title: CHD7_T720A.homo_male_01

description: Library name: CHD7_T720A_homo_male_01


title: CHD7_T720A.het_male_03

status: Public on Jun 16 2025

type: SRA

city: Houston

first: Maria

middle: Elisa

last: Ruiz Echartea

state: Texas

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: Library name: CHD7_T720A_het_male_03

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: heart

tag: strain

tag: genotype

value: CHD7 T720A heterozygous

tag: Sex

value: male


title: M2KO_H3K36me3_1_IP

city: New York

first: Yicheng

last: Long

state: New York

address: 413 East 69th Street

department: Biochemistry, CVRI

institute: Weill Cornell Medicine

library_source: genomic

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.

molecule: genomic DNA

organism: Homo sapiens

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).

tag: cell line

tag: cell type

value: human pluripotent stem cells

value: MTF2 KO

tag: treatment

value: CHIP_H3K36me3 antibody


title: Liver_PHx_DAY3_1

city: Portland

first: Teresa

last: Zimmers

state: OR

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 Liver

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 Liver

value: Day3 post 70% hepatectomy


title: CHD7_T720A.het_female_01

description: Library name: CHD7_T720A_het_female_01

value: female


title: Liver_PHx_DAY1_4

description: RNAs cleaned up, DNaseI treated


title: mMA9_Kat6b-sgRNA_rep1

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description: Library name: mMA9-Cas9_RNA_FP_Kat6b_sg1-sg2_7d_REP1_200712_GATCAG_S9

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)

molecule: polyA RNA

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_H3K27me3_IP

value: MTF2-FLAG H3K36me3-binding mutant

value: CHIP_H3K27me3 antibody


title: CHD7_T720A.het_male_02

description: Library name: CHD7_T720A_het_male_02


title: Liver_PHx_DAY1_3

description: RNAs cleaned up, DNaseI treated


title: mMA9_Kat6a-sgRNA_rep4

description: Library name: mMA9-Cas9_RNA_FP_Kat6a_sg1-sg2_7d_REP4_200712_ACTTGA_S8


title: M2D1_H3K27me3_IP


title: mMA9_LUC-sgRNA_rep1

description: Library name: mMA9-Cas9_RNA_FP_sgLUC_7d_REP1_200712_CACCGG_S25

value: non-targeting control


title: CHD7_T720A.het_male_01

description: Library name: CHD7_T720A_het_male_01


title: mMA9_Kat6a-sgRNA_rep3

description: Library name: mMA9-Cas9_RNA_FP_Kat6a_sg1-sg2_7d_REP3_200712_CAGATC_S7


title: Liver_PHx_DAY1_2

description: RNAs cleaned up, DNaseI treated


title: Liver_PHx_DAY1_5

description: RNAs cleaned up, DNaseI treated


title: CHD7_WT_male_03

description: Library name: CHD7_WT_male_03

value: WT


title: M2C2_H3K27me3_IP

value: MTF2-FLAG DNA-binding mutant


title: mMA9_Kat6a-sgRNA_rep2

description: Library name: mMA9-Cas9_RNA_FP_Kat6a_sg1-sg2_7d_REP2_200712_GCCAAT_S6


title: Liver_PHx_DAY1_1

description: RNAs cleaned up, DNaseI treated


title: M2C1_H3K27me3_IP


title: M2B2_H3K27me3_IP

value: MTF2-FLAG SUZ12-binding mutant


title: Liver_Control_2

description: RNAs cleaned up, DNaseI treated


title: Liver_Control_3

description: RNAs cleaned up, DNaseI treated


title: CHD7_WT_male_01

description: Library name: CHD7_WT_male_01

value: heart


title: M2B1_H3K27me3_IP


title: M2A2_H3K27me3_IP

value: MTF2-FLAG WT


title: D13.s4E.A3S1.ASS04

city: Bristol

first: Lindsay

last: Nicholson

address: Biomedical Sciences Building

department: Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

description: Library name: Sample23

data_processing:
usegalaxy.eu
adapter removal and FastQC
RNA STAR (2.7.8a, using mm10) to align reads. Gene expression  quantified by featureCounts
DGE analysis in R (4.3.1) using voom normalisation in limma(3.56.2) and GSEA using fgsea(1.26.0)
Assembly: mm10
Supplementary files format and content: tab delimited text file with raw counts for each sample

source_name: Spleen

extract_protocol:
Eyes or spleens were were dissected and single cell suspensions produced by mechanical disruption and filtering through a 70 micron filter. Sorted cells were acquired using a 4-laser Fortessa X-20 flow cytometer and data analysis completed using FlowJo software.
Samples were prepared and sequenced using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following the manurfacturer's protocol.

treatment_protocol: Induction of experimental autoimmune uveoretinitis by transfer of pathogenic cells obtained from mice immunised with IRBP 629-643 (EAHYARPEIAQRARA).

value: Spleen

value: CD4 T cell


title: mMA9_Kat7-sgRNA_rep3

description: Library name: mMA9-Cas9_RNA_FP_Hbo1_sg1-sg2_7d_REP3_200712_GTGAAA_S19


title: mMA9_Kat7-sgRNA_rep4

description: Library name: mMA9-Cas9_RNA_FP_Hbo1_sg1-sg2_7d_REP4_200712_GTGGCC_S20


title: D13.s4E.A3S2.ASS04

description: Library name: Sample24


title: mMA9_Kat7-sgRNA_rep2

description: Library name: mMA9-Cas9_RNA_FP_Hbo1_sg1-sg2_7d_REP2_200712_GTCCGC_S18


title: D13.s4E.A2S2.ASS04

description: Library name: Sample22


title: Whole Heart, Cilia Mut, e9.5, rep1

city: New Haven

first: Kathryn

last: Berg

state: Connecticut

address: 333 Cedar St.

department: Genetics

institute: Yale University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned with Cell Ranger (v3.0.1).
Assembly: mm10
Supplementary files format and content: Matrix, Barcodes, and Features files from Cell Ranger(v3.0.1)

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 age

value: embyonic day 9.5


title: D13.s4E.A2S1.ASS04

description: Library name: Sample21


title: mMA9_Kat7-sgRNA_rep1

description: Library name: mMA9-Cas9_RNA_FP_Hbo1_sg1-sg2_7d_REP1_200712_GTAGAG_S17


title: Whole Heart, Cilia Het, e9.5, rep2

description: 10x Genomics


title: M2A1_H3K27me3_IP

value: human pluripotent stem cells


title: CHD7_WT_male_02

description: Library name: CHD7_WT_male_02

value: male


title: C455, T cell lymphoma, biol rep 4

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

data_processing:
Cutadapt was used to remove unwanted sequences (e.g., adapters, poly-A tails, etc.) and low-quality reads on the FASTQ files provided by the sequencing facility. FASTQC6 and MULTIQC7 were both used to check the quality of reads. The STAR aligner tool8 was used to map the reads to the GRCm39 mouse reference genome, obtained from ENSEMBL (https://www.ensembl.org/Mus_musculus/Info/Index). Htseq-count was used to obtain gene counts. Finally, we performed a naive pre-filtering step to remove low count genes by only keeping those transcripts with an average count across all samples bigger than one. We used the R/Bioconductor package DESeq2 to perform differential gene expression (DE) analysis of the Htseq transcript counts. Genes with an adjusted P-value (p adj) < 0.05 and absolute log2 fold change (logFC)≥1 were considered significantly differentially expressed. Finally, read counts were normalized by the DESeq2 normalization method of variance stabilizing transformation (VST), to be used primarily for visualization. Figures for this analysis were generated using DESeq2.
Assembly: mm39
Supplementary files format and content: Processed data files are in txt format and contain raw read counts

source_name: ALK+ Hdac1KO, thymic lymphoma

extract_protocol:
Snap frozen tumor tissue was lyzed in homogenization buffer. Nuclei were pelleted by centrifugation (5 min, 4°C, 350 rcf). The supernatant was mixed with Trizol and chloroform, vortexed and centrifuged (15 min, 4°C, 21,000 rcf).  The aqueous layer was mixed with an equal volume of 100% ethanol and passed through a QIAgen RNeasy column. The QIAgen RNeasy protocol was followed and samples were eluted in 27 µL Elution Buffer. 3 µL of 10 x TurboTM DNase Buffer and 1 µL of TurboTM Dnase enzyme was added and the samples were incubated (30 min, 37°C). 70 µL of RNase-free water and 350 µL of QIAgen RLT Buffer were added. 250 µL of 100% ethanol was added and the samples were applied to the column and washed 2 x with RPE. Samples were eluted in RNase-free water.
Quantseq, https://www.lexogen.com/quantseq-family/

value: ALK+ Hdac1KO, thymic lymphoma

value: NPM-ALK+ CRE+ HDAC1delta/delta


title: D13.s4E.B1S2.ASS03

description: Library name: Sample20


title: M2D2_Input


title: Liver_Control_1

description: RNAs cleaned up, DNaseI treated

value: Bulk Liver

value: Day3 post 70% hepatectomy


title: C424, T cell lymphoma, biol rep 3


title: M2D1_Input

value: MTF2-FLAG H3K36me3-binding mutant


title: D13.s4E.A2S.ASS03

description: Library name: Sample19


title: M2C2_Input


title: B966, T cell lymphoma, biol rep 2


title: Whole Heart, Cilia Het, e9.5, rep1

description: 10x Genomics


title: M2C1_Input


title: M2B2_Input


title: Whole Heart, Cilia Mut, e9.5, rep2

description: 10x Genomics


title: D13.s4T.A3S2.ASS04

description: Library name: Sample17


title: B 840, T cell lymphoma, biol rep 1


title: Whole Heart, Wildtype, e9.5, rep1

description: 10x Genomics


title: Whole Heart, Wildtype, e9.5, rep2

description: 10x Genomics


title: D13.s4E.A1S.ASS03

description: Library name: Sample18


title: Whole Heart, Wildtype, e9.5, rep3

description: 10x Genomics


title: C453, T cell lymphoma, biol rep 4

source_name: ALK+, thymic lymphoma

value: ALK+, thymic lymphoma

value: NPM-ALK+ HDAC1 fl/fl


title: D13.s4T.A3S1.ASS04

description: Library name: Sample16


title: M2B1_Input


title: Aged_run3

city: Stanford

first: Yu Xin

last: Wang

state: California

address: 269 Campus Dr

institute: Stanford University School of Medicine

description: mRNA

data_processing:
Cell and UMI barcodes were extracted using Drop-seq_tools-1.12.
Hisat 2 for alignment.
Cells were filtered for mitochondrial RNA counts (<5%) and total gene counts (200<n<2000) and genes were filtered for expression in at least 3 cells.
Gene expression were log(x+1) normalized, regressed for total UMI counts and mitochondrial RNA content; then expression was scaled to max of 10.
Sequencing runs were integrated using HarmonyPy. Myogenic cells were subset after clustering.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: h5ad (AnnData)

source_name: Skeletal muscle cells

growth_protocol: Skeletal muscle cells were isolated from uninjured (contralateral) and injured (days 3, 6, 10 post injury) TA and GA muscle of young and aged mice. Myogenic cells were enriched by magnetic bead activated cell sorting by negative depletion of lineage (CD45, CD11b, CD31, Sca1) and positive selection for a7-integrin+ cells.

