title: sample 903, sham, Vehicle

description: Library name: 903.H_S75

value: Vehicle (V)


title: GP5d p53-KO clone2 DMSO Rep1

status: Public on Jun 16 2025

type: SRA

city: Helsinki

first: Divyesh

last: Patel

address: University of Helsinki

department: Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine,

country: Finland

institute: University of Helsinki

description: GP5d_p53_KO_clone2_gene_expression_counts.tsv

library_source: transcriptomic

data_processing:
Trim Galore v.0.6.7 was used to remove adaptor/overepresented sequences, discarding reads left with < 20 bp. FastQC v.0.11.9 was used for quality control.
Reads were also aligned with STAR v.2.5.3a (Dobin et al. 2013).
Gene counts were quantified by using HTSeq-count v.0.11.2 (Anders et al. 2015)
Diffential expression analysis was performed with DESeq2 v.1.32.0 (Love et al. 2014).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene expression counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Colon

growth_protocol: GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. OE19 and LNCAP-1F5 cells were cultured in RPMI supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA stranded mRNA-seq kit for Illumina (Roche) as per manufacturer’s instruction

treatment_protocol:
Cells were treated with distinct chromatin modifier enzyme inhibitors. For DNMT inhibition, cells were treated with 500 nM/L DAC (MedChemExpress, HY-A0004). Media containing DAC were replaced each day for three days. For HDAC inhibition, cells were treated with 500 nmol/L SB939 (MedChemExpress, HY-13322) for 18 hours. For SETDB1 inhibition, cells were treated with 500 nM/L Mitramycin A (MedChemExpress, HY-A0122) for 24 hours. For co-inhibition of DNMT and HDAC, cells were treated with 500 nM/L DAC. DAC containing media were replaced each day for three days followed by 500 nmol/L SB939 for 18 hours and collected for RNA isolation and ChIP-seq. For co-inhibition of DNMT and SETDB1, cells were treated with 500 nM/L DAC. Media containing DAC were replaced each day for three days followed by 500 nM/L Mitramycin A for 24 hours. For co-inhibition of HDAC and SETDB1, GP5d and OE19 cells were treated with 500 nM/L SB939 for 18 hours followed by 500 nM/L Mitramycin A for 24 hours. For DMSO control, cells were treated with DMSO (Fisher, BP231). Media containing DMSO were replaced each day for four days. For p53 reintroduction in GP5d p-53 KO cells, cells were transfected with p53 expressing pIRES2-EGFP-p53 WT plasmid (addgene # 49242). After 24 hours of transfection, cells were treated with combination of DAC (72 hours) and SB939 (18 hours) for co-inhibition of DNMT and HDAC or DMSO control (96 hours).
Generation of GP5d p53-KO and GP5d KAP1 heterozygous cell line is described in Sahu et al., Nat. Gen. (2022)

tag: tissue

value: Colon

tag: cell line

tag: cell type

value: Colon  adenocarcinoma

tag: genotype

tag: treatment

value: DMSO Control


title: HT29_ABE_sgQ311*_48hpi2

city: Dresden

first: Frank

last: Buchholz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

description:
Library name: H_311_48_2
Column name in raw_counts.csv: H_311_48_2

data_processing:
Aligned to the human genome GRCh38/hg38 using STAR v2.7.3a for paired-end reads.
Aligned reads fed through featureCounts v2.0.6 of the subread package to generate the count matrix.
Assembly: GRCh38
Supplementary files format and content: Count matrix with sample IDs for columns and Ensembl gene IDs for rows.

growth_protocol: A431 and PANC-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. HT-29 cells were maintained in McCoy's 5a Medium supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads following Novogene NGS RNA Library Prep Set protocol. Briefly, after fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The non-directional library was complete following end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: All cell lines were infected first with an ABE-GFP-PuroR lentivirus. Then, following puromycin selection, cells were infected with a mutation-targeting sgRNA-TdTomato lentivirus. RNA was isolated at 36, 48 and 72 hours post infection

value: Human Adenocarcinoma; Colorectal

value: ABE + Q311*-correcting-gRNA lentivirus


title: OE19, HDACi-SETDB1i Rep2

description: OE19_Co-inhibition_treatments_gene_expression_counts.tsv

source_name: Esophagus

value: Esophagus

value: Esophageal  adenocarcinoma

value: Wild-type

value: HDAC SETDB1 co-inhibition


title: HT29_ABE_sgQ311*_36hpi

description:
Library name: H_311_36_1
Column name in raw_counts.csv: H_311_36_1_1


title: HT29_ABE_sgQ311*_36hpi2

description:
Library name: H_311_36_2
Column name in raw_counts.csv: H_311_36_2


title: HT29_ABE_sgR273H_72hpi2

description:
Library name: H_273_72_2
Column name in raw_counts.csv: H_273_72_2

value: ABE + R273H-correcting-gRNA lentivirus


title: sample 902, sham, Vehicle

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

country: USA

institute: NYU Langone Health

description: Library name: 902.H_S74

data_processing:
Quality control of sequencing reads was assessed using FastQC v0.11.7 and MultiQC v1.9
Reads were mapped to the mouse reference genome (mm10) using STAR v2.6.1d
Genomic features were assigned using Subread featureCounts v1.6.3
Assembly: mm10
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

organism: Mus musculus

source_name: ventricular myocardium

growth_protocol: Tissues were collected from mice (In-vivo experiment). At sacrifice, mice were anesthetized with ketamine/xylazine and perfused with PBS. Heart tissue was collected and frozen at -80C.

extract_protocol:
Total RNA was extracted from ventricular myocardium using the RNeasy Mini Kit (Qiagen, Hilden, Germany) as per the manufacturer’s protocol
RNA sequencing was performed by the NYU School of Medicine Genome Technology Center on an Illumina Novaseq 6000 instrument.

treatment_protocol: Heart tissue from mice was collected and frozen at -80C after sacrifice, as per the growth protocol.

value: ventricular myocardium

tag: strain

tag: age

value: adult

tag: Sex

value: male

tag: sample id

tag: surgery

value: sham

tag: bacteria


title: HT29_ABE_sgVEGF_48hpi2

description:
Library name: H_VEGF_48_2
Column name in raw_counts.csv: H_VEGF_48_2

value: ABE + VEGFA3-control gRNA lentivirus


title: GP5d p53-KO clone2 DMSO Rep3


title: OE19, HDACi-SETDB1i Rep1


title: sample 901, sham, Vehicle

description: Library name: 901.H_S73


title: OE19, DNMTi-SETDB1i  Rep3

value: DNMT SETDB1 co-inhibition


title: HT29_ABE_sgR273H_48hpi

description:
Library name: H_273_48_1
Column name in raw_counts.csv: H_273_48_1_1


title: HT29_ABE_sgR273H_48hpi2

description:
Library name: H_273_48_2
Column name in raw_counts.csv: H_273_48_2


title: scRNA-seq_co-culture

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Library name: Sample01

library_source: transcriptomic single cell

data_processing:
Counts generated using Cell Ranger with ncbiRefSeq.2024-02-14
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cell line

growth_protocol: The co-cultureed ESCs/EpiSCs were cultured on 0.1% gelatin-coated dishes at 37°C in a 5% CO2 atmosphere in BRD0705/IWR1 medium, on feeders. For BRD0705/IWR conditions, 8 µM BRD0705 (Cayman Chemical) and 2.5 µM IWR-1 (Selleckchem) were added to the N2B27 medium. DMEM/F12-N2 medium was prepared by adding 1 ml of N2 (Gibco) 100× stock solution to 100 ml of DMEM/F12. For Neurobasal/B27 medium, 2 ml of B27 (Gibco) and 2 mM L-glutamine were added to 100 ml of Neurobasal medium. N2B27 medium was prepared by mixing DMEM/F12-N2 medium with Neurobasal/B27 medium at a 1:1 ratio, followed by the addition of 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
ESCs/EpiSCs cultured in BRD0705/IWR1 medium were trypsinized and dissociated into the single-cell. According to the manufacturer's instructions, single-cell RNA sequencing was performed with the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1.
According to the manufacturer's instructions, single-cell RNA sequencing was performed with the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1.

value: ESCs

value: WT


title: HT29_ABE_sgR273H_36hpi2

description:
Library name: H_273_36_2
Column name in raw_counts.csv: H_273_36_2_1

value: Colon


title: OE19, DNMTi-SETDB1i  Rep2


title: HT29_ABE_sgR273H_36hpi

description:
Library name: H_273_36_1
Column name in raw_counts.csv: H_273_36_1


title: HT29_ABE_sgR273H_72hpi

description:
Library name: H_273_72_1
Column name in raw_counts.csv: H_273_72_1_1


title: A431_ABE_sgVEGF_72hpi

description:
Library name: A_VEGF_72_1
Column name in raw_counts.csv: A_VEGF_72_1

source_name: Skin; Epidermis

value: Skin; Epidermis

value: Human Epidermoid Carcinoma


title: A431_ABE_sgVEGF_48hpi2

description:
Library name: A_VEGF_48_2
Column name in raw_counts.csv: A_VEGF_48_2


title: Whole Heart, Ncx1 Mutant, e9.5

city: New Haven

first: Kathryn

last: Berg

state: Connecticut

address: 333 Cedar St.

department: Genetics

institute: Yale University

description:
Library name: mut
10x Genomics

data_processing:
Reads were aligned with Cell Ranger (v6.1.0).
Assembly: mm10
Supplementary files format and content: Matrix, Barcodes, and Features files from Cell Ranger(v6.1.0)

molecule: polyA RNA

source_name: Embryonic heart

extract_protocol:
Flashfrozen hearts were homogenized with a TissueLyser II (Qiagen), filtered through a 40 uM strainer and centrifuged at 1200g, 5 minutes, 4C. Resuspended nuclei were FACs sorted for quality and fractionated with the 10x Genomics Chomium iX according to manufacturer's protocol.
The 10x Genomics Chromium Single Cell Reagent Kit (v3.1) was used to generated expression libraries. Libraries were sequenced with a NovaSeq 6000 (Illumina).

value: Embryonic heart

tag: developmental stage

value: embyonic day 9.5


title: OE19, DMSO Rep6

value: Esophagus

value: Esophageal  adenocarcinoma

value: DMSO Control


title: A431_ABE_sgVEGF_48hpi

description:
Library name: A_VEGF_48_1
Column name in raw_counts.csv: A_VEGF_48_1_1


title: OE19, DNMTi-SETDB1i  Rep1

value: Wild-type


title: A431_ABE_sgVEGF_36hpi2

description:
Library name: A_VEGF_36_2
Column name in raw_counts.csv: A_VEGF_36_2


title: Whole Heart, Wildtype, e9.5

description:
Library name: wt
10x Genomics


title: A431_ABE_sgVEGF_72hpi2

description:
Library name: A_VEGF_72_2
Column name in raw_counts.csv: A_VEGF_72_2


title: OE19, DMSO Rep5


title: A431_ABE_sgVEGF_36hpi

description:
Library name: A_VEGF_36_1
Column name in raw_counts.csv: A_VEGF_36_1_1


title: A431_ABE_sgR273H_72hpi2

description:
Library name: A_273_72_2
Column name in raw_counts.csv: A_273_72_2

value: ABE + R273H-correcting-gRNA lentivirus


title: Mandible, rep 3

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

description:
Library name: Mandible_8
10 Genomics (3' GEX)

