title: Sample_4_male

status: Public on Mar 17 2020

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

data_processing:
ase call files  for the samples were converted to fastq files using the mkfastq utility in cellRanger
FASTQ files were aligned to the mm10 mouse genome and quantified with the cellRanger count utility
We used Seurat for the single-cell analysis. We performed a QC step to identify and remove cells that were potential outliers. This included removing potential multiplets  (i.e., cells that had clear outlier gene expression) and cells that had approximately ten percent or more of mitochondrial gene expression (i.e., cells that were likely to have high technical variation). After filtering out these suspect cells, we then normalized and log-transformed the data (using the 'LogNormalize' method), regressed out unwanted sources of technical variation (i.e., the number of detected molecules and mitochondrial contribution to gene expression), and scaled the counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data files are comma-separated matrix text files that contain CellRanger gene counts for each cell surveyed.

source_name: Full Brain

extract_protocol:
Brains were removed from healthy adult mice, digested to a single-cell suspension, stained, and then run through a cell sorter to isolate all YFP-expressing cells. Isolated cells were washed and then prepped for single-cell sequencing.
Libraries were prepared for single-cell sequencing according to manufacturer's instructions using the Chromium Next GEM Single-cell 3’ Reagent Kit (10xGenomics) to extract RNA, barcode, and create a cDNA library.
10X Genomics Chromium scRNA-seq

treatment_protocol: Mice were injected with 2 doses of tamoxifen at 6 weeks of age to induce recombination and flourescently label all cells expressing PDGFRα with YFP.

value: C57B6J; PDGFRalpha-CreER +/-;  YFP F/+

tag: date of isolation

value: 8-10 weeks


title: Sample_2_male

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

value: 17 weeks


title: Sample_5_female

value: 9-10 weeks


title: Sample_6_male


title: Sample_3_female


title: Sample_1_female

value: 17-20 weeks


title: sample_10_B_cells

status: Public on Mar 18 2020

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description: Bisulfite-converted DNA

library_source: genomic

data_processing:
Basecalls was performed using CASAVA
After trimming for low-quality bases (Phred score<30) and reads with a length <40 bp with TrimGalore, the reads were aligned to the human genome (GRCh37) using Bismark with paired end mode and default setting . For ACCEL-NGS Methyl-Seq DNA Library, as recommended by the manufacturer, 15 bp were trimmed on 5' and 3' of both reads.
Duplicate reads were removed using Picard tools and reads with more than 10% unconverted CHG or CHH cytosines were filtered out
SNP calling was performed with BisSNP using default settings, except for the maximum coverage filter set at 200. Heterozygous SNPs with less than 5 reads per allele were filtered out. In addition, SNP with multiple mapping positions were filtered out, as well as SNPs with more than one minor allele with allele frequency>0.05. or deviating significantly from Hardy-Weinberg equilibrium based on exact tests corrected for multiple tests. C/T and G/A SNPs were assessed after filtering out reads mapping to the C/T strand.
ASM calling was performed after separating the SNP-containing reads by allele using R. After Bismark methylation extractor is applied, CpG methylation calls by allele are retrieved using allele tagged read IDs. Paired reads with ambiguous SNP calling (i.e., called as REF allele on one paired end and ALT allele on the other) were discarded.
genome build: GRCh37
processed data files format and content: Processed files per sample contain difference in methylation percentage at the CpG level between the alternate and reference alleles for each SNPs associated with high confidence ASM (observed in >2 biological samples) if the given sample was informative. The columns include chromosome, start and end of the CpG (reported on positive strand), difference in methylayion percentage and SNP ID. The unique identifier in these files is the CpG coordinate AND SNP ID.

molecule: genomic DNA

organism: Homo sapiens

source_name: B cells

extract_protocol:
DNA extracted using phenol-chloroform protocol after RNAse treatment. DNA was bisulfite converted with the EZ DNA methylation kit (Zymo).
For Nextera transposase-based library approach, genomic DNA was first tagmented using Nextera XT transposome and end repair was performed using 5mC. After bisulfite conversion, Illumina adapters and custom bisulfite converted adapters are attached by limited cycle PCR. Illumina TruSeq DNA Methylation Kit and ACCEL-NGS Methyl-Seq DNA Library kit were used according to the manufacturer’s instructions.

tag: subject id

tag: cancer status

value: non-cancer

tag: organ

value: blood

tag: library

value: TruSeq DNA Methylation Kit


title: Patient 3

type: RNA

city: Munich

first: Oliver

last: Weigert

address: Max-Lebsche-Platz 30

country: Germany

institute: Experimental Leukemia and Lymphoma Research

hyb_protocol: See manufacturer's website http://www.nanostring.com

scan_protocol: maschine: NanoString nCounter MAX system; scan protocol: 555 fields of view (FOV)

data_processing: The normalization was performed under default settings in nSolver 4.0 software.

source_name: lymph node_diagnostic_biopsy

label_protocol: NanoString nCounter technology

growth_protocol: formalin-fixed paraffin-embedded tissue

extract_protocol: ExpressArt FFPE Clear RNAready kit (AmpTec) or the AllPrep FFPE (Qiagen)

tag: gender

value: female

tag: ffs

tag: protein exchange

tag: copy number gain


title: KO 4-8 ATAC-seq

city: Stanford

first: Andrey

last: Krokhotin

state: CA

address: 279 Campus Drive W

institute: HHMI

data_processing:
RNA-seq sequenced reads were trimmed for adaptor sequence using trim_galore with parameters ---paired --illumina, then kallisto quant (version 0.44.0)  was used to quantify transcripts. DESeq2 was used for gene differential expression analysis.  Change in gene expression between two conditions was defined as significant if absolute log2 fold change > 0.5 and FDR<5%. ComplexHeatmap package was used to generate heatmap.
ATAC-seq sequenced reads were trimmed for adaptor sequence and aligned to the mouse genome (mm9) using bowtie2. Paired reads with up to 2 kb separation were used (-X2000). Positions of Tn5 inserts were determined as a read start position offset by +4 bp for reads aligned to + strand and as a read start position offset by -5 bp for reads aligned to – strand. MACS2 was used for peak calling on Tn5 inserts positions. The following parameters were used --shift -75 --extsize 150 --nomodel -p 0.01. Peaks were merged across all conditions using bedtools. Principal component analysis and differential peak calling were performed using DESeq2. Change in gene expression between two conditions was defined as significant if absolute log2 fold change > 0.5 and FDR<5%.
Genome_build: RNA-seq data were aligned to mm10; ATAC-seq data were aligned to mm9
Supplementary_files_format_and_content: tab-delimited tsv files include transcript counts and TPM values for each RNA-seq Sample

source_name: primary cortical neurons

extract_protocol:
Neurons were washed and collected in ice-cold PBS usinga cell lifter (Corning #3008), and then counted using a Countess II FL cell counter (Applied Biosystems).
Accessible chromatin from 55,000 neurons per biological sample were transposed and tagged using Tn5(Nextera DNA Sample Prep Kit from Illumina, cat# FC-121-1030). Libraries were quantified by PCR using a PhiX library (Illumina cat# TG-110-3001) standard curve and then multiplexed at a 1:1 ratio

tag: cell type

value: cortical neurons derived from E16.5 embryos cultured for 7 days in vitro

tag: treatment

value: 2h TTX/APV

tag: genotype

value: ACTL6B -/-


title: KO 3-2 ATAC-seq


title: WT 4-3 ATAC-seq

value: wild type


title: WT 3-7 ATAC-seq


title: KO 2-3 ATAC-seq


title: KO 3-3 ATAC-seq


title: WT 4-4 ATAC-seq


title: WT 4-4 6h-KCl RNA-seq

extract_protocol:
Neurons were washed 1x with ice-cold PBS and collected with 1 mL per 6-well TRIzol (Life Technologies, cat# 15596081). Total RNA was extracted and DNAse treated using the DirectZol kit(Zymo Research cat# R2060). RNA quality was confirmed by Bioanalyzer (Agilent)
Individual RNA libraries were prepared with unique barcodes using the SMARTer Stranded Total RNA Sample Prep HI Kit (Clontech cat# 634874). Libraries were quantified by PCR using a PhiX library (Illumina cat# TG-110-3001) standard curve and then multiplexed at a 1:1 ratio.

value: 7h TTX/APV and 6h KCl


title: KO 3-5 ATAC-seq


title: KO 4-7 ATAC-seq


title: WT 4-2 ATAC-seq


title: WT 4-4 6h control RNA-seq

value: 7h TTX/APV


title: WT 3-4 ATAC-seq


title: WT 3-7 6h-KCl RNA-seq


title: WT 4-4 1h-KCl RNA-seq

value: 2h TTX/APV and 1h KCl


title: WT 4-2 6h control RNA-seq


title: WT 4-3 1h-KCl RNA-seq


title: WT 3-7 6h control RNA-seq


title: WT 4-2 1h-KCl RNA-seq


title: WT 3-4 1h-KCl RNA-seq


title: KO 3-5 RNA-seq


title: KO 4-8 RNA-seq


title: KO 4-7 RNA-seq


title: KO 2-3 RNA-seq


title: KO 3-2 RNA-seq


title: KO 1-1 ATAC-seq


title: WT 4-2 6h-KCl RNA-seq


title: KO 1-1 RNA-seq


title: WT 3-4 6h control RNA-seq


title: WT 3-7 RNA-seq


title: WT 4-4 RNA-seq


title: WT 4-3 RNA-seq


title: mES_Mll2KO_100nM5dAza_mRRBS_rep1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: fragmented genomic DNA

data_processing:
Basecalls were performed using  bcl2fastq.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For PRO-seq analyses, PRO-seq raw data were trimmed by cutadapt 1.14 and Trimmomatic 0.33. Each sample was next mapped to the mouse and fruit fly genome assemblies (mm9 and dm3, respectively) using Bowtie. The number of fly reads on each experiment was used to normalize the corresponding genome-wide strand-specific profiles.
For CRISPR screen sequencing, reads were aligned to the sgRNAs using Bowtie1. For CRISPR screen counts, the enrichment of individual guides was calculated as the log2 ratios ‘Sorted cells’ and ‘Total population’, with each sgRNA with a log2FC > 1 considered as enriched.
For mRRBS, well-observed CpG positions were obtained by performing an analysis of variance (ANOVA)–like test for differential methylation with the DSS v2.26.0 R/Bioconductor package and quantified using the SeqMonk platform (v1.40.1) with the bisulfite feature methylation pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: embryonic stem cell

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) and RNAse free DNaseI (Sigma) was used to eliminate DNA contamination.
For ChIPseq, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). Sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, and reverse-crosslinking and submitted for library preparation.
For PROseq, nuclei were isolated by Dounce homogenizer with loose pestle. Nuclei were subjected to nuclear run-on in the presence of biotin-11-ATP/GTP/CTP/UTP and Drosophila S2 spike-in nuclei. Biotinylated nascent RNA was purified by Dynabeads M-280 streptavidin.
For mRRBS, genomic DNA was digested with MspI (New England BioLabs) before size selection of 100- to 250-bp fragments with solid-phase reversible immobilization beads (MagBio Genomics). DNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

treatment_protocol: differentiation protocol: 1500 ESCs were cultured in 25 µL of EB differentiation medium on the lid of 150-mm culture plates for 6 d. EB differentiation medium was composed of DMEM supplemented with 15% FBS (Gemini Bio-Products), 1× GlutaMAX (Gibco), 1× MEM nonessential amino acids (Gibco), 1× β-mercaptoethanol (Gibco), and 1× penicillin–streptomycin (Gibco).