extract_protocol:
DropSeq using a dolomite single-cell RNA-seq chip 2 (Dolomite, cat: 3200583) was used with 311 units/ul for the beads and cells.
KAPA HiFi HotStart ReadyMix (KAPA Biosytems, cat: KK2602) and tagmentation by the Nextera XT DNA Library Preparation Kit (Illumina, cat: FC-131-1096), DASH depletion of mitochondrial DNA.

treatment_protocol: Skeletal muscle injuries were induced by intramuscular injection of 20uL of notexin.

tag: age

value: aged (18-24 month)

value: Skeletal muscle cells

value: mix of uninjured and injured by notexin

tag: injury time points


title: M2A2_Input

value: MTF2-FLAG WT


title: D13.s4T.A2S2.ASS04

description: Library name: Sample15

value: Spleen


title: Aged_run2

description: mRNA


title: C413, T cell lymphoma, biol rep 2


title: M2A1_Input


title: D13.s4T.A2S1.ASS04

description: Library name: Sample14

value: CD4 T cell


title: Aged_run1

description: mRNA


title: D13.e4E.A1R.ASS04

description: Library name: Sample13

source_name: Eye

value: Eye


title: M2D2_SUZ12_IP

value: CHIP_SUZ12 antibody


title: C348, T cell lymphoma, biol rep 1


title: R331_ES_7

city: Hous

first: Gregory

middle: Jude

last: Guthrie

state: TX

address: 1100 Bates St

department: Pediatrics

data_processing:
Mapping performed with hisat2 v2.0.5 with parameter --dta --phred33; ;
Novel Gene prediction was performed with StringTie v1.3.3 with default parameters to assemble sets of transcript isoforms from bam files;
GffCompare v0.10.6 with default parameter settings compared StringTie assemblies to referenence annotation files to sort new genes from known genes.
FeatureCounts v1.5.0-p3 with default parameters was used to count the read numbers. RPKM of each gene was then calculated using the length of the genes and the counts mapped to the gene.
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: comma separated csv files contain raw read counts for each Sample

organism: Sus scrofa

source_name: liver

extract_protocol:
Liver RNA was extracted using the Qiagen RNAeasy mini prep kit. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1 µg RNA was used for construction of library sequences.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: liver

tag: diet

value: ENT

tag: surgery

value: sham


title: mMA9_Kat6a-sgRNA_rep1

description: Library name: mMA9-Cas9_RNA_FP_Kat6a_sg1-sg2_7d_REP1_200712_ACAGTG_S5

value: hematopoietic

value: mouse myeloid leukemia (AML)


title: U2F-NC-5

city: Hengyang

first: Hongye

last: Yan

state: Hunan

address: 69 Chuanshan Road

country: China

institute: The First Affiliated Hospital of University of South China

data_processing:
RNA-seq reads were filtered to get clean reads using FastQ (v0.20.0).
The clean reads were aligned to the human genome GRCh38.p13 using STAR (v2.7.9a)
Read counts were quantified by RSEM (1.3.3)
Differential gene expression analysis was done using DEseq2 package (v1.38.3)
P value was adjusted using the Benjamini–Hochberg method
Assembly: hg38
Supplementary files format and content: csv, gene expression for all samples

source_name: Forebrain Organoid

growth_protocol: Human forebrain organoids were cultured in media reported in published protocols

extract_protocol:
Qiagen miRNeasy Mini Kit was used to extract total RNA
Sequencing libraries were prepared for RNA-seq using standard Illumina protocols

treatment_protocol: MTK (final concentration is 20 ng/ml and 400 ng/ml) was added to the organoid culture media. 7 days post MTK exposure, total RNA was extracted.

value: Forebrain Organoid

value: Human induced pluripotent stem cells

value: control


title: M2D1_SUZ12_IP

value: human pluripotent stem cells

value: MTF2-FLAG H3K36me3-binding mutant


title: P331_IB_4

value: IL

value: BDL


title: U2F-NC-2


title: M2C1_SUZ12_IP

value: MTF2-FLAG DNA-binding mutant


title: D13.e4E.B1R.ASS03

description: Library name: Sample10


title: D13.e4E.B1L.ASS03

description: Library name: Sample11


title: D13.e4E.A1L.ASS04

description: Library name: Sample12


title: Q331_IB_5


title: N331_EB_5


title: U2F-NC-3


title: U2F-NC-1


title: M2C2_SUZ12_IP


title: M2B2_SUZ12_IP

value: MTF2-FLAG SUZ12-binding mutant


title: C452, T cell lymphoma, biol rep 3

value: ALK+, thymic lymphoma

value: NPM-ALK+ HDAC1 fl/fl


title: D13.e4E.A2L.ASS03

description: Library name: Sample09

value: Eye

value: CD4 T cell


title: M331_IB_3

value: liver


title: D13.e4E.A2R.ASS03

description: Library name: Sample08


title: M2B1_SUZ12_IP

value: CHIP_SUZ12 antibody


title: L353_IS_9

value: sham


title: U2F-NC-4


title: D13.e4T.A3L.ASS04

description: Library name: Sample07


title: U2F-MTK400-4

value: MTK (final concentration 400 ng/ml)


title: M2A2_SUZ12_IP

value: MTF2-FLAG WT


title: M2A1_SUZ12_IP


title: D13.e4T.A2R.ASS04

description: Library name: Sample06


title: L353_IS_10


title: K353_SB_8

value: SL


title: M2D2_FLAG_IP

value: CHIP_FLAG antibody


title: K348_SS_2


title: U2F-MTK400-2

value: Forebrain Organoid

value: Human induced pluripotent stem cells


title: U2F-MTK20-5

value: MTK (final concentration 20 ng/ml)


title: D13.e4T.A1L.ASS04

description: Library name: Sample04


title: U2F-MTK400-1


title: K336_IB_8

value: IL

value: BDL


title: M2D1_FLAG_IP

value: human pluripotent stem cells

value: MTF2-FLAG H3K36me3-binding mutant


title: M2C2_FLAG_IP

value: MTF2-FLAG DNA-binding mutant


title: M2C1_FLAG_IP


title: D13.e4T.B1LG.ASS03

description: Library name: Sample02

value: Eye


title: K331_ES_6

value: ENT


title: U2F-MTK20-4


title: U2F-MTK400-5


title: M2B2_FLAG_IP

value: MTF2-FLAG SUZ12-binding mutant


title: U2F-MTK20-3


title: I348_SB_2

value: liver


title: D13.e4T.B1R.ASS03

description: Library name: Sample01

value: CD4 T cell


title: I335_IB_7


title: U2F-MTK400-3

value: MTK (final concentration 400 ng/ml)


title: M2B1_FLAG_IP


title: U2F-MTK20-2


title: I331_IB_2


title: D13.e4T.A1R.ASS04

description: Library name: Sample05


title: OB12_B1S

description: Library name: Sample12

extract_protocol:
Eyes or spleens were dissected and single cell suspensions produced by mechanical disruption and filtering through a 70 micron filter. Sorted cells were acquired using a 4-laser Fortessa X-20 flow cytometer and data analysis completed using FlowJo software.
Samples were prepared and sequenced using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following the manurfacturer's protocol.

treatment_protocol: Induction of experimental autoimmune uveoretinitis by immunisation with  IRBP(RBP3) peptide 1-20 (GPTHLFQPSLVLDMAKVLLD)

value: Spleen


title: M2A2_FLAG_IP

value: MTF2-FLAG WT


title: U2F-MTK20-1


title: OB11_A3S

description: Library name: Sample11


title: D13.e4T.B1L.ASS03

description: Library name: Sample03


title: M2A1_FLAG_IP

value: CHIP_FLAG antibody


title: H352_IS_8

value: sham


title: H353_ES_12


title: OB10_B3S

description: Library name: Sample10


title: MM-28-2

city: Nanjing

first: Xiaolong

last: Shao

state: Jiangsu

address: Nanjing Agricultural University,  No.1 Weigang

institute: Nanjing Agricultural University

description:
Library name: Sample 8
WT at  28℃ in Minimal medium(MM)

data_processing:
RNA-seq reads were mapped to the Pseudomonas syringae pv. actinidiae str. Shaanxi_M228 - Assembly GCF_000344475.3 using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Assembly: Pseudomonas syringae pv. actinidiae str. Shaanxi_M228 - Assembly GCF_000344475.3
Supplementary files format and content: txt files were generated from RNA-seq, containing raw read counts mapped to each gene.

source_name: strain

growth_protocol: Minimal medium(MM)

extract_protocol:
RNAprep Pure Bacteria Kit (Tiangen, DP430)
NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina)

treatment_protocol: The wild type Psa_M228 strain was cultured in MM at 28℃ for 2 hours and then transferred to 16℃ for 5 more hours, while the control group was cultured at 28℃ for a total of 7 hours.