data_processing:
Sample capture 3’ GEX library FASTQ files were processed with the 10X Genomics CellRanger Software Suite v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest). CellRanger count was used to demultiplex and process cell barcodes, align reads derived from the 3’ end of transcripts to the mm10 genome, and construct a gene-by-cell unique molecular identifier counts matrix.
Downstream single-cell analysis was performed in R v4.1.0 using the Seurat single-cell analysis pipeline.
Filtering: The following quality control filtering criteria were applied to each cell from each sample: gene number between 600 and 6000 genes and mitochondrial content > 20%. Filtering reduced cell numbers by about 5% per sample.  Cell cycle scores for the S phase (DNA synthesis; 43 genes) and G2M phase (54 genes) were calculated per cell using the genes lists provided by Seurat.
Normalization: Gene expression within each sample was normalized using SCTransform with regularization (vst.flavor = “v2”) using the “glmGamPoi” method.14 Mitochondrial content and differences in cell cycle score were regressed out (vars.to.regress= “percent.mt”, “CC.difference”) during normalization.
Data Set Integration: 3,000 gene features were selected for finding cell-cell anchors across data sets for data set alignment or “integration” with Seurat CCA to remove batch effects from the different captures.The UMAP was constructed using the top 20 principal components. Clustering was done using the Louvain algorithm with the top 20 PCs at multiple clustering resolutions.
Cell type Annotation: To aid in the identification of CD11b+ subpopulations and determine the optimal clustering resolution, SingleR, an automated celltype classification tool was applied using the MouseRNAData and ImmGenData from the CellDex R package.
Differential Gene Expression on Cd11b+ cell populations: Used FindAllMarkers() to find genes that are up- and down-regulated in each subpopulation versus all other cells at resolution =0.1 with the following settings: method=wilcox, logfc.threshold=0.3, assay=SCT, min.pct=0.2, only.pos=FALSE.
Differential Gene Expression on between Femur and Mandible:we Used the Wilcoxon rank sum test in FindMarkers() with the following settings:  method=wilcox, logfc.threshold=0.25, assay=SCT, min.pct=0.1, only.pos=FALSE. Genes are considered DE if FDR < 0.05.
Assembly: mm10 (from 10X Genomics)
Supplementary files format and content: Decomposed counts matrix (features.tsv, matrix.mtx, and barcodes.tsv) from cellranger that can be imported into R with Seurat Read10X() function.
Supplementary files format and content: Differential gene expression results table containing the up- and down-regulated genes for each subpopulation (DEG_Results_UpandDownregulated_Subpopulation_MarkersRes0.1.txt ) using the Wilcoxon Rank Sum test from FindAllMarkers. Format = TSV. Table contains the log2FC (logFC column) of expression between each cluster (cluster column) for each gene (gene column). The percentage of cells expressing the gene in the cluster in question is indicated in the "pct.1" column. The percentage of all other cells expressing the gene is indicated in "pct.2" column.

source_name: Mandible

extract_protocol:
Primary bone marrow macrophages (BMMs) were harvested from the femurs and tibiae of 2-month-old male and female C57Bl/6J mice. Femurs and tibiae were dissected, and adherent tissue was removed. The ends of the bones were cut, and the marrow was flushed from the inner compartments. Mandibles were dissected in two portions, a right and left side, and adherent tissue was removed. The molar teeth of each mandibular section were extracted, and tooth sockets were flushed. The condylar and incisal portions of the mandible were cut, and the marrow space was flushed from the inner compartments. From both the mandibular and femoral derived bone marrow cells were positively selected using CD11b microbeads and magnetic column isolation (Miltenyi Biotec, catalog #130-097-142) following manufacturer’s instructions. Briefly, flushed cells were pelleted and resuspended in MACS buffer (phosphate–buffered saline (PBS), pH 7.2, 0.5% bovine serum albumin, 2 mM EDTA). The cells then were incubated with CD11b microbeads for 15 minutes. The cells were then rinsed for 10 mins with MACS buffer. Following incubation, the cells were applied to the MACS column in a magnetic field. The columns were rinsed three times. The columns were then removed from magnetic field and flushed with 5 mL of MACS buffer to elute bound CD11b+ cells. Six samples (3 femoral and 3 mandibular) were submitted for single-cell RNA sequencing.
Single cell captures targeting 10,000 cells each were performed by 10X Genomics ST G chip for 3’ gene expression at UMN Genomic Center.

value: Mandible

value: Male

value: 2 months


title: OE19, DMSO Rep4

description: OE19_Co-inhibition_treatments_gene_expression_counts.tsv


title: A431_ABE_sgR273H_72hpi

description:
Library name: A_273_72_1
Column name in raw_counts.csv: A_273_72_1


title: Mandible, rep 2

description:
Library name: Mandible_7
10 Genomics (3' GEX)


title: A431_ABE_sgR273H_48hpi2

description:
Library name: A_273_48_2
Column name in raw_counts.csv: A_273_48_2


title: GP5d, HDACi-SETDB1i  Rep3

description: GP5d_Co-inhibition_treatments_gene_expression_counts.tsv

value: Colon  adenocarcinoma

value: HDAC SETDB1 co-inhibition


title: A431_ABE_sgR273H_48hpi

description:
Library name: A_273_48_1
Column name in raw_counts.csv: A_273_48_1_2


title: Mandible, rep 1

description:
Library name: Mandible_6
10 Genomics (3' GEX)


title: A431_ABE_sgR273H_36hpi

description:
Library name: A_273_36_1
Column name in raw_counts.csv: A_273_36_1


title: GP5d, HDACi-SETDB1i Rep2


title: Femur, rep 3

description:
Library name: Femur_7
10 Genomics (3' GEX)

source_name: Femur

value: Femur


title: OE CUT&Tag

city: Shanghai

first: Wangsheng

last: Wang

state: Please Select

address: 845 Lingshan Rd.

country: China

institute: Shanghai Jiao Tong University

description: Library name: Sample 2

library_source: genomic

data_processing:
Raw reads were trimmed with Trim Galore software (version 0.4.5)
Trimmed reads were mapped to the human (Homo sapiens) hg38 genome obtained from UCSC genome browser database using Bowtie2 (version 2.5.4)
Duplicated reads were discarded by MarkDuplicates.jar program in Picard tools (version 1.119). Then, reads were sorted with SAMtools (version 1.2.0).
MACS2 (version 1.1) was used to call peak with the parameters set to ‘-f BAMPE --broad -q 0.05 --nolambda’.
TE regions were partitioned into ‘H3K9me3- enriched TEs’ and ‘Other TEs’ by robust k-means analysis with two clusters using R package pheatmap (version 1.0.12).Differential analysis of H3K9me3 signal enriched in TE region was performed by Manorm. (version 1.3.0).
Assembly: hg38
Supplementary files format and content: NC.bw, A9.bw
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: amnion

extract_protocol:
0.1 million cells were collected and sequentially incubated sequentially with ConA beads, primary antibody (anti-H3K9me3 antibody, #A-4036, EpiGentek) and secondary antibody (Goat anti-Rabbit IgG, Vazyme)
hyperactive PG-TN5/PA-TN5 Transposon was used for each CUT&Tag reaction, and CUT&Tag libraries were constructed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro protocol (Vazyme, #TD904).

value: amnion

tag: time

value: 72 hours

value: fibroblasts

tag: chip antiboy

value: H3K9me3 (Epigentek, A-4036)

value: transfection of nS100A9 overexpression vector


title: GP5d, HDACi-SETDB1i Rep1

value: Colon


title: NC CUT&Tag

description: Library name: Sample 1

value: transfection of control vector


title: Whole Heart, Ncx1 Heterozygous, e9.5

description:
Library name: het
10x Genomics

value: Embryonic heart

value: embyonic day 9.5


title: Sublibrary 8 of snRNA-seq library using “split-pool” combinatorial barcoding technology

city: Rochester

first: Duan

last: Liu

email: liud25@gmail.com, liu.duan@mayo.edu

address: 200 1st ST SW

department: MPET

institute: Mayo Clinic

description: Library name: sublibrary8

data_processing:
Raw sequencing data were processed by using the Parse Bioscience pipeline (v1.2.0) with default settings to align sequencing reads to the human genome (hg38). Sample loading information was included in the" WT 100K Sample Loading Table_V1.3.0.xlsm" file (attached).
Downstream integrated single cell data processing, such as doublet filtering, dimensionality reduction, differential expression analysis and clustering, were performed using Seurat (v.5.0.3)
Assembly: hg38
Supplementary files format and content: .mtx; Processed matrix data at single cell-level
Supplementary files format and content: .cvs; Summary of single nuclei information includes barcode, sample belongs, gene counts, transcript counts, nCount, nFeature, seurat cluser and cell type annotation.
Supplementary files format and content: .xlsm; Sample loading information for single-nuclei RNA barcoding. Required for processing the raw sequencing data using Parse Bioscience pipeline.

molecule: nuclear RNA

source_name: neural organoids

growth_protocol: Neural organoids were generated from human iPSCs using the STEMdiff™ Dorsal Forebrain Organoid Differentiation Kit, and were maintened by using the STEMdiff™ Neural Organoid Maintenance Kit, according to the manufacturer’s protocol.

extract_protocol:
Single nuclei were isolated from fresh organoids and were fixed by using the Parse Evercode Nuclei Fixation v2 kit according to the manufacturer’s protocol.
Single-nuclei sequencing libraries were prepared using the Parse Evercode WT v2 Kit according to the manufacturer’s protocol.

value: neural organoids


title: GP5d, DNMTi-SETDB1i  Rep3

value: Wild-type

value: DNMT SETDB1 co-inhibition


title: Sublibrary 7 of snRNA-seq library using “split-pool” combinatorial barcoding technology

description: Library name: sublibrary7


title: Femur, rep 1

description:
Library name: Femur_1
10 Genomics (3' GEX)

value: Female


title: Sublibrary 6 of snRNA-seq library using “split-pool” combinatorial barcoding technology

description: Library name: sublibrary6


title: GP5d, DNMTi-SETDB1i  Rep2


title: Sublibrary 4 of snRNA-seq library using “split-pool” combinatorial barcoding technology

description: Library name: sublibrary4


title: GP5d, DNMTi-SETDB1i  Rep1


title: Sublibrary 5 of snRNA-seq library using “split-pool” combinatorial barcoding technology

description: Library name: sublibrary5


title: Sublibrary 3 of snRNA-seq library using “split-pool” combinatorial barcoding technology

description: Library name: sublibrary3


title: Young untreated male 8

city: Fort Collins

first: Thomas

last: LaRocca

state: Colorado

address: 1582 Campus Delivery

department: Health and Exercise Science

institute: Colorado State University

description: Library name: YM8

data_processing:
Aligned to the mm10 genome using STAR
Ran TEtranscripts to get gene and TE expression
Assembly: mm10
Supplementary files format and content: Normalized counts to mean library size

source_name: Skeletal Muscle

extract_protocol:
RNA was isolated from muscle samples using the Zymo Direct-zol RNA miniprep kit (Zymo Research) according to the manufacturer’s protocol, including a DNase treatment to remove genomic DNA
Library preparation was performed using PolyA RNA selection kits (Tecan), followed by sequencing on an Illumina NovaSeq 6000 platform to generate > 40M 150 bp paired-end reads per sample.

treatment_protocol: The treatment group was provided with 3TC (National Drug Code: 33342-002-07, manufactured by Macleods Pharmaceuticals) in drinking water at 2 mg/mL (a human-equivalent therapeutic dose used in other studies) for 6 weeks

value: Skeletal Muscle

value: Untreated


title: GP5d, DMSO Rep6

value: Colon  adenocarcinoma

value: DMSO Control


title: Young untreated male 2

description: Library name: YM2


title: Sublibrary 1 of snRNA-seq library using “split-pool” combinatorial barcoding technology

description: Library name: sublibrary1


title: A431_ABE_sgR273H_36hpi2

description:
Library name: A_273_36_2
Column name in raw_counts.csv: A_273_36_2

value: Skin; Epidermis

value: Human Epidermoid Carcinoma

value: ABE + R273H-correcting-gRNA lentivirus


title: PHF1KO12_H3K36me3_IP

city: New York

first: Yicheng

last: Long

address: 413 East 69th Street

department: Biochemistry, CVRI

institute: Weill Cornell Medicine

data_processing:
For ChIP-seq, adapter sequences were trimmed from the read pairs using Cutadapt (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were aligned to the human reference genome (hg38) using BWA (MEM). Properly paired read alignments with mapping scores greater than 30 were used for downstream analysis. PCR duplicates were removed using Picard MarkDuplicates. Peak calling was performed with MACS2 with the options of ‘macs2 callpeak -g hs -f BAMPE --keep-dup all --bdg’. Bigwig files were generated using bedGraphToBigWig tool. Peak metaplots and heatmaps were generated on pooled replicates using deepTools.
Assembly: hg38, Gencode GENCODE basic gene annotation (v42)
Supplementary files format and content: For ChIP-seq, the .bw files are the bigwig Peak files for each ChIP IP samples generated using MACS2 followed by bedGraphToBigWig tool. The de-duplicated bam files are included for all input samples.