value: embryonic stem cell

tag: cell line

tag: drug treatment

tag: genotype/variation


title: mES_Mll2KO_DMSO_mRRBS_rep3

description: fragmented genomic DNA

value: DMSO


title: mES_Mll2KO_100nM5dAza_mRRBS_rep2

description: fragmented genomic DNA


title: mES_WT_DMSO_mRRBS_rep3

description: fragmented genomic DNA

value: WT


title: mES_Mll2KO_100nM5dAza_mRRBS_rep3

description: fragmented genomic DNA


title: mES_Mll2KO_DMSO_mRRBS_rep1

description: fragmented genomic DNA


title: mES_Mll2KO_100nM5dAzaRNA_rep2

description:
Mll2KO
total RNA

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For PRO-seq analyses, PRO-seq raw data were trimmed by cutadapt 1.14 and Trimmomatic 0.33. Each sample was next mapped to the mouse and fruit fly genome assemblies (mm9 and dm3, respectively) using Bowtie. The number of fly reads on each experiment was used to normalize the corresponding genome-wide strand-specific profiles.
For CRISPR screen counts, the enrichment of individual guides was calculated as the log2 ratios ‘Sorted cells’ and ‘Total population’, with each sgRNA with a log2FC > 1 considered as enriched.
For mRRBS, well-observed CpG positions were obtained by performing an analysis of variance (ANOVA)–like test for differential methylation with the DSS v2.26.0 R/Bioconductor package and quantified using the SeqMonk platform (v1.40.1) with the bisulfite feature methylation pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: ESCs were grown in N2B27 media supplemented with LIF (2i/LIF) and 5dAza.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) and RNAse free DNaseI (Sigma) was used to eliminate DNA contamination.
For ChIPseq, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). Sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, and reverse-crosslinking and submitted for library preparation.
For PROseq, nuclei were isolated by Dounce homogenizer with loose pestle. Nuclei were subjected to nuclear run-on in the presence of biotin-11-ATP/GTP/CTP/UTP and Drosophila S2 spike-in nuclei. Biotinylated nascent RNA was purified by Dynabeads M-280 streptavidin.
For mRRBS, genomic DNA was digested with MspI (New England BioLabs) before size selection of 100- to 250-bp fragments with solid-phase reversible immobilization beads (MagBio Genomics). DNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit.
For CRISPR screen sequencing, reads were aligned to the sgRNAs using Bowtie1.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

treatment_protocol:
For shRNA knockdown, ESCs were infected with lentivial shRNA in the presense of 10ug/ml polybrene for 24 hours and then selected with 2 ug/ml puromycin for 72h before harvest for ChIP-seq or RNA-seq experiments.
For sgRNA knockdown, ESCs were infected with lentivial sgRNA in the presense of 10ug/ml polybrene for 24 hours and then selected with 2 ug/ml puromycin for 7days before harvest for ChIP-seq or RNA-seq experiments.

value: 100nM 5dAza for 4 days

tag: genotype/variant


title: mES_WT_DMSO_mRRBS_rep2

description: fragmented genomic DNA


title: mES_WT_DMSO_mRRBS_rep1

description: fragmented genomic DNA


title: mES_Mll2KO_DMSO_mRRBS_rep2

description: fragmented genomic DNA


title: WT 3-4 RNA-seq


title: mES_Mll2KO_0dAzaRNA_rep2

description:
Mll2KO
total RNA


title: mES_WT_0dAzaRNA_rep2

description:
WT
total RNA


title: WT 3-7 1h-KCl RNA-seq


title: KO 3-3 RNA-seq


title: mES_Mll2KO_0dAzaRNA_rep1

description:
Mll2KO
total RNA


title: mES_Mll2KO_sgNTRNA_rep2

description:
Mll2KO
total RNA

tag: shRNA/sgrna

value: sgNT


title: mES_WT_0dAzaRNA_rep1

description:
WT
total RNA


title: mES_Mll2KO_sgDnmt1RNA_rep2

description:
Mll2KO
total RNA


title: mES_Mll2KO_sgNTRNA_rep1

description:
Mll2KO
total RNA


title: mES_Mll2KO_sgDnmt1RNA_rep1

description:
Mll2KO
total RNA


title: mES_WT_sgNTRNA_rep2

description:
WT
total RNA


title: mES_Mll2KO_shCXXC1mRRBS_rep3

description:
Mll2KO
fragmented genomic DNA


title: mES_WT_sgNTRNA_rep1

description:
WT
total RNA


title: mES_Mll2KO_shNTmRRBS_rep3

description:
Mll2KO
fragmented genomic DNA

value: shNT


title: mES_WT_shNTmRRBS_rep3

description:
WT
fragmented genomic DNA


title: mES_Mll2KO_shCXXC1mRRBS_rep2

description:
Mll2KO
fragmented genomic DNA


title: mES_Mll2KO_shCXXC1mRRBS_rep1

description:
Mll2KO
fragmented genomic DNA


title: mES_WT_shNTmRRBS_rep2

description:
WT
fragmented genomic DNA


title: mES_Mll2KO_shNTmRRBS_rep1

description:
Mll2KO
fragmented genomic DNA


title: mES_WT_shNTmRRBS_rep1

description:
WT
fragmented genomic DNA


title: mES_Mll2KO_shNT_Set1aChIP

description:
Mll2KO
fragmented genomic DNA

tag: chip antibody

value: Set1a (Homemade, #919)


title: mES_Mll2KO_shCXXC1PRO_rep1

description:
Mll2KO
Nacent RNA

data_processing:
Library strategy: PRO-seq
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For PRO-seq analyses, PRO-seq raw data were trimmed by cutadapt 1.14 and Trimmomatic 0.33. Each sample was next mapped to the mouse and fruit fly genome assemblies (mm9 and dm3, respectively) using Bowtie. The number of fly reads on each experiment was used to normalize the corresponding genome-wide strand-specific profiles.
For CRISPR screen counts, the enrichment of individual guides was calculated as the log2 ratios ‘Sorted cells’ and ‘Total population’, with each sgRNA with a log2FC > 1 considered as enriched.
For mRRBS, well-observed CpG positions were obtained by performing an analysis of variance (ANOVA)–like test for differential methylation with the DSS v2.26.0 R/Bioconductor package and quantified using the SeqMonk platform (v1.40.1) with the bisulfite feature methylation pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.


title: mES_Mll2KO_shCXXC1_Set1aChIP

description:
Mll2KO
fragmented genomic DNA


title: mES_Mll2KO_shCXXC1PRO_rep2

description:
Mll2KO
Nacent RNA


title: mES_Mll2KO_shNTPRO_rep2

description:
Mll2KO
Nacent RNA


title: WT 4-2 RNA-seq


title: mES_WT_shNTPRO_rep2

description:
WT
Nacent RNA


title: mES_WT_shNT_Set1aChIP

description:
WT
fragmented genomic DNA


title: mES_TMutant_shCXXC1RNA_rep2_ep

description:
Set1bKO, Mll2△SET, Set1a△SET
total RNA

value: Set1bKO, Mll2deltaSET, Set1adeltaSET


title: mES_Mll2KO_shNTPRO_rep1

description:
Mll2KO
Nacent RNA


title: mES_WT_shNTPRO_rep1

description:
WT
Nacent RNA


title: mES_TMutant_shNTRNA_rep2_ep

description:
Set1bKO, Mll2△SET, Set1a△SET
total RNA


title: mES_Mll2dSET_shCXXC1RNA_rep2_ep

description:
Mll2△SET
total RNA


title: mES_Mll2dSET_shNTRNA_rep2_ep

description:
Mll2△SET
total RNA


title: mES_WT_shNTRNA_rep2_ep

description:
WT
total RNA


title: mES_TMutant_shNTRNA_rep1_ep

description:
Set1bKO, Mll2△SET, Set1a△SET
total RNA


title: mES_Mll2dSET_shNTRNA_rep1_ep

description:
Mll2△SET
total RNA


title: mES_Mll2KO_shNTRNA_rep2

description:
Mll2KO
total RNA


title: mES_WT_shNTRNA_rep1_ep

description:
WT
total RNA


title: mES_Mll2dSET_shCXXC1RNA_rep1_ep

description:
Mll2△SET
total RNA


title: mES_Mll2KO_shNTmRRBS_rep2

description:
Mll2KO
fragmented genomic DNA


title: mES_WT_shNTRNA_rep2

description:
WT
total RNA


title: mES_Mll2KO_shCXXC1RNA_rep2

description:
Mll2KO
total RNA


title: mES_WT_shNTRNA_rep1

description:
WT
total RNA


title: mES_WTRNA_rep1

description:
WT
total RNA


title: mES_Sorted_population_Mll2KO

description:
Mll2KO Cas9
sgRNA PCR

data_processing:
Library strategy: PCR sgRNA
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For PRO-seq analyses, PRO-seq raw data were trimmed by cutadapt 1.14 and Trimmomatic 0.33. Each sample was next mapped to the mouse and fruit fly genome assemblies (mm9 and dm3, respectively) using Bowtie. The number of fly reads on each experiment was used to normalize the corresponding genome-wide strand-specific profiles.
For CRISPR screen counts, the enrichment of individual guides was calculated as the log2 ratios ‘Sorted cells’ and ‘Total population’, with each sgRNA with a log2FC > 1 considered as enriched.
For mRRBS, well-observed CpG positions were obtained by performing an analysis of variance (ANOVA)–like test for differential methylation with the DSS v2.26.0 R/Bioconductor package and quantified using the SeqMonk platform (v1.40.1) with the bisulfite feature methylation pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

value: Brie library (sgRNA library)

value: Mll2KO Cas9


title: mES_Mll2KORNA_rep2

description:
Mll2KO
total RNA


title: mES_Mll2KORNA_rep1

description:
Mll2KO
total RNA


title: mES_Sorted_population_WT

description:
WT Cas9
sgRNA PCR

value: WT Cas9


title: mES_Mll2KO_shNTRNA_rep1

description:
Mll2KO
total RNA


title: mES_input_H3K4me3ChIP_rep1

description:
WT
fragmented genomic DNA

value: H3K4me3 (Homemade, #28)


title: mES_Mll2KO_shCXXC1_H3K4me3ChIP_rep1

description:
Mll2KO
fragmented genomic DNA


title: mES_Mll2KO_shCXXC1RNA_rep1

description:
Mll2KO
total RNA


title: mES_Total_population_WT

description:
WT Cas9
sgRNA PCR


title: mES_Mll2KO_shNT_H3K4me3ChIP_rep2

description:
Mll2KO
fragmented genomic DNA


title: mES_Total_population_Mll2KO

description:
Mll2KO Cas9
sgRNA PCR


title: mES_WTRNAseq_rep2

description:
WT
total RNA


title: mES_TMutant_shCXXC1RNA_rep1_ep

description:
Set1bKO, Mll2△SET, Set1a△SET
total RNA


title: mES_Mll2KO_shCXXC1_H3K4me3ChIP_rep2

description:
Mll2KO
fragmented genomic DNA


title: mES_input_Mll2ChIP_H3K4me3ChIP_rep2

description:
WT
fragmented genomic DNA

value: Mll2 (Homemade, #9173)


title: mES_WT_shNT_H3K4me3ChIP_rep1

description:
WT
fragmented genomic DNA


title: mES_Mll2KO_shNT_H3K4me3ChIP_rep1

description:
Mll2KO
fragmented genomic DNA


title: mES_Mll2KO_Mll2ChIP_rep2

description:
Mll2KO
fragmented genomic DNA


title: RNA from healthy control  H16

city: Suzhou

first: Xingbo

last: Mo

address: Renai Road

country: China

institute: Soochow University

description: healthy control

hyb_protocol: Standard Affymetrix Hybridization Protocol

scan_protocol: Standard Affymetrix scan Protocol

data_processing: AGCC software（Affymetrix® GeneChip® Command Console® Software）

label: biotin

label_protocol: Standard Affymetrix biotin label Protocol

growth_protocol: 15-ml peripheral blood was collected and stored in sodium-citrate-supplemented vacuum tubes. PBMCs were isolated using density gradient centrifugation using Lymphoprep (Sigma, life science, USA).