value: strain

value: bacteria

value: WT

tag: batch


title: OB09_A2S

description: Library name: Sample09


title: H336_IS_5

value: IL


title: MM-28-1

description:
Library name: Sample 7
WT at  28℃ in Minimal medium(MM)

organism: Pseudomonas syringae pv. actinidiae str. Shaanxi_M228


title: MM-16-2

description:
Library name: Sample 2
WT at  16℃ in Minimal medium(MM)


title: H335_IS_3


title: M2A_1_Input

value: human pluripotent stem cells


title: M2KO_1_Input

value: MTF2 KO


title: OB07_C1R

description: Library name: Sample07


title: MM-16-1

description:
Library name: Sample 1
WT at  16℃ in Minimal medium(MM)


title: OB08_C1L

description: Library name: Sample08


title: M2A_K27me3_2_IP

value: CHIP_H3K27me3 antibody


title: H331_EB_4

value: BDL


title: OB06_B1R

description: Library name: Sample06

value: Eye


title: C.necator, ammonium sulfate, 48h, biol rep3

city: Binghamton

first: Sha

last: Jin

state: NEW YORK

address: 4400 Vestal Parkway East

institute: Binghamton University

description:
Library name: S3_3
Column name in Raw_Counts_All_Saplmes.txt: S3_3_fpkm and S3_3_count

data_processing:
The sequenced reads/raw reads often contain low quality reads or reads with adaptors, which will affect the quality of downstream analysis. To avoid this, it's necessary to filter the raw reads and get the clean reads. (1)Remove reads with adapter contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Algorithm for mapping sequences:appropriate software is chosen according to the characteristics of the reference genome. In general, Bowtie2 is chosen for the genomes of bacteria and other species with a high gene density. The mismatch parameter is set to two, and other parameters are set to default. In general, the total mapped rate should be more than 70%, and the percentage of reads that can be mapped to multiple sites in the reference genome should be less than 10%, if there is no contamination and a correct reference genome is chosen.
FeatureCounts software was used to analyze the gene expression levels in this experiment. The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.
Assembly: ASM928v2
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM value of each sample

organism: Cupriavidus necator

source_name: Bacterium

growth_protocol: The C.necator was fermented under 37 degree for 48h. The carbon and nitrogen source was lactic acid and ammonium salts (sulfate/nitrite as indicated), respectively.

extract_protocol:
The RNA was extracted using RNeasy protect bacteria mini kit (Qiagen), 1ug of total RNA was used for the construction of libraries.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: The C.necator was feed with different nitrogen source as indicated.

value: Gram-negative bacterium

value: Feed with ammonium sulfate

tag: time


title: M2A_K27me3_1_IP


title: G353_SS_9

value: liver

value: SL


title: OB05_B1L

description: Library name: Sample05

value: CD4 T cell


title: M2A_SUZ12_1_IP

value: MTF2-FLAG WT

value: CHIP_SUZ12 antibody


title: M2A_SUZ12_2_IP


title: OB04_B3R

description: Library name: Sample04


title: C.necator, ammonium sulfate, 48h, biol rep1

description:
Library name: S3_1
Column name in Raw_Counts_All_Saplmes.txt: S3_1_fpkm and S3_1_count


title: C.necator, ammonium sulfate, 48h, biol rep2

description:
Library name: S3_2
Column name in Raw_Counts_All_Saplmes.txt: S3_2_fpkm and S3_2_count


title: G352_SS_7

value: sham


title: M2A_FLAG_2_IP

value: CHIP_FLAG antibody


title: OB03_B3L

description: Library name: Sample03


title: G351_IS_7


title: M2A_FLAG_1_IP


title: G336_ES_10

value: ENT


title: C.necator, ammonium sulfate, 30h, biol rep2

description:
Library name: S2_2
Column name in Raw_Counts_All_Saplmes.txt: S2_2_fpkm and S2_2_count

value: WT


title: M2KO_K27me3_2_IP


title: C.necator, ammonium sulfate, 30h, biol rep3

description:
Library name: S2_3
Column name in Raw_Counts_All_Saplmes.txt: S2_3_fpkm and S2_3_count


title: OB01_A2L

description: Library name: Sample01


title: C.necator, ammonium sulfate, 30h, biol rep1

description:
Library name: S2_1
Column name in Raw_Counts_All_Saplmes.txt: S2_1_fpkm and S2_1_count


title: M2KO_K27me3_1_IP


title: C.necator, ammonium sulfate, 12h, biol rep3

description:
Library name: S1_3
Column name in Raw_Counts_All_Saplmes.txt: S1_3_fpkm and S1_3_count


title: M2KO_SUZ12_2_IP


title: 03535400003CXCR4KO

city: London

first: Antal

last: Rot

state: England

address: Charterhouse Square

department: Center of Microvascular Research

institute: Queen Mary University London

description: 10x Genomics

data_processing:
The 3.1.0 pipeline version of Cell Ranger was used
Seurat R package Hao et al. was used to filter low quality cells
Assembly: GRCm38
Supplementary files format and content: tab-seperated values files and matrix files

source_name: bone marrow

extract_protocol:
Bone marrow (BM) cells were depleted of CD11b+, CD5+, B220+ and Ly6G+ cells by magnetic cell sorting (Miltenyi Biotec, Bergisch Gladbach, Germany) and stained with anti-CD71, anti-Ter119 as well as lineage markers anti-CD11b, anti-CD19, anti-CD3 and anti-Gr1 antibodies. The Lin-CD71+Fscint/ hi cell population was FACS sorted on Aria II (BD Biosciences, San Jose, CA, USA), fixed in 80 % methanol on ice and stored at – 80 °C.
Single-cell RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics, Pleasanton, CA, USA)

treatment_protocol: 100μl of 5 mg /mL of tamoxifen solution was injected i.p. per mouse (CXCR4 flox flox, CXCR4 flox flox UBC-Cre-ERT2) on 3 consecutive days and tissues were harvested and analyzed on the day following the last injection

value: bone marrow

value: CD71 positive

value: CXCR4 flox/flox UBC-Cre-ERT2

value: tamoxifen


title: F351_SB_5

value: BDL


title: 03535400003CXCR4WT

description: 10x Genomics

value: CXCR4 flox flox


title: F348_SS_1


title: M2KO_SUZ12_1_IP

value: human pluripotent stem cells

value: MTF2 KO


title: 03535600002ACKR1WT

description: 10x Genomics

value: wild-type


title: C.necator, ammonium sulfate, 12h, biol rep1

description:
Library name: S1_1
Column name in Raw_Counts_All_Saplmes.txt: S1_1_fpkm and S1_1_count

value: Gram-negative bacterium

value: Feed with ammonium sulfate


title: Aged_PGE2_3

data_processing:
Default Illumina base calling implementation.
Reads were trimmed, and then mapped to concatenated human and mouse genome using Bowtie 2.
Reads mapping to chrM and those with MAPQ <10 were removed.
Peaks were called with MACS 2.
BPNet neural network model was applied to learn regulatory DNA logic for predicting accessibility.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: narrowPeak, bigWig

source_name: Muscle stem cells

growth_protocol: a7-integrin+ CD34+ MuSCs were prospectively isolated by FACS from young or aged C57BL/6 mice. Cells were pelleted, resuspended in MuSC culture media (DMEM+15% FBS+bFGF) with or without 2h.

extract_protocol:
Cells were pelleted and permeabilized in hypotonic buffer with 0.1% IGEPAL CA-630. Nuclei were treated with transposase from Illumina (Cat FC-121-1030).
Fragments were amplified with NEBNext PCR master mix and Nextera indices for 8-12 cycles.

treatment_protocol: Vehicle (0.1% DMSO) or prostaglandin E2 (PGE2, 1000x in DMSO) was added to the media at the time of cell seeding.

value: aged (20-25 months)

value: Muscle stem cells

value: 2 hours


title: M2KO_FLAG_2_IP

value: CHIP_FLAG antibody


title: F331_EB_3

value: liver

value: ENT


title: Aged_PGE2_2


title: OB02_A2R

description: Library name: Sample02

value: Eye

value: CD4 T cell


title: M2KO_FLAG_1_IP


title: E352_EB_9


title: C.necator, ammonium nitrate, 48h, biol rep2

description:
Library name: N3_2
Column name in Raw_Counts_All_Saplmes.txt: N3_2_fpkm and N3_2_count

value: WT

value: Feed with ammonium nitrite


title: G335_EB_6

value: BDL


title: S12C2_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, undifferentiated


title: C.necator, ammonium nitrate, 48h, biol rep1

description:
Library name: N3_1
Column name in Raw_Counts_All_Saplmes.txt: N3_1_fpkm and N3_1_count


title: S12C2_1

value: human pluripotent stem cells


title: G331_IB_1

value: IL


title: Aged_PGE2_1


title: C.necator, ammonium nitrate, 30h, biol rep3

description:
Library name: N2_3
Column name in Raw_Counts_All_Saplmes.txt: N2_3_fpkm and N2_3_count

value: Gram-negative bacterium


title: C.necator, ammonium sulfate, 12h, biol rep2

description:
Library name: S1_2
Column name in Raw_Counts_All_Saplmes.txt: S1_2_fpkm and S1_2_count

value: Feed with ammonium sulfate


title: E348_IS_6

value: sham


title: Aged_vehicle_3

value: aged (20-25 months)

value: Muscle stem cells

value: Vehicle (DMSO 0.1%)


title: Aged_vehicle_2

value: 2 hours


title: S12C1_2


title: C.necator, ammonium nitrate, 30h, biol rep2

description:
Library name: N2_2
Column name in Raw_Counts_All_Saplmes.txt: N2_2_fpkm and N2_2_count


title: E335_IS_2

value: liver


title: C.necator, ammonium nitrate, 30h, biol rep1

description:
Library name: N2_1
Column name in Raw_Counts_All_Saplmes.txt: N2_1_fpkm and N2_1_count


title: C.necator, ammonium nitrate, 48h, biol rep3

description:
Library name: N3_3
Column name in Raw_Counts_All_Saplmes.txt: N3_3_fpkm and N3_3_count


title: Aged_vehicle_1


title: S12C1_1


title: C.necator, ammonium nitrate, 12h, biol rep2

description:
Library name: N1_3
Column name in Raw_Counts_All_Saplmes.txt: N1_3_fpkm and N1_3_count


title: Young_PGE2_2

value: young (8-20 weeks)


title: E329_EB_2

value: ENT


title: Young_PGE2_1


title: F335_IB_6


title: S12B2_1

value: SUZ12-FLAG PRC2.1- mutant


title: E331_ES_5


title: C.necator, ammonium nitrate, 12h, biol rep1

description:
Library name: N1_2
Column name in Raw_Counts_All_Saplmes.txt: N1_2_fpkm and N1_2_count

value: WT

value: Feed with ammonium nitrite


title: S12B2_2


title: Young_vehicle_2


title: Young_vehicle_1


title: S12B1_1


title: E351_SB_4

value: SL

value: BDL


title: Ferret 9028 Bleomycin Replicate 2

city: South San Francisco

first: Ian

last: Driver

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

data_processing:
Illuina BCL files where proccessed to fastq format using bcl2fastq v2.2.0.
To generate a count matrix, the sequenced files from each independent sample were processed through 10X Genomics Cell Ranger software v7.1.0, using defualt include intron mode.
Assembly: Mustela putorius furo (domestic ferret) reference built from NCBI genome ASM1176430v1.1
Supplementary files format and content: Tab separated value files and matrix files containing raw UMI counts for all genes and all barcodes above Cellranger automated cutoff

molecule: nuclear RNA

organism: Mustela putorius furo

source_name: lung

extract_protocol:
Lung nuclei from saline and bleomycin injured ferrets were isolated using a CST buffer as described previously. Snap frozen lung tissues (50 mg) were immediately placed into a nuclei isolation using CST buffer (20 mM Tris-HCl pH 7.5, 292 mM NaCl, 2 mM CaCl2, 42 mM MgCl2, 1% CHAPS, and 2% BSA) and homogenized using a dounce homogenizer to mechanically dissociate nuclei from cells. The resulting homogenate was filtered through a 40 µm strainer, and nuclei were pelleted by centrifugation at 300 × g for 2 minutes at 4°C. Nuclei were resuspended in 0.04% BSA buffer to a final concentration of 1,000 nuclei/µl.
Single-nuclei RNA sequencing (snRNA-seq) libraries were prepared using the 10x Genomics 5' Kit v2, following the manufacturer's protocol (10X Genomics). Libraries were sequenced on an Illumina Nextseq 550 platform using 75-cycle paired-end sequencing, using 8bp for index read 28bp for R1 and 56bp for R2.