growth_protocol: hiPSCs were maintained on vitronectin in StemFlex medium supplemented with 25 U/mL penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
For ChIP-seq, hiPSCs at 70-80% confluency were collected by Accutase treatment and crosslinked with 1% formaldehyde in PBS at room temperature for 10 min. The crosslinking reaction was quenched by adding one volume of 1.25 M glycine to 10 volumes of PBS for 2 min. Cells were washed in ice-cold PBS and cell pellets stored at -80°C. Aliquots of 10 million cells were lysed in 1 mL ChIP lysis buffer (800 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% sodium deoxycholate, 1X protease inhibitor cocktail) on ice for 30 min. Lysates were sonicated in MilliTubes (Covaris, Cat#520135) with the Covaris S220 focused-ultrasonicator at 4°C for 10 min at a PIP of 140 W, a duty factor of 5%, and 200 cycles/burst. Lysate was cleared by centrifugation at 16,000xg for 10 min at 4°C, and supernatant was collected. For each IP, 1 mL chromatin dilution buffer (25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 1X protease inhibitor cocktail) together with 20 ng spike-in chromatin from Drosophila melanogaster S2 cells was added to the cleared lysate from 2.5-5.0 million cells. Chromatin samples were incubated with 2-4 μg of anti-CBX7 (4 μL), anti-FLAG (2 μL), anti-H2AK119ub (5 μL), anti-H3K27me3 (6 μL), anti-H3K36me3 (3 μL), anti-H3K4me3 (4 μL), anti-JARID2 (4 μL), anti-MTF2 (5 μL), anti-RING1B (7 μL), or anti-SUZ12 (4 μL) antibody at 4°C overnight. A spike-in antibody against the Drosophila-specific histone variant H2Av was added to all chromatin samples. Then, 25 μl of washed Pierce Protein A/G Magnetic Beads (Thermo Fisher, 88803) were added to the IP solution to incubate at room temperature for 2 h. Beads were washed twice with 1 mL of LSB buffer (20 mM Tris pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), HSB buffer (20 mM Tris pH 8.0, 2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1% Triton X-100), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% sodium deoxycholate, 1% Igepal), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Chromatin was then eluted by incubating the beads with 120 μl of elution buffer (100 mM sodium bicarbonate, 1% SDS) for 20 min at room temperature. Formaldehyde crosslinking was reversed by adding 5 μL of 5 M NaCl and incubating at 65°C for 3 h. Protein and RNA were removed by adding 14 μL of 1M Tris pH 8, 3 μL of 500 mM EDTA, 3 μL of proteinase K, and 1 μL of 1 mg/mL RNase A and incubating at 37°C for 1 h. DNA was extracted by phenol-chloroform-isoamyl extraction followed by ethanol precipitation. DNA samples were resuspended in 30 μl of 10 mM Tris pH 8.0 and quantified using a Qubit fluorometer (Invitrogen).
For ChIP-seq, between 2 ng and 100 ng of each sample was used for library preparation using the KAPA HyperPlus Kit according to the manufacturer’s instructions, except for skipping the fragmentation step. DNA libraries were pooled and sequenced on a NovaSeq 6000 or NovaSeq X Plus using a 150-cycle kit (paired end, 2 x 150 bp).

value: human pluripotent stem cells

value: PHF1 KO

value: CHIP_H3K36me3 antibody


title: PHF1KO11_H3K36me3_IP


title: Young untreated female 8

description: Library name: YF8


title: PHF1C8_H3K36me3_IP

value: PHF1-FLAG DNA-binding mutant


title: GP5d, DMSO Rep4

value: Colon


title: PHF1C7_H3K36me3_IP


title: Femur, rep 2

description:
Library name: Femur_6
10 Genomics (3' GEX)

value: Femur

value: Male

value: 2 months


title: Young untreated female 3

description: Library name: YF3


title: LNCAP_1F5 p53-KO, DNMTi-HDACi Rep3

description: LNCAP_1F5_p53_KO_all_treatments_gene_expression_counts.tsv

source_name: Prostate

value: Prostate

value: Prostate adenocarcinoma

value: DNMT HDAC co-inhibition


title: PHF1B6_H3K36me3_IP

value: PHF1-FLAG SUZ12-binding mutant


title: Young untreated female 1

description: Library name: YF2

value: Skeletal Muscle

value: Untreated


title: PHF1B3_H3K36me3_IP


title: LNCAP_1F5 p53-KO, DNMTi-HDACi Rep2


title: PHF1A3_H3K36me3_IP

value: PHF1-FLAG WT


title: PHF1A2_H3K36me3_IP


title: Old 3TC treated male 5

description: Library name: DMO5

value: 3TC treated


title: PHF19KO4_H3K36me3_IP

value: PHF19 KO


title: Sublibrary 2 of snRNA-seq library using “split-pool” combinatorial barcoding technology

description: Library name: sublibrary2

value: neural organoids


title: LNCAP_1F5 p53-KO, DNMTi-HDACi Rep1


title: LNCAP_1F5 p53-KO, SETDB1i Rep3

value: SETDB1 inhibition


title: PHF19C3_H3K36me3_IP

value: human pluripotent stem cells

value: PHF19-FLAG DNA-binding mutant

value: CHIP_H3K36me3 antibody


title: PHF19KO2_H3K36me3_IP


title: Young untreated male 1

description: Library name: YM1


title: PHF19C2_H3K36me3_IP


title: GP5d, DMSO Rep5

value: Colon

value: Colon  adenocarcinoma

value: Wild-type

value: DMSO Control


title: LNCAP_1F5 p53-KO, SETDB1i Rep2

value: Prostate

value: Prostate adenocarcinoma


title: LNCAP_1F5 p53-KO, SETDB1i Rep1


title: PHF19B1_H3K36me3_IP

value: PHF19-FLAG SUZ12-binding mutant


title: Old 3TC treated female 8

description: Library name: DFO8

value: Skeletal Muscle


title: PHF19A10_H3K36me3_IP

value: PHF19-FLAG WT


title: Old 3TC treated female 5

description: Library name: DFO5


title: PHF19KO4_FLAG_IP

value: CHIP_FLAG antibody


title: LNCAP_1F5 p53-KO, HDACi Rep3

value: HDAC inhibition


title: PHF19KO2_FLAG_IP

value: PHF19 KO


title: Old 3TC treated female 4

description: Library name: DFO4

value: 3TC treated


title: PHF19C3_FLAG_IP


title: PHF19C2_FLAG_IP


title: Old untreated male 6

description: Library name: CMO6

value: Untreated


title: LNCAP_1F5 p53-KO, HDACi Rep2


title: LNCAP_1F5 p53-KO, HDACi Rep1


title: Old 3TC treated male 2

description: Library name: DMO2


title: Old untreated male 3

description: Library name: CMO3


title: Old 3TC treated male 1

description: Library name: DMO1


title: PHF19B5_H3K36me3_IP

value: human pluripotent stem cells


title: LNCAP_1F5 p53-KO, DNMTi Rep3

value: DNMT  inhibition


title: LNCAP_1F5 p53-KO, DNMTi Rep2


title: PHF19A5_FLAG_IP


title: Old untreated female 3

description: Library name: CFO3


title: PHF19A5_H3K36me3_IP

value: CHIP_H3K36me3 antibody


title: LNCAP_1F5 p53-KO, DNMTi Rep1


title: PHF19A10_FLAG_IP


title: Old untreated female 2

description: Library name: CFO2


title: S12C2_H3K4me3_IP

value: SUZ12-FLAG PRC2.2- mutant

value: CHIP_H3K4me3 antibody


title: S12B1_H3K4me3_IP

value: SUZ12-FLAG PRC2.1- mutant


title: S12B2_H3K4me3_IP


title: S12C1_H3K4me3_IP


title: S12A2_H3K4me3_IP

value: SUZ12-FLAG WT


title: LNCAP_1F5 p53-KO, DMSO Rep3

value: Prostate

value: DMSO Control


title: S12A1_H3K4me3_IP


title: Old untreated female 1

description: Library name: CFO1


title: PHF19B5_FLAG_IP

value: PHF19-FLAG SUZ12-binding mutant


title: S12C1_CBX7_IP

value: CHIP_CBX7 antibody


title: Old untreated male 1

description: Library name: CMO1

value: Skeletal Muscle


title: PHF19B1_FLAG_IP

value: CHIP_FLAG antibody


title: S12B1_CBX7_IP


title: S12B2_CBX7_IP


title: LNCAP_1F5 p53-KO, DMSO Rep1

value: Prostate  adenocarcinoma


title: LPSKD3

city: Hefei

first: Minglu

last: Ji

address: China

institute: Anhui Medical University

description: Library name: Simble6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse renal tubular epithelial cells

growth_protocol: mTEC were magnitic sorted, and treated withDMEM/F12 culture medium supplemented with 5% Fetal bovine serum

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the LPS group and the LPSKD group, cells were transfected with negative control and siRNA respectively in 6 - well plate. Subsequently, the cells were stimulated with LPS (20 μg/ml) at a density of approximately 1×10^6 cells per dish and cultured for 24 hours.

value: Mouse renal tubular epithelial cells


title: S12A2_CBX7_IP


title: LPSKD2

description: Library name: Simble5


title: LNCAP-1F5, DNMTi-HDACi Rep3

description: LNCAP_1F5_all_treatments_gene_expression_counts.tsv

value: Wild-type

value: DNMT HDAC co-inhibition


title: S12A1_CBX7_IP

value: human pluripotent stem cells


title: LPSKD1

description: Library name: Simble4


title: S12C2_RING1B_IP

value: CHIP_RING1B antibody


title: LNCAP-1F5, DNMTi-HDACi Rep2


title: S12C1_RING1B_IP


title: LPS3

description: Library name: Simble3


title: S12B2_RING1B_IP


title: LNCAP-1F5, DNMTi-HDACi Rep1


title: LPS2

description: Library name: Simble2


title: S12A2_RING1B_IP


title: S12A1_RING1B_IP


title: LNCAP_1F5 p53-KO, DMSO Rep2

value: Prostate adenocarcinoma


title: S12C2_CBX7_IP

value: SUZ12-FLAG PRC2.2- mutant


title: LNCAP-1F5, SETDB1i Rep3

value: SETDB1 inhibition


title: LPS1

description: Library name: Simble1


title: S12C1_H2AK119Ub_IP

value: CHIP_H2AK119ub antibody


title: LNCAP-1F5, SETDB1i Rep2


title: S12B2_H2AK119Ub_IP

value: SUZ12-FLAG PRC2.1- mutant


title: LPSKD IP

description: Library name: Sample4

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The clean reads were mapped to the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks.
Called peaks were then annotated using R package ChIPseeker.
HOMER (http://homer.ucsd.edu/homer/download.html，v4.11.1) were used to find de novo and known motif.
ifferential peaks analysis was performed using R package  Diffbind for experimental design with replication.
Assembly: GRCm38
Supplementary files format and content: bigWig

source_name: epithelial cells

extract_protocol:
Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. Extract chromatin from cross-linked cells by adding Lysis Buffer
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X) and End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min.  And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15min. USER Enzyme was added to remove base U of adaptor at 37°C for 5min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads.

treatment_protocol: In the LPS group and the LPSKD group, cells were transfected with negative control and siRNA respectively in 15-cm large dishes. Subsequently, the cells were stimulated with LPS (20 μg/ml) at a density of approximately 1×10⁷ cells per dish and cultured for 24 hours.

