title: BT245-KO-5AZA-R2

data_processing:
Data processing. Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple control metrics were obtained using FASTQC (v0.11.2), samtools (v0.1.19), BEDtools (v2.17.0) and custom scripts.
Gene expression analysis. The remaining clean set of reads were then aligned to the reference genome build hg19 (GRCh37) with STAR (v2.3.0e) using the default parameters. Multimapping reads (MAPQ<1) were discarded from downstream analyses. Gene expression levels were estimated by quantifying uniquely mapped reads falling into exonic regions defined by the ensGene annotation set from Ensembl (GRCh37; N=60234 genes) using featureCounts (v1.4.4). Normalization (mean-of-ratios), variance-stabilized transformations of the data, as well as differential expression analysis, were performed using DESeq2. Unless otherwise stated, all reported p-values have been adjusted for multiple testing using the Benjamini-Hochberg procedure.
Repeat element expression analysis. The clean set of rRNA-depleted RNA-seq reads were aligned to the human repeat genome, as previously described. The reference repeat sequences were downloaded from Repbase (v23.03) (http://www.girinst.org/repbase). We then combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus repeat element sequences. All subsequent steps closely mirror those detailed for gene expression analysis. Normalization (library size) factors derived from canonical genes (Ensembl ensGene annotation) using mean-of-ratios as described above were used to normalize repeat elements.
Genome_build: hg19
Supplementary_files_format_and_content: Raw abundance measurements of Ensembl genes
Supplementary_files_format_and_content: Raw abundance measurements of Repbase repeat elements

source_name: Tumor-derived cell-line

value: glioma tumor


title: BT245-KO-COMBO-R1

status: Public on May 13 2019

type: SRA

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy mini kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2000, 2500 and 4000 platforms.

tag: genotype

tag: treatment

value: Panobinostat + 5-azacytidine

tag: tissue


title: BT245-KO-COMBO-R2


title: BT245-KO-5AZA-R1


title: 2469_brain_h3k27ac

library_source: genomic

data_processing:
Sequence reads were aligned to the human genome (HG19) using Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012) under default settings. PCR duplicates were removed using PICARD tools generating .BAM files (Li et al., 2009). Read processing and alignment for analysis of repeat elements was performed separately (see below for details). Significant peaks were identified using Model-Based Analysis for ChIP-seq (MACS 1.4) (Zhang et al., 2008)with a p value cutoff of 1e-9.  Peaks were annotated using HOMER (v3.12) (Heinz et al., 2010) with promoter regions classified as any peak within +/- 2.5 kb of a transcriptional start site (TSS), and enhancer region greater than 2.5 kb from a TSS. Peaks were also annotated using ChIP-atlas annotating distal enhancers to genes based upon public CHIA-PET datasets. Super enhancers were identified using the ROSE algorithm with exclusion of peaks within +/- 2.5 kb of a TSS and a stitch distance of 12.5 kb. For visualization of H3K27 acetylation profiles, BAM alignment files were normalized to RPKM values using DeepTools (Ramirez et al., 2014) and visualized in Integrated Genome Viewer (v2.3.40).
Genome_build: hg19

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction ~5% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below). ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 6ug of H3K27ac antibody (Diagenode, C15410196), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail (Life Technologies) at 65°C for 30 min followed by 2ul Proteinase K (Thermo Fisher Scientific) at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: sample type

value: Tumor

tag: chip antibody


title: BT245-KO-PANO-R2

value: Panobinostat


title: BT245-KO-DMSO-R2


title: BT245-5AZA-R2


title: BT245-5AZA-R1


title: BT245-KO-DMSO-R1


title: BT245-KO-PANO-R1


title: R4.6

city: Miami

first: Alexander

last: Agoulnik

state: FL

department: Human and Molecular Genetics

country: USA

institute: Florida International University Herbert Wertheim College of Medicine

data_processing:
Partek Flow
STAR aligner
Differentially expressed genes were identified using Gene Specific Analysis (GSA)
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with ratio, fold-change and p-values

source_name: TGF-β1 + DMSO

growth_protocol: LX-2 cells were grown in 2% FBS DMEM media.

extract_protocol:
Cells were lysed using Trizol and total RNA was isolated by column purification using a GeneJET RNA purification kit following manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with recombinant human TGF-β1, with DMSO or ML290 (5 µM) for 72h in 2% FBS DMEM.