treatment_protocol: Ferrets were injured with 3 doses of bleomycin or saline control at 1 week interval, the lung tissues were harvested at 6-8 weeks post the injury. The collectedlLung tissues were immediately snap frozen and grounded in liquid nitrogen prior to being  placed into a nuclei isolation using CST buffer for nuclei isolation.

value: Bleomycin

value: lung


title: Ferret 9028 Bleomycin Replicate 1


title: S12A2_2

value: human pluripotent stem cells

value: SUZ12-FLAG WT

value: RNA-seq, undifferentiated


title: D348_SB_1


title: Young_run2

description: mRNA

value: Skeletal muscle cells

value: mix of uninjured and injured by notexin


title: Young_run1

description: mRNA


title: Ferret 6872 Bleomycin Replicate 1


title: D352_SB_7


title: D335_ES_9

value: sham


title: S12A1_2


title: Ferret 6294 Bleomycin Replicate 2


title: 4293_APP-PS1-12M-Ki67-

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using bcl2fastq2 v.2.20
Alignment and quatification with Kallisto version 0.43.1 using the default parameters
reads mapped to each transcript against the RefSeq mm38 annotation download on March 2018
Normalization using DeSeq2 and batch correction using SVA10
Genome_build: mm38
Supplementary_files_format_and_content: comma separated file including batch-corrected DeSeq2 rlog counts for each Sample.

growth_protocol: cell isolation protocol: For obtaining RNA from proliferating microglia the cells have to undergo fixation as the proliferation maker Ki67 is an intranuclear protein. APP/PS1 mice and WT at 4, 6, and 12 months were intracardially perfused with PBS and the brains were collected in ice cold HBSS. The brains were homogenized using the Adult brain dissociation kit according to the manufacturer’s instructions. The brain homogenates were resuspended in 7 mL HBSS, strained through 40 µM strainer and 3 mL Percoll were added to obtain a final 30 % of Percoll solution. The samples were subsequently underlayered with 2 mL 70% Percoll solution using a syringe. The samples were centrifuged at 500g with slow acceleration and no brake at 16 °C for 28 min. Microglial cells were recovered from the Percoll interphase, washed with PBS, centrifuged at 400g for 5 min at 4 °C. Thus, the pellet was re-suspended in 4 % PFA in PBS and incubated for 15 min on ice. After fixation, the cells were washed with PBS, followed by a wash in staining buffer containing 0.1 % RNAse free BSA and 1:400 RNasin plus  in PBS, centrifuged at 330g for 3 min at 4 °C. The pellet was resuspended in 200 µL staining buffer and frozen in -80 °C until further use.

extract_protocol:
Briefly, to lyse the sorted cells, the samples were thawed at RT, 75µl of PKD buffer was added and incubated for 1 h at 56 °C at 300 rpm for reverse cross-linking.  Samples were then centrifuged at 20000g for 20 min.  For RNA extraction, the miRNeasy FFPE Kit was used following manufacturer’s instructions to obtain 14 µl of RNA.  Samples were quantified using a High Sensitivity D5000 DNA assay on an Agilent 2200 Tapestation.
Purified full-length cDNA was processed to NGS libraries using the Nextera XT DNA library preparation and the Nextera XT Index kits (Illumina). In short, cDNA was diluted to 200 pg/µl, 100 pg were tagmented. Tagmentation was terminated and primer mix and buffers were added and tagmented cDNA was PCR amplified. The finished NGS libraries were purified using Ampure XP Beads at a 1:1 ratio and eluted in 15 µl of nuclease-free water before quantification and QC using a High Sensitivity D5000 DNA assay on an Agilent 2200 Tapestation.
Nextseq500 high output chemistry V1, 75 bp SR or 75 bp & 75 bp PE

treatment_protocol: The samples were thawed, permeabilized in permeabilization buffer containing 0.1 % Triton-X100 and 1:200 Fc-block in staining buffer for 10 min on ice, and centrifuged at 500g at 4°C. The samples were stained in 100 µl primary antibody mix and incubated for 30 min on ice on slow rotation. After centrifugation at 400g for 3 min at 4°C, the samples were stained with secondary anti-rabbit Alexa 647  in 200 µl staining buffer for 20 min. The antibody concentrations for Ki67 and secondary antibody were titrated. The samples were washed with staining buffer, centrifuged at 500g for 3 min at 4 °C and resuspended in 500 µL staining buffer containing DAPI (10 µg/mL). Unstained samples and fluorescence minus one were used as controls. CD45 and CD11b positive microglia were gated as Ki67 positive and Ki67 negative cells and DAPI staining confirmed that cells containing nuclei were sorted. Using BD FACSAria II 400 proliferating or non-proliferating microglia respectively were collected in 1.5 mL RNase free containing 25 µL PKD buffer supplemented with 1:16 proteinase K  and ERCC spike in controls , snap frozen on dry ice and stored at −80°C until further processing.

value: male

tag: age in months

tag: tissue/cell type

value: microglia


title: D329_ES_2

value: liver


title: S12A1_1


title: D353_EB_10

value: ENT


title: S12B1_2

value: SUZ12-FLAG PRC2.1- mutant


title: 4292_APP-PS1-12M-Ki67-


title: Ferret 6294 Bleomycin Replicate 1


title: 4290_WT-12M-Ki67-

value: WT


title: M2KO_1

value: MTF2 KO


title: Ferret 6872 Bleomycin Replicate 2


title: C353_SS_8

value: SL


title: 4289_APP-PS1-12M-Ki67+


title: C352_SS_6


title: M2KO_2


title: S12A2_1


title: 4288_APP-PS1-12M-Ki67+


title: Ferret 4665 Bleomycin Replicate 1


title: Ferret 0869 Bleomycin Replicate 2


title: C351_SS_4


title: C335_ES_8


title: Ferret 4665 Bleomycin Replicate 2


title: D351_SS_5


title: 4287_WT-12M-Ki67+


title: M2D2_2

value: MTF2-FLAG H3K36me3-binding mutant


title: B353_IB_11

value: IL

value: BDL


title: 4286_WT-12M-Ki67+


title: B352_SB_6


title: Ferret 9078 Saline Replicate 2

value: Saline

value: lung


title: Ferret 0869 Bleomycin Replicate 1

value: Bleomycin


title: 4277_APP-PS1-12M-Ki67-


title: M2D1_1

value: human pluripotent stem cells

value: RNA-seq, undifferentiated


title: Ferret 9078 Saline Replicate 1


title: M2C2_2

value: MTF2-FLAG DNA-binding mutant


title: B351_SB_3


title: 4276_APP-PS1-12M-Ki67-

value: male


title: 4275_WT-12M-Ki67-

value: microglia


title: M2C2_1


title: B348_EB_8

value: liver


title: M2C1_2


title: Ferret 8849 Saline Replicate 1


title: M2D2_1


title: Ferret 8849 Saline Replicate 2


title: B336_IS_4

value: sham


title: M2C1_1


title: 4274_WT-12M-Ki67-


title: B335_IS_1


title: B331_ES_4

value: ENT


title: 4272_APP-PS1-12M-Ki67+


title: M2D1_2


title: M2B2_2

value: MTF2-FLAG SUZ12-binding mutant


title: Ferret 4626 Saline Replicate 2


title: 4273_APP-PS1-12M-Ki67+


title: B329_EB_1


title: Ferret 4626 Saline Replicate 1


title: Ferret 0359 Saline Replicate 2


title: M2B2_1


title: Ferret 0359 Saline Replicate 1


title: M2B1_2


title: 4270_WT-12M-Ki67+

value: WT


title: Ectodermal cells (H1), 20 mM EtOH 3

type: genomic

city: Helsinki

first: Nina

last: Kaminen-Ahola

address: Haartmaninkatu 8

department: Department of Medical and Clinical Genetics

country: Finland

institute: University of Helsinki

description: Ectodermal cells (H1), 20 mM EtOH, EPIC2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were scanned using iScan system and standard recommended Illumina scanner settings.

data_processing:
The raw DNAm dataset was pre-processed, quality-controlled, and filtered with ChAMP R package using the minfi method. Data was filtered using detection P-values and bead count values with default thresholds. Probes were normalized with noob in minfi R package, and BMIQ in wateRmelon R package. Following normalization, probes located in sex chromosomes and probes binding to polymorphic and off-target sites were filtered.
Average Beta

label: Cy3 and Cy5

label_protocol: The Infinium MethylationEPIC array uses direct hybridization without labeled nucleotides. After hybridization, labeled nucleotides were arred during primer extension step.

growth_protocol: hESCs were differentiated into the three germ layers by using the STEMdiff Trilineage Differentiation kit (Stemcell Technologies). Differentiation was performed according to the manufacturer’s instructions, and the medium was changed daily. Endodermal and mesodermal cells were collected after five days and ectodermal cells after seven days.

extract_protocol: DNA were extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The medium was supplemented with EtOH (≥ 99.5 p-%) at a final concentration of 20 mM or 70 mM. Exposure was started at the same time as the differentiation (day 1). The exposure durations were four days (96 h) for endodermal and mesodermal cells, and six days (144h) for ectodermal cells.

