq and ATACseq, urothelial organoids were cultured in advanced DMEM/F12 (#12634010, Gibco) [supplemented with B27 (2% v/v, #17504044, Gibco), Noggin conditioned medium (10% v/v), R-spondin conditioned medium (10% v/v), EGF (50ng/ml, #AF-100-15, PeproTech), Y-27632 (10µM, #S1049, Selleckchem), A83-01 (0.5µM, #S7692, Selleckchem), N-Acetyl-L-cysteine (1.25mM, #A9165, Millipore Sigma), Primocin (1% v/v, #ant-pm-2, InvivoGen), Penicillin-Streptomycin (1% v/v, #15140122, Gibco), L-Glutamine (1% v/v, 25030081, Gibco), and GlutaMAX (1% v/v, #35050061, Gibco)]. For single cell RNAseq, live urothelial cells were sorted out as DAPI-/EpCAM+/nlsEGFP+.

extract_protocol:
In RNAseq, total RNA was extracted with Trizol reagent following the manufacture's instruction. ATACseq was performed using standard protocol (Jason D Buenrostro, et al. Natur Methods, 06 October, 2013). For each control and Kmt2c/d KO group, 50K cells were proceessed for transposase treatment. ChIPseq was performed using standard ChIP protocol (Shipra Shukla, et al. Cancer Cell, 16 November, 2017). Ten million cells were used for each antibody. Cut_n_Run was performed using standard protocol (Peter J Skene, et al. Nature Protocols, 12 April, 2018). For each control and Kmt2c/d KO group, 250K cells were used. DNA fragments from ChIPseq and Cut_n_Run were extracted with cycle/gel purification kit (#740609, TAKARA). In scRNAseq, 5K live cells in each mouse were processed for encapsulation and library preparation.
RNAseq libraries were prepared using standard Illumina polyA library preparation protocol. Single cell RNAseq libraries were prepared with 10X genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 according to manufacturer’s specifications. ATACseq, ChIPseq and CUT_n_RUN libraries were prepared using standard Illumina epigenetic library preparation protocol
RNAseq and scRNAseq:poly (A) capture; ATACseq, CUT_n_RUN, and ChIPseq: epigenetic library.

treatment_protocol: In CRISPR system, urothelial cells were edited with CRISPR/Cas9 (pLentiCRISPR_v2 one vector system). In Cre-Loxp system, urothelial cells from Tmprss2-CreERT2-IRES-nlsEGFP;Kmt2cf/f;Kmt2df/f mouse were infected with Adeno-mCherry (Control) and Adeno-mCherry-P2A-Cre (Kmt2c/d dKO). In scRNAseq, live urothelial cells from Tmprss2-CreERT2-IRES-nlsEGFP;Kmt2cf/f;Kmt2df/f mice with or without 3-month tamoxifen treatment (2 doses, 3mg/dose) were isolated as Kmt2c/d KO (n=3 mice) and Control group (n=4 mice), respectively.