extract_protocol: Total RNA was extracted from PBMCs using Trizol (Invitrogen, Carlsbad, California, USA)and quantified by using NanoDrop ND-1000 (Thermo Scientific, Wilmington, Delaware, USA) spectrophotometer.

treatment_protocol: Trizol reagent (Invitrogen, Catalogue No. 15596026, USA) was added to avoid RNA degradation.

value: female

tag: tissue

value: peripheral blood mononuclear


title: RNA from healthy control  H18

description: healthy control


title: mES_WT_shNT_H3K4me3ChIP_rep2

description:
WT
fragmented genomic DNA


title: mES_input_Mll2ChIP_rep1

description:
WT
fragmented genomic DNA


title: F1-Lupus CMP rep.3

city: Athens

first: Maria

last: Grigoriou

state: Papagou

address: Soranou Efesiou 4

country: Greece

institute: BRFAA

description:
CMP6
F1-L.3
Lupus-prone
mRNA-Seq
processed data file: cpm_CMP.csv

data_processing:
Illumina RTAv.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence (q<30), then mapped to mm10 whole genome using STAR v2.6.
Counts Per Million (CPM) were calculated using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.csv: Comma-separated text files include normalized expression values (CPM) for each dataset.

source_name: Bone Marrow

extract_protocol:
LSK and CMP cells were isolated using flow cytometry cell sorting. RNA was harvested using NucleoSpin® RNA XS.
Illumina TruSeq RNA Sample Prep Kit v2 was used with 500ng of total RNA for the construction of sequencing libraries.

tag: strain/background

value: NZB/W F1

tag: disease state

value: Lupus

tag: age

value: Old

value: CMP


title: F1-Lupus CMP rep.1

description:
CMP4
F1-L.1
Lupus-prone
mRNA-Seq
processed data file: cpm_CMP.csv


title: F1-Prediseased CMP rep.2

description:
CMP2
F1-P.2
mRNA-Seq
Lupus-prone
processed data file: cpm_CMP.csv

value: Prediseased

value: Young


title: RNA from healthy control  H14

description: healthy control

tag: gender


title: RNA from healthy control  H13

description: healthy control


title: RNA from healthy control  H12

description: healthy control


title: RNA from healthy control  H15

description: healthy control


title: RNA from healthy control  H17

description: healthy control


title: F1-Prediseased CMP rep.1

description:
CMP1
F1-P.1
Lupus-prone
mRNA-Seq
processed data file: cpm_CMP.csv


title: B6-Old LSK rep.3

description:
HSC12
B6.O3
mRNA-Seq
processed data file: cpm_LSK.csv

value: Wild-type

value: Normal

value: LSK


title: RNA from healthy control  H10

description: healthy control


title: B6-Old LSK rep.2

description:
HSC11
B6.O2
mRNA-Seq
processed data file: cpm_LSK.csv


title: RNA from healthy control  H11

description: healthy control


title: mES_WT_Mll2ChIP_rep2

description:
WT
fragmented genomic DNA

value: embryonic stem cell

value: WT


title: RNA from healthy control  H07

description: healthy control


title: RNA from healthy control  H09

description: healthy control


title: B6-Old LSK rep.1

description:
HSC10
B6.O1
mRNA-Seq
processed data file: cpm_LSK.csv


title: RNA from healthy control  H05

description: healthy control


title: mES_Mll2KO_Mll2ChIP_rep1

description:
Mll2KO
fragmented genomic DNA


title: mES_WT_Mll2ChIP_rep1

description:
WT
fragmented genomic DNA


title: F1-Lupus CMP rep.2

description:
CMP5
F1-L.2
Lupus-prone
mRNA-Seq
processed data file: cpm_CMP.csv


title: B6-Young LSK rep.3

description:
HSC9
B6.Y3
mRNA-Seq
processed data file: cpm_LSK.csv


title: F1-Prediseased CMP rep.3

description:
CMP3
F1-P.3
Lupus-prone
mRNA-Seq
processed data file: cpm_CMP.csv


title: RNA from healthy control  H03

description: healthy control


title: RNA from healthy control  H08

description: healthy control


title: RNA from healthy control  H04

description: healthy control


title: RNA from healthy control  H06

description: healthy control


title: B6-Young LSK rep.2

description:
HSC8
B6.Y2
mRNA-Seq
processed data file: cpm_LSK.csv


title: RNA from healthy control  H02

description: healthy control


title: RNA from healthy control  H01

description: healthy control


title: B6-Young LSK rep.1

description:
HSC7
B6.Y1
mRNA-Seq
processed data file: cpm_LSK.csv


title: F1-Prediseased LSK rep.2

description:
HSC5
F1.P2
Lupus-prone
mRNA-Seq
processed data file: cpm_LSK.csv


title: F1-Prediseased LSK rep.3

description:
HSC6
F1.P3
Lupus-prone
mRNA-Seq
processed data file: cpm_LSK.csv


title: F1-Prediseased LSK rep.1

description:
HSC4
F1.P1
Lupus-prone
mRNA-Seq
processed data file: cpm_LSK.csv


title: F1-Lupus LSK rep.2

description:
HSC2
F1.L2
Lupus-prone
mRNA-Seq
processed data file: cpm_LSK.csv


title: RNA from RA pateint P27

description: rheumatoid arthritis


title: F1-Lupus LSK rep.1

description:
HSC1
F1.L1
Lupus-prone
mRNA-Seq
processed data file: cpm_LSK.csv


title: mES_Mll2KO_100nM5dAzaRNA_rep1

description:
Mll2KO
total RNA

value: 100nM 5dAza for 4 days


title: RNA from RA pateint P26

description: rheumatoid arthritis


title: RNA from RA pateint P25

description: rheumatoid arthritis


title: RNA from RA pateint P24

description: rheumatoid arthritis


title: Lytic_H3K4me1_ChIPseq

city: Los Angeles

first: Angela

last: Park

address: 1501 San Pablo St, ZNI 521

department: Molecular Microbiology and Immunology

institute: University of Southern California

data_processing:
Reads were trimmed based on quality score from both ends using Partek Flow and aligned  to hg19 genome using bowtie 2. Peak calling and annotation were done using HOMER
Reads were trimmed based on quality score from both ends using Partek Flow
Reads were aligned to hg19 genome using bowtie 2
(ChIP-Seq) Peak calling was done using HOMER (H3K27ac peaks used -size 1000)
(ChIP-Seq) Peak annotation was done using HOMER; TSS peaks were removed
(ChIP-Seq) Motif analysis was done using HOMER
(ChIP-Seq) Heatmaps and profiles were generated using NGSPlot (-SC global, -G hg19, -L 10000)
(ChIP-Seq) Potential superenhancers were identified using HOMER (-sytle super)
(4C-Seq) Genomic interactions were identified using 4cseqpipe (hg19 genome used; -stat_type linear_mean -trend_resolution 1000)
(GROSeq) Peak calling and annotation done using HOMER (-style groseq)
(GROSeq) NGSPlot used to generate heatmaps and profiles  (-SC global, -G hg19, -L 10000)
Genome_build: hg19
Supplementary_files_format_and_content: peaks

growth_protocol: RPMI1640 + 10% FBS + 1% Pen/Strep + 20ug/ml Hygromycin

extract_protocol:
Cells were fixed with 1% formaldehyde and total nuclei was extracted
KAPA HyperPrep kit

treatment_protocol: 1ug/ml doxycycline for 24 h

tag: infection

value: KSHV

tag: replication

value: Lytic

value: rabbit anti-H3K4me1 (Abcam 8895 lot# GR3283236-1)


title: Lytic_H3K27ac_ChIPseq-set2

value: rabbit anti-H3K27ac (Active Motif 39133 lot# 28518012)


title: RNA from RA pateint P22

description: rheumatoid arthritis

value: female

value: peripheral blood mononuclear


title: RNA from RA pateint P23

description: rheumatoid arthritis


title: RNA from RA pateint P21

description: rheumatoid arthritis


title: Latent_H3K27ac_ChIPseq-set2

value: Latent


title: RNA from RA pateint P20

description: rheumatoid arthritis


title: Latent_H3K4me1_ChIPseq


title: Latent_H3K27ac_ChIPseq-set1


title: Latent_MYCenhancer_4Cseq

data_processing:
Library strategy: 4C-seq
Reads were trimmed based on quality score from both ends using Partek Flow and aligned  to hg19 genome using bowtie 2. Raw files were directly used for analysis with 4cseqpipe
Reads were trimmed based on quality score from both ends using Partek Flow
Reads were aligned to hg19 genome using bowtie 2
(ChIP-Seq) Peak calling was done using HOMER (H3K27ac peaks used -size 1000)
(ChIP-Seq) Peak annotation was done using HOMER; TSS peaks were removed
(ChIP-Seq) Motif analysis was done using HOMER
(ChIP-Seq) Heatmaps and profiles were generated using NGSPlot (-SC global, -G hg19, -L 10000)
(ChIP-Seq) Potential superenhancers were identified using HOMER (-sytle super)
(4C-Seq) Genomic interactions were identified using 4cseqpipe (hg19 genome used; -stat_type linear_mean -trend_resolution 1000)
(GROSeq) Peak calling and annotation done using HOMER (-style groseq)
(GROSeq) NGSPlot used to generate heatmaps and profiles  (-SC global, -G hg19, -L 10000)
Genome_build: hg19
Supplementary_files_format_and_content: peaks

extract_protocol: We followed a previous published protocol (Stadhouders et al., 2013 Nat Protocol)


title: RNA from RA pateint P28

description: rheumatoid arthritis


title: RNA from RA pateint P18

description: rheumatoid arthritis


title: RNA from RA pateint P19

description: rheumatoid arthritis


title: Latent_MYCpromoter_4Cseq


title: RNA from RA pateint P17

description: rheumatoid arthritis


title: MDA_STRIP1_3

city: Lund

first: Chris

middle: Denis

last: Madsen

address: Scheelevägen 2

department: Laboratory Medicine

country: Sweden

institute: Lund University

data_processing:
Demultiplexing: Demultiplexing step (bcl2fastq2) involves in reorganizing the FASTQ files based on the sample index information, and generating the statistics and reporting files.
Masking step: Masking step (bowtie2) performs masking of ribosomal RNA, PhiX and repeats sequences.
Read Mapping: Mapping step (Tophat/bowtie2) performs reads alignment to the reference genome (hg38).
Expression counts: Expression count step (Cufflinks 2.2.1) perform counting reads for transcripts.  The reference gtf file (UCSC_hg38_knownGenes_22sep2014.gtf) was used to run cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited files containing gene isoform level FPKM values as obtained from the Cufflinks software package

source_name: MDA-MB-231 breast cancer cells

growth_protocol: Cells were maintained in DMEM high glucose with 10% FBS and 1% Pen-strep at 37℃

extract_protocol:
Cells were harvested 72 hours post-transfection using Rneasy kit (Qiagen) and treated with DNase I.
Library was prepared according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.
TruSeq® Stranded mRNA Library Prep

treatment_protocol: Cells were transfected using Lipofectamine 2000 reagent for siControl (Ctr) and siSTRIP1 (40A)