value: epithelial cells

value: mTEC


title: LNCAP-1F5, SETDB1i Rep1

value: Prostate


title: S12C2_H2AK119Ub_IP


title: LPS IP

description: Library name: Sample3


title: S12B1_H2AK119Ub_IP


title: S12A2_H2AK119Ub_IP

value: SUZ12-FLAG WT


title: S12A1_H2AK119Ub_IP


title: LNCAP-1F5, HDACi Rep3

value: HDAC inhibition


title: LNCAP-1F5, HDACi Rep2


title: PHF19KO2_Input

value: PHF19 KO


title: LPSKD input

description: Library name: Sample2


title: PHF19KO4_Input


title: PHF19C3_Input

value: PHF19-FLAG DNA-binding mutant


title: LNCAP-1F5, HDACi Rep1

value: Prostate  adenocarcinoma


title: S12B1_RING1B_IP


title: PHF19C2_Input


title: LGAS6826

city: St. Louis

first: Steven

last: Funk

address: 660 S. Euclud Ave

institute: Washington University

data_processing:
CellRanger
Assembly: mm10
Supplementary files format and content: Normalized, scaled, curated, and annotated CellRanger count matrix in .rds format

source_name: murine kidney cortex

value: murine kidney cortex

value: 2 years

value: high fat diet


title: PHF19B5_Input

value: human pluripotent stem cells

value: PHF19-FLAG SUZ12-binding mutant


title: LGAS6435


title: LNCAP-1F5, DNMTi Rep3

value: Wild-type

value: DNMT  inhibition


title: PHF19B1_Input


title: PHF19A5_Input

value: PHF19-FLAG WT


title: LNCAP-1F5, DNMTi Rep2


title: LGAS7707


title: LNCAP-1F5, DNMTi Rep1


title: PHF19KO2_SUZ12_IP

value: CHIP_SUZ12 antibody


title: PHF19A10_Input


title: PHF19KO4_SUZ12_IP


title: PHF19C3_SUZ12_IP


title: LGAS6436

value: floxed control


title: LNCAP-1F5, DMSO Rep3

value: DMSO Control


title: PHF19B5_SUZ12_IP


title: PHF19B1_SUZ12_IP


title: LGAS6393


title: LGAS7705


title: PHF19A10_SUZ12_IP


title: PHF19C2_SUZ12_IP


title: LNCAP-1F5, DMSO Rep1

value: Prostate


title: LPS input

description: Library name: Sample1

value: epithelial cells

value: mTEC


title: PHF19A5_SUZ12_IP


title: PHF1KO12_FLAG_IP

value: PHF1 KO

value: CHIP_FLAG antibody


title: E17.5

city: Beijing

first: PAN

last: YUWEI

state: Beijing

address: 2 West Yuanmingyuan Road

department: College of biological sciences

institute: China Agriculture University

data_processing:
Raw FASTQ reads were mapped to the mouse mm10 reference genome (GRCm38.93.dna/GRCm38.93.gtf) using Cell Ranger Version 7.2.0. Digitized count matrices were pre-processed and doublets/multiplets were simulated using DoubletFinder (version 2.0.4) with default parameters. Singlet cells were kept and used for downstream query analyses if and only if they met the following collective quality control metrics: (a) 500 < genes/cell < 7000; (b) cells contained no more than 15% of mitochondrial gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small intestine

growth_protocol: Mice were kept on a 12-hour light-dark cycle. The morning with visible vaginal plug were considered as embryonic day 0.5 (E0.5)

extract_protocol:
Small intestines were excised from E15.5, E17.5 embryos or P7 mice, cut longitudinally in ice-cold PBS to remove the contents. The epithelium was separated from the mesenchyme by gentle shaking, followed by 70 μm cell sieve filtration.  The remaining mesenchymal flakes were prepared as described above for the separation of MCs from the P14 intestine to obtain a single-cell suspension. The resulting fractions of both mesenchymal and epithelial cells were combined and filtered through a 40 μm cell sieve, then incubated with antibodies on ice for 15 minutes in PBS containing 2 % FBS. The primary antibodies employed were anti-CD31-APC (eBiosciences, 17-0311-82, 1: 500), anti-CD326 (Epcam)-PeCy7 (eBiosciences, 25-9326-42, 1: 500) and anti-CD45-APC (eBiosciences, 17-0451-82, 1: 500). Fixable Viability Dye eFluor™ 450 (eBiosciences, 65-0863-14, 1: 1000) was applied to identify dead cells. After several washes in ice-cold PBS, cells sorting was performed on BD FACS Arial 3.0 machin. The 450-/Epcam+ and 450-/Epcam-/CD31-/CD45- cells were sorted into EP tubes in single-cell mode by FACS.
Chromium Single Cell 3ʹ v2 libraries were sequenced with a Novaseq 6000 sequencer (Illumina), with the following sequencing parameters: read 1, 150 cycles; i7 index, 8 cycles and read 2, 150 cycles.

treatment_protocol: To obtain the intestine from E15.5, E17.5 embryos and P7mice, uterus was first dissected from pregnant mice at indicated time point. the whole small intestine was then isolate and subjected to single cells.

value: Small intestine

value: wild type

value: untreated


title: P7


title: PHF1C8_FLAG_IP

value: PHF1-FLAG DNA-binding mutant


title: PHF1C7_FLAG_IP

value: human pluripotent stem cells


title: sgCtrl_2

city: Dongguan

first: Zhou

last: Junzhi

state: Guangdong

address: Xincheng Road 1#, Songshan Lake

institute: Guangdong Medicine University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by fastp v0.20.1 for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v2.7.7a with default parameters.Annotation file of Ensembl release 76 (GRCh38) transcriptome gff file was provided to STAR as gene model.
raw reads count aligned to each gene were calculated by FeatureCount v2.0.0
Assembly: hg38
Supplementary files format and content: xls files; Matrix table with raw gene counts for each gene by every sample
Supplementary files format and content: xls files; include FPKM values for each gene by everySample

extract_protocol:
RNA was isolated from 1-2x10^6 cells stored in TRIzol reagent following manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: sgL1 and sgCtrl

value: breast cancer cell line

value: sgCtrl


title: E15.5


title: sgCtrl_1


title: PHF1B3_FLAG_IP

value: PHF1-FLAG SUZ12-binding mutant


title: PHF1KO11_FLAG_IP


title: PHF1A3_FLAG_IP

value: PHF1-FLAG WT


title: P14_4

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp（0.12.2）
Trimmed sequence reads were mapped toGRCm39 using hisat2（2.0.5）
Read count extraction and normalization were performed using featureCounts（1.5.0-p3）
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: small intestinal mesenchyme

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: The whole intestines obtained from E17.5 or P14 wild-type mice were subjected to EDTA to remove the epithelium. Then, the remaining part of the small intestine was isolate and subjected to RNA extraction

value: small intestinal mesenchyme


title: LNCAP-1F5, DMSO Rep2

value: Prostate  adenocarcinoma

value: Wild-type


title: sgL1_6


title: PHF1A2_FLAG_IP


title: P14_3


title: sgL1_5


title: PHF19KO4_H3K27me3_IP

value: PHF19 KO

value: CHIP_H3K27me3 antibody


title: P14_2


title: sgL1_4


title: PHF19C3_H3K27me3_IP

value: PHF19-FLAG DNA-binding mutant


title: PHF19C2_H3K27me3_IP


title: E17_4


title: sgCtrl_3


title: PHF19B1_H3K27me3_IP

value: PHF19-FLAG SUZ12-binding mutant


title: PHF19KO2_H3K27me3_IP


title: PHF19A10_H3K27me3_IP

value: PHF19-FLAG WT


title: P14_1


title: sgL1_3


title: sgL1_2


title: PHF1B6_FLAG_IP

value: CHIP_FLAG antibody


title: E17_3

value: wild type


title: PHF1KO12_H3K27me3_IP

value: PHF1 KO


title: PHF1KO11_H3K27me3_IP


title: E17_2


title: PHF19A5_H3K27me3_IP


title: sgL1_1


title: PHF1C8_H3K27me3_IP

value: PHF1-FLAG DNA-binding mutant


title: H3K27me3_TMD8_IRF4_2

city: Boston

first: Geoffrey

middle: M

last: Nelson

state: MA

address: 45 Shattuck St

department: BCMP

institute: Harvard Medical School

data_processing:
E.coli-derived reads were first removed and the remainder were mapped to the hg38 genome build with bowtie v1.2.2.
Signal was quantified at differentially accessible ATAC-seq peaks via make_heatmap (available at https://github.com/AdelmanLab/NIH_scripts) and metagenes were created within R v4.2.1.
Enriched gene ontologies at these ATAC-seq peaks with an H3K4me3 fold change >= 1.5 were determined using clusterProfiler v4.4.4.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
For each sample, nuclei from three technical triplicates replicates were extracted by incubating cells on ice for 10 min in Nuclei Extraction buffer (NE: 20 mM HEPES–KOH, pH 7.9; 10 mM KCl; 0.1% Triton X-100; 20% Glycerol; 0.5mM spermidine; 1x complete protease inhibitor [Roche # 11836170001]), collecting by centrifugation (600 g, 3 min, 4ºC), discarding the supernatant, and resuspending at [100 µl / 500K nuclei] sample in NE buffer. For each target 500K nuclei were immobilized onto Concanavalin-A beads (EpiCypher #21-1401) and incubated overnight (4ºC with gentle rocking) with 0.5 µg of antibody (IgG, H3K4me3, H3K4me1, H3K27me3, and H3K27Ac.
CUT&TAG enriched DNA was purified using the Monarch DNA Cleanup kit (New England Biolabs #T1030S), and 10 ng used to prepare sequencing libraries with the Ultra II DNA Library Prep kit (New England Biolabs #E7645S). Libraries were sequenced to 150 base pairs on an Illumina Novaseq using pair-end mode by Novogene (Sacramento, CA).

tag: antibody

value: Diffuse large B-cell lymphoma

value: IRF4 siRNA


title: PHF1B6_H3K27me3_IP

value: human pluripotent stem cells


title: E17_1


title: cKO 4

source_name: Total small intestine

treatment_protocol: Uterus was first dissected from pregnant mice at E15.5. After quick genotyping, the whole small intestine was isolate and subjected to RNA extraction

value: Total small intestine

value: unprocessed E15.5 embryo

value: Slmapfl/fl; Derom-Cre

value: Dermo-Cre drived Slmap knockout


title: PHF1C7_H3K27me3_IP


title: PHF19B5_H3K27me3_IP


title: H3K4me1_TMD8_IRF4_2


title: cKO 3


title: PHF1A2_H3K27me3_IP

value: PHF1-FLAG WT


title: H3K4me3_TMD8_IRF4_2


title: H3K27me3_TMD8_IRF4_1


title: S12C1_CMd15_2

data_processing:
For RNA-seq, adapter sequences were trimmed from the read pairs using Cutadapt (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were aligned to the human reference genome (hg38) using STAR with GENCODE basic gene annotation (v42). Read counts were calculated as transcripts per million (TPM) using uniquely mapped reads counted using featureCounts in a strand-specific way. Differential expression analysis between the mutant and WT lines was performed by modeling read counts in a generalized linear model accounting for cell lines. Fold change and p-values were calculated using DESeq2, in which two-sided Wald tests for regression coefficients of interest were performed.
Assembly: hg38, Gencode GENCODE basic gene annotation (v42)
Supplementary files format and content: For RNA-seq, the fCounts files contains the raw read number counts with number of reads mapped to gene bodies (defined by the featureCounts tool using the GENCODE v42 annotation)

extract_protocol:
total RNA was extracted using TRIzol and purified using the Direct-zol RNA MiniPrep kit according to the manufacturer’s instructions. RNA concentration was measured with a Qubit fluorometer (Invitrogen), and RNA quality was determined using a TapeStation (Agilent Technologies).
RNA-seq libraries were prepared from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase according to the manufacturer’s instructions. Libraries were pooled and sequenced on a NovaSeq 6000 or NovaSeq X Plus using a 150-cycle kit (paired end, 2 x 150 bp).