tag: cell line

tag: cell type

value: hepatic stellate cell line


title: BT245-PANO-R2


title: BT245-COMBO-R2


title: BT245-PANO-R1


title: DIPGXIII-KO-PANO-R1


title: DIPGXIII-KO-5AZA-R1


title: DIPGXIII-COMBO-R2


title: DIPGXIII-COMBO-R1


title: DIPGXIII-COMBO-R3


title: DIPGXIII-KO-DMSO-R1


title: DIPGXIII-KO-PANO-R2


title: R4.4


title: DIPGXIII-5AZA-R2


title: DIPGXIII-5AZA-R1


title: DIPGXIII-PANO-R2


title: DIPGXIII-PANO-R3


title: DIPGXIII-DMSO-R2


title: DIPGXIII-KO-5AZA-R2


title: DIPGXIII-KO-DMSO-R2


title: DIPGXIII-PANO-R1


title: DIPGXIII-DMSO-R1


title: BT245-DMSO-D6


title: BT245-DMSO-D7


title: DIPGXIII-KO-COMBO-R2


title: BT245-NKO-P16


title: BT245-NKO-P31


title: BT245-NKO-P17


title: BT245-NKO-P30


title: BT245-KO-C2P6


title: BT245-KO-C4


title: DIPGXIII-NKO-C12


title: DIPGXIII-NKO-C8


title: BT245-KO-C2


title: DIPGXIII-KO-C5


title: BT245-KO-C5P4


title: G477


title: DIPGXIII-5AZA-R3


title: DIPGXIII-KO-C10


title: BT245-NKO-P18


title: MB-i4i5ZRS_L13769-2

city: Berlin

first: Christina

last: Paliou

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: MB-i4i5ZRS_L13769-1_L13769-2_merged_MAPQ30.KR_10kb.WashU.txt

data_processing:
Raw sequencing reads were preprocessed with cutadapt v1.15 (Martin, 2011) to trim potential low quality bases (-q 20 -m 25) and Illumina sequencing adapters (-a and -A option with Illumina TruSeq adapter sequences according to the cutadapt documentation) at the 3’ end of reads. Next, sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0 (Wingett et al., 2015) (no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) for short read mapping. The trimming of sequencing adapters in the first step would not have been necessary, because potentially remaining sequencing adapter in reads from valid ligation products should also be removed by the truncation after ligation sites implemented in the HiCUP pipeline. In case replicates were available, they were combined after the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 (Durand et al., 2016) was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing (Durand et al., 2016; Knight and Ruiz, 2013; Rao et al., 2014). For binning and normalization, only the genomic region chr5:27,800,001- 30,600,000 enriched in the DNA-capturing step was considered. Therefore, only reads pairs mapping to this region were kept, shifted by the offset of 27,800,000 bp and imported with Juicer tools using a custom chrom.sizes file which contained only the length of the enriched region (2.8 Mb). Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb and 10kb resolution and coordinates were shifted back to their original values. Subtraction maps were generated from KR normalized maps, which were normalized in a pair-wise manner before subtraction. To account for differences between two maps in their distance-dependent signal decay, maps were scaled jointly across their sub-diagonals. Therefore, the values of each sub-diagonal of one map were divided by the sum of this sub-diagonal and multiplied by the average of these sums from both maps. Afterwards, the maps were scaled by 10^6 / total sum. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 97-th  percentile were truncated for visualization purposes.
In order to obtain more fine-grained interaction profiles for selected loci, we defined 10kb viewpoint regions and generated virtual Capture-C-like profiles based on the filtered, unique read-pairs that were also used for the cHiC maps. A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region, while the other read mapped outside of it. The reads outside of the viewpoint were counted per restriction fragment and read counts were binned afterwards to 1 kb bins. In case a fragment was overlapping more than one bin, the read count was distributed proportionally. Afterwards, the each binned profiles wasere smoothed by averaging over a running window of 5 bins and scaled by 10^3 / sum of all its counts on chr5. The viewpoint and a window ± 5kb around it were not considered for the computation of the scaling factor. The profiles were generated with custom Java code using htsjdk v2.12.0  (https://samtools.github.io/htsjdk/). Virtual Capture-C viepoint: Shh promoter (chr5:28,789,001-28,799,000)

organism: Mus musculus

source_name: Embryonic Midbrain

growth_protocol: Limbs from 34-5 somite-stage (E10.5) mouse embryos were microdissected in PBS.

extract_protocol:
Tissues were homogenized in Collagenase solution, fixes with 2% FA at room temperature, 10 min and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor). Upon PBS wash, samples were snap-frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 2 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

tag: strain

tag: development stage

value: delta-CTCF i4i5ZRS


title: FLHL-Lprom_L14195-2

description: FLHL-Lprom_L14195-1_L14195-2_merged_MAPQ30.KR_10kb.WashU.txt

source_name: Embryonic Limb Bud


title: FLHL-WT-Rep3_L12944-2

description:
FLHL-WT_L12944-1-2_L12945_merged_MAPQ30.KR_10kb.WashU.txt
vC_WT_FLHL_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

value: wild type


title: MB-i4i5ZRS_L13769-1


title: FLHL-i4i5ZRSreg_L16376-1

description:
FLHL-i4i5ZRSreg_L16376-1_L16376-2_merged_MAPQ30.KR_10kb.WashU.txt
vC_i4i5ZRSreg_FLHL_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

value: delta-CTCF i4i5ZRSreg


title: FLHL-ZRSreg_L14197-2

description:
FLHL-ZRSreg_L14197-1_L14197-2_merged_MAPQ30.KR_10kb.WashU.txt
vC_ZRSreg_FLHL_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

value: delta-RSreg


title: Rad21-FLHL-E105-i4i5ZRS-Mm-Rep1-L13980

description: ΔCTCF i4i5ZRS

data_processing:
Single-end reads from ChIP-seq experiments were mapped with Bowtie-2.2.6 (Langmead and Salzberg, 2012) to reference genome mm9. Mapped reads were filtered for mapping quality ≥10, and duplicates were removed using samtools (https://github.com/samtools/samtools).
Reads were extended (chromatin modifications: 300bp, transcription factors: 200bp) and scaled (one million / total of unique reads) to produce coverage tracks. For figure display purposes, ChIP-seq BigWig files were merged using the bigWigMerge from UCSC tools. BigWig files were visualized in the UCSC browser.
Genome_build: mm9
Supplementary_files_format_and_content: bw