value: MDA-MB-231 breast cancer cells

tag: sirna


title: RNA from RA pateint P15

description: rheumatoid arthritis


title: RNA from RA pateint P16

description: rheumatoid arthritis


title: MDA_STRIP1_2


title: RNA from RA pateint P12

description: rheumatoid arthritis


title: MDA_STRIP1_1


title: Lytic_H3K27ac_ChIPseq-set1


title: MDA_Ctrl_3

value: siControl


title: F1-Lupus LSK rep.3

description:
HSC3
F1.L3
Lupus-prone
mRNA-Seq
processed data file: cpm_LSK.csv

value: NZB/W F1

value: Lupus

value: Old

tag: cell type


title: MDA_Ctrl_2


title: MDA_Ctrl_1


title: RNA from RA pateint P10

description: rheumatoid arthritis


title: RNA from RA pateint P09

description: rheumatoid arthritis


title: RNA from RA pateint P14

description: rheumatoid arthritis


title: elf6-ref6-jmj13-htr10_rep3

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

institute: Max Planck Insititue for Biology

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.4.1.
Reads were aligned to the Arabidopsis genome (TAIR10) using the STAR aligner version 2.5.2a.
Transcripts per million (TPM) values were generated using Kallisto version 0.43.1 (21) with an index built on TAIR10 cDNA sequences.
Differential gene expression analysis of htr10, elf6;ref6;jmj13 and elf6;ref6;jmj13;htr10 was performed using DESeq2 1.22.2 for transcripts that had 10 counts or more in at least one sample.
Differentially expressed genes (DEGs) were classified as having a p-value < 0.1 after correction for multiple testing (i.e. adjusted p-value).
Genome_build: TAIR10 cDNA sequences (Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz)
Supplementary_files_format_and_content: *.tsv: Kallisto quantification abundance.tsv output

organism: Arabidopsis thaliana

source_name: elf6;ref6;jmj13;htr10 homozygous mutant pollen

extract_protocol:
RNA-seq libraries were generated from total RNA of mature pollen using Smart-seq2.
Smart-seq2

value: Mature pollen

tag: ecotype


title: elf6-ref6-jmj13-htr10_rep1

tag: genotype


title: elf6-ref6-jmj13-htr10_rep2


title: RNA from RA pateint P07

description: rheumatoid arthritis


title: RNA from RA pateint P06

description: rheumatoid arthritis


title: RNA from RA pateint P13

description: rheumatoid arthritis


title: Macrophage Untreated #4

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were adapter-trimmed and quality-filtered with Trimmomatic.
High quality fastq files were aligned to the human genome by using STAR.
Gene read counts were calculated with featureCounts.
Differential gene expression was performed with DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: gene counts, tabular

molecule: polyA RNA

source_name: Macrophage Untreated

extract_protocol:
Total RNA isolation was performed with RNeasy Mini Kit (QIAGEN).
RNA libraries were generated starting from 1 µg of total RNA. RNA quality was assessed by using a Tape Station instrument (Agilent). To avoid over-representation of 3’ends, only high-quality RNA with RNA Integrity Number (RIN) ≥ 8 was used.

value: Macrophages

tag: treated with

value: none (untreated)


title: Macrophage Untreated #3


title: Macrophage VEGFR3 #4

source_name: Macrophage VEGFR3


title: Macrophage Untreated #1


title: RNA from RA pateint P04

description: rheumatoid arthritis


title: RNA from RA pateint P02

description: rheumatoid arthritis


title: elf6-ref6-jmj13_rep2

source_name: elf6;ref6;jmj13 homozygous mutant pollen


title: RNA from RA pateint P08

description: rheumatoid arthritis


title: RNA from RA pateint P01

description: rheumatoid arthritis


title: Macrophage VEGFR3 #3


title: elf6-ref6-jmj13_rep1


title: Macrophage VEGFR3 #2


title: RNA from RA pateint P11

description: rheumatoid arthritis


title: Macrophage VEGFR3 #1


title: htr10_rep3

source_name: htr10 homozygous mutant pollen


title: Lymphatic Untreated #4

source_name: Lymphatic Untreated

value: Lymphatic endothelial cells


title: htr10_rep2


title: RNA from RA pateint P03

description: rheumatoid arthritis


title: Macrophage Untreated #2


title: RNA from RA pateint P05

description: rheumatoid arthritis


title: Lymphatic Untreated #3


title: Lymphatic Untreated #2


title: elf6-ref6-jmj13_rep3


title: WT_rep3

source_name: wild type pollen

value: wild type


title: Lymphatic Untreated #1


title: WT_rep2


title: htr10_rep1


title: Lymphatic VEGFR3 #4

source_name: Lymphatic VEGFR3


title: WT_rep1


title: H3K4me3_rep2

description:
anti-H3K4me3_rep1 IP from Input_A_rep2
H3K4me3.merged.log2r.bw
narrow_H3K4me3_peaks.narrowPeak
broad_H3K4me3_peaks.broadPeak

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.4.1.
Reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 version 2.1.0.
Reads were filtered for a MAPQ score > 10 using SAMtools version 1.3 and subsequently filtered for duplicate reads using Picard tools MarkDuplicates version 1.141.
Biological replicates were subsequently merged for downstream analysis after confirming high correlation among replicates.
For data visualization, log2 ratio bigwig coverage files relative to input were generated using the deepTools version 2.5.0.1 utility bamCoverage with a bin size of 10 bp.
Peaks were called using the MACS2 version 2.1.0 callpeak function using -f BAMPE --broad --broad-cutoff 0.1 -g 1.2e8
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: *.bw: Normalized log2 ratio coverage of histone marks relative to relevant input sample. Data is generated from merged replicates.
Supplementary_files_format_and_content: *.narrowPeak: MACS2 narrowPeaks generated from merged replicates.
Supplementary_files_format_and_content: *.broadPeak: MACS2 broadPeaks generated from merged replicates.

source_name: Sperm nuclei

extract_protocol:
Sperm nuclei from an ProHTR10:HTR10-Clover line were isolated by FACS and stored at -80°C in Cryopreservation Buffer (50 mM Tris-Cl pH 8.0, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 1 mM PMSF, 1x Roche protease inhibitor cocktail). Sperm mononucleosomes were generated by micrococcal nuclease (MNase, New England Biolabs) digestion. Aliquots of frozen sperm nuclei were thawed on ice and subsequently subjected to MNase digestion in MNase digestion buffer (1x NEB MNase reaction buffer, 1.5 mM DTT, 5% PEG 6000). EDTA was added to a final concentration of 10 mM to stop the MNase digestion. Nuclei were lysed by adding Triton X-100 and sodium deoxycholate to a final concentration of 0.1% each, incubated on ice for 15 minutes and then vortexed. Soluble material containing mononucleosomes were recovered after centrifugation and subjected to immunoprecipitation. Sequencing libraries were prepared using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on an Illumina Hiseq 2500 to generate 50 bp paired-end reads.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs)

tag: chip-antibody

value: anti-H3K4me3 (Abcam, ab8580)


title: htr10_rep4


title: Lymphatic VEGFR3 #1


title: Lymphatic VEGFR3 #2


title: H3K4me3_rep3

description:
anti-H3K4me3_rep1 IP from Input_A_rep3
H3K4me3.merged.log2r.bw
narrow_H3K4me3_peaks.narrowPeak
broad_H3K4me3_peaks.broadPeak


title: H3K4me3_rep1

description:
anti-H3K4me3_rep1 IP from Input_A_rep1
H3K4me3.merged.log2r.bw
narrow_H3K4me3_peaks.narrowPeak
broad_H3K4me3_peaks.broadPeak


title: Input_B_rep3

description: Mnase-digested chromatin input DNA


title: Input_B_rep2

description: Mnase-digested chromatin input DNA


title: H3.10_rep2

description:
anti-GFP_rep1 IP from Input_B_rep2
HTR10.merged.log2r.bw

value: anti-GFP (Thermo Scientific, A-11122)


title: H3.10_rep3

description:
anti-GFP_rep1 IP from Input_B_rep3
HTR10.merged.log2r.bw


title: H3K27me3_rep1

description:
anti-H3K27me3_rep1 IP from Input_A_rep2
H3K27me3.merged.log2r.bw
narrow_H3K27me3_peaks.narrowPeak
broad_H3K27me3_peaks.broadPeak

value: anti-H3K27me3 (Millipore, 07-449)


title: Input_B_rep1

description: Mnase-digested chromatin input DNA


title: H3K27me1_rep1

description:
anti-H3K27me1_rep1 IP from Input_A_rep1
H3K27me1.merged.log2r.bw
narrow_H3K27me1_peaks.narrowPeak
broad_H3K27me1_peaks.broadPeak

value: anti-H3K27me1 (Millipore, 17-643)


title: H3K27ac_rep3

description:
anti-H3K27ac_rep1 IP from Input_A_rep3
H3K27ac.merged.log2r.bw
narrow_H3K27ac_peaks.narrowPeak
broad_H3K27ac_peaks.broadPeak

value: anti-H3K27ac (Abcam, ab4729)


title: H3K27ac_rep2

description:
anti-H3K27ac_rep1 IP from Input_A_rep2
H3K27ac.merged.log2r.bw
narrow_H3K27ac_peaks.narrowPeak
broad_H3K27ac_peaks.broadPeak


title: H3K27ac_rep1

description:
anti-H3K27ac_rep1 IP from Input_A_rep1
H3K27ac.merged.log2r.bw
narrow_H3K27ac_peaks.narrowPeak
broad_H3K27ac_peaks.broadPeak


title: Lymphatic VEGFR3 #3


title: H3K27me3_rep2

description:
anti-H3K27me3_rep1 IP from Input_A_rep3
H3K27me3.merged.log2r.bw
narrow_H3K27me3_peaks.narrowPeak
broad_H3K27me3_peaks.broadPeak


title: H3.10_rep1

description:
anti-GFP_rep1 IP from Input_B_rep1
HTR10.merged.log2r.bw


title: Input_A_rep2

description: Mnase-digested chromatin input DNA


title: Input_A_rep3

description: Mnase-digested chromatin input DNA


title: Input_A_rep1

description: Mnase-digested chromatin input DNA


title: TAZ-3

city: Saint John

first: Tony

last: Reiman

state: NB

address: 100 Tucker Park Rd

country: Canada

institute: University of New Brunswick

description: Replicate 3

data_processing:
RNA-seq reads were mapped using the Two-mapping step strategy with STAR (version 2.3.0) and Bowtie2 (version 2.0.0) using hg19 version of index files.
parameters used are as follows with STAR: --chimSegmentMin 18 --chimScoreMin 12
parameters used are as follows with Bowtie2: --local --very-sensitive-local --mm
FPKM values were calculated using StringTie (version 1.3.3b)
parameters used are as follows with Stringtie: -Be
Genome_build: hg19
Supplementary_files_format_and_content: GTF files  with FPKM and TPM values

source_name: multiple myeloma cell line

growth_protocol: KMM1 cells were transduced with lentivirus expressing TAZ or empty vector control; RNA was extracted 4 days after transduction

extract_protocol:
RNA was extracted using RNAeasy minikit
RNA was quantified and integrity was analyzed on Agilent Tape Station. Samples with RNA integration number of greater than 8 were selected for library preparation. Poly-A enrichment of mRNA was performed from 15ug of total RNA (Dyna beads mRNA direct Micro Kit). All samples were spiked in with ERCC spike in mix (Life Technologies) before poly-A enrichment for performance assessment of libraries. 100ng of poly-A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module (RNA Seq V2 kit, Life Technologies). Size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape. 50ng of fragmented poly A enriched RNA was used to prepare whole transcriptome library using RNA seq V2 kit( Life Technologies ) following manufacturer recommended protocols . Yield and size distribution of the  library was assessed on Agilent Tape Station using D1000 screen tape. Barcoded libraries were equally pooled and amplified onto Ion Sphere™ Particles (ISPs) supplied by Ion Pi HiQ OT2 kit (Life Technologies). ISPs loaded with libraries were sequenced on Ion Torrent Proton sequencer using Ion PI chip V3. Two samples were pooled together and sequenced in one chip (Ion PI HiQ sequencing kit).