value: SUZ12-FLAG PRC2.2- mutant

value: RNA-seq, day 15 cardiomyocyte


title: S12C2_CMd15_1


title: S12C1_CMd15_1


title: cKO 2


title: S12B2_CMd15_2

value: SUZ12-FLAG PRC2.1- mutant


title: cKO 1


title: H3K27ac_TMD8_IRF4_1


title: Ctrl 4

value: Slmapfl/fl

value: Control


title: H3K4me1_TMD8_IRF4_1


title: PHF1B3_H3K27me3_IP

value: PHF1-FLAG SUZ12-binding mutant

value: CHIP_H3K27me3 antibody


title: H3K27ac_TMD8_IRF4_2


title: Ctrl 3


title: S12B1_CMd15_1


title: S12B2_CMd15_1


title: S12B1_CMd15_2


title: S12A2_CMd15_2

value: SUZ12-FLAG WT


title: PHF1A3_H3K27me3_IP


title: Ctrl 2


title: H3K4me3_TMD8_IRF4_1


title: S12A1_CMd15_2


title: H3K27me3_TMD8_Ctr_2

value: control


title: S12A2_CMd15_1


title: S12A1_CMd15_1


title: M2KO1_CMd15_1

value: MTF2 KO


title: Ctrl 1


title: M2KO1_CMd15_2


title: M2D2_CMd15_2

value: MTF2-FLAG H3K36me3-binding mutant


title: H3K4me1_TMD8_Ctr_2

value: Diffuse large B-cell lymphoma


title: T1_TAZko_181310

city: Cologen

first: Lioba

last: Ester

address: Joseph Stelzmann Str. 26

institute: University of Cologne

data_processing:
CellRanger
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: isolated nuclei from isolated glomeruli

extract_protocol:
Mice at 4 weeks of age were euthanized by cervical dislocation. Kidneys were perfused with magnetic beads to isolate glomeruli, as described before.72 In brief, kidneys were removed and perfused with magnetic beads (Dynabeads m-450 Epoxy, ThermoFisher Scientific). Subsequently, kidneys were minced and placed in a digestion solution (1 mg/mL Collagenase Type II (Worthington), 1 mg/mL Protease (Sigma-Aldrich, P5147) and 0.1 U/mL DNase I (AppliChem) in HBSS) and then purified by sieving and a magnet. Nuclei from glomeruli were isolated using Nuclei Isolation Kit: Nuclei EZ Prep (Sigma, NUC101-1KT). Briefly, cells were lysed with EZ buffer supplemented with 1xPIM (Roche) and 0.1% RNAse inhibitor (NEB, M0314L) and single nuclei were obtained using a 30 µm strainer.
Single nuclei suspensions in 1XPBS containing 0,04% BSA (700-1200 nuclei/µL concentration) were processed with the Chromium Next GEM Single Cell 3ʹ Kit v3.1 with dual indices, aiming for a target of 10,000 cells/sample. Cells and the appropriate master mix were loaded on a Chromium Next GEM Chip G and run on the Chromium Controller to generate Gel Bead-In-EMulsions (GEMs) according to the manufacturers’ protocol. After incubation, the GEMs were broken and the pooled fractions were recovered. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient amounts for library construction. Library preparation was performed, including End Repair, A-tailing, Adaptor Ligation and PCR. The final libraries were quantified (Qubit) and validated (Tape Station), pooled and the pool was then quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing instrument with 29+89bp read length.

value: isolated nuclei from isolated glomeruli

value: TAZpKO


title: T2_TAZko_181311


title: H3K4me3_TMD8_Ctr_2


title: M2D1_CMd15_2

value: human pluripotent stem cells


title: M2D1_CMd15_1


title: YE2_YAPko_early_181309

value: YAPpKO


title: M2C2_CMd15_2

value: MTF2-FLAG DNA-binding mutant


title: M2C2_CMd15_1


title: M2C1_CMd15_2


title: H3K4me1_TMD8_Ctr_1


title: M2B2_CMd15_2

value: MTF2-FLAG SUZ12-binding mutant


title: YE1_YAPko_early_181308


title: YL2_YAPko_late_181307


title: H3K27me3_TMD8_Ctr_1


title: H3K27ac_TMD8_Ctr_1


title: M2B2_CMd15_1

value: RNA-seq, day 15 cardiomyocyte


title: YL1_YAPko_late_181306


title: H3K4me3_TMD8_Ctr_1


title: M2C1_CMd15_1


title: M2B1_CMd15_1


title: H3K27ac_TMD8_Ctr_2


title: wt2_wildtype_181305

value: wildtype


title: M2A2_CMd15_2

value: MTF2-FLAG WT


title: PHF1KO12_Input

value: PHF1 KO


title: M2D2_CMd15_1


title: M2A2_CMd15_1


title: M2A1_CMd15_2


title: PHF1KO11_Input


title: M2A1_CMd15_1


title: M2KO1_CMd8_2

value: RNA-seq, day 8 cardiac progenitor


title: PHF1C8_Input

value: PHF1-FLAG DNA-binding mutant


title: D2-mdx

city: Montreal

first: Natasha

middle: C

last: Chang

state: Québec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

description: 10X genomics

data_processing:
Reads were processed with Cell Ranger (version 3.0.1)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hindlimb muscle

extract_protocol:
Lower hindlimbs of two mice were dissected, and dissociated with a collagenase B / dispase II solution with the gentleMACS Octo Dissociator with Heaters. Lysates were then filtered through a 100 μm filter and cells pelleted by centrifugation. Cell pellets were resuspended in red blood cell lysis buffer and washed with FACS buffer (5% FBS, 1 mM EDTA in PBS). After incubation with antibodies, MuSCs were sorted based on negative lineage markers (Cd11b−, Sca1−, Cd45−, Cd31−) and positive selection markers α7-integrin and VCAM1. Cell sorting was performed using a BD FACSAriaTM III (BD Biosciences).
Cell were captured on the 10X Genomics Chromium platform and subjected to single cell transcriptomic sequencing. Following satellite cell isolation, the single-cell RNA-sequencing libraries were prepared using the 10X Genomics NextGen scRNA 3’ V3.1 (10X Genomics, Pleasanton, CA) with approximately 10,000 satellite cells from each strain. Libraries were then sequenced with an Illumina NovaSeq6000 sequencer (Illumina, San Diego, CA).

value: hindlimb muscle

value: Muscle stem cell

value: 14 weeks


title: M2KO1_CMd8_1

value: MTF2 KO


title: DBA

description: 10X genomics

value: 13 weeks


title: S12C2_CMd15_2

value: SUZ12-FLAG PRC2.2- mutant


title: M2D2_CMd8_2

value: MTF2-FLAG H3K36me3-binding mutant


title: M2B1_CMd15_2

value: human pluripotent stem cells


title: M2D1_CMd8_2


title: M2C2_CMd8_2


title: M2D1_CMd8_1


title: PHF1B6_Input

value: PHF1-FLAG SUZ12-binding mutant


title: PHF1C7_Input


title: M2D2_CMd8_1


title: B10

description: 10X genomics

value: 15 weeks


title: NC_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by fastp v0.20.1 for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v2.7.7a with default parameters.Annotation file of Ensembl release 76 (GRCh38) transcriptome gff file was provided to STAR as gene model.
raw reads count aligned to each gene were calculated by FeatureCount v2.0.0
Assembly: mm10
Supplementary files format and content: xls files; Matrix table with raw gene counts for each gene by every sample
Supplementary files format and content: xls files; include FPKM values for each gene by everySample

source_name: mouse embryonic fibroblast cell (MEF)

treatment_protocol: Ufl1-ko and control

value: mouse embryonic fibroblast cell (MEF)

value: NC


title: PHF1B3_Input


title: M2C1_CMd8_2

value: MTF2-FLAG DNA-binding mutant


title: NC_2


title: PHF1A3_Input

value: PHF1-FLAG WT


title: wt1_wildtype_181304

value: isolated nuclei from isolated glomeruli

value: wildtype


title: PHF1A2_Input


title: M2C1_CMd8_1

value: RNA-seq, day 8 cardiac progenitor


title: M2B2_CMd8_2

value: MTF2-FLAG SUZ12-binding mutant


title: M2B2_CMd8_1


title: NC_1


title: M2B1_CMd8_2


title: PHF1KO12_SUZ12_IP

value: PHF1 KO

value: CHIP_FLAG antibody


title: KO_3


title: M2B1_CMd8_1


title: M2A2_CMd8_2

value: MTF2-FLAG WT


title: PHF1KO11_SUZ12_IP


title: KO_2


title: M2A2_CMd8_1


title: mdx

description: 10X genomics

value: hindlimb muscle

value: Muscle stem cell

value: 11 weeks


title: M2C2_CMd8_1

value: human pluripotent stem cells


title: M2A1_CMd8_2


title: M2A1_CMd8_1


title: KO_1


title: M2KO1_CMd1_1

value: MTF2 KO

value: RNA-seq, day 1 mesoderm


title: PHF1B6_SUZ12_IP

value: PHF1-FLAG SUZ12-binding mutant


title: BMDMs, RANKL+Vitamin D and K, rep_3

city: Guangzhou

first: Yang

last: Zhao

address: No. 253 Industrial Avenue

institute: Zhujiang hospital of southern medical university

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: raw counts and FPKM values for each Sample

source_name: primary bone marrow derived macrophages

growth_protocol: Primary bone marrow derived macrophages were maitained in α-MEM medium containing 10% fetal bovine serum, 1% Penicillin-Streptomycin, and 20 ng/ml macrophage colony-stimulating factor (M-CSF).

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: For osteoclastogenesis, cells were incubated with M-CSF (20 ng/mL) and RANKL (100 ng/mL) in the presence or absence of vitamins D (1000 nM) and vitamin K (20 μM) or vehicle for 48 hours.

value: primary bone marrow derived macrophages

value: RANKL+Vitamin D and K


title: BMDMs, RANKL+Vitamin D and K, rep_2


title: PHF1C8_SUZ12_IP

value: PHF1-FLAG DNA-binding mutant


title: M2D1_CMd1_2

value: MTF2-FLAG H3K36me3-binding mutant


title: M2D2_CMd1_1


title: M2KO1_CMd1_2


title: M2D1_CMd1_1


title: PHF1C7_SUZ12_IP


title: BMDMs, RANKL+Vitamin D and K, rep_1


title: M2C2_CMd1_2

value: MTF2-FLAG DNA-binding mutant


title: PHF1B3_SUZ12_IP


title: PHF1A3_SUZ12_IP

value: PHF1-FLAG WT


title: BMDMs, RANKL, rep_3

value: RANKL


title: M2C1_CMd1_2


title: M2C2_CMd1_1


title: BMDMs, RANKL, rep_2


title: M2C1_CMd1_1


title: M2B2_CMd1_2

value: MTF2-FLAG SUZ12-binding mutant


title: S12C2_H3K36me3_IP

value: SUZ12-FLAG PRC2.2- mutant

value: CHIP_H3K36me3 antibody


title: BMDMs, RANKL, rep_1


title: M2B1_CMd1_2


title: S12C1_H3K36me3_IP


title: M2B1_CMd1_1


title: BMDMs, PBS, rep_3

value: PBS


title: M2A2_CMd1_2

value: MTF2-FLAG WT


title: S12B2_H3K36me3_IP

value: SUZ12-FLAG PRC2.1- mutant


title: M2A2_CMd1_1

value: human pluripotent stem cells


title: BMDMs, PBS, rep_2


title: M2A1_CMd1_2


title: S12B1_H3K36me3_IP


title: BMDMs, PBS, rep_1


title: S12A2_H3K36me3_IP

value: SUZ12-FLAG WT


title: Zea mays B73, primary and seminal root tips (0-1mm), 2 h water treatment, RNA-seq cellular transcription data, biorep 4