source_name: Limb

growth_protocol: Limb bud and midbrain were micro-dissected from 34-5 somite stage (E10.5) mouse embryos

extract_protocol:
Histone modifications were immunoprecipitated with the respective antibody (Lee et al., 2006, Jerkovic et al., 2017) and trascription factor ChIPs were performed with the  iDeal ChIP-seq kit for Transcription Factors (Cat. No. C01010055) according to guidelines.
We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate chromatin modification ChIP and 20μg for CTCF and RAD21 ChIP. ChIP for H3K27ac (Diagenode: C15410174), H3K36me3 K3K36me3 (Abcam:ab9050), CTCF (Diagenode:C15410210) and RAD21 (Abcam: ab992) was then performed as in Lee et al., 2006.
Libraries were prepared using the Nextera adaptors and sequenced 50 or 75bp reads.

treatment_protocol: Tissues were homogenized with Collagenase solution, fixed with 1% FA crosslinking for 10 minutes at room temperature,  cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor) and upon PBS wash, snap frozen and stored in -80°C. Material was sonicated either in in buffer 3 for sonication (Lee et al.,) for chromatin modifications or sonication buffer included in the iDeal ChIP-seq kit for Transcription Factors (Cat. No. C01010055).

value: deltaCTCF i4i5ZRS

tag: embryonic stage

value: Embryonic day 10.5

value: Rad21 (Abcam:ab992)


title: Rad21-FLHL-E105-WT-Rep1-L12247

description: Wildtype

value: Wildtype


title: H3K27ac-FLHL-E105-Lprom-Mm-Rep1-L10228

description:
Lmbr1Δprom/Δprom
H3K27ac-FLHL-E105-Lprom-Mm-Merge.bw

source_name: Midbrain

value: H3K27Ac (Diagenode:C15410174)


title: Rad21-FLHL-E105-i4i5-Mm-Rep1-L14967

description: ΔCTCF i4i5

value: deltaCTCF i4i5


title: H3K27ac-FLHL-E105-Lprom-Mm-Rep2-L14766


title: H3K27ac-FLHL-E105-WT-Mm-Rep2-L14765

description:
Wildtype
H3K27ac-FLHL-E105-WT-Mm-Merge.bw


title: H3K27ac-FLHL-E105-WT-Mm-Rep1-L14764


title: CTCF-FLHL-E105-i4i5ZRS-Mm-Rep2-L13978

description: ΔCTCF i4i5ZRS

value: CTCF (Diagenode:C15410210)


title: CTCF-FLHL-E105-i4i5-Mm-Rep2-L14966

description: ΔCTCF i4i5


title: FLHL-ZRSreg_L14197-1

description:
ΔZRSreg
FLHL-ZRSreg_L14197-1_L14197-2_merged_MAPQ30.KR_10kb.WashU.txt

data_processing:
Library strategy: Capture Hi-C
Raw sequencing reads were preprocessed with cutadapt v1.15 (Martin, 2011) to trim potential low quality bases (-q 20 -m 25) and Illumina sequencing adapters (-a and -A option with Illumina TruSeq adapter sequences according to the cutadapt documentation) at the 3’ end of reads. Next, sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0 (Wingett et al., 2015) (no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) for short read mapping. The trimming of sequencing adapters in the first step would not have been necessary, because potentially remaining sequencing adapter in reads from valid ligation products should also be removed by the truncation after ligation sites implemented in the HiCUP pipeline. In case replicates were available, they were combined after the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 (Durand et al., 2016) was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing (Durand et al., 2016; Knight and Ruiz, 2013; Rao et al., 2014). For binning and normalization, only the genomic region chr5:27,800,001- 30,600,000 enriched in the DNA-capturing step was considered. Therefore, only reads pairs mapping to this region were kept, shifted by the offset of 27,800,000 bp and imported with Juicer tools using a custom chrom.sizes file which contained only the length of the enriched region (2.8 Mb). Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb and 10kb resolution and coordinates were shifted back to their original values. Subtraction maps were generated from KR normalized maps, which were normalized in a pair-wise manner before subtraction. To account for differences between two maps in their distance-dependent signal decay, maps were scaled jointly across their sub-diagonals. Therefore, the values of each sub-diagonal of one map were divided by the sum of this sub-diagonal and multiplied by the average of these sums from both maps. Afterwards, the maps were scaled by 106 / total sum. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 97-th  percentile were truncated for visualization purposes.
In order to obtain more fine-grained interaction profiles for selected loci, we defined 10kb viewpoint regions and generated virtual Capture-C-like profiles based on the filtered, unique read-pairs that were also used for the cHiC maps. A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region, while the other read mapped outside of it. The reads outside of the viewpoint were counted per restriction fragment and read counts were binned afterwards to 1 kb bins. In case a fragment was overlapping more than one bin, the read count was distributed proportionally. Afterwards, the each binned profiles wasere smoothed by averaging over a running window of 5 bins and scaled by 103 / sum of all its counts in the enriched region on chr5. The viewpoint and a window ± 5kb around it were not considered for the computation of the scaling factor. The profiles were generated with custom Java code using htsjdk v2.12.0  (https://samtools.github.io/htsjdk/). Virtual Capture-C viepoint: Shh promoter (chr5:28,789,001-28,799,000)
Supplementary_files_format_and_content: bedgraph, txt