value: ectodermal cells

value: 20 mM EtOH


title: A352_ES_11


title: M2B1_1


title: 4320_WT-6M-Ki67-


title: Ectodermal cells (H1), 20 mM EtOH 2


title: A351_SS_3

value: SL


title: M2A2_2

value: MTF2-FLAG WT


title: Ectodermal cells (H1), 20 mM EtOH 1


title: A348_IB_9

value: IL

value: BDL


title: Ectodermal cells (H1), Control 4-2

description: Ectodermal cells (H1), Control, EPIC2, same biological sample as ECC4

value: control


title: M2A2_1

value: human pluripotent stem cells


title: 4269_APP-PS1-6M-Ki67-


title: 4294_APP-PS1-6M-Ki67+


title: Ectodermal cells (H1), Control 3-2

description: Ectodermal cells (H1), Control, EPIC2, same biological sample as ECC3


title: 4267_WT-6M-Ki67-


title: Ectodermal cells (H1), Control 2-2

description: Ectodermal cells (H1), Control, EPIC2, same biological sample as ECC2


title: 4271_WT-12M-Ki67+


title: A331_ES_3


title: A353_IB_10


title: RAD21 rep2

city: Freiburg im Breisgau

first: Maximilian

middle: Christian

last: von der Linde

address: Stefan-Meier-Straße 17

department: Institute for Medical Bioinformatics and Systems Medicine (IBSM)

institute: University Medical Center Freiburg

data_processing:
The 3' adaptors were removed using cutadapt (v1.4.2, Read1: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and trimmed reads with a length of less than 18bp were discarded.
The trimmed reads were aligned to GRCh38.14 (Genome Reference Consortium Human Build 38), GCA_000001405.29 using bowtie
genome-wide coverage tracks were computed using bedtools (v2.27, bedtools genomecov -split -bg, bedtools genomecov  -split -bg -strand '+' ,bedtools genomecov -split -bg -strand '-') and bedGraphToBigWig from the kent-tools (bedGraphToBigWig v4, bedGraphToBigWig -blockSize=256 -itemsPerSlot=1024)ignoreDuplicates --nomalizeUsing CPM --exactScaling for H3 WT and KD
Assembly: GRCh38.14 (Genome Reference Consortium Human Build 38), GCA_000001405.29
Supplementary files format and content: bigwig format files containing the information about genome coverage

source_name: Ramos

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

extract_protocol:
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, libraries were prepared following the NEB Next Ulta II DNA library kit. Libraries were amplified with the kappa library amplification qCR master mix

value: Ramos

value: Burkitt's Lymphoma

value: untreated


title: A336_EB_7


title: 4268_APP-PS1-6M-Ki67-

value: male

value: microglia


title: A329_ES_1

value: liver

value: sham


title: Ectodermal cells (H1), Control 1-2

description: Ectodermal cells (H1), Control, EPIC2, same biological sample as ECC1


title: Mesodermal cells (H1), 20 mM EtOH 3

description: Mesodermal cells (H1), 20 mM EtOH, EPIC2

value: mesodermal cells


title: CTCF rep1


title: 4265_APP-PS1-6M-Ki67+


title: retrospective, acute leukemia, AL_038

city: Boston

first: Salvatore

last: Benfatto

state: Massachusetts

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Library name: AL_038

data_processing:
Pod5 raw data files were processed using dorado (v. 0.3.2)
The methylation calls were extracted from the bam files using the modkit tool (v. 0.1.13)
Assembly: hg19
Supplementary files format and content: txt files restricted to the CpGs positions of our reference cohort and containing the methylation status of the covered CpGs.
Supplementary files format and content: txt files containing the methylation status of all the covered CpGs.

source_name: Peripheral Blood

extract_protocol:
Collected samples were processed to obtain DNA. DNA was extracted using the Qiagen DNeasy Blood and Tissue DNA extraction kit (Qiagen, Cat. no 69506), following manufacturer’s instructions for non-nucleated blood specimens. For every patient sample retrieved, 150-200 μL of specimen was mixed with 20 μL of proteinase K, adjusting the volume to 220 μL with PBS. Then 200 μL of ALT lysis buffer was added and samples were gently vortexed. To complete the cell lysis step, samples were incubated for 10 minutes at 56° C. For DNA precipitation, 200 μL of 100% ethanol was added to the samples. This mixture was then placed into a mini column and centrifuged for 1 minute at 8000 rpm. The mini column was placed into a new collection tube and a first washing step was performed adding 500 μL of buffer AW1 and centrifuging for 1 minute at 8000 rpm. The collection tube was discarded and a second washing step was done using 500 μL of AW2 buffer, centrifuging for 3 minutes at 14000 rpm. Finally, the DNA was eluted from the column by adding 200 μL of elution buffer and centrifuging for 1 minute at 8000 rpm. The elution step was repeated several times to increase DNA recovery and DNA quantification was done using the Qubit fluorometer (ThermoFisher Scientific, Cat. no. Q33238).
Retrospective samples: samples were processed using the Rapid Barcoding Kit 24 V14 (Oxford Nanopore Technologies, Cat. no. SQK-RBK114.24), according to the manufacturer's instructions. Prospective samples: DNA was extracted as described above. DNA was then prepared using the Rapid Sequencing Kit V14 (Oxford Nanopore Technologies, Cat. no. LSK-RAD114).

value: Peripheral Blood


title: RAD21 rep1


title: CTCF rep2


title: 4263_WT-6M-Ki67+

value: WT


title: Mesodermal cells (H1), 20 mM EtOH 2

value: 20 mM EtOH


title: retrospective, acute leukemia, AL_037

description: Library name: AL_037

source_name: Bone Marrow

value: Bone Marrow


title: 4262_WT-6M-Ki67+


title: retrospective, acute leukemia, AL_036

description: Library name: AL_036


title: Mesodermal cells (H1), 20 mM EtOH 1


title: Ta, RNA,replicate3

city: Shanghai

first: xu

last: wu

address: 83 Fenyang Road

institute: EENT Hospital, Fudan University

data_processing:
We used Solexa pepline software for image processing and base recognition. Fastq software  was used to assess the sequencing quality of trimmed reads, which are then aligned to a reference genome using Hisat2  software. StringTie software was employed to estimate transcript abundance by referencing an official database, resulting in the generation of RNA transciptome expression profiles.
Assembly: GRCh38
Supplementary files format and content: gene_count.csv

source_name: auricular cartilage

extract_protocol:
Chondrocytes were rapidly immersed in Trizol (Sigma-Aldrich, St. Louis, MO, USA) reagent  for preservation, followed by RNA extraction using chloroform and precipitation with isopropyl alcohol. The resulting RNA precipitates underwent two washes with 70% ethanol, drying, and subsequent dissolution in RNase-free water. The quantity and quality of the RNA samples were assessed using a NanoDrop ND-1000 spectrophotometer..
1.5ug of total RNA for each group was used to conduct transcriptome sequencing by Illuminate NovaSeq 6000.

value: auricular cartilage

value: primary chondrocyte


title: M2A1_1

city: New York

first: Yicheng

last: Long

address: 413 East 69th Street

institute: Weill Cornell Medicine

value: MTF2-FLAG WT

value: RNA-seq, undifferentiated


title: Ta, RNA,replicate2


title: Mesodermal cells (H1), Control 4-2

description: Mesodermal cells (H1), Control, EPIC2, same biological sample as MC4

value: control


title: retrospective, acute leukemia, AL_035

description: Library name: AL_035


title: 4266_WT-6M-Ki67-


title: retrospective, acute leukemia, AL_039

description: Library name: AL_039


title: 4369_WT-4M-Ki67+


title: Mesodermal cells (H1), Control 3-2

description: Mesodermal cells (H1), Control, EPIC2, same biological sample as MC3


title: Nif, RNA,replicate3


title: 4330_APP-PS1-4M-Ki67-


title: Mesodermal cells (H1), Control 2-2

description: Mesodermal cells (H1), Control, EPIC2, same biological sample as MC2


title: retrospective, acute leukemia, AL_034

description: Library name: AL_034


title: retrospective, acute leukemia, AL_033

description: Library name: AL_033


title: Ta, RNA,replicate1


title: Nif, RNA,replicate2


title: Endodermal cells (H1), 20 mM EtOH 3

description: Endodermal cells (H1), 20 mM EtOH, EPIC2

value: endodermal cells


title: Mesodermal cells (H1), Control 1-2

description: Mesodermal cells (H1), Control, EPIC2, same biological sample as MC1


title: 4329_APP-PS1-4M-Ki67+


title: retrospective, acute leukemia, AL_031

description: Library name: AL_031


title: Nif, RNA,replicate1


title: P3, RNA,replicate3


title: 4308_APP-PS1-4M-Ki67+


title: retrospective, acute leukemia, AL_030

description: Library name: AL_030


title: Endodermal cells (H1), 20 mM EtOH 2


title: 4371_WT-4M-Ki67-


title: Endodermal cells (H1), 20 mM EtOH 1


title: P3, RNA,replicate2


title: 4307_APP-PS1-4M-Ki67+


title: retrospective, acute leukemia, AL_029

description: Library name: AL_029


title: P3, RNA,replicate1


title: 4301_APP-PS1-4M-Ki67-


title: P3, scRNA,replicate3

data_processing:
Raw reads are processed through an internal pipeline to generate gene expression profiles. Briefly, cell barcodes and UMIs were extracted after filtering reads in the absence of multiple t-tails. Read2 contains RNA sequences. Cell ranger uses STAR (V2.7.11) to compare Read2 to a reference genome GRCh38, and selects the uniquely matched sequence for subsequent analysis. Reads for the same cell barcode, UMI, and gene were combined to calculate the number of UMIs per gene per cell. The UMI count table for each cell barcode was used for further analysis.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz/features.tsv.gz/matrix.mtx.gz

extract_protocol:
Chondrocytes were digested into single-cell suspension and mixed with 10× barcodes and Master Mix(10× Genomics Chromium, Capital Biotechnology, Beijing, China).
Single-cell library was constructed according to the manufacturer’s instructions. High-throughput sequencing was performed on the Illumina NovaSeq platform.