value: multiple myeloma cell line

tag: cell line

value: TAZ vector


title: TAZ-2

description: Replicate 2


title: TAZ-1

description: Replicate 1


title: H3K27me1_rep2

description:
anti-H3K27me1_rep1 IP from Input_A_rep3
H3K27me1.merged.log2r.bw
narrow_H3K27me1_peaks.narrowPeak
broad_H3K27me1_peaks.broadPeak


title: WPI-3

description: Replicate 3

value: Empty vector control


title: WPI-2

description: Replicate 2


title: Sample 27: APP-V717F mutated SH-SY5Y cell line - AG494 treated

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to the Human Primeview Microarray (Affymetrix Catalog # 901837) for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

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

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

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: SH-SY5Y cells were differentiated for 3-4 days in neurobasal medium supplemented with B27, glutamax, 10 μM retinoic acid and 50 ng/mL Brain-Derived Neurotrophic Factor (BDNF). Then, medium was renewed in the presence of the indicated concentration of drugs and cells treated for 72 hours.

extract_protocol: Cells were lysed with RTL buffer (Qiagen) for RNA extraction using the RNAeasy mini kit (Qiagen).

treatment_protocol: All drugs were dissolved in DMSO, and controls of cells treated with DMSO were run in parallel, at a final concentration of 0.1% DMSO. SH-SY5Y cells were treated for 72 hours in the presence of the drugs or the vehicle.

value: APP-V717F mutated

tag: treatment

value: AG494 treated


title: Sample 29: PSEN1-M146V mutated SH-SY5Y cell line - NOSCA treated

value: PSEN1-M146V mutated

value: NOSCA treated


title: Sample 28: APP-V717F mutated SH-SY5Y cell line - NOSCA treated


title: Sample 30: PSEN1-M146V mutated SH-SY5Y cell line - PALBO treated

value: PALBO treated


title: Sample 26: Wild Type SH-SY5Y cell line - PALBO treated

value: Wild Type


title: WPI-1

description: Replicate 1


title: Sample 24: Wild Type SH-SY5Y cell line - AG494 treated


title: Sample 25: Wild Type SH-SY5Y cell line - NOSCA treated


title: Sample 22: APP-V717F mutated SH-SY5Y cell line - DMSO

value: DMSO


title: Sample 20: PSEN1-M146V mutated SH-SY5Y cell line - PALBO treated


title: Sample 23: PSEN1-M146V mutated SH-SY5Y cell line - DMSO


title: Sample 19: PSEN1-M146V mutated SH-SY5Y cell line - NOSCA treated


title: Sample 17: APP-V717F mutated SH-SY5Y cell line - AG494 treated


title: Sample 18: APP-V717F mutated SH-SY5Y cell line - NOSCA treated


title: Sample 16: Wild Type SH-SY5Y cell line - PALBO treated


title: Sample 14: Wild Type SH-SY5Y cell line - AG494 treated


title: 5FU_FO897_SC_Transcriptome

city: Boston

first: Duluxan

last: Sritharan

state: MA

address: 240 Longwood Avenue, Bldg. C

institute: Harvard University

data_processing:
Cellranger v2.2.0 (with default parameters) was used to process single-cell RNA sequencing datasets prepared using CellRanger V2 Chemistry
Cellranger v3.0.2 (with default parameters) was used to process single-cell RNA sequencing datasets prepared using CellRanger V3 Chemistry
Genome_build: mm10
Supplementary_files_format_and_content: H5 - CellRanger single-cell count matrix

source_name: Bone marrow LSK

extract_protocol:
Cells were sorted by FACS and encapsulated by 10x
Libraries were prepared according to 10x Chromium single-cell RNA protocols. Library was sequenced on an Illumina NextSeq sequencer

value: Bone marrow LSK

value: No dox

tag: system

value: cCARLIN


title: 5FU_FO892_SC_1_Transcriptome


title: Sample 12: APP-V717F mutated SH-SY5Y cell line - DMSO


title: 5FU_FO892_SC_2_Transcriptome


title: 5FU_FO817_SC_Transcriptome

value: Dox


title: 5FU_FO898_SC_Transcriptome


title: 5FU_SB133_SC_Transcriptome

extract_protocol:
Cells were sorted by FACS and encapsulated by 10x
Libraries were prepared according to 10x Chromium single-cell RNA protocols. Library was sequenced on an Illumina HiSeq sequencer


title: Sample 10: PSEN1-M146V mutated SH-SY5Y cell line - PALBO treated


title: Sample 11: Wild Type SH-SY5Y cell line - DMSO

description: Wild Type SH-SY5Y cell line - DMSO

source_name: Wild Type SH-SY5Y cell line - DMSO


title: MT_CFX

city: Seoul

first: Jong Seung

last: Kim

address: Anan-ro 145

department: Department of Chemistry

country: South Korea

institute: Korea University

description: Gene expression data from human breast cancer cell lines.

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

label: Biotin

source_name: Human breast cancer cell lines

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: For microarray analysis, MDA-MB-231 cells (3 × 10e6 cells) were seeded in 100 mm dishes and were allowed to adhere for at least 24 h.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cells treated with 10 µM Mt-CFX, 10 µM CFX, and 1% DMSO as a control for 72 h.

value: Triple negative breast cancer

value: Mt-CFX


title: Sample 9: PSEN1-M146V mutated SH-SY5Y cell line - NOSCA treated


title: 5FU_FO837_SC_Transcriptome


title: Sample 21: Wild Type SH-SY5Y cell line - DMSO

description: Wild Type SH-SY5Y cell line - DMSO


title: Control

value: DMSO control


title: CFX

value: CFX


title: EB_FO864_SC_RH_Transcriptome


title: Sample 13: PSEN1-M146V mutated SH-SY5Y cell line - DMSO


title: Sample 15: Wild Type SH-SY5Y cell line - NOSCA treated


title: EB_FO864_SC_LH_Transcriptome


title: Sample 8: APP-V717F mutated SH-SY5Y cell line - NOSCA treated


title: Sample 6: Wild Type SH-SY5Y cell line - PALBO treated


title: Sample 7: APP-V717F mutated SH-SY5Y cell line - AG494 treated


title: Sample 5: Wild Type SH-SY5Y cell line - NOSCA treated


title: EB_FO864_SC_RF_Transcriptome


title: EB_FO864_SC_LF_Transcriptome


title: 5FU_SB133_SC_Amplicon

extract_protocol:
Cells were sorted by FACS and encapsulated by 10x
Amplified cDNA libraries were prepared according to 10x Chromium single-cell protocols. From this, the CARLIN amplicon was amplified by nested PCR using primers specific to the sequences surrounding CARLIN. Libraries were indexed and sequenced on an Illumina MiSeq sequencer.


title: 5FU_FO898_SC_Amplicon


title: 5FU_FO892_SC_1_Amplicon


title: 5FU_FO837_SC_Amplicon


title: 5FU_FO892_SC_2_Amplicon


title: BbHB_R2

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

description:
Replicate experiment 2
yeast-like cells

data_processing:
Illumina HiSeq™ 2500 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files include gene ID, gene length, reads number and RPKM values for each gene in two replicates.

organism: Beauveria bassiana

source_name: In vivo hyphal bodies

growth_protocol: Conidia suspension (5 μl,10^5 conidia ml^-1) of  Beauveria bassiana wild type were  injected into the hemocoel of Galleria mellonella. The infected insects were incubated at 25 °C for 3.5 days

extract_protocol: Total RNA was extracted using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA), and then the double-stranded cDNA was prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: The hemolymph was collected by centrifuging, generating a mixed sample of B. bassiana hyphal bodies and host cells.

tag: strain

tag: culture time

value: 3.5 days

value: hyphal bodies


title: EB_FO864_SC_LH_Amplicon


title: BbHB_R1

description:
Replicate experiment 1
yeast-like cells

tag: tissue


title: Sample 3: PSEN1-M146V mutated SH-SY5Y cell line - DMSO


title: Sample 4: Wild Type SH-SY5Y cell line - AG494 treated


title: 5FU_FO817_SC_Amplicon


title: EB_FO864_SC_RH_Amplicon


title: EB_FO864_SC_RF_Amplicon


title: mES_Mll2KOSuz12KO_EB_6days_RNA_rep2

description: total RNA

data_processing:
Basecalls were performed using  bcl2fastq.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For PRO-seq analyses, PRO-seq raw data were trimmed by cutadapt 1.14 and Trimmomatic 0.33. Each sample was next mapped to the mouse and fruit fly genome assemblies (mm9 and dm3, respectively) using Bowtie. The number of fly reads on each experiment was used to normalize the corresponding genome-wide strand-specific profiles.
For CRISPR screen sequencing, reads were aligned to the sgRNAs using Bowtie1. For CRISPR screen counts, the enrichment of individual guides was calculated as the log2 ratios ‘Sorted cells’ and ‘Total population’, with each sgRNA with a log2FC > 1 considered as enriched.
For mRRBS, well-observed CpG positions were obtained by performing an analysis of variance (ANOVA)–like test for differential methylation with the DSS v2.26.0 R/Bioconductor package and quantified using the SeqMonk platform (v1.40.1) with the bisulfite feature methylation pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: embryonic stem cell

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) and RNAse free DNaseI (Sigma) was used to eliminate DNA contamination.
For ChIPseq, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). Sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, and reverse-crosslinking and submitted for library preparation.
For PROseq, nuclei were isolated by Dounce homogenizer with loose pestle. Nuclei were subjected to nuclear run-on in the presence of biotin-11-ATP/GTP/CTP/UTP and Drosophila S2 spike-in nuclei. Biotinylated nascent RNA was purified by Dynabeads M-280 streptavidin.
For mRRBS, genomic DNA was digested with MspI (New England BioLabs) before size selection of 100- to 250-bp fragments with solid-phase reversible immobilization beads (MagBio Genomics). DNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

value: Embryonic body differentiation

tag: drug treatment

tag: genotype/variation


title: mES_Mll2KO_EB_6days_DMSORNA_rep3

description: total RNA


title: mES_Mll2KOSuz12KO_EB_6days_RNA_rep3

description: total RNA


title: mES_Mll2KO_EB_6days_100nM5dAzaRNA_rep2

description: total RNA


title: mES_Mll2KO_EB_6days_DMSORNA_rep2

description: total RNA


title: mES_WT_EB_6d_DMSORNA_rep2

description: total RNA

value: WT


title: mES_Mll2KO_EB_6days_100nM5dAzaRNA_rep3

description: total RNA


title: EB_FO864_SC_LF_Amplicon


title: TissuePanel_SB214_Skin_Epithelial

source_name: Skin epithelial

extract_protocol:
Cells were sorted by FACS and resuspended in Trizol
RNA of up to 1ug or 150,000 cells was reverse transcribed using a CARLIN-specific UMI-tagged primer. The CARLIN array was then PCR amplified by nested PCR before indexing and sequencing via MiSeq