value: deltaZRSreg


title: FLHL-i4i5ZRS_L13768-2

description:
ΔCTCF i4i5ZRS
vC_i4i5ZRS_FLHL_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph
FLHL-i4i5ZRS_L13768-1_L13768-2_merged_MAPQ30_KR_10kb.WashU.txt


title: DIPGXIII-KO-COMBO-R1

value: glioma tumor


title: HSJ-030-C8


title: FLHL-i4i5ZRS_L13768-1


title: ESC_WT_G4_L13065-1

description:
wild type
ESC-WT-G4_L13065-2-L13736-2_merged_MAPQ30.KR_10kb.WashU.txt
vC_ESCs_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

source_name: Embryonic Stem Cells


title: FLHL-Lprom_L14195-1

description:
Lmbr1Δprom/Δprom
FLHL-Lprom_L14195-1_L14195-2_merged_MAPQ30.KR_10kb.WashU.txt


title: WT_E8.5_1b

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

description: Single-cell RNA-sequencing of 10 wild-type E8.5 mouse embryos (library b)

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", version 1.3.1, default parameters). The count pipeline was run jointly on multiple sequencing runs of the same experiment. Genomic reference: "refdata-cellranger-mm10-1.2.0", prepared by 10x Genomics.
For experiments with multiple libraries, all libraries were aggregated using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("aggr pipeline", version 1.3.1, default parameters). The output of Cell Ranger "count" was aggregated and normalized to the same sequencing depth and then the gene-barcode matrices were recomputed on the combined data. Sample aggregation was evaluated with normalizing for sequencing depth differences in the libraries. Normalized UMI counts used the 'mapped' normalization mode. Analysis of the data was based on the normalized UMI counts.
Genome_build: mm10
Supplementary_files_format_and_content: For all samples there is one tar gz archive containing the gene-barcode matrices as produced by the Cell Ranger pipeline. They contain the MEX-formatted UMI count matrices of each sample, or if multiple libraries where sequence, the aggregated gene-barcode matrix. Samples names consist of genotype (WT: wild-type, EED: Eed KO), developmental state (E6.5, E7.0, E7.5, E8.0, E8.5, experiment number (1, 2) with respect to genotype and stage and, if aggregated, library number (a, b). 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix...Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

molecule: polyA RNA

source_name: whole embryo

growth_protocol: Preimplantation embryos were cultured in pre-gassed 25 ul KSOM supplemented with 1/2 amino acids (Millipore) under mineral oil at 37ºC and 5% CO2.  After ~84 hours post-fertilization, cavitated blastocysts were transferred into the uterine horns of pseudopregnant females in clutches of 10-15 per horn.

extract_protocol:
Wild-type (WT) and Eed null (Eed KO) embryos were isolated from surrogate mice. Outermost extraembryonic tissues (yolk sac, trophectoderm derived tissues) were preserved if possible. The 4-10 embryos isolated per experiment were washed in 1xPBS/0.4%BSA, pooled without pre-selection and subjected to tissue dissociation in 200 µl TrypLE Express (Gibco) for 40-60 minutes at 37ºC, with pipetting in 5 minute intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40 µM. Cells were washed twice with 1ml 1xPBS/0.4%BSA and centrifugation for 5 minutes at 1200 rpm. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomic, Chromium™ Single Cell 3’ v2).
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v2), with the exception of fewer PCR cycles in cDNA amplification and sample index PCR than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 230 Mio paired end reads and parameters as described in the manual.

treatment_protocol: B6D2F1 oocytes were isolated from 5-10 week old female mice ~12h after a hormone priming superovulation regime (5 IU PSMG and 5IU hCG delivered 46 hours afterwards) and stored in 25 ul droplets of pregassed KSOM media with 1/2 amino acids (Millipore) at 37ºC and 5%C02 .  Zygotes were generated by intracytoplasmic sperm injection of decapitated B6/CAST F1 strain sperm and cultured to E3.5 blastoycsts prior to uterine transfer into pseudopregnant CD-1 strain females (~25-35 g).  Post-implantation embryos were isolated according to the embryonic day with a 24 hour offset to accommodate developmental delay as a result of uterine transfer (see extract protocol).  Experimental samples were additionally injected with a cocktail of 3 discrete gRNA's targeted to exons of Eed and Cas9 mRNA synthesized by in vitro transcription at concentrations of 33.3 ng/ul per gRNA and 200 ng/ul for Cas9.  gRNA/Cas9 injections occurred within 6-8 hours post fertilization, followed by equivalent culture in KSOM media to the blastocyst stage as the control.