title: Endodermal cells (H1), Control 3-2

description: Endodermal cells (H1), Control, EPIC2, same biological sample as ENC3


title: retrospective, acute leukemia, AL_028

description: Library name: AL_028


title: P1, scRNA,replicate3


title: retrospective, acute leukemia, AL_027

description: Library name: AL_027


title: 4284_WT-4M-Ki67-


title: Endodermal cells (H1), Control 4-2

description: Endodermal cells (H1), Control, EPIC2, same biological sample as ENC4


title: retrospective, acute leukemia, AL_026

description: Library name: AL_026


title: 4310_WT-4M-Ki67+


title: 4300_WT-4M-Ki67+


title: Endodermal cells (H1), Control 1-2

description: Endodermal cells (H1), Control, EPIC2, same biological sample as ENC1


title: retrospective, acute leukemia, AL_025

description: Library name: AL_025


title: retrospective, acute leukemia, AL_032

description: Library name: AL_032


title: P6, scRNA,replicate3


title: 4282_WT-4M-Ki67-


title: P6, scRNA,replicate2


title: Endodermal cells (H1), Control 2-2

description: Endodermal cells (H1), Control, EPIC2, same biological sample as ENC2


title: MN10_WT_Rep1_ontDNA_org_hiPS6_human

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description: Library name: MN10_WT_Rep1_ontDNA_org_hiPS6_human

data_processing:
The resulting long read DNA sequencing data was basecalled and mapped to the reference genome (hg38) using dorado (version 0.5.1) with model dna_r10.4.1_e8.2_400bps_sup@v4.1.0 and --modified-bases-model dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2. Visualization was performed using methylartist (version 1.2.6).
The resulting long-read RNA seq data was basecalled using dorado (version 0.7.1) with model rna004_130bps_sup@v3.0.1 and --modified-bases-models using dorado's model rna004_130bps_sup@v3.0.1_m6A_GRACH@v1. Reads were then mapped using minimap2 (-ax splice -uf -k14 -y) using hg38 as the reference genome. Visualization was done using the sorted and indexed bam file (samtools 1.16.1) on IgV (version 2.18.2)
Assembly: GRCh38
Supplementary files format and content: Alignment files as output from dorado basecaller (DNA) or minimap2 (RNA)

extract_protocol:
High molecular weight DNA was extracted from frozen pellets (500 000-1 million cells) using the Nanobind HMW DNA Extraction kit (PacBio) following the manufacturer’s instructions. The final product was eluted in 100 μL of Buffer EB. DNA concentration and quality were assessed with Nanodrop and Qubit.
RNA was extracted from one hiPS cell pellet (3 million cells) using the Trizol RNA extraction protocol (Trizol reagent [Invitrogen #15596026]). The NEBNext High Input Poly(A) mRNA Isolation Module (NEB #E3370S) protocol was used to select the mRNA for long-read direct RNA sequencing.
Libraries for long-read DNA seq were prepared using SQK-LSK109 Ligation Sequencing kit (Oxford Nanopore Technologies)
The library for long-read direct RNA sequencing was prepared according to manufacturer’s protocol and using the Direct RNA Sequencing Kit (SQK-RNA004) from Oxford Nanopore Technologies.
DNA libraries were sequenced using a FLO-PRO002 PromethION Flow Cell R9 Version on a PromethION (Oxford Nanopore Technologies) at SciLifeLab.
The sample for long-read RNAseq was sequenced using a PromethION 2 Solo IT on a PromethION RNA Flow Cell (FLO-PRO004RA).

tag: lentivirus

tag: type

value: organoid

tag: target gene

tag: crispr guide_rna


title: Mouse cell, cellSp_713_EE_3, rep 3

city: Shenzhen

first: Jian-Kang

last: Zhu

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

institute: Southern University of Science and Technology

description: Library name: hepa1-6 713split-3

data_processing:
FASTQ generation: Illumina bcl-convert v4.0
Read trimming: Trimmomatic v0.38  SLIDINGWINDOW:5:15 HEADCROP:3 AVGQUAL:15 LEADING:5 TRAILING:5 MINLEN:80.
Alignment: BSMAP v2.90 to mm39  -n 0 -v 0.08 -g 1 -p 48.
Methylation ratios: methratio.py, BSMAP package
DMCs: Radmeth v1.0  coverage >= 5×, Q < 0.05, Δβ > 0.10.
DMRs: metilene v0.2-8  --mincpgs 3 --mode 1 -mtc 2; keep regions P < 0.05, Δβ > 0.10, >= 5 CpGs, length > 50 bp.
Assembly: mm10
Supplementary files format and content: xls format table with chr, pos, strand, context, rate, depth, nC
Supplementary files format and content: csv format table with chr,start,end,meth.diff,qvalue,annotation,gene_annot

extract_protocol:
Genomic DNA was isolated from mouse liver tissue or Hepa1-6 liver cells with the QIAamp DNA Mini kit (Qiagen), quantified by Qubit fluorometry, fragment size verified on a Fragment Analyzer, and spiked with 0.5 % unmethylated λ-DNA as a bisulfite-conversion control.
One µg gDNA was sheared (~250 bp) on a Bioruptor, end-repaired, A-tailed and ligated to 5-mC Illumina adapters; DNA was bisulfite-converted (EZ DNA Methylation-Gold, Zymo), PCR-amplified (8–12 cycles, KAPA HiFi Uracil+), size-selected with AMPure XP beads, QC’d on a Bioanalyzer, quantified by qPCR, and sequenced as 2 × 150 bp reads on an Illumina NovaSeq X Plus.


title: MN10_WT_Rep1_ontDNA_iPSC_hiPS6_human

description: Library name: MN10_WT_Rep1_ontDNA_iPSC_hiPS6_human

value: hiPSC


title: P3, scRNA,replicate2

tag: tissue


title: Mouse cell, cellSp_713_EE_2, rep 2

description: Library name: hepa1-6 713split-2

tag: cell line


title: 4280_WT-4M-Ki67+

tag: strain

tag: Sex

value: male

tag: genotype


title: 4279_APP-PS1-4M-Ki67+

value: microglia


title: P1, scRNA,replicate2

tag: cell type


title: MN10_WT_Rep1_ontDNA_iPSC_hiPS48_human

description: Library name: MN10_WT_Rep1_ontDNA_iPSC_hiPS48_human


title: Mouse cell, cellSp_713_EE_1, rep 1

description: Library name: hepa1-6 713split-1


title: 4261_WT-4M-Ki67-


title: P6, scRNA,replicate1


title: 4283_APP-PS1-4M-Ki67-


title: Mouse cell, cellSp_573_EE_3, rep 3

description: Library name: hepa1-6 573split-3


title: MN07_LacZ_hiPS6_Rep1_ontRNA

description: Library name: MN07_LacZ_hiPS6_Rep1_ontRNA

value: LacZ


title: Mouse cell, cellSp_573_EE_2, rep 2

description: Library name: hepa1-6 573split-2


title: P3, scRNA,replicate1


title: P1, scRNA,replicate1


title: 4258_APP-PS1-4M-Ki67-


title: Mouse cell, cellSp_573_EE_1, rep 1

description: Library name: hepa1-6 573split-1


title: CORT 4h

type: RNA

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45C with 60 rpm onGeneChip™ Hybridization Oven 645. GeneChips were washed and stained in the GeneChip™ Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G.

data_processing: The data were analyzed with the Microarray Data Analysis Tool using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: CORT 4h exposed mice eye

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: C57BL/6J male mice were kept under 12h light 12 dark conditions for 1 week.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions of DNA/RNA/Protein Extraction Kit.

treatment_protocol: Unanesthetized 8-week-old male mice were used in this study. For microarray analysis, 7 weeks old male mice (N = 6) were adrenalectomized and superior cervical ganglionectomized, as in our previous report. Two weeks after, mice were treated with drugs at ZT2, when IOP is low, with a single drop (30 μL) of L-NE (1 mM/0.1% DMSO PBS) or dobutamine (1 mM/0.1% DMSO PBS) using a micropipette into bilateral eyes. During instillation, the mice were gently restrained with their necks held back. After 4 h, total RNA of vehicle- or NE-treated eyes was extracted using the DNA/RNA/Protein Extraction Kit (#DRP100, Presto) at ZT6 and pooled for microarray analysis (N = 1).

tag: tag

value: Tissue


title: 4257_WT-4M-Ki67+


title: control scRNA-seq

first: xuelian

last: wang

address: Ruijin er road No.197

institute: Ruijin hospital

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) using default parameters. The CellRanger mkfastq command was used to generate Fastq files. Subsequently, data were mapped to the pre-build mouse reference genome (mm10, version 1.2.0).
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: aorta

extract_protocol:
In brief, after rinsing with 1% PBS for three times, the adventitia were cut and digested with an enzyme digestion [2mg/mL collagenase type Ⅰ (Invitrogen; 17018-029), 2 mg/ml disapase Ⅱ（Sigma; C2-BIOC） in Hank’s balance salt solution containg calcium and magesium] for 2h at 37℃. The cell suspension was strained through a 70 μm filter, washed twice in the 1×PBS and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albumin, then subjected to scRNA-seq.
The scRNA-seq was conducted using the Standard 10x Chromium Single Cell 3′ v3 protocol by 10X Genomics GemCode Technology. In summary, single cells were individually tagged with a unique 10x Barcode and unique molecular identifier through the encapsulation into Gel Bead-In-Emulsions. Sequences sharing identical 10x Barcodes were then classified as originating from the same cell. The resultant cDNA library was prepared and subjected to sequencing on the Nova PE150 platform.

value: aorta

value: Aortic adventitial cells

value: wide type

tag: treatment


title: Ang II scRNA-seq

value: angiotensin II


title: Mouse cell, cellSp_EE_2, rep 2

description: Library name: hepa1-6 PC384-2


title: 3'mRNAseq multiplexed pool 2, mixed cell types and treatments

description:
Library name: 3_mRNAseq_pool2
Sequencing was performed using a strategy where 3'-UTRs were sequenced from mRNA fragments. In the process, samples are pooled into two libraries, where each sample is labeled with unique sample barcodes. After alignment each sample is demultiplexed using drop-seq tools and 12bp long barcodes.

data_processing:
Sequencing with 75 cycles produced 21 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 62 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was inspected using FastQC and multiQC to ensure the quality of sequencing results (Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc; Ewels P. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016). Subsequently, reads were filtered to remove low quality reads and reads shorter than 20 bp using Trimmomatic (Bolgeret al. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. 2014).
Reads passing the filter were then processed further using Drop-seq tools and the pipeline originally suggested in Drop-seq paper (v. 2.4.1, Macosko et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015). In brief, the raw, filtered read libraries were converted to sorted BAM files using Picard tools (http://broadinstitute.github.io/picard). This was followed by tagging reads with sample specific barcodes and unique molecular identifiers (UMIs). Tagged reads were then trimmed for 5’ adapters and 3’ poly A tails. Alignment ready reads were converted from BAM formatted files to fastq files that were used as an input for STAR aligner (Dobin A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013).
Alignments were done using data from GENCODE Release 38 human genome (GRCh38.p13) and comprehensive gene annotation files (Frankish A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019) with default STAR settings. Following the alignment, the uniquely aligned reads were sorted and merged with previous unaligned tagged BAM file to regain barcodes and UMIs lost during the alignment step. Next, annotation tags are added to aligned and barcode tagged BAM files to complete the alignment process. Finally, Drop-seq tools are used to detect and correct systematic synthesis errors present in sample barcode sequences. Digital expression matrices are then created by counting the total number of unique UMI sequences (UMI sequences that differ only by a single base are merged together) for each transcript.
DESeq2 was then used to identify differentially expressed genes (Love MI. et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014).
Assembly: GENCODE Release 38 human genome (GRCh38.p13) and comprehensive gene annotation files.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: List of samples and sample specific barcodes used for pooling (MS xlsx format).