value: Skin epithelial


title: TissuePanel_SB213_Skin_Epithelial


title: Sample 2: APP-V717F mutated SH-SY5Y cell line - DMSO

value: APP-V717F mutated


title: mES_Mll2KOSuz12KO_EB_6days_RNA_rep1

description: total RNA


title: mES_Mll2KO_EB_6days_100nM5dAzaRNA_rep1

description: total RNA


title: mES_WT_EB_6d_DMSORNA_rep3

description: total RNA


title: 5FU_FO897_SC_Amplicon


title: mES_Mll2KO_EB_6days_DMSORNA_rep1

description: total RNA


title: TissuePanel_SB214_Lung_Monocytes

source_name: Lung monocytes

value: Lung monocytes


title: mES_WT_EB_6d_DMSORNA_rep1

description: total RNA


title: TissuePanel_SB214_Lung_Mesenchymal

source_name: Lung Pdgfra+

value: Lung Pdgfra+


title: mES_input_Mll2KOSuz12KO_DMSO_H3K27me3_rep2

description: fragmented genomic DNA

value: embryonic stem cell

value: DMSO


title: Sample 1: Wild Type SH-SY5Y cell line - DMSO

description: Wild Type SH-SY5Y cell line - DMSO

value: Wild Type


title: TissuePanel_SB214_Lung_Epithelial

source_name: Lung EPCAM+

value: Lung EPCAM+

value: cCARLIN


title: mES_input_Mll2KO_100nM5dAza_H3K27me3_rep2

description: fragmented genomic DNA


title: mES_input_Mll2KO_DMSO_H3K27me3_rep2

description: fragmented genomic DNA


title: mES_Mll2KOSuz12KO_DMSO_H3K27me3_rep2

description: fragmented genomic DNA

tag: chip antibody

value: H3K27me3(Homemade, #67)


title: mES_Mll2KO_100nM5dAza_H3K27me3_rep2

description: fragmented genomic DNA


title: TissuePanel_SB214_Intestine_Epithelial

source_name: Intestine EPCAM+

value: Intestine EPCAM+

value: Dox


title: mES_Mll2KO_DMSO_H3K27me3_rep2

description: fragmented genomic DNA


title: TissuePanel_SB213_Lung_Epithelial


title: mES_input_WT_DMSO_H3K27me3_rep2

description: fragmented genomic DNA


title: mES_input_Mll2KOSuz12KO_DMSO_H3K27me3_rep1

description: fragmented genomic DNA


title: TissuePanel_SB214_BM_Mesenchymal

source_name: Bone marrow Pdgfra+

value: Bone marrow Pdgfra+


title: TissuePanel_SB213_Intestine_Epithelial


title: TissuePanel_SB213_Lung_Mesenchymal


title: mES_input_Mll2KO_100nM5dAza_H3K27me3_rep1

description: fragmented genomic DNA


title: TissuePanel_SB226_Liver_Mesenchymal

source_name: Liver Pdgfra+

value: Liver Pdgfra+


title: TissuePanel_SB214_BM_Monocytes

source_name: Bone marrow monocytes

value: Bone marrow monocytes


title: TissuePanel_SB213_BM_Mesenchymal


title: mES_WT_DMSO_H3K27me3_rep2

description: fragmented genomic DNA


title: TissuePanel_SB213_BM_Monocytes


title: mES_input_WT_DMSO_H3K27me3_rep1

description: fragmented genomic DNA


title: mES_Mll2KOSuz12KO_DMSO_H3K27me3_rep1

description: fragmented genomic DNA


title: TissuePanel_FO916_Intestine

source_name: Intestine

extract_protocol:
Tissues were dissected, snap frozen, and the RNA extracted using Trizol
RNA of up to 1ug or 150,000 cells was reverse transcribed using a CARLIN-specific UMI-tagged primer. The CARLIN array was then PCR amplified by nested PCR before indexing and sequencing via MiSeq

value: Intestine

value: No dox


title: mES_Mll2KO_100nM5dAza_H3K27me3_rep1

description: fragmented genomic DNA


title: mES_Mll2KO_DMSO_H3K27me3_rep1

description: fragmented genomic DNA


title: TissuePanel_FO916_Gonad

source_name: Gonad

value: Gonad


title: TissuePanel_SB213_Lung_Monocytes


title: mES_WT_DMSO_H3K27me3_rep1

description: fragmented genomic DNA

value: WT


title: TissuePanel_FO916_Skin

source_name: Skin

value: Skin


title: TissuePanel_SB225_Liver_Mesenchymal


title: TissuePanel_FO916_Heart

source_name: Heart

value: Heart


title: TissuePanel_FO916_Lung

source_name: Lung

value: Lung


title: TissuePanel_FO916_Kidney

source_name: Kidney

value: Kidney


title: TissuePanel_FO912_Gonad


title: mES_Mll2KOSuz12KO#3RNA_double_rep2

description: total RNA

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For PRO-seq analyses, PRO-seq raw data were trimmed by cutadapt 1.14 and Trimmomatic 0.33. Each sample was next mapped to the mouse and fruit fly genome assemblies (mm9 and dm3, respectively) using Bowtie. The number of fly reads on each experiment was used to normalize the corresponding genome-wide strand-specific profiles.
For CRISPR screen counts, the enrichment of individual guides was calculated as the log2 ratios ‘Sorted cells’ and ‘Total population’, with each sgRNA with a log2FC > 1 considered as enriched.
For mRRBS, well-observed CpG positions were obtained by performing an analysis of variance (ANOVA)–like test for differential methylation with the DSS v2.26.0 R/Bioconductor package and quantified using the SeqMonk platform (v1.40.1) with the bisulfite feature methylation pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) and RNAse free DNaseI (Sigma) was used to eliminate DNA contamination.
For ChIPseq, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). Sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, and reverse-crosslinking and submitted for library preparation.
For PROseq, nuclei were isolated by Dounce homogenizer with loose pestle. Nuclei were subjected to nuclear run-on in the presence of biotin-11-ATP/GTP/CTP/UTP and Drosophila S2 spike-in nuclei. Biotinylated nascent RNA was purified by Dynabeads M-280 streptavidin.
For mRRBS, genomic DNA was digested with MspI (New England BioLabs) before size selection of 100- to 250-bp fragments with solid-phase reversible immobilization beads (MagBio Genomics). DNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit.
For CRISPR screen sequencing, reads were aligned to the sgRNAs using Bowtie1.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

value: embryonic stem cell

tag: genotype/variant


title: TissuePanel_FO912_Intestine


title: mES_Mll2KOSuz12KO#4RNA_double_rep2

description: total RNA


title: mES_Mll2KOSuz12KO#2RNA_double_rep2

description: total RNA


title: mES_input_Mll2KO_DMSO_H3K27me3_rep1

description: fragmented genomic DNA

value: DMSO


title: TissuePanel_FO916_Brain

source_name: Brain

value: Brain

value: cCARLIN


title: TissuePanel_FO916_Liver

source_name: Liver

value: Liver


title: mES_Mll2KOSuz12KO#1RNA_double_rep2

description: total RNA

source_name: embryonic stem cell


title: mES_Mll2KOSuz12KO#4RNA_double_rep1

description: total RNA


title: mES_Mll2KORNA_double_rep2

description: total RNA


title: TissuePanel_FO916_Spleen

source_name: Spleen

value: Spleen


title: mES_Mll2KOSuz12KO#2RNA_double_rep1

description: total RNA


title: mES_Mll2KOSuz12KO#3RNA_double_rep1

description: total RNA


title: TissuePanel_FO916_Muscle

source_name: Muscle

value: Muscle


title: TissuePanel_FO912_Skin

value: Dox


title: TissuePanel_FO912_Heart


title: mES_Mll2KORNA_double_rep1

description: total RNA


title: mES_Mll2KOSuz12KO#1RNA_double_rep1

description: total RNA


title: TissuePanel_FO912_Kidney


title: TissuePanel_FO912_Lung


title: mES_WTRNA_double_rep1

description: total RNA


title: TissuePanel_FO912_Brain


title: mES_input_H3K27me3_rep2

description: fragmented genomic DNA

tag: shRNA/sgrna

value: shNT


title: mES_Mll2KO_shCXXC1_H3K27me3_rep2

description: fragmented genomic DNA

value: H3K27me3 (Homemade, #67)


title: TissuePanel_FO912_Muscle


title: TissuePanel_FO912_Liver


title: mES_Mll2KO_shNT_H3K27me3_rep2

description: fragmented genomic DNA


title: TissuePanel_FO912_Spleen


title: mES_WTRNA_double_rep2

description: total RNA


title: InVivoPhylogeny_Rep2_Gr_L

source_name: Bone marrow granulocytes

value: Bone marrow granulocytes


title: mES_input_H3K27me3_rep1

description: fragmented genomic DNA


title: mES_WT_shNT_H3K27me3_rep2

description: fragmented genomic DNA


title: InVivoPhylogeny_Rep2_BCell_L

source_name: Bone marrow B cell

value: Bone marrow B cell


title: InVivoPhylogeny_Rep2_Gr_R


title: InVivoPhylogeny_Rep2_BCell_R


title: mES_Mll2KO_shCXXC1_H3K27me3_rep1

description: fragmented genomic DNA


title: mES_Mll2KO_shNT_Set1aChIP_rep2

description: fragmented genomic DNA

value: Set1a (Homemade, #919)


title: mES_WT_shNT_H3K27me3_rep1

description: fragmented genomic DNA

value: WT


title: mES_input_Set1aChIP

description: fragmented genomic DNA


title: mES_Mll2KO_shNT_H3K27me3_rep1

description: fragmented genomic DNA


title: InVivoPhylogeny_Rep2_Heart

source_name: Mouse heart

value: Mouse heart


title: mES_Mll2KO_shCXXC1_Set1aChIP_rep2

description: fragmented genomic DNA


title: InVivoPhylogeny_Rep2_Skin

source_name: Mouse skin

value: Mouse skin


title: mES_WT_shNT_Set1aChIP_rep2

description: fragmented genomic DNA


title: InVivoPhylogeny_Rep2_Colon

source_name: Mouse colon

value: Mouse colon


title: InVivoPhylogeny_Rep2_Muscle_L

source_name: Mouse muscle

value: Mouse muscle


title: InVivoPhylogeny_Rep2_Intestine

source_name: Mouse intestine

value: Mouse intestine


title: InVivoPhylogeny_Rep2_Brain_R

source_name: Mouse brain

value: Mouse brain


title: InVivoPhylogeny_Rep2_Brain_L

value: cCARLIN


title: wt_20_M.w1001

type: genomic

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

description: Ip-BrdU of Wild type 20' after release in S-Phase

hyb_protocol: DNA was hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array (5-bp resolution) using the GeneChip Hybridization, Wash, and Stain kit (Affymetrix, PN 900720).