value: B6D2F1 maternal strain crossed with B6/CAST F1 males

value: embryo

tag: developmental stage

value: wild-type


title: WT_E8.0_1a

description: Single-cell RNA-sequencing of 10 wild-type E8.0 mouse embryos (library a)


title: WT_E7.5_2

description: Single-cell RNA-sequencing of 4 wild-type E7.5 mouse embryos


title: WT_E7.0_1

description: Single-cell RNA-sequencing of 9 wild-type E7.0 mouse embryos


title: WT_E8.0_1b

description: Single-cell RNA-sequencing of 10 wild-type E8.0 mouse embryos (library b)


title: WT_E6.5_1

description: Single-cell RNA-sequencing of 10 wild-type E6.5 mouse embryos


title: T4: chronic lymphocytic leukemia 4 (Cytogenetics_Array)

type: genomic

city: Brno

first: Karla

last: Plevova

address: Kamenice 5

department: Central European Institute of Technology

country: Czech Republic

institute: Masaryk University

hyb_protocol: Cytogenetic Array 2.7M CytoScan HD/Cytogenetic Array 2.7M

data_processing: Chromosome Analysis Suite

label: biotin

source_name: peripheral blood

extract_protocol: DNA blood & tissue isolation kit, Qiagen

tag: gender

value: M

value: peripheral blood

tag: diagnosis

value: chronic lymphocytic leukemia


title: T3: chronic lymphocytic leukemia 3 (Cytogenetics_Array)

scan_protocol: Cytogenetic Array 2.7M CytoScan HD/Cytogenetic Array 2.7M


title: T2: chronic lymphocytic leukemia 2 (Cytogenetics_Array)

label_protocol:
Cytogenetic Array 2.7M
CytoScan HD/Cytogenetic Array 2.7M


title: Exp Az-2

city: Beijing

first: Xing

last: Chen

address: Chengfu Road 202

country: China

institute: Peking University

description: RNA fragment

data_processing:
Adaptors were removed by using cutadapt (version 1.17). Low-quality reads were filtered by using fastq_quality_filter (version 0.0.13). The filtered reads were mapped to the human genome (hg38) using bowtie (version 1.1.1) with maximum 2 mismatches.
The clusters were analyzed using the default settings of PARalyzer (version 1.5) with following modifications: the minimum read count was set to 5 and the minimum T-C conversion count was set to 2.
The clusters were mapped to the human transcriptome (UCSC) using BEDTools (version 2.24.0).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt files include read counts for each cluster. bed files include position of each cluster

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in 10-cm dishes (one dish for each group). HeLa cells were grown in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin at 37 ℃ in a 5% CO2 atmosphere.

extract_protocol:
Follow the OG-CLAP protocol.
The cDNA library was constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1) following manufacturer’s instruction.

treatment_protocol: After the cells reached 50% confluence, GalNAz was added to the medium of Exp group to a final concentration of 100 μM. After 30 h of culturing, 4SU was added to the medium of both Exp group and noAz group to a final concentration of 200 μM. Then the cells were cultured for 16 h, followed by an additional labeling pulse with 100 μM 4SU for 2 h.

value: Epithelial

tag: passages

value: A HeLa cell line derived from ATCC HeLa cells


title: Exp Az-3

description: RNA fragment


title: WT_E7.5_1

description: Single-cell RNA-sequencing of 7 wild-type E7.5 mouse embryos


title: Control B-1

description: RNA fragment


title: DIPGXIII-KO-C10P5_H3K27ac

data_processing:
Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (Bolger et al., 2014) (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple quality control metrics were obtained using FASTQC (v0.11.2), samtools (Li et al., 2009) (v0.1.19), BEDtools (Quinlan and Hall, 2010) (v2.17.0) and custom scripts.   Reads were processed as described for RNAseq, and then aligned using the human repeat genome as reference, as previously described (Solovyov et al., Cell Reports 2018). Repbase reference genome was used (Bao et al., 2015) (v23.03) (http://www.girinst.org/repbase). Since Repbase largely consists of family consensus sequences, reads are assigned to these sequences regardless of where and how many times they are present in the genome, mitigating mapping uncertainty. We combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus elements, and counted the number of reads mapping into each of these elements using featureCounts (MAPQ>3). Differential enrichment of H3K27ac at the consensus sequences were then calculated using DESeq2 (Love et al., 2014). The inverse of ChIP-Rx spike-in scaling factors (i.e. 1/rx) were supplied to DESeq2 as normalization factors (i.e. size factors).
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

source_name: H3.3K27M-KO_Tumor-derived cell-line

value: Tumor-derived cell-line

value: H3K27ac antibody (Diagenode, C15410196)


title: BT245-KO-C4P6_H3K27ac


title: T5: chronic lymphocytic leukemia 5 (Cytogenetics_Array)


title: Control B-2

description: RNA fragment


title: G477-LPG

data_processing:
The ATAC-seq libraries were sequenced with 125 bp paired-end reads and trimmed for Nextera sequencing adaptors using trimgalore with default settings. The trimmed reads were then mapped to hg19. Reads were filtered to remove duplicates, unmapped or poor quality (phred33<30) reads, mitochondrial reads, and those overlapping the ENCODE blacklist (Carroll et al., 2014).
Following alignment, accessible chromatin regions/peaks were called using MACS2. Default parameters were used, except for the following: --keep-dup all -B --nomodel --SPMR -q 0.05 --slocal 6250 --llocal 6250. The signal intensity was calculated as the fold enrichment of the signal per million reads in a sample over a modelled local background using the bdgcmp function in MACS2 (Zhang et al., 2008). Custom scripts along with the bedtools suite were used to identify chromatin accessibility peaks unique to specific groups of samples and to identify overlaps with H3K27ac peaks. ENCODE’s Genome Structure Correction tool (Bickel et al., 2011) was used to calculate the significance of the change in agreement between the H3K27ac and ATAC-seq signal.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: H3.3K27WT patient-derived cell line