growth_protocol: Human embryonic stem cells (hESCs) were cultured in E8 Medium (Gibco) on Matrigel (Corning) coated plates at 37 °C and 5% CO2. Culture media was routinely replaced every day. Cells were passaged using 0.5 mM EDTA. hESCs were differentiated into the three germ layers by using the STEMdiff Trilineage Differentiation kit (Stemcell Technologies). Differentiation was performed according to the manufacturer’s instructions, and the medium was changed daily. Endodermal and mesodermal cells were collected after five days and ectodermal cells after seven days.

extract_protocol:
RNA were extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer's instructions.
Custom library construction protocol using 3' RNA-Seq (Drop-seq-like) library construction strategy.

treatment_protocol: The medium was supplemented with EtOH (≥ 99.5 p-%) at a final concentration of 20 mM or 70 mM. Exposure was started at the same time as the differentiation (day 1). The exposure durations were four days (96 h) for endodermal and mesodermal cells, and six days (144h) for ectodermal.

value: endodermal, mesodermal, ectodermal cells

value: control, 20 mM EtOH, 70 mM EtOH

tag: pool


title: Mouse cell, cellSp_EE_3, rep 3

description: Library name: hepa1-6 PC384-3


title: hAoSMCs, miR-15a mimic, rep2

city: Munich

first: Lars

last: Maegdefessel

address: Ismaninger Strasse 22

institute: Technical University of Munich

data_processing:
After cluster generation, the library preparations were sequenced on an Illumina NovaSeq PE150 platform and >40M paired-end reads were generated for each sample. Raw data (raw reads) of fastq format were cleaned by removing reads containing adapter sequence, reads containing poly-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data was calculated. All downstream analyses were based on the clean, high-quality data.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to quantify reads mapped to each gene. FPKM of each gene was calculated based on the length of the gene and its mapped reads. Differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting p-values were adjusted for false discovery rate using the Benjamini and Hochberg’s approach. At this point, data was released by the commercial vendor and all subsequent analyses were performed independently by our group. Genes with an adjusted p-value <=0.05 and absolute fold-change >=1.5 were defined as differentially expressed.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: raw data (.fq), counts matrix (gene_count.xls), fpkm counts matrix (gene_fpkm.xls)

growth_protocol: Primary human aortic smooth muscle cells (hAoSMCs, lot nr 3003) were purchased from Cell Applications (San Diego, USA) and cultured in complete Human SMC Growth Medium (Cell Applications; 311-500), supplemented with 1% PenStrep. Cells were seeded in 6-well plates at 125.000 cells/well and kept in growth medium overnight.

extract_protocol:
RNA was harvested by pooling two wells of each condition to assure adequate RNA concentration. Extraction was performed using miRNeasy Tissue/Cells Advanced Mini Kit (Qiagen), following the manufacturer’s protocol, including an on-column DNAse digestion step.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP. The directional library was complete after 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. The clustering of the index-coded samples was performed according to the manufacturer’s instructions.

treatment_protocol: Next morning, cells were starved for 24h in OptiMEM (Gibco, ThermoFisher Scientific) + 2% FBS + 1% PenStrep. Shortly before transfection, medium was changed back to full growth medium as per above. Transfection of miRNA-modulators (miRVana miRNA mimic/inhibitor/scrambled control, ThermoFisher Scientific) was performed using Lipofectamine RNAiMAX (ThermoFisher Scientific) in accordance with manufacturer’s manual and using 7.2 µl RNAiMAX per well and a final modulator concentration of 50nM. Cells were then cultured for 48h.

value: miR-15a mimic


title: L-NE 4h

source_name: NE 4h exposed mice eye


title: 3'mRNAseq multiplexed pool 1, mixed cell types and treatments

description:
Library name: 3_mRNAseq_pool1
Sequencing was performed using a strategy where 3'-UTRs were sequenced from mRNA fragments. In the process, samples are pooled into two libraries, where each sample is labeled with unique sample barcodes. After alignment each sample is demultiplexed using drop-seq tools and 12bp long barcodes.


title: Vehcle 4h

source_name: Vehcle 4h exposed mice eye


title: Mouse cell, cellSp_EE_1, rep 1

description: Library name: hepa1-6 PC384-1


title: hAoSMCs, scrambled control, rep3

source_name: Primary human aortic smooth muscle cells

value: scrambled control oligo


title: Mouse cell, cellSF01_EE_6, rep 6

description: Library name: hepa1-6 PC402+cr31214-3


description: Library name: MN07_WT_Rep1_cutnrun_hiPS6_IgG_L1_CRISPRi

data_processing:
CUT&RUN reads were aligned to the human and yeast genomes (hg38 and R64-1-1 respectively) using bowtie2 (–local –very-sensitive- local –no-mixed –no-discordant –phred33 -I 10 -X 700)
BAM files were indexed using samtools (version 1.16.1) and converted to bigwig files using deeptools bamCoverage (version 2.5.4) (--normalizeUsingRPKM)
Assembly: GRCh38
Supplementary files format and content: Bigwigs for genome browser visualization
Library strategy: CUT&Run

extract_protocol:
CUT&RUN experiments were done following the protocol described in Skene&Henikoff  2018 (Skene & Henikoff, 2017). 300.000 cells per condition per antibody were used to do the analysis. For H3K4me3 CUT&RUN, standard CUT&RUN protocol was used. For the dCas9 CUT&RUN, a light crosslinking step was added.
For CUT&RUN analysis Illumina sequencing libraries were prepared using the Hyperprep kit (KAPA) with unique dual indexed adapters (KAPA).
CUT&RUN libraries were sequenced on a Nextseq500 instrument (paired end, 2x75bp).

tag: batch


title: UWBBRCA

first: Cong

last: Wang

address: 639, Longmi Avenue

institute: China Pharmaceutical University

description:
Library name: sample2
UWBBRCA_FPKM

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster GenerationSystem using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) accordingtothemanufacturer’s instructions. After cluster generation, the library preparationsweresequenced on a Novaseq 6000 platform and 150 bp stand-specific paired-endreadswere generated.
Raw data (raw reads) of fastq format were firstly processed through in-houseperlscripts. In this step, clean data (clean reads) were obtained by trimmingreadscontaining adapter, ploy-N or with low quality from raw data. At the sametime, Q20, Q30 and GC content of the clean data were calculated. All the downstreamanalyses were performed based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded fromgenomewebsite directly. Index of the reference genome was built using hisat2-2.0.4andpaired-end clean reads were mapped to the reference genome. STARusedthemethodof Maximal Mappable Prefix(MMP) which can generate a precise mappingresult forjunction reads
Stringtie-1.3.3b ）was used to count the read numbers mapped to each gene. AndthenFPKM was calculated, which expected number of Fragments Per Kilobaseoftranscript sequence per Millions base pairs sequenced. FPKMis a simple andmostlycommon used expression level normalization method. It normalizes for bothsequencing depth and genome size.
Differential expression analysis of two conditions/groups(at least two biological replicates per condition/group) was performed usingtheedgeR.It provide statistical routines for determining differential expression indigital geneexpression data using a model based on the negative binomial distribution.
Theresulting P-values were adjusted using the Benjamini and Hochberg’s approachforcontrolling the false discovery rate . Genes with an adjusted P-value <0.05wereassigned as differentially expressed ones.
Assembly: mm9
Supplementary files format and content: csv file include FPKM values for each samples

source_name: Cell Line

growth_protocol: 50% RPMI 1640, 50% MEGM, and 3% FBS, and penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using RNA-easy Isolation Reagent(Vazyme),
A total of 1 µg total RNA per sample was used as input material for thelncRNAlibrary preparation. Strand-specific libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations and index codes were added to attribute sequences to eachsample.Briefly, ribosome RNA was depleted from total RNA. Fragmentation was carriedoutusing divalent cations under elevated temperature in NEBNext First StrandSynthesisReaction Buffer(5X). First strand cDNA was synthesized using randomhexamerprimer and M-MuLV Reverse Transcriptase (RNase H-). Second strandcDNAsynthesis was subsequently performed using DNA Polymerase I and RNase Hwiththeincorporation of dUTP instead of dTTP. Remaining overhangs were convertedintoblunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNAfragments, NEBNext Adaptor with hairpin loop structure were ligated for hybridization.In order to select cDNA fragments of preferentially 150-200 bp in length, thelibraryfragments were purified with AMPure XP system.Then USER Enzyme (NEB, USA) was used to digest the second strand withsize-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 minat 95°Cbefore PCR. Then PCR was performed with Phusion High-Fidelity DNApolymerase, Universal PCR primers and Index (X) Primer. And then, PCR products were purified(AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer2100 system.

treatment_protocol: no treatment

value: Cell Line

value: Tumor cell

value: WT

value: no


description: Library name: MN07_WT_Rep1_cutnrun_hiPS6_H3K9me3_L1_CRISPRi

value: hiPSC


title: hAoSMCs, scrambled control, rep2

value: Primary human aortic smooth muscle cells


title: 4260_WT-4M-Ki67-

value: male

value: microglia


title: UWB

description:
Library name: sample1
UWB_FPKM

value: BRCA1 Knockout


title: Mouse cell, cellSF01_EE_5, rep 5

description: Library name: hepa1-6 PC402+cr31214-2


title: hAoSMCs, miR-15a mimic, rep3


title: hAoSMCs, scrambled control, rep1


description: Library name: MN07_WT_Rep1_cutnrun_hiPS6_H3K4me3_L1_CRISPRi


title: Mouse cell, cellSF01_EE_4, rep 4

description: Library name: hepa1-6 PC402+cr31214-1


title: A549 cells, Merge_3

city: Gangneung-si

first: Young-Joo

last: Kim

state: Gangwon-do

address: 679, Saimdang-ro

country: South Korea

institute: Korea Institute of Science and Technology

description: Library name: Merge_3

data_processing:
The low quality sequence reads with less than 30 PHRED score and adapter sequence reads were trimmed using a Trim Galore tool.
Sequence reads were mapped to the human reference genome (GENCODE: GRCh38, release 47) using TopHat2 tool with default parameters.
RNA abundance was estimated by as the FPKM values according to GTF (GENCODE: GRCh38, release 45) using Cufflinks tool Genome_build
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: Tab-delimited text files include log2(FPKM+1) values for each sample
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: A549 cells were grown in RPMI with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from each sample using the RNeasy total RNA extraction kit (Qiagen) according to manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus

treatment_protocol: A549 cells were plated into 6-well plates at 3 × 105 cells/well and incubated for 24 hours before being treated with untreated (mock), CBD, Etoposdie, and combined.