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G.

data_processing: Signals were normalized with TAS 1.1.02 (Affymetrix) using quantile normalization. Analysis results were stored in log2 scale for signal intensity and in −10 × log10 scale for P values. Probe signals were analyzed using perfect matches only with a bandwidth of 300 bp. P-value intervals were generated using the following parameters: cutoff, 10−5; maximum gap, 80 bp; min run, 40 bp. Significant intervals were scored as active origins when signal intensity was above a threshold arbitrarily set at 50% of the signal range and when BrdU tracks were larger than 1 kb. Replication profiles (signal log ratio) were displayed with IGB 6.1  Bar files correspond to signal intensities (signal log ratio of BrdU IP relative to WCE) and can be displayed with IGB (Integrated genome Brower).

organism: Saccharomyces cerevisiae

source_name: WT

label_protocol: Purified immunoprecipitated DNA was amplified using the WGA2 GenomePlex Complete Whole Genome Amplification kit (Sigma) with the addition of 0.1 mM dUTP in the amplification reaction. Amplified DNA (7 μg) was fragmented and labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling kit (Affymetrix, PN 900812) according to the manufacturer's recommendations.

growth_protocol: Cells were grown in YPD at 25°C

extract_protocol: Standard protocol for BrdU-IP chip. For immunoprecipitation of BrdU-labeled DNA, 1.5 × 10e9 cells were lysed five times for 2 min each time in NIB buffer (17% (v/v) glycerol, 50 mM MOPS buffer, 150 mM potassium acetate, 2 mM magnesium chloride, 500 μM spermidine and 150 μM spermine, pH 7.2) with zirconium beads on a Vibrax shaker (VXR basic, Ika) at 4 °C. DNA was isolated using Qiagen genomic DNA extraction kit and sonicated to yield an average DNA size of 300–600 bp. For each immunoprecipitation, 10 μl of mouse anti-BrdU IgG1 (BD Bioscience, 555627) was prebound to Dynabeads M-280 sheep anti-mouse IgG (Invitrogen, 112.01D) and added to the denatured purified DNA.

treatment_protocol: Samples were released from alpha-factor arrest in the presence or not of HU (200mM) and collected at the indicated time post G1 release

value: Untreated

tag: cell-cycle phase

value: S-Phase 20min

tag: antibody

value: anti-BrDU


title: wt_30_M.w1001

description: Ip-BrdU of Wild type 30' after release in S-Phase

value: S-Phase 30min


title: rad53_30_M.w1001

description: Ip-BrdU of rad53-11 30' after release in S-Phase


title: InVivoPhylogeny_Rep2_Lung_R

source_name: Mouse lung

tag: cell type

value: Mouse lung

value: Dox


title: TKO-LPS-3h

city: Beijing

first: Xiang

last: Zhang

address: Tsinghuayuan Street

institute: Tsinghua University

data_processing:
Data were filtered by SOAPnuke (v1.5.2) to get clean data.
Bowtie2 (v2.2.5) was used to map clean reads to reference gene with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar and  HISAT (v2.0.4) was used to reference genome with the following parameters: -p8--phred64 --sensitive -I 1 -X 1000..
Gene expression levels were quantified using RSEM (v1.2.12)
Differential expressed genes between WT and TKO BMDMs were defined as FDR < 0.001 and absolute value of log2 ratio (TKO/WT) > 1.
Genome_build: mouse (mm10)
Supplementary_files_format_and_content: Excel file contains quantified gene expression level as FPKM and FDR for differential expression analysis.

source_name: Macrophages

growth_protocol: Bone marrows cells from WT and TKO mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol:
RNA was isolated using total  RNA purification kit (GeneMark) and total RNA was polyA enriched.
1.mRNA was isolated, purified and fragmented and cDNA was synthesis 2. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments 3. cDNA fragments were amplified by PCR with adapters from previous step. 4.The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library.

treatment_protocol: BMDMs from WT and TKO mice were stimulated with 10 ng/ml LPS for 3 h.

value: Bone marrow-derived macrophages

tag: genotype


title: InVivoPhylogeny_Rep2_Liver_2

source_name: Mouse liver

value: Mouse liver


title: InVivoPhylogeny_Rep2_Liver_1


title: mec1_30_M.w1001

description: Ip-BrdU of mec1-1sml1-1 30' after release in S-Phase


title: wt_40_M.w1001

description: Ip-BrdU of Wild type 40' after release in S-Phase

value: S-Phase 40min


title: WT-LPS-3h


title: 018_yH2A_mec1_1_tel1_1sml1_1_30min

description: Ip-yH2A of mec1_1_sml1_1 tel1-1_30' after release in S-Phase

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step  with ratio relative to Input (IP) or relative to G1 (ADNg)

growth_protocol: Cells were grown on YPD at 25°C

extract_protocol:
Standard protocol for preparation of yeast genomic DNA, chromatin immunoprecipitation and micrococcal nuclease digestion
NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumia)_Sequencer:HiSeq 4000 (1x51 nt)

treatment_protocol: Samples were either collected from G1 synchronised cultures or from cell released from alpha-factor arrest into S phase for 60 minutes in the presence of 200 mM HU (hydroxyurea).

value: α-yH2A antibody


title: TKO without stimulation

value: TKO


title: InVivoPhylogeny_Rep2_Muscle_R


title: WT without stimulation

value: WT


title: InVivoPhylogeny_Rep1_HSC_R

source_name: Mouse hematopoietic stem cell

extract_protocol:
Cells were sorted by FACS and resuspended in Trizol
RNA of up to 1ug or 150,000 cells was reverse transcribed using a CARLIN-specific UMI-tagged primer. The CARLIN array was then PCR amplified before indexing and sequencing via MiSeq

value: Mouse hematopoietic stem cell


title: InVivoPhylogeny_Rep1_Lung_R

extract_protocol:
Tissues were dissected, snap frozen, and the RNA extracted using Trizol
RNA of up to 1ug or 150,000 cells was reverse transcribed using a CARLIN-specific UMI-tagged primer. The CARLIN array was then PCR amplified before indexing and sequencing via MiSeq


title: 017_yH2A_mec1_1_sml1_1_30min

description: Ip-yH2A of mec1_1_sml1_1 30' after release in S-Phase


title: InVivoPhylogeny_Rep1_Muscle_R

value: Mouse muscle


title: BrdU_rad9delta_30min

description:
Ip-BrdU of rad9delta 30' after release in S-Phase
BrdU-IP-Seq

data_processing:
Library strategy: BrdU-IP-Seq
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step  with ratio relative to Input (IP) or relative to G1 (ADNg)

source_name: ADNg

value: anti-BrDU Antibody No. ABIN93885


title: InVivoPhylogeny_Rep1_Liver_1


title: InVivoPhylogeny_Rep1_Brain_R

value: Mouse brain


title: ADNg_WT_Async

description:
Input of Wild type in Async
input

value: Async


title: 016_yH2A_mec1_1_sml1_1_G1

description: Ip-yH2A of mec1_1_sml1_1 in G1 phase of the cell cycle

value: Untreated


title: InVivoPhylogeny_Rep1_MPP_R

source_name: Mouse multipotent progenitor cell

value: Mouse multipotent progenitor cell

value: cCARLIN


title: BrdU_mec1-1sml1-1_30min

description:
Ip-BrdU of mec1-1sml1-1 30' after release in S-Phase
BrdU-IP-Seq

value: S-Phase 30min

value: anti-BrDU Antibody No. ABIN93884


title: BrdU_WT_30min

description:
Ip-BrdU of Wild type 30' after release in S-Phase
BrdU-IP-Seq

value: anti-BrDU Antibody No. ABIN93883


title: InVivoPhylogeny_Rep1_HSC_L

value: Dox


title: InVivoPhylogeny_Rep1_MPP_L


title: InVivoPhylogeny_Rep2_Lung_L

value: Mouse lung


title: InVivoPhylogeny_Rep1_Skin

value: Mouse skin


title: InVivoPhylogeny_Rep1_Heart

value: Mouse heart


title: 161_ADNg_rad53delta-pGAL-SML1_G1

description:
Input ofrad53delta-pGAL-SML1 (overexpressing sml1 in presence of Galactose) in G1 phase of the cell cycle in presence of Galactose(2%)
input


title: 160_ADNg_pGAL-SML1_90min

description:
Input of pGAL-SML1 (overexpressing sml1 in presence of Galactose) 45' after release in S-Phase in presence of Galactose(2%)
input

value: S-Phase 90min


title: InVivoPhylogeny_Rep1_Colon

value: Mouse colon


title: 159_ADNg_pGAL-SML1_45min

description:
Input of pGAL-SML1 (overexpressing sml1 in presence of Galactose) 30' after release in S-Phase in presence of Galactose(2%)
input

value: S-Phase 45min


title: 158_ADNg_pGAL-SML1_G1

description:
Input of pGAL-SML1 (overexpressing sml1 in presence of Galactose) in G1 phase of the cell cycle in presence of Galactose(2%)
input


title: InVivoPhylogeny_Rep1_Intestine

value: Mouse intestine


title: InVivoPhylogeny_Rep1_Brain_L


title: 156_yH2A_rad53delta-pGAL-SML1_45min

description:
Ip-yH2A of rad53delta-pGAL-SML1 (overexpressing sml1 in presence of Galactose) 30' after release in S-Phase in presence of Galactose(2%)
ChIP-Seq, α-yH2A antibody

value: anti-H2A-S128_Gift from A. Verreault_AV137


title: 157_yH2A_rad53delta-pGAL-SML1_90min

description:
Ip-yH2A of rad53delta-pGAL-SML1 (overexpressing sml1 in presence of Galactose) 45' after release in S-Phase in presence of Galactose(2%)
ChIP-Seq, α-yH2A antibody


title: InVivoPhylogeny_Rep1_Lung_L


title: InVitroPhylogeny_Gen2_7

data_processing:
Library strategy: DNA-seq
Cellranger v2.2.0 (with default parameters) was used to process single-cell RNA sequencing datasets prepared using CellRanger V2 Chemistry
Cellranger v3.0.2 (with default parameters) was used to process single-cell RNA sequencing datasets prepared using CellRanger V3 Chemistry
Genome_build: mm10
Supplementary_files_format_and_content: H5 - CellRanger single-cell count matrix

source_name: Mouse embryonic stem cells

growth_protocol: Cells were cultured on mouse embryonic fibroblast feeder layers in embryonic stem cell medium with LIF

extract_protocol:
Cells were trypsinized, pelleted and resuspended in DNA lysis buffer
Up to 250ng gDNA was input into an initial UMI tagging reaction using a primer specific to the CARLIN region. Following this the CARLIN array + UMI was amplified in a PCR reaction before indexing and sequencing via MiSeq

value: Mouse embryonic stem cells


title: InVivoPhylogeny_Rep1_Liver_2

value: Mouse liver


title: 155_yH2A_rad53delta-pGAL-SML1_G1

description:
Ip-yH2A ofrad53delta-pGAL-SML1 (overexpressing sml1 in presence of Galactose) in G1 phase of the cell cycle in presence of Galactose(2%)
ChIP-Seq, α-yH2A antibody


title: InVitroPhylogeny_Gen2_6


title: 152_yH2A_pGAL-SML1_G1

description:
Ip-yH2A of pGAL-SML1 (overexpressing sml1 in presence of Galactose) in G1 phase of the cell cycle in presence of Galactose(2%)
ChIP-Seq, α-yH2A antibody


title: InVitroPhylogeny_Gen2_5


title: 154_yH2A_pGAL-SML1_90min

description:
Ip-yH2A of pGAL-SML1 (overexpressing sml1 in presence of Galactose) 45' after release in S-Phase in presence of Galactose(2%)
ChIP-Seq, α-yH2A antibody


title: 130_ADNg_rad53-11_G1

description:
Input of rad53-11 30' in G1 phase of the cell cycle
input

value: Untreated


title: 107_ADNg_rad53-11_30min

description:
Input of rad53-11 30' after release in S-Phase
input


title: 103_ADNg_WT_30min

description:
Input of Wild type 30' after release in S-Phase
input

value: WT


title: InVitroPhylogeny_Gen2_3

value: cCARLIN


title: 163_ADNg_rad53delta-pGAL-SML1_90min

description:
Input of rad53delta-pGAL-SML1 (overexpressing sml1 in presence of Galactose) 45' after release in S-Phase in presence of Galactose(2%)
input


title: 162_ADNg_rad53delta-pGAL-SML1_45min

description:
Input of rad53delta-pGAL-SML1 (overexpressing sml1 in presence of Galactose) 30' after release in S-Phase in presence of Galactose(2%)
input