extract_protocol:
Adherent cell cultures were dissociated and 100 000 cells were washed twice in cold PBS at 4°C. Cells were resuspended in 100 uL Hypotonic Cell Lysis Buffer (0.1% Sodium Citrate Tribasic Dihydrate, 0.1% Triton X-100) and titurated until cells were dissolved. Samples were incubated on ice 30 minutes, centrifuged at 2000 g for 5 minutes at 4°C, and pellet resuspended in 100 uL Normal Cell Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), titurated, incubated on ice 30 minutes, centrifuged at 2000 g for 5 minutes at 4°C, and supernatant removed. The transposase reaction was carried out by titurating in 25 uL per sample in TD Buffer (10 mM Tris-HCl, pH 8.00, 5 mM Magnesium Chloride) with 5 uL Transposase (Illumina Nextera Kit), and incubated at 37°C for 30 minutes, and 8.5 uL of 100mM EDTA was added, samples transferred to ice, and DNA recovered using MinElute PCR Purification columns (Qiagen).
Libraries were generated by PCR in 50 uL reaction (25 uL sample, 10 uL 5x Phusion HF buffer, 0.5 uL Phusion Polymerase, 1 uL 10mM dNTPs, 0.5 uL of each custom Illumina primers at 12.5 uM). The PCR reaction followed 98°C for 30 seconds, followed by 12 cycles of 98°C for 10s, 63°C for 30s, 72°C for 1 min, followed by 72°C for 5 min. DNA was recovered using GeneRead Purification columns (Qiagen). The libraries were sequenced to 50 million reads per sample on Illumina HiSeq 2500 using Nextera Sequencing Primers.

tag: cell line background

tag: genotype/variation

tag: sample info

value: H3.3K27WT patient-derived cell line


title: G477-P14


title: Exp Az-1

description: RNA fragment


title: DIPGXIII-P18

source_name: H3.3K27M patient-derived cell line

value: DIPGXIII

value: H3.3K27M patient-derived cell line


title: BT245-DMSO-D5

tag: genotype


title: DIPGXIII-P15


title: BT245-COMBO-R1

tag: treatment

value: Panobinostat + 5-azacytidine


title: pcGBM2-P15


title: DIPGXIII-KO-C5P8

source_name: Crispr/Cas9 H3.3K27M-KO clone

value: Crispr/Cas9 H3.3K27M-KO clone


title: DIPGVI-P16

value: DIPGVI


title: DIPGXIII-KO-C10P5


title: DIPGXIII-KO-C10P10


title: Thiamet-G TG-2

data_processing:
Reads were mapped to the human genome (hg19) using Tophat and only uniquely mapped reads were allowed for subsequent analysis.
The splicing pattern analysis and PSI calculation was performed by using MISO with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include PSI value for each alternative splicing event ...

extract_protocol:
Total RNA was extracted by TRIzol following the manufacturer’s instructions. For each replicate, mRNA was purified from 3 µg total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After the cells reached 70% confluence, the cells were treated with 100 µM 5S, 10 µM TG, or an equal amount of DMSO for 48 h.


title: Zebrafish fin pigment cells

city: Seattle

first: Victor

last: Lewis

state: Washington

address: 1959 NE Pacific St., UW-HSB H502

department: Biology

institute: University of Washington

description: Data collected from zebrafish fin pigment cells. Single-cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 2 of their single-cell solutions kit.

data_processing:
Expression matrix files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.

organism: Danio rerio

source_name: Dorsal and anal fins

growth_protocol: Fish were maintained at ~28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac (Aquafauna) followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WT(ABb), a derivative of inbred ABwp, Tg(tyrp1b:palm-mCherry)wp.rt11 ,Tg(pnp4a:palmmCherry)wp.rt10

extract_protocol: 10X genomics V1 protocol following manufacturer recommendations.

treatment_protocol: Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation, we extracted distal dorsal fin regions (~10 mm standard length, SL; n=20) and proximal interstripe anal fin regions (~14 mm SL; n=10). Tissue was enzymatically dissociated with Liberase (0.25 mg/mL in dPBS) at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re-suspended in 1% BSA / 5% FBS in dPBS and DAPI (0.1 μg/mL, 15 min) before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels, single cells were isolated by sequentially gating cells according to their SSC-A vs. FSC-A, FSC-H vs FSC-W and SSC-H vs SSC-W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild-type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence, and then cells from transgenic fish were purified according to these gates. All samples were kept on ice, except during Liberase incubation, and then sorted chilled.