city: Austin

first: Lorenzo

last: Concia

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

description: Library name: Z.mays_B73_Primary+SeminalRoot_0-1mm_2h_water_cellular_BR4

data_processing:
Adapter trimming (trimmomatic-0.36 PE -phred33 -validatePairs ILLUMINACLIP:/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:5 TRAILING:5 MINLEN:20)
Contaminants filtration (sortmerna -ref contaminants.fasta -reads $SAMPLE.input.fw.fastq -reads $SAMPLE.input.rv.fastq --out2 True --kvdb $SAMPLE.kvdb --readb $SAMPLE.readb --idx-dir sortmerna.idx-dir --zip-out Yes --fastx true --blast '1 cigar qcov qstrand' --paired_in true --other $SAMPLE.processed)
Read mapping (STAR --genomeDir STAR_2.7.10b.GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterMultimapNmax 1 --readFilesIn $SAMPLE.fw.fastq $SAMPLE.rv.fastq --outFileNamePrefix $SAMPLE.mapped)
Alignments filtering (samtools view -bh -f 0x2 $SAMPLE.bam)
Alignments deduplication (umi_tools dedup -I $SAMPLE.bam -S $SAMPLE.deduplicated.bam --umi-separator=":" --paired )
Genomic coverage (bamCoverage --binSize 50 --normalizeUsing RPGC --effectiveGenomeSize 2209328549 --outFileFormat bigwig --filterRNAstrand forward --bam $SAMPLE.deduplicated.bam --outFileName $SAMPLE.deduplicated.fw.bw )
Read count (htseq-count -f bam --order=pos --stranded=reverse -a 0 -t exon -i gene --nonunique=fraction --mode=union --counts_output=$SAMPLE.counts.tsv $SAMPLE.deduplicated.bam Zm-B73-REFERENCE-NAM-5.0_genomic.with_scaffolds.GENE.coding+non_coding+pseudo.EXONS.gff)
Assembly: GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.fasta
Supplementary files format and content: bigwig files with read density coverage
Supplementary files format and content: tables with raw read counts

organism: Zea mays

source_name: Terminal 1 mm of primary and seminal roots

growth_protocol: B73 seeds were surface sterilized with 1% sodium hypochlorite; 0.05% Tween 20 for 15 min at room temperature, rinsed 4X with 1-2 volumes of autoclaved dH2O and  imbibed overnight in autoclaved dH2O with stirring and aeration. The next day the imbibed seeds were surface sterilized again but this time with 0.5% sodium hypochlorite; 0.05% Tween 20 for 15 min at room temperature, rinsed 4X with 1-2 volumes of autoclaved dH2O and germinated in sterilized 6.5" by 10" glass casserole dishes lined with paper towels dampened with sterile water. The dishes were covered with a transparent lid, and the seeds were germinated at 28 °C for 3 days under continuous light (Feit Electric OneSync LED light system) adjusted to a 3000 K soft white color temperature and 300–400 lx..

extract_protocol:
The terminal 1mm root tip tissue tissue was ground with mortar and pestle in liquid nitrogen and RNA was extracted using TRIzol from Invitrogen #15596026. DNA was removed from the RNA using the Invitrogen Turbo DNA Free kit. Ribosomal RNA was removed from the DNase-treated samples using the Qiagen QIAseq FastSelect-rRNA removal kit for plants (Qiagen # 334315). QIA FasSelect was designed to be incorporated into the library preparation kit protocols. Please see the library construction protocol  for details.
RNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library kit for Illumina (NEB # E7760S) in combination with NEBNext Multiplex Oligos for Illumina, Unique Dual Index UMI Adaptors RNA set 1 (NEB # E7416S) and the Qiagen QIAseq FastSelect plant ribosomal RNA removal kit. Immediately prior to the library construction, we followed the QIAseq FastSelect-rRNA removal kit instructions as it pertained to making libraries using the NEBNext Ultra II Directional RNA Library kit for Illumina. Per the QIAseq FastSelect guidelines, we used a mass input of 1 ug of total cellular RNA in a total volume of 4 ul and mixed it with 4 ul of the NEBNext First strand Synthesis reaction buffer, 1ul of the NEB random primers and 1 ul of the QIAseq FAstSelect rRNA plant reagent. We then followed the QIAseq FastSelect guidlelines for intact RNA (RIN > 7) (See Table 7 of the Qiagen kit manual) for the simulatneous fragmentation (15 min at 94 °C) of RNAs and hybridization of the QIAseq FastSelect reagent to RNAs. We then immediately proceeded to the “First Sstrand cDNA Ssynthesis Reaction” (Step 4.2) of the NEBNext Ultra II Directional RNA Library Prep instruction manual.

treatment_protocol: The B73 seedlings were incubated 2 hours in milli-q water at 28 C with gentle swirling (~65 rpm) to aerate prior to root tip dissection

tag: cultivar

value: 3-days after germination

value: seedlings incubated 2 h in water prior to root tip dissection


title: 5neg

city: Portland

first: Timothy

middle: J

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

data_processing:
Reads were aligned to the mouse reference genome using STAR version 2.7.9a
Total read counts for annotated genes were determined using the featureCounts program.
Mapping quality was evaluated using RSeQC and MultiQC. Samples from two mice had greater than 20% of reads distributed among ‘Other_intergenic’ features, suggesting high genomic DNA contamination, so these mice were excluded from mouse transcriptome analysis and used only for ribosomal sequence analysis.
Reads that were unmapped to mouse genome were mined for ribosomal RNA (rRNA) sequences using Ribodetector (Deng et al., 2022), using the ‘–ensure rrna’ setting to limit hits to high-confidence assignments.
High-confidence rRNA reads from Ribodetector were subsequently classified with stringent cutoffs (threshold = 70%) using IdTaxa (Murali et al., 2018) against the Genome Taxonomy Database (GTDB) release 207.
Assembly: GRCm39
Supplementary files format and content: count matrix output from featureCounts program

extract_protocol:
RNA was isolated from captures using ZymoResearch Quick-RNA FFPE Miniprep, cat#R1008
mRNA sequencing libraries were prepared with the SMART-Seq Stranded Kit (Takara Bio, cat#634442) using ribosomal RNA depletion

value: Small intestine

value: intestinal

value: WT


title: PHF1A2_SUZ12_IP

value: CHIP_FLAG antibody


title: S12A1_H3K36me3_IP


title: Zea mays B73, primary and seminal root tips (0-1mm), 2 h water treatment, RNA-seq cellular transcription data, biorep 1

description: Library name: Z.mays_B73_Primary+SeminalRoot_0-1mm_2h_water_cellular_BR1

value: Terminal 1 mm of primary and seminal roots


title: M2A1_CMd1_1

value: RNA-seq, day 1 mesoderm


title: 4neg


title: M2B2_CMd1_1


title: S12C2_H3K27me3_IP

value: CHIP_H3K27me3 antibody


title: IRKO_IP_3

first: Wenqiang

last: Chen

address: 1 Joslin Pl, Room 610

department: Joslin Diabetes Center

description: Library name: Sample 5

data_processing:
Sequencing reads were filtered and stored in the FASTQ format prior to data analysis. The clean reads were aligned to mouse reference genome (Mus_musculus) by Bowtie2 on a standard reference genome version GCF_000001635.26_GRCm38.p6).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: FASTQ
Supplementary files format and content: CSV file includes FPKM values for each sample

organism: Mus

source_name: whole brain

extract_protocol:
ribosome-bound mRNA are isolated with a Direct-zol RNA Microprep Kit (R2062, Zymo)
Library sequencing was performed on the DNBSEQ platform with an average generation about 4.50G Gb bases per sample.

value: whole brain

value: Microglia

value: KO


title: IRKO_IP_2

description: Library name: Sample 4


title: 5pos


title: IRKO_IP_1

description: Library name: Sample 3


title: 4pos


title: M2D2_CMd1_2

value: MTF2-FLAG H3K36me3-binding mutant


title: MG_IP_2

description: Library name: Sample 2

value: Ctr


title: S12B2_H3K27me3_IP

value: SUZ12-FLAG PRC2.1- mutant


title: MG_IP_1

description: Library name: Sample 1


title: 3neg


title: RNA-seq of plankponic PAO1-3

first: Jiayu

last: Gu

address: Xingangxi street

institute: SCSIO

description: Library name: Sample 12

data_processing:
The libraries were sequenced on a NovaSeq 6000 S4 (Illumina). The obtained raw data were evaluated with FastQC (v0.10.1), and contamination and adapter sequences were removed with Cutadapt (version 1.9.1).Cleaned dataweremapped to the MPAO1/PAO1 genome with bowtie2 (v2.2.6), and the expression profiling was calculated with Htseq (V 0.6.1). The differential gene expression analysis was performed using EdgeR54 (R-3.1.2) with each subline genomes.
Assembly: PAO1 genome(GenBank ID: AE004091) and MPAO1 (GenBank ID:PRJNA438597)
Supplementary files format and content: raw counts and FPKM for each Sample

organism: Pseudomonas aeruginosa

growth_protocol: The assay was performed at room temperature with modified M9 medium containing 47.8mM Na2HPO4, 22mM KH2PO4, 6.8mM NH4Cl, 18.7mM NaCl, 100 μM CaCl2, 2mM MgSO4 and 0.1% glucose. For inoculation, 1ml fresh overnight cultures were injected into the inlet of medical silicone catheters (3mm inner diameter × 400mm length) (Forbest Manufacturing Corporation, Shenzhen, China), taking care to avoid any bubbles. Inoculated catheters were left static for 1 h before flow initiation to allow colonization on the inner catheter surface. Then, flow was initiated with a peristaltic pump with a flow rate of 0.1 ml min−1 for each channel. At indicated time points, phages were collected from the effluents and biofilm cells inside the catheter were collected by cutting the catheter open. Fresh M9 medium was supplied daily and total assay runtime lasted for 6 days depending on the readout.

extract_protocol:
Overnight PAO1 and MPAO1 planktonic cultures in M9 medium (OD600 ~ 3) were collected by centrifugation at 12,000 g for 30 s at 4 °C.The biofilm cells on the inner surface of themedical catheter were collected at day 6 by cutting 5mm at the middle of the catheter, and cells were collected by centrifugation. Total RNA was isolated and quality control was performed with Agilent RNA ScreenTape (Lot: 0201937-152). rRNA was removed with the Ribo-off rRNA Depletion Kit (Bacteria) (Vazyme, # N407-C1).
To prepare cDNA libraries, 1 μg total RNA was used for cDNA synthesis amplification (11 cycles) using VAHTS Total RNA-seq (Bacteria) Library Prep Kit for Illumina (Lot:7E582A1) according to the manufacturer’s instructions.

tag: sample group

value: plankponic PAO1


title: S12B1_H3K27me3_IP

data_processing:
For ChIP-seq, adapter sequences were trimmed from the read pairs using Cutadapt (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were aligned to the human reference genome (hg38) using BWA (MEM). Properly paired read alignments with mapping scores greater than 30 were used for downstream analysis. PCR duplicates were removed using Picard MarkDuplicates. Peak calling was performed with MACS2 with the options of ‘macs2 callpeak -g hs -f BAMPE --keep-dup all --bdg’. Bigwig files were generated using bedGraphToBigWig tool. Peak metaplots and heatmaps were generated on pooled replicates using deepTools.
Assembly: hg38, Gencode GENCODE basic gene annotation (v42)
Supplementary files format and content: For ChIP-seq, the .bw files are the bigwig Peak files for each ChIP IP samples generated using MACS2 followed by bedGraphToBigWig tool. The de-duplicated bam files are included for all input samples.