title: 096_ADNg_WT_G1

description:
Input of Wild type in G1 phase of the cell cycle
input


title: InVivoPhylogeny_Rep1_Muscle_L

value: Mouse muscle


title: InVitroPhylogeny_Gen2_1


title: InVitroPhylogeny_Gen2_2


title: Diversity_SB214_4

extract_protocol:
Granulocytes were sorted by FACS and resuspended in Trizol
RNA of up to 1ug or 150,000 cells was reverse transcribed using a CARLIN-specific UMI-tagged primer. The CARLIN array was then PCR amplified by nested PCR before indexing and sequencing via MiSeq

value: Bone marrow granulocytes


title: InVitroPhylogeny_Gen2_8


title: Diversity_SB214_3


title: 153_yH2A_pGAL-SML1_45min

description:
Ip-yH2A of pGAL-SML1 (overexpressing sml1 in presence of Galactose) 30' after release in S-Phase in presence of Galactose(2%)
ChIP-Seq, α-yH2A antibody


title: 043_yH2A_WT-GAL_30min

description:
Ip-yH2A of Wild type in G1 phase of the cell cycle 30' after release in S-Phase in presence of Galactose(1%)
ChIP-Seq, α-yH2A antibody

value: WT-GAL

value: S-Phase 30min


title: sm-m8

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Fastq files were aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

source_name: chondrocyte

growth_protocol: Primary chondrocytes were isolated from mouse femoral heads. the chondrocytes were seeded in a 24-well plate at a density of 1.0*105 cells/well and cultured with 10% fetal bovine serum (FBS; Gibco) in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco) plus 1% penicillin and streptomycin (10000 U/mL, Gibco) at 37oC and 5% CO2. Afterwards, chondrocytes were collected without passaging following a 4 d of culture.

extract_protocol: RNA was extracted using Qiagen RNeasy kit (Cat#74104) with 10mg of total RNA for the construction of Clonetech SMARTer sequencing libraries.

value: SM/J

value: cartilage

tag: age

value: post natal day 21

tag: Sex

value: male


title: 049_yH2A_GALRNR-GAL_30min

description:
Ip-yH2A of GAL RNR (overexpressing RNR in presence of Galactose) 30' after release in S-Phase  in presence of Galactose(1%)
ChIP-Seq, α-yH2A antibody

value: GALRNR-GAL


title: Diversity_SB214_2

source_name: Bone marrow granulocytes

value: Dox


title: Diversity_SB214_1


title: InVitroPhylogeny_Gen2_4


title: sm-m7


title: 040_yH2A_WT-GAL_G1

description:
Ip-yH2A of Wild type in G1 phase of the cell cycle in presence of Galactose(1%)
ChIP-Seq, α-yH2A antibody


title: Diversity_SB213_3


title: 035_Rpb3_WT_30min

description:
Ip-RPB3 of Wild type 30' after release in S-Phase
ChIP-Seq, α-Rpb3 antibody

value: Anti-RPB3 antibody [1Y26] (ab202893)


title: Diversity_SB213_1


title: Diversity_FO916_R_125K

value: No dox


title: Diversity_SB213_2


title: sm-m5


title: Diversity_FO916_R_25K


title: Diversity_SB213_4


title: Diversity_FO916_R_5K


title: sm-m6


title: sm-m4


title: Diversity_FO915_R_25K


title: sm-m3


title: 046_yH2A_GALRNR-GAL_G1

description:
Ip-yH2A of GAL RNR (overexpressing RNR in presence of Galactose) in G1 phase of the cell cycle in presence of Galactose(1%)
ChIP-Seq, α-yH2A antibody

value: anti-H2A-S128_Gift from A. Verreault_AV137


title: 034_Rpb3_WT_G1

description:
Ip-RPB3 of Wild type in G1 phase of the cell cycle
ChIP-Seq, α-Rpb3 antibody


title: 031_Rpb1-PS2_WT_30min

description:
Ip-RNA polymerase II CTD repeat YSPTSPS (phospho S2) of Wild type 30' after release in S-Phase
ChIP-Seq, α-Rpb1-PS2 antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade


title: 029_Rpb1-PS2_WT_G1

description:
Ip-RNA polymerase II CTD repeat YSPTSPS (phospho S2) of Wild type in G1 phase of the cell cycle
ChIP-Seq, α-Rpb1-PS2 antibody

value: Untreated


title: sm-m2


title: 028_Cdc45-3PK_WT_50min

description:
Ip-PK of Wild type with Cdc45-PK 50' after release in S-phase
ChIP-Seq, α-PK antibody

value: WT

value: S-Phase 50min

value: Anti-PK (anti-V5 tag)_AbD Serotec_MCA1360G


title: Diversity_FO914_R_25K

value: Bone marrow granulocytes

value: cCARLIN


title: Diversity_FO913_R_125K


title: 036_yH2A_WT_HU-60min

description:
Ip-yH2A of Wild type 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-yH2A antibody

value: S-Phase + HU-60min


title: Diversity_FO913_R_5K


title: 027_Cdc45-3PK_WT_40min

description:
Ip-PK of Wild type with Cdc45-PK 40' after release in S-phase
ChIP-Seq, α-PK antibody

value: S-Phase 40min


title: Diversity_FO912_R_125K


title: 026_Cdc45-3PK_WT_30min

description:
Ip-PK of Wild type with Cdc45-PK 30' after release in S-phase
ChIP-Seq, α-PK antibody

value: S-Phase 30min


title: sm-m1

value: SM/J

value: cartilage

value: post natal day 21


title: sm-f7

value: female


title: Diversity_FO912_R_5K

value: Dox


title: 025_Cdc45-3PK_WT_20min

description:
Ip-PK of Wild type with Cdc45-PK 20' after release in S-phase
ChIP-Seq, α-PK antibody

value: S-Phase 20min


title: Diversity_FO912_R_25K


title: Diversity_FO915_R_125K

value: No dox


title: 024_Cdc45-3PK_WT_G1

description:
Ip-PK of Wild type with Cdc45-PK in G1 phase of the cell cycle
ChIP-Seq, α-PK antibody


title: sm-f6


title: Diversity_FO915_R_5K


title: Diversity_FO916_L_125K


title: Diversity_FO916_L_25K


title: Diversity_FO916_L_5K


title: 023_Cdc45-3PK_WT_50min


title: sm-f5


title: Diversity_FO915_L_125K


title: Diversity_FO914_R_5K


title: sm-f8


title: sm-f4


title: Diversity_FO915_L_25K


title: Diversity_FO915_L_5K


title: sm-f3


title: 022_Cdc45-3PK_WT_40min


title: Diversity_FO913_R_25K


title: 021_Cdc45-3PK_WT_30min


title: Diversity_FO914_R_125K


title: sm-f2


title: Diversity_FO914_L_25K


title: Diversity_FO913_L_125K


title: 020_Cdc45-3PK_WT_20min


title: Diversity_FO913_L_25K


title: Diversity_FO913_L_5K


title: lg-m8

value: LG/J

value: male


title: Diversity_FO912_L_125K


title: 015_yH2A_WT_30min

description:
Ip-yH2A of Wild type 30' after release in S-Phase
ChIP-Seq, α-yH2A antibody

value: WT

value: Untreated

value: anti-H2A-S128_Gift from A. Verreault_AV137


title: Diversity_FO912_L_25K

value: Bone marrow granulocytes


title: Diversity_FO912_L_5K

value: cCARLIN


title: Diversity_FO217_3

extract_protocol:
Granulocytes were sorted by FACS and resuspended in Trizol
RNA of up to 1ug or 150,000 cells was reverse transcribed using a CARLIN-specific UMI-tagged primer. The CARLIN array was then PCR amplified before indexing and sequencing via MiSeq


title: lg-m7


title: 014_Ddc2-HA_WT_50min

description:
Ip-HA of Wild type with Ddc2-HA 50' after release in S-Phase
ChIP-Seq, α-HA antibody

value: S-Phase 50min

value: Anti-HA_Santa Cruz_SC-7392


title: Diversity_FO914_L_125K


title: lg-m6


title: lg-m5


title: Diversity_FO215_3


title: Diversity_FO217_1


title: 012_Ddc2-HA_WT_30min

description:
Ip-HA of Wild type with Ddc2-HA 30' after release in S-Phase
ChIP-Seq, α-HA antibody

value: S-Phase 30min


title: lg-m4


title: Diversity_FO914_L_5K


title: Diversity_FO215_2


title: sm-f1

value: SM/J


title: Diversity_FOND2_1K


title: 019_Cdc45-3PK_WT_G1

value: Anti-PK (anti-V5 tag)_AbD Serotec_MCA1360G


title: 011_Ddc2-HA_WT_20min

description:
Ip-HA of Wild type with Ddc2-HA 20' after release in S-Phase
ChIP-Seq, α-HA antibody


title: lg-m3

value: cartilage

value: post natal day 21


title: 013_Ddc2-HA_WT_40min

description:
Ip-HA of Wild type with Ddc2-HA 40' after release in S-Phase
ChIP-Seq, α-HA antibody

value: S-Phase 40min


title: 010_Ddc2-HA_WT_G1

description:
Ip-HA of Wild type with Ddc2-HA in G1 phase of the cell cycle
ChIP-Seq, α-HA antibody


title: Diversity_FOND2_125K


title: lg-m2


title: Diversity_FO217_2

value: Dox


title: 009_yH2A_WT_50min

description:
Ip-yH2A of Wild type 50' after release in S-Phase
ChIP-Seq, α-yH2A antibody


title: lg-m1


title: 008_yH2A_WT_40min

description:
Ip-yH2A of Wild type 40' after release in S-Phase
ChIP-Seq, α-yH2A antibody


title: Diversity_FOND1_5K

value: No dox


title: Diversity_FOND1_25K


title: Diversity_FO215_1


title: Diversity_FOND1_125K


title: lg-f8

value: LG/J

value: female


title: Diversity_FO803

value: No Dox


title: 007_yH2A_WT_30min

value: WT

value: Untreated


title: Diversity_FO397_1K

value: Bone marrow granulocytes


title: Diversity_FOND2_5K

value: cCARLIN


title: 006_yH2A_WT_20min

description:
Ip-yH2A of Wild type 20' after release in S-Phase
ChIP-Seq, α-yH2A antibody

value: S-Phase 20min

value: anti-H2A-S128_Gift from A. Verreault_AV137


title: Diversity_FOND2_25K


title: lg-f7


title: Diversity_FO397_25K


title: 005_yH2A_WT_50min

value: S-Phase 50min


title: lg-f6


title: Diversity_FO397_125K


title: Diversity_FO395_1K


title: Diversity_FO395_25K


title: Diversity_FO395_5K


title: lg-f5


title: Diversity_FOND1_1K


title: 004_yH2A_WT_40min


title: lg-f4


title: 003_yH2A_WT_30min

value: S-Phase 30min


title: Diversity_FO395_125K


title: Inducible_FO406_2K

value: iCARLIN


title: 002_yH2A_WT_20min


title: lg-f2

value: cartilage


title: lg-f3

value: post natal day 21


title: Inducible_FO406_10K


title: Inducible_FO406_50K


title: Inducible_FO406_250K


title: lg-f1


title: 001_yH2A_WT_G1

description:
Ip-yH2A of Wild type in G1 phase of the cell cycle
ChIP-Seq, α-yH2A antibody


title: Diversity_FO397_5K


title: Inducible_FO409_2K


title: Inducible_FO409_10K


title: Inducible_FO409_50K


title: Inducible_FO409_250K