value: Lung

value: Lung adenocarcinoma

value: Combination treatment (combination of 15 μM Etoposide +  20 μM CBD) for 24 hours


title: hAoSMCs, miR-15a inhibitor, rep2

value: miR-15a inhibitor


description: Library name: MN07_WT_Rep1_cutnrun_hiPS48_IgG_L1_CRISPRi


title: A549 cells, Merge_2

description: Library name: Merge_2


description: Library name: MN07_WT_Rep1_cutnrun_hiPS48_H3K9me3_L1_CRISPRi


title: Mouse cell, cellSF01_EE_3, rep 3

description: Library name: hepa1-6 PC402+cr51214-3


title: A549 cells, Merge_1

description: Library name: Merge_1


title: hAoSMCs, miR-15a inhibitor, rep1


title: Mouse cell, cellSF01_EE_2, rep 2

description: Library name: hepa1-6 PC402+cr51214-2


description: Library name: MN07_WT_Rep1_cutnrun_hiPS48_H3K4me3_L1_CRISPRi


title: Mouse cell, cellSF01_EE_1, rep 1

description: Library name: hepa1-6 PC402+cr51214-1


title: A549 cells, Eto_3

description: Library name: Eto_3

value: Etoposide treatment for 24 hours


title: hAoSMCs, miR-15a mimic, rep1


title: Mouse cell, cellMock_3, rep 3

description: Library name: hepa1-6 con-3


title: A549 cells, Eto_2

description: Library name: Eto_2


description: Library name: MN07_gRNA1_Rep1_cutnrun_hiPS6_dCas9_L1_CRISPRi


title: OE19 Input

first: Divyesh

last: Patel

address: University of Helsinki

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

data_processing:
FastQC v.0.11.9 was used for quality control and determination of read lengths of raw data.
Raw reads were mapped with bowtie2 v.2.4.1 (bowtie2 --very-sensitive) to the reference genome.
Picard v.2.23.4 was used to remove duplicates (MarkDuplicates -REMOVE_DUPLICATES false -ASSUME_SORT_ORDER coordinate).
Samtools v.1.7 was used to filter reads with MAPQ smaller than 20 and remove marked duplicates (samtools view -F 1024 -b -q 20).
Peaks were called with MACS2 v.2.2.7.1 (macs2 callpeak -g hs --keep-dup all).
Peaks overlapping with ENCODE blacklisted regions were removed from the narrowPeak and summit files with bedtools v.2.29.2 (bedtools subtract -A).
A RPKM normalized bigwig file was created with deepTools v.3.5.0 (bamCoverage --binSize 50 --normalizeUsing RPKM).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for the Input samples)

growth_protocol: GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. OE19 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:
Cells were formaldehyde cross-linked and sonicated chromatin was immunoprecipitated by using Dynal-bead coupled antibodies. Immunoprecipitated DNA was purified and used to prepare ChIP-seq library for Illumina sequencing.
Immunoprecipitated DNA was end-repaired, dA tailed and adapter ligated. Adaptor ligated DNA was PCR enriched as described earlier (Sahu et al., Nat. Gen. 2022).

treatment_protocol: GP5d and OE19 cells were co-inhibited with DNMT and HDAC. Cells were treated with 500 nM/L 5-aza-2'-deoxycytidine. DAC containing media  were replaced each day for three days. Cells were treated with 500 nmol/L SB939 for 18 hours.

value: Esophageal  adenocarcinoma

tag: chip antibody

value: input


description: Library name: MN07_LacZ_Rep1_cutnrun_hiPS6_dCas9_IgG_L1_CRISPRi

value: LacZ


title: OE19  Control, H3K4me3, Rep2

value: Diagenode, C15410003


title: Mouse cell, cellMock_2, rep 2

description: Library name: hepa1-6 con-2


title: OE19  Control, H3K4me3, Rep1


description: Library name: MN07_LacZ_Rep1_cutnrun_hiPS6_dCas9_L1_CRISPRi


title: Mouse cell, cellMock_1, rep 1

description: Library name: hepa1-6 con-1


title: hAoSMCs, miR-15a inhibitor, rep3


title: OE19  Control, H3K27ac, Rep2

value: Diagenode, C15410196


title: Mouse liver, Sp_713_EE_6, Day 30, rep 6

description: Library name: X348-6

source_name: liver

value: liver


title: A549 cells, CBD_2

description: Library name: CBD_2

value: Cannabidiol treatment for 24 hours


title: OE19  Control, H3K27ac, Rep1


description: Library name: MN07_gRNA1_Rep1_cutnrun_hiPS6_H3K9me3_L1_CRISPRi

value: hiPSC


description: Library name: MN07_gRNA1_Rep1_cutnrun_hiPS6_H3K4me3_L1_CRISPRi


title: Mouse liver, Sp_713_EE_4, Day 30, rep 4

description: Library name: X348-4


title: OE19  DNMTi-HDACi, H3K4me3, Rep2


title: OE19  DNMTi-HDACi, H3K4me3, Rep1


title: A549 cells, Mock_3

description: Library name: mock_3

value: non-treatment


title: A549 cells, CBD_1

description: Library name: CBD_1


title: MN07_LacZ_Rep1_hiPS6_IgG_L1_CRISPRi

description: Library name: MN07_LacZ_Rep1_hiPS6_IgG_L1_CRISPRi


title: A549 cells, Mock_2

description: Library name: mock_2


title: Mouse liver, Sp_713_EE_3, Day 30, rep 3

description: Library name: X348-3


title: MN07_LacZ_Rep1_hiPS6_H3K9me3_L1_CRISPRi

description: Library name: MN07_LacZ_Rep1_hiPS6_H3K9me3_L1_CRISPRi


title: OE19  DNMTi-HDACi, H3K27ac, Rep2


title: A549 cells, Mock_1

description: Library name: mock_1


title: Mouse liver, Sp_713_EE_2, Day 30, rep 2

description: Library name: X348-2


title: OE19  DNMTi-HDACi, H3K27ac, Rep1


title: A549 cells, Eto_1

description: Library name: Eto_1


title: MN07_LacZ_Rep1_hiPS6_H3K4me3_L1_CRISPRi

description: Library name: MN07_LacZ_Rep1_hiPS6_H3K4me3_L1_CRISPRi


title: Mouse liver, Sp_713_EE_1, Day 30, rep 1

description: Library name: X348-1


title: cg6

city: Jerusalem

first: Daniel

middle: S

last: Goldenberg

state: Select State

address: Kiryat Hadassah, P.O.B. 12000

department: The Goldyne Savad Institute of Gene and Cell Therapy

country: Israel

institute: Hadassah University Hospital

data_processing:
Quality assessment measures were first applied to FASTQ files with FastQC v0.11.8 tool.
Reads were next aligned to the transcriptome (HSA GRCh38) using Salmon v1.10.0.
Differential gene expressions were explored with DESeq2
Assembly: hg38
Supplementary files format and content: Tab delimited text file including raw counts per sample.

growth_protocol: DMEM, 37grad. C

extract_protocol:
micro miRNeasy kit with an additional DNAse treatment on column (Qiagen, Hilden, Germany ID 217084 and 79254).
Libraries were prepared using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen, Vienna,  Austria), which was followed by an amplification step according to the manufacturer’s instructions.

value: HCC

value: control

value: No treatment


title: A549 cells, CBD_3

description: Library name: CBD_3

value: Lung


title: GP5d DNMTi-HDACi, H3K4me3, Rep2

value: Colon adenocarcinoma


title: Mouse liver, Sp_573_EE_6, Day 30, rep 6

description: Library name: X342-6


title: cg5


title: Mouse liver, Sp_713_EE_5, Day 30, rep 5

description: Library name: X348-5


title: GP5d DNMTi-HDACi, H3K4me3, Rep1


title: cg3


title: OVOL1 OX 3

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

institute: Weizmann Institute of Science

description: Library name: MDA_231_OVOL1_OX_c3_3

data_processing:
Libraries were sequenced by the Illumina NextSeq 500
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154))
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Assembly: hg38
Supplementary files format and content: OVOL1_RNA-Seq.xlsx - Raw and normalized counts (genes in rows and samples in columns)

growth_protocol: Cells were maintained in RPMI medium supplemented with 10% FBS, 1% Penicillin-Streptomycin solution

extract_protocol:
RNA was isolated using Trizol reagent following manufacturer protocol
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

treatment_protocol: MDA-MB-231 cells were stably transfected with plasmid harboring Arrdc4 overexpression

value: Breast Cancer

value: OVOL1 overexpression


title: OVOL1 OX 4

description: Library name: MDA_231_OVOL1_OX_c3_4


title: Mouse liver, Sp_573_EE_5, Day 30, rep 5

description: Library name: X342-5


title: Mouse liver, Sp_573_EE_4, Day 30, rep 4

description: Library name: X342-4


title: cg1


title: OVOL1 OX 2

description: Library name: MDA_231_OVOL1_OX_c3_2


title: OVOL1 OX 1

description: Library name: MDA_231_OVOL1_OX_c3_1


title: GP5d DNMTi-HDACi, H3K27ac, Rep1


description: Library name: MN07_gRNA1_Rep1_cutnrun_hiPS6_IgG_L1_CRISPRi


title: Control 4

description: Library name: MDA_231_empty_6_3_c4_1

value: WT


title: ko11


title: GP5d DNMTi-HDACi, H3K27ac, Rep2


title: Mouse liver, Sp_573_EE_2, Day 30, rep 2

description: Library name: X342-2


title: ko5


title: Mouse liver, Sp_573_EE_1, Day 30, rep 1

description: Library name: X342-1


title: GP5d p53-KO, DNMTi-HDACi Rep2

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 geneexpression counts for each sample.

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. Cells were treated with 500 nmol/L SB939 for 18 hours and collected for RNA isolation and ChIP-seq. For DMSO control, cells were treated with DMSO (Fisher, BP231). Media containing DMSO were replaced each day for four days.
Generation of GP5d p53-KO and GP5d KAP1 heterozygous cell line is described in Sahu et al., Nat. Gen. (2022)

value: DNMT HDAC co-inhibition

tag: time

value: 96 hours


title: Mouse liver, Sp_EE_18, Day 120, rep 6

description: Library name: X330-6


title: ko2


title: ko1