value: pigment cells

value: Untreated


title: Thiamet-G TG-1


title: DIPGVI-P14


title: R088

data_processing:
Data processing. Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple control metrics were obtained using FASTQC (v0.11.2), samtools (v0.1.19), BEDtools (v2.17.0) and custom scripts.
Gene expression analysis. The remaining clean set of reads were then aligned to the reference genome build hg19 (GRCh37) with STAR (v2.3.0e) using the default parameters. Multimapping reads (MAPQ>3) were discarded from downstream analyses. Gene expression levels were estimated by quantifying uniquely mapped reads falling into exonic regions defined by the ensGene annotation set from Ensembl (GRCh37; N=60234 genes) using featureCounts (v1.4.4). Normalization (mean-of-ratios), variance-stabilized transformations of the data, as well as differential expression analysis, were performed using DESeq2. Unless otherwise stated, all reported p-values have been adjusted for multiple testing using the Benjamini-Hochberg procedure.
Repeat element expression analysis. The clean set of rRNA-depleted RNA-seq reads were aligned to the human repeat genome, as previously described. The reference repeat sequences were downloaded from Repbase (v23.03) (http://www.girinst.org/repbase). We then combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus repeat element sequences. All subsequent steps closely mirror those detailed for gene expression analysis. Normalization (library size) factors derived from canonical genes (Ensembl ensGene annotation) using mean-of-ratios as described above were used to normalize repeat elements.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

source_name: Tumor


title: Ac4-5SGlcNAc 5S-1


title: R006


title: DMSO NC-2


title: Ac4-5SGlcNAc 5S-2


title: P0.5 fiber rep2

city: Bronx

first: Ales

last: Cvekl

state: NY

address: 1300 Morris Park Avenue, Ullman 123

department: The Departments Ophthalmology and Visual Sciences, Genetics

institute: Albert Einstein College of Medicine

data_processing:
Adapters were trimmed using trim-galore (v 0.4.1)
Trimmed reads were then mapped to mm10 using Bowtie2 (v2.3.3.1)
Reads with low mapping quality, mapped to mitochondrial or found duplicated were removed using SAMtools (v1.2) and picard (v 2.1.1)
MACS2 (2.1. 0) was used for peak calling
Genome_build: mm10
Supplementary_files_format_and_content: Narrowpeak files for each pooled sample

source_name: lens fiber

extract_protocol:
After cell dissociation using freshly microdissected lens epithelium and fiber, the nuclei were extracted using cell lysis buffer
The ATAC-seq libraries were prepared using standard ATAC-seq protocols as described by Buenrostro JD et al 2013 Nature Methods

tag: tissue

value: lens


title: P0.5 fiber rep1


title: P0.5 epithelium rep2

source_name: lens epithelium


title: P0.5 epithelium rep1


title: chronic lymphocytic leukemia 9

data_processing:
bcl2fastq for base calling and demultiplexing
Adapter sequences were trimmed from raw reads using Trimmomatic software (version 0.32)
STAR alignment
htseq-count script for read counting from BAM files
edgeR rpkm() function for data normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM log2 values for all samples

source_name: Peripheral blood CLL cell

extract_protocol:
TriReagent with isopropanol precipitation, DNase treatment
RNA libraries were prepared for sequencing using TruSeq® Stranded Total RNA kit (Illumina) with Ribo-Zero ribosomal RNA depletion, 1 ul of RNA treated by DNase was used as an input.

tag: disease state

value: chronic lymphocytic leukemia (CLL)

value: B-lymphocytes

value: Peripheral blood

tag: chromosomal abnormalities

value: chromothripsis


title: chronic lymphocytic leukemia 5


title: chronic lymphocytic leukemia 6


title: chronic lymphocytic leukemia 10


title: chronic lymphocytic leukemia 8


title: E14.5 fiber rep1


title: Control B-3

description: RNA fragment

value: Epithelial


title: chronic lymphocytic leukemia 4


title: E14.5 epithelium rep2


title: E14.5 fiber rep2


title: PS14-1547


title: chronic lymphocytic leukemia 3


title: DMSO NC-1

value: A HeLa cell line derived from ATCC HeLa cells


title: CTCF-FLHL-E105-i4i5ZRSreg-Mm-Rep1-L12999

data_processing:
Single-end reads from ChIP-seq experiments were mapped with Bowtie-2.2.6 (Langmead and Salzberg, 2012) to reference genome mm9. Mapped reads were filtered for mapping quality ≥10, and duplicates were removed using samtools (https://github.com/samtools/samtools).
Reads were extended (chromatin modifications: 300bp, transcription factors: 200bp) and scaled (one million / total of unique reads) to produce coverage tracks. For figure display purposes, ChIP-seq BigWig files were merged using the bigWigMerge from UCSC tools. BigWig files were visualized in the UCSC browser.
Genome_build: mm9

value: delta-CTCF i4i5ZRSreg

value: Embryonic day 10.5

tag: chip antibody

value: CTCF (Diagenode:C15410210)


title: chronic lymphocytic leukemia 2

tag: cell type


title: E14.5 epithelium rep1

tag: strain


title: BT245-KO-C4P6

data_processing:
Data processing. Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple control metrics were obtained using FASTQC (v0.11.2), samtools (v0.1.19), BEDtools (v2.17.0) and custom scripts.
Gene expression analysis. The remaining clean set of reads were then aligned to the reference genome build hg19 (GRCh37) with STAR (v2.3.0e) using the default parameters. Multimapping reads (MAPQ<1) were discarded from downstream analyses. Gene expression levels were estimated by quantifying uniquely mapped reads falling into exonic regions defined by the ensGene annotation set from Ensembl (GRCh37; N=60234 genes) using featureCounts (v1.4.4). Normalization (mean-of-ratios), variance-stabilized transformations of the data, as well as differential expression analysis, were performed using DESeq2. Unless otherwise stated, all reported p-values have been adjusted for multiple testing using the Benjamini-Hochberg procedure.
Repeat element expression analysis. The clean set of rRNA-depleted RNA-seq reads were aligned to the human repeat genome, as previously described. The reference repeat sequences were downloaded from Repbase (v23.03) (http://www.girinst.org/repbase). We then combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus repeat element sequences. All subsequent steps closely mirror those detailed for gene expression analysis. Normalization (library size) factors derived from canonical genes (Ensembl ensGene annotation) using mean-of-ratios as described above were used to normalize repeat elements.
Genome_build: hg19
Supplementary_files_format_and_content: Raw abundance measurements of Ensembl genes
Supplementary_files_format_and_content: Raw abundance measurements of Repbase repeat elements