tag: rnaseq

value: Single cell RNAseq


title: P28 cortical astrocytes rep4

value: astrocyte

tag: genotype


title: Control_scRNAseq_Rep3


title: Control_scRNAseq_Rep2


title: L3_nonLSC_rep1

description: Samples from patient #L3

value: Bone marrow


title: P28 cortical astrocytes rep3

value: WT


title: L3_LSC_rep3

description: Samples from patient #L3

value: CD34+CD38-CD58- bone marrow mononuclear cells


title: Peripheral blood_EoE_001

description: Hive CLX gravity-based scRNA-seq


title: Peripheral blood_EoE_002

description: Hive CLX gravity-based scRNA-seq


title: P28 cortical microglia rep3


title: P28 cortical astrocytes rep2


title: Peripheral blood_control_003

description: Hive CLX gravity-based scRNA-seq

value: control


title: WT_PROcap_Rep1

tag: cell line

value: Mouse bladder urothelial cells

value: Urothelial cells


title: L3_LSC_rep1

description: Samples from patient #L3

tag: tissue


title: L3_LSC_rep2

description: Samples from patient #L3


title: Kmt2c_Kmt2d_dKO_CUTnRUN_SET1A_Rep1

tag: ChIP


title: L3_nonLSC_rep3

description: Samples from patient #L3


title: Peripheral blood_control_002

description: Hive CLX gravity-based scRNA-seq


title: L2_nonLSC_rep3

description: Samples from patient #L2

value: IKZF1 mutation=12.07%;  BCR-ABL=107.5%;  IGH rearrangement


title: Control_CUTnRUN_SET1A_Rep1


title: P28 cortical astrocytes rep5

tag: developmental stage


title: P28 cortical astrocytes rep1


title: P28 cortical neurons rep5

value: neuron


title: L2_nonLSC_rep2

description: Samples from patient #L2


title: Control_CUTnRUN_MENIN_Rep1

value: MENIN


title: Peripheral blood_control_001

description: Hive CLX gravity-based scRNA-seq


title: P28 cortical neurons rep4


title: Control_scRNAseq_Rep1


title: L2_nonLSC_rep1

description: Samples from patient #L2


title: F_SC_withoutPSCR

city: Campinas

first: Mônica

last: Barbosa de Melo

state: Sao Paulo

address: Avenue Candido Rondon, 400. Cidade Universitária

department: Center for Molecular Biology and Genetic Engineering - CBMEG

country: Brazil

institute: Campinas University

data_processing:
Read quality was assessed by FastQC v0.11.5
Sequence reads were mapped to GRCh38.88 using STAR version 2.5.2
Read count extraction were performed using FeatureCounts algorithm from Rsubread
Assembly: GRCh38.88
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol Reagent (Ambion Life Technologies, Carlsbad CA, USA), and a commercial RNeasy mini Kit (Qiagen GmbH, Hilden, Germany), according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA-Seq v2 kit (Illumina, San Diego, CA, USA) according to manufacturer’s protocol.

value: peripheral blood

value: Endothelial colony-forming cells (ECFCs)


title: P28 cortical neurons rep3

value: cortex


title: AP_SC_withoutPSCR


title: Kmt2c_Kmt2d_dKO_CUTnRUN_H3K27me3_Rep1

city: New York


title: L2_LSC_rep3

description: Samples from patient #L2


title: P28 cortical neurons rep2


title: L2_LSC_rep2

description: Samples from patient #L2


title: Kmt2c_Kmt2d_dKO_CUTnRUN_H3K4me3_Rep1


title: Kmt2c_Kmt2d_dKO_CUTnRUN_MENIN_Rep1


title: Control_CUTnRUN_H3K27me3_Rep1


title: M_SC_withPSCR


title: Control_CUTnRUN_H3K4me3_Rep1


title: L1_nonLSC_rep3

description: Samples from patient #L1

value: CD34+CD38-CD58+, CD34+CD38+CD58-, and CD34+CD38+CD58+ bone marrow mononuclear cells


title: Kmt2c_Kmt2d_dKO_CUTnRUN_H3K4me2_Rep1


title: J_SC_withPSCR


title: JK_SC_withPSCR


title: ACD

city: Xiamen

first: Lingjuan

last: Zhang

address: Xiangan South Street

institute: Xiamen University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ear skin

extract_protocol:
Skin biopsies were minced and digested with collagenase D and DNase1 to isolate single skin cells as previously described (Zhang et al., 2019; Zhang et al., 2021).
Libraries were generated from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v2. cDNA libraries were sequenced on an Illumina Novaseq6000 platform (Illumina).

value: ear skin

tag: strain

value: ICR

value: 7~8 weeks

tag: treatment

value: DNFB-elicited ACD ear skin samples


title: P28 cortical neurons rep1


title: L2_LSC_rep1

description: Samples from patient #L2

value: Bone marrow


title: Kmt2c_Kmt2d_dKO_scRNAseq_Rep3

value: Single cell RNAseq


title: CTRL

tag: age

value: Healthy control  ear skin samples


title: N_SC_withPSCR


title: L1_nonLSC_rep1

description: Samples from patient #L1


title: L1_nonLSC_rep2

description: Samples from patient #L1


title: Control_CUTnRUN_H3K4me2_Rep1


title: Kmt2c_Kmt2d_dKO_CUTnRUN_H3K4me1_Rep1


title: D_SC_withPSCR


title: Control_CUTnRUN_H3K4me1_Rep1


title: APD_SC_withoutPSCR


title: L1_LSC_rep2

description: Samples from patient #L1

value: CD34+CD38-CD58- bone marrow mononuclear cells