value: human pluripotent stem cells


title: RNA-seq of plankponic PAO1-2

description: Library name: Sample 11


title: Zea mays B73, primary and seminal root tips (0-1mm), 2 h water treatment, RNA-seq cellular transcription data, biorep 2

description: Library name: Z.mays_B73_Primary+SeminalRoot_0-1mm_2h_water_cellular_BR2

tag: tissue

value: 3-days after germination


title: Zea mays B73, primary and seminal root tips (0-1mm), 2 h water treatment, RNA-seq cellular transcription data, biorep 3

description: Library name: Z.mays_B73_Primary+SeminalRoot_0-1mm_2h_water_cellular_BR3

value: seedlings incubated 2 h in water prior to root tip dissection


title: 3pos

value: Small intestine


title: RNA-seq of plankponic PAO1-1

description: Library name: Sample 10

tag: cell line


title: IRKO_IP_4

description: Library name: Sample 6

tag: cell type


title: S12A2_H3K27me3_IP

tag: genotype

value: SUZ12-FLAG WT


title: RNA-seq of biofilm PAO1-3

description: Library name: Sample 9

value: biofilm PAO1


title: RNA-seq of biofilm PAO1-2

description: Library name: Sample 8


title: 2pos

value: intestinal

value: WT

tag: treatment


title: S12A1_H3K27me3_IP


title: S12C1_H3K27me3_IP

value: SUZ12-FLAG PRC2.2- mutant


title: RNA-seq of biofilm PAO1-1

description: Library name: Sample 7


title: 1neg


title: RNA-seq of plankponic MPAO1-2

description: Library name: Sample 5

value: plankponic MPAO1


title: RNA-seq of plankponic MPAO1-1

description: Library name: Sample 4


title: RNA-seq of plankponic MPAO1-3

description: Library name: Sample 6


title: RNA-seq of biofilm MPAO1-3

description: Library name: Sample 3

value: biofilm MPAO1


title: S12B2_Input


title: RNA-seq of biofilm MPAO1-2

description: Library name: Sample 2


title: RNA-seq of biofilm MPAO1-1

description: Library name: Sample 1


title: Quad_PHx_DAY7_5

first: Teresa

last: Zimmers

address: 2730 S Moody Ave

department: CDCB

institute: OHSU

description: RNAs cleaned up, DNaseI treated

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p –countReadPairs -Q 10”.
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.40.2) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: The excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts

source_name: Bulk quadriceps

growth_protocol: 12 to 14 weeks old male mice were used

extract_protocol:
Total RNAs were extracted from nitrogen frozen bulk livers or quadriceps tissues using QIAzol lysis reagent (Qiagen, #79306). RNA cleanup and DNAse treatment were performed using the RNeasy cleanup kit (Qiagen, #74204) and DNaseI
KAPA totalRNA

treatment_protocol: Animals were subjected to sham surgery or 70% partial hepatectomy. On day3 post-surgery, animals were euthanized, then livers and quadriceps were collected to extract total RNA for subsequent RNA0sequencing experiment. 3 sham control animals and 5 partial hepatectomy animals were used.

value: Bulk quadriceps

value: Day3 post 70% hepatectomy


title: S12B1_Input


title: OE, D4, F+ rep 2

first: Daniel

last: Garry

state: Minnesota

address: 2231 6th Street SE, Suite 4-156

department: Lillehei Heart Institute

institute: University of Minnesota

description: Library name: iEtv2_Dox_D4_Flk1Pos_2_S48

data_processing:
Adapter trimming was performed using Trim_Galore, followed by alignment of raw reads to the Mus musculus genome (UCSC version mm10) using Bowtie2 (v2.2.4). Peak calling was carried out with MACS2 (v1.4.2) using the 'callpeak' function with the options --shift 100 and --extsize 200.
Assembly: Mus musculus reference genome mm10 (GRCm38)
Supplementary files format and content: ATAC-seq peaks and coverage were provided as BED and BigWig files, respectively.

source_name: Embryoid bodies

extract_protocol:
EBs from different time points (i.e., D2, D3, and D4 for WT EBs, and D3 and D4 for OE EBs) were collected and dissociated in a 0.25% trypsin solution at 37 °C for 3 minutes. Trypsin was then inactivated using culture medium containing 10% FBS. Collected cells were centrifuged at 500g for 5 minutes and washed once with ice-cold PBS. Single cells from differentiated EBs at D3 and D4 (with and without doxycycline) were sorted using FACS for FLK1+ and PDGFRa+ as described above. The ATAC reaction was performed with nuclei extracted from 50,000 cells using Tn5 transposase (Illumina). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.
The process below closely mirrors the methods outlined in Buenrostro, Wu ,Chang, et. al (2015) with only minor changes, namely that 1) we use our own custom indices for barcoding and 2) a final double-sided bead size- selection is performed on the final pool prior to sequencing. In brief, purified and tagmented DNA is incorporated with UMGC created Nextera-based indices and undergo 5 cycles of PCR. An aliquot of this product is then taken for qPCR to assess how many more PCR cycles are needed. After interpretation of the qPCR data, the remainder of the sample is amplified another 5-10 cycles. Final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen). Libraries are then pooled equal-mass based on the ratio of library between 200-1000 bp and undergo a double-sided bead size-selection (1.0x, 0.85x). The final pool is validated for size distribution using capillary electrophoresis and quantified using both fluorimetry (Qubit) and via Q-PCR to assess library functionality. The pool is normalized to the appropriate sequencing concentration based on qPCR results.

value: Embryoid bodies

value: iHA-Etv2 (inducible HA-tagged Etv2) ESCs

value: Embryonic stem cell-Embryoid body (ES-EB)

value: OE

value: Doxycycline


title: Quad_PHx_DAY7_4

description: RNAs cleaned up, DNaseI treated


title: OE, D4, -/- rep 2

description: Library name: iEtv2_Dox_D4_DoubleNeg_2_S46


title: 2neg


title: Quad_PHx_DAY7_3

description: RNAs cleaned up, DNaseI treated


title: S12A2_Input

extract_protocol:
For ChIP-seq, hiPSCs at 70-80% confluency were collected by Accutase treatment and crosslinked with 1% formaldehyde in PBS at room temperature for 10 min. The crosslinking reaction was quenched by adding one volume of 1.25 M glycine to 10 volumes of PBS for 2 min. Cells were washed in ice-cold PBS and cell pellets stored at -80°C. Aliquots of 10 million cells were lysed in 1 mL ChIP lysis buffer (800 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% sodium deoxycholate, 1X protease inhibitor cocktail) on ice for 30 min. Lysates were sonicated in MilliTubes (Covaris, Cat#520135) with the Covaris S220 focused-ultrasonicator at 4°C for 10 min at a PIP of 140 W, a duty factor of 5%, and 200 cycles/burst. Lysate was cleared by centrifugation at 16,000xg for 10 min at 4°C, and supernatant was collected. For each IP, 1 mL chromatin dilution buffer (25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 1X protease inhibitor cocktail) together with 20 ng spike-in chromatin from Drosophila melanogaster S2 cells was added to the cleared lysate from 2.5-5.0 million cells. Chromatin samples were incubated with 2-4 μg of anti-CBX7 (4 μL), anti-FLAG (2 μL), anti-H2AK119ub (5 μL), anti-H3K27me3 (6 μL), anti-H3K36me3 (3 μL), anti-H3K4me3 (4 μL), anti-JARID2 (4 μL), anti-MTF2 (5 μL), anti-RING1B (7 μL), or anti-SUZ12 (4 μL) antibody at 4°C overnight. A spike-in antibody against the Drosophila-specific histone variant H2Av was added to all chromatin samples. Then, 25 μl of washed Pierce Protein A/G Magnetic Beads (Thermo Fisher, 88803) were added to the IP solution to incubate at room temperature for 2 h. Beads were washed twice with 1 mL of LSB buffer (20 mM Tris pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), HSB buffer (20 mM Tris pH 8.0, 2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1% Triton X-100), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% sodium deoxycholate, 1% Igepal), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Chromatin was then eluted by incubating the beads with 120 μl of elution buffer (100 mM sodium bicarbonate, 1% SDS) for 20 min at room temperature. Formaldehyde crosslinking was reversed by adding 5 μL of 5 M NaCl and incubating at 65°C for 3 h. Protein and RNA were removed by adding 14 μL of 1M Tris pH 8, 3 μL of 500 mM EDTA, 3 μL of proteinase K, and 1 μL of 1 mg/mL RNase A and incubating at 37°C for 1 h. DNA was extracted by phenol-chloroform-isoamyl extraction followed by ethanol precipitation. DNA samples were resuspended in 30 μl of 10 mM Tris pH 8.0 and quantified using a Qubit fluorometer (Invitrogen).
For ChIP-seq, between 2 ng and 100 ng of each sample was used for library preparation using the KAPA HyperPlus Kit according to the manufacturer’s instructions, except for skipping the fragmentation step. DNA libraries were pooled and sequenced on a NovaSeq 6000 or NovaSeq X Plus using a 150-cycle kit (paired end, 2 x 150 bp).

value: human pluripotent stem cells


title: OE, D4, -/- rep 1

description: Library name: iEtv2_Dox_D4_DoubleNeg_1_S45


title: OE, D3, F+ rep 2

description: Library name: iEtv2_Dox_D3_Flk1Pos_2_S18


title: S12A1_Input


title: OE, D3, -/- rep 2

description: Library name: iEtv2_Dox_D3_DoubleNeg_2_S16


title: Quad_PHx_DAY7_2

description: RNAs cleaned up, DNaseI treated


title: S12C2_MTF2_IP

value: CHIP_MTF2 antibody


title: Quad_PHx_DAY7_1

description: RNAs cleaned up, DNaseI treated


title: S12C1_Input


title: OE, D3, -/- rep1

description: Library name: iEtv2_Dox_D3_DoubleNeg_1_S15


title: S12C2_Input


title: Quad_PHx_DAY3_5

description: RNAs cleaned up, DNaseI treated


title: 1pos

value: Small intestine


title: OE, D3, F+ rep 1

description: Library name: iEtv2_Dox_D3_Flk1Pos_1_S17


title: Control, D4, P+ rep 2

description: Library name: iEtv2_D4_PDGFRaPos_2_March15_S32

value: Control


title: S12B2_MTF2_IP

value: SUZ12-FLAG PRC2.1- mutant


title: Control, D4, P+ rep 1

description: Library name: iEtv2_D4_PDGFRaPos_1_March15_S31


title: Control, D4, +/+ rep 2

description: Library name: iEtv2_D4_DoublePos_2_March15_S34


title: OE, D4, F+ rep 1

description: Library name: iEtv2_Dox_D4_Flk1Pos_1_S47


title: Quad_PHx_DAY3_4

description: RNAs cleaned up, DNaseI treated


title: Control, D4, +/+ rep 1

description: Library name: iEtv2_D4_DoublePos_1_March15_S33


title: S12B1_MTF2_IP


title: Control, D4, F+ rep 1

description: Library name: iEtv2_D4_Flk1Pos_1_March15_S29


title: Control, D4, -/- rep 2

description: Library name: iEtv2_D4_DoubleNeg_2_S24


title: S12A2_MTF2_IP

value: SUZ12-FLAG WT


title: Control, D4, -/- rep 1

description: Library name: iEtv2_D4_DoubleNeg_1_S23


title: Control, D3, P+ rep 2

description: Library name: iEtv2_D3_PDGFRaPos_2_S12


title: Quad_PHx_DAY3_3

description: RNAs cleaned up, DNaseI treated


title: Quad_PHx_DAY3_2

description: RNAs cleaned up, DNaseI treated


title: Control, D4, F+ rep 2

description: Library name: iEtv2_D4_Flk1Pos_2_March15_S30


title: Control, D3, -/- rep 1

description: Library name: iEtv2_D3_DoubleNeg_1_S5


title: Quad_PHx_DAY1_5

description: RNAs cleaned up, DNaseI treated


title: Quad_PHx_DAY3_1

description: RNAs cleaned up, DNaseI treated


title: Quad_PHx_DAY1_4

description: RNAs cleaned up, DNaseI treated


title: S12A1_MTF2_IP


title: Control, D3, -/- rep 2

description: Library name: iEtv2_D3_DoubleNeg_2_S6


title: Control, D3, P+ rep 1

description: Library name: iEtv2_D3_PDGFRaPos_1_S11


title: Control, D3, F+ rep 2

description: Library name: iEtv2_D3_Flk1Pos_2_Feb28_S10


title: Quad_PHx_DAY1_3

description: RNAs cleaned up, DNaseI treated


title: S12C1_MTF2_IP


title: Control, D3, +/+ rep 1

description: Library name: iEtv2_D3_DoublePos_1_S13


title: Control, D2, -/- rep 2

description: Library name: iEtv2_D2_DoubleNeg_2_S2


title: S12B1_FLAG_IP

value: CHIP_FLAG antibody


title: S12C1_FLAG_IP

value: SUZ12-FLAG PRC2.2- mutant


title: Quad_PHx_DAY1_2

description: RNAs cleaned up, DNaseI treated


title: S12C2_FLAG_IP


title: Control, D3, F+ rep 1

description: Library name: iEtv2_D3_Flk1Pos_1_Feb28_S9


title: Control, D3, +/+ rep 2

description: Library name: iEtv2_D3_DoublePos_2_S14


title: ESC2i-rep3

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Library name: Sample06

data_processing:
Counts generated using Salmon with GENCODE vM24
Assembly: mm10
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: cell line

growth_protocol: The ESCs were cultured on 0.1% gelatin-coated dishes at 37°C in a 5% CO2 atmosphere. DMEM/F12-N2 medium was prepared by adding 1 ml of N2 (Gibco) 100× stock solution to 100 ml of DMEM/F12. For Neurobasal/B27 medium, 2 ml of B27 (Gibco) and 2 mM L-glutamine were added to 100 ml of Neurobasal medium. N2B27 medium was prepared by mixing DMEM/F12-N2 medium with Neurobasal/B27 medium at a 1:1 ratio, followed by the addition of 0.1 mM β-mercaptoethanol (Sigma). For ESC-2i, 3 µM CHIR-99021 (Selleckchem), 1 µM PD0325901 (Selleckchem) were added to the N2B27 medium (2i). B6D2F1 ESCs were derived and expanded under 2i conditions in N2B27 medium, on feeders. For ESC-BRD0705/PD03, 8 µM BRD0705 (Cayman Chemical) and 1 µM PD0325901 (Selleckchem) were added to the N2B27 medium. B6D2F1-ESC were derived and expanded  in BRD0705/PD03  N2B27 medium, on feeders.

extract_protocol:
ESCs cultured in different medium were trypsinized and dissociated into the single-cell. Total RNA was extracted using the GeneJET RNA purification kit. For RNA-seq library preparation, 1 g total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with RiboZero (Illumina).
For RNA-seq library preparation, 1 g total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with RiboZero (Illumina).

value: ESCs

value: WT


title: Quad_PHx_DAY1_1

description: RNAs cleaned up, DNaseI treated

value: Bulk quadriceps


title: S12A1_FLAG_IP


title: Control, D2, -/- rep 1

description: Library name: iEtv2_D2_DoubleNeg_1_S1


title: ESC2i-rep2

description: Library name: Sample05


title: Naive CD4 T cells from FAKfl/fl mice were transduced with RV-Cre and stimulated in vitro into Th17 cells.

city: Seoul

first: Gap Ryol

last: Lee

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

country: South Korea

institute: Sogang University

description: Library name: FakKO Th17

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: spleen

growth_protocol: Control or FAK KO naive CD4 T cells were stimulated with plate-bound anti-CD3ε (10 μg/ml) and soluble anti-CD28 (5 μg/ml) antibodies and cultured for 3 days under Th17-polarizing conditions.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: For Th17-polarization, mouse recombinant IL-6 (50 ng/ml), human recombinant TGFβ1 (1 ng/ml), mouse recombinant TNF-alpha (1 ng/ml), mouse recombinant IL-1beta (2 ng/ml), anti-mouse IFNgamma (5 μg/ml), and anti-mouse IL-4 (5 μg/ml) were treated.

value: spleen

value: primary cell

value: T lymphocyte

value: FAK-deficient

value: Th17 polarizing conditions


title: Naive CD4 T cells from FAKfl/fl mice were transduced with control RV and stimulated in vitro into Th17 cells.

description: Library name: Control Th17


title: S12A2_FLAG_IP

first: Yicheng

last: Long

address: 413 East 69th Street


title: Quad_Control_3

description: RNAs cleaned up, DNaseI treated

value: Day3 post 70% hepatectomy


title: S12B2_FLAG_IP

value: human pluripotent stem cells


title: M2E2_H3K36me3_IP

value: MTF2-FLAG H3K36me3-binding mutant #2

value: CHIP_H3K36me3 antibody


title: ESC-BRD0705/PD03-rep3

description: Library name: Sample03


title: Quad_Control_2

description: RNAs cleaned up, DNaseI treated


title: Quad_Control_1

description: RNAs cleaned up, DNaseI treated


title: CHD7_T720A.homo_female_03

city: Houston

first: Maria

middle: Elisa

last: Ruiz Echartea

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Library name: CHD7_T720A_homo_female_03

data_processing:
Paired-end reads were trimmed using TrimGalore
Trimmed fastq files were mapped using STAR
Features were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample

source_name: heart

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen), following the manufacturer's protocol.
RNA libraries were prepared using the QIAseq Stranded Total RNA library Kit (Qiagen) with an input of 100 ng RNA.  Ribosomal RNA depletion was performed using the QIAseq FastSelect HMR kit (Qiagen).  RNA was then fragmented, reverse-transcribed into cDNA, and ligated with Illumina sequencing adaptors.  Size selection for libraries was performed using SPRIselect beads (Beckman Coulter), and library purity was assessed on the Tapestation 4200 (Agilent) using the High Sensitivity DNA 1000 tape, targeting a size of approximately 300 bp.

value: heart

tag: strain

value: CHD7 T720A homozygous

value: female


title: mMA9_MLL1n-sgRNA_rep4

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

description: Library name: mMA9-Cas9_RNA_Kuhn_MLL1_sg2-sg3_7d_REP4_200712_GGTAGC_S24

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the mouse genome (mm10) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final deduped .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Assembly: mm10
Supplementary files format and content: .tdf files encoding coverage data for visualization in genome browser for all samples
Supplementary files format and content: .txt file containing regularized normalized gene counts (rlog counts)
Supplementary files format and content: .txt file containing differentially expressed genes of knockouts vs control (DeSeq2 output)

source_name: hematopoietic

growth_protocol: mouse AML cell line grown in RPMI+20%FBS+5%Pen/Strep (Gibco) supplemented with SCF (25ng/ml), IL3 (25ng/ml) and IL6 (25ng/ml) at 5% CO2 and 37°C

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen) accoding to the manufacturer's instructions
Poly-A tail selection and library preparation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

treatment_protocol: Cells were stably transduced with Cas9 and selected with blasticidine for 7 days. Subsequently, sgRNAs targeting Kat6a, Kat6b, Kat7, Mll1 or non-targeting control (LUC) were lentivirally transduced and selected for with puromycin. Cells were harvested and analyzed 7d after viral transduction with the sgRNAs

value: hematopoietic

value: mouse myeloid leukemia (AML)


title: M2D2_H3K36me3_IP

institute: Weill Cornell Medicine

value: MTF2-FLAG H3K36me3-binding mutant


title: ESC-BRD0705/PD03-rep1

description: Library name: Sample01

value: ESCs

value: WT


title: Liver_PHx_DAY7_5

description: RNAs cleaned up, DNaseI treated

source_name: Bulk Liver

value: Bulk Liver


title: ESC-BRD0705/PD03-rep2

description: Library name: Sample02


title: M2E1_H3K36me3_IP


title: mMA9_MLL1n-sgRNA_rep3

description: Library name: mMA9-Cas9_RNA_Kuhn_MLL1_sg2-sg3_7d_REP3_200712_GAGTGG_S23


title: M2C2_H3K36me3_IP

value: MTF2-FLAG DNA-binding mutant


title: CHD7_T720A.het_female_03

description: Library name: CHD7_T720A_het_female_03

value: CHD7 T720A heterozygous


title: Liver_PHx_DAY7_4

description: RNAs cleaned up, DNaseI treated


title: M2D1_H3K36me3_IP


title: CHD7_T720A.homo_female_01

description: Library name: CHD7_T720A_homo_female_01


title: ESC2i-rep1

description: Library name: Sample04


title: mMA9_MLL1n-sgRNA_rep2

description: Library name: mMA9-Cas9_RNA_Kuhn_MLL1_sg2-sg3_7d_REP2_200712_CGTACG_S22


title: CHD7_T720A.het_female_02

description: Library name: CHD7_T720A_het_female_02


title: Liver_PHx_DAY7_3

description: RNAs cleaned up, DNaseI treated


title: M2C1_H3K36me3_IP


title: Liver_PHx_DAY7_2

description: RNAs cleaned up, DNaseI treated


title: mMA9_MLL1n-sgRNA_rep1

description: Library name: mMA9-Cas9_RNA_Kuhn_MLL1_sg2-sg3_7d_REP1_200712_GTTTCG_S21


title: Liver_PHx_DAY7_1

description: RNAs cleaned up, DNaseI treated


title: mMA9_LUC-sgRNA_rep4

description: Library name: mMA9-Cas9_RNA_FP_sgLUC_7d_REP4_200712_CAGGCG_S28

value: non-targeting control


title: M2B1_H3K36me3_IP

value: MTF2-FLAG SUZ12-binding mutant


title: CHD7_T720A.homo_female_02

description: Library name: CHD7_T720A_homo_female_02


title: CHD7_WT_female_03

description: Library name: CHD7_WT_female_03


title: Liver_PHx_DAY3_5

description: RNAs cleaned up, DNaseI treated

value: Day3 post 70% hepatectomy


title: mMA9_LUC-sgRNA_rep3

description: Library name: mMA9-Cas9_RNA_FP_sgLUC_7d_REP3_200712_CACTCA_S27


title: M2A2_H3K36me3_IP

value: human pluripotent stem cells

value: MTF2-FLAG WT


title: CHD7_WT_female_02

description: Library name: CHD7_WT_female_02


title: Liver_PHx_DAY3_4

description: RNAs cleaned up, DNaseI treated


title: Liver_PHx_DAY3_3

description: RNAs cleaned up, DNaseI treated


title: M2A1_H3K36me3_IP

value: CHIP_H3K36me3 antibody


title: mMA9_LUC-sgRNA_rep2

description: Library name: mMA9-Cas9_RNA_FP_sgLUC_7d_REP2_200712_CACGAT_S26


title: M2KO_H3K36me3_2_IP

value: MTF2 KO


title: CHD7_T720A.homo_male_02

description: Library name: CHD7_T720A_homo_male_02

value: heart

value: CHD7 T720A homozygous

value: male


title: CHD7_T720A.homo_male_03

description: Library name: CHD7_T720A_homo_male_03


title: Liver_PHx_DAY3_2

description: RNAs cleaned up, DNaseI treated


title: M2B2_H3K36me3_IP


title: mMA9_Kat6b-sgRNA_rep3

description: Library name: mMA9-Cas9_RNA_FP_Kat6b_sg1-sg2_7d_REP3_200712_GGCTAC_S11

value: hematopoietic

value: mouse myeloid leukemia (AML)


title: M2A_H3K36me3_2_IP


title: mMA9_Kat6b-sgRNA_rep4

description: Library name: mMA9-Cas9_RNA_FP_Kat6b_sg1-sg2_7d_REP4_200712_CTTGTA_S12


title: CHD7_WT_female_01

description: Library name: CHD7_WT_female_01

value: female


title: mMA9_Kat6b-sgRNA_rep2

description: Library name: mMA9-Cas9_RNA_FP_Kat6b_sg1-sg2_7d_REP2_200712_TAGCTT_S10


title: M2A_H3K36me3_1_IP