source_name: Tumor-derived cell-line

value: glioma tumor


title: NC3

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

country: United Kingdom

institute: aSciStance Ltd

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim Galore version: 0.4.1 (a wrapper for Cutadapt 1.8.1 with parameters  -f fastq -e 0.1 -q 20 -O 1 and FastQC)
Reads were mapped to GRCh38 whole genome using HiSAT2 v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Counts were produced using SeqMonk 0.34. All reads overlapping an exon were counted, all reads from all exons of all isoforms added, counting each one once.
Counts Per Million reads (CPM) were calculated dividing reads from all exons of all isoforms by the size of the library in reads, multiplied by 1 million.
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts Per Million reads (CPM)

source_name: engineered neural crest cells

extract_protocol:
Total RNA was extracted from cultures using RNeasy mini from Qiagen. DNA contamination was removed from the samples using DNA-free™ DNA Removal Kit from Ambion (Thermofisher).
cDNA synthesis and Illumina libraries were performed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit from TAKARA.

value: hPSC-epi-derived neural crest progeniteurs

tag: es line


title: NC2


title: NC1


title: Sample_Group_2__Neonatal_NSC_replicate3

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

data_processing:
Sequencing data is analyzed for quality and contamination. Following the initial assessment, Bowtie2 is used to map the spike-in DNA before the analysis moves to the trimming and filtering steps where RNA-seq reads are preprocessed to improve the quality of data input for read mapping. The open-source tools used for trimming of adapters are FastqMcf, part of the ea-utils package, and cutadapt, with PRINSEQ used in the quality filtering step.Once the data preprocessing step has detected and removed N’s at the ends of reads, trimmed sequencing adapters, and filtered reads for quality and length. FastQC is then re-run to analyze the trimmed reads, allowing a before and after comparison. The summary report generated provides a quality assurance check to validate the processed set of input data used in the subsequent read mapping step. The improved set of sequence reads are merged, if needed, using SeqPrep then mapped to the reference genome using Bowtie, an ultrafast, memory- efficient short read aligner, followed by generation of a mapping rate summar. Using the open-source software BEDTools and SAMtools, read alignment and read coverage tracks are generated and deployed to the genome browser. The final steps of the analysis are abundance determination and differential expression analysis by DEseq. Abundance levels for ncRNAs (miRNAs, tRNAs, rRNAs, lincRNAs, piRNAs, snoRNAs), antisense transcripts, coding genes and repeat elements (LTR, LINE, SINE,and tandem repeats) are determined, then a summary of reads overlapping each of these annotations in the reference genome is created using SAMtools using R. Finally, differences in expression of ncRNA, antisense transcripts, and repeat elements between samples are calculated. The analysis produces outputs that include read alignment and coverage tracks for the genome browser, annotations to the reference genome, as well as abundance determination and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Read Counts and Differential Expression data

source_name: NSC EV

extract_protocol:
Trizol Extraction and SeraMir Exosome RNA column purification
Illumina small RNA preparation kit

value: subventricular zone

value: primary neural stem cells (NSCs)


title: Sample_Group_2__Neonatal_NSC_replicate2


title: DIPGXIII-DMSO-R3


title: Sample_Group_2__Neonatal_NSC_replicate1


title: Sample_Group_1_Astrocytes_replicate3

source_name: Astrocyte EV

value: cortical astrocytes


title: LMSMC4

source_name: engineered smooth muscle cells

value: hPSC-lpm-derived smooth muscle cells


title: WT_E8.5_1a

source_name: whole embryo

value: B6D2F1 maternal strain crossed with B6/CAST F1 males

value: embryo

value: wild-type


title: Sample_Group_1_Astrocytes_replicate2


title: HCASMC4

source_name: coronary artery smooth muscle cells

value: Primary cells from adult patient


title: Sample_Group_1_Astrocytes_replicate1


title: LMSMC3


title: DIPGXIII-P17

value: DIPGXIII

value: Tumor-derived cell-line

value: H3.3K27M patient-derived cell line


title: LMSMC2


title: HCASMC2


title: chronic lymphocytic leukemia 1

value: chronic lymphocytic leukemia (CLL)

value: B-lymphocytes

value: Peripheral blood

value: chromothripsis


title: FLHL-i4i5ZRSreg_L16376-2

data_processing:
Raw sequencing reads were preprocessed with cutadapt v1.15 (Martin, 2011) to trim potential low quality bases (-q 20 -m 25) and Illumina sequencing adapters (-a and -A option with Illumina TruSeq adapter sequences according to the cutadapt documentation) at the 3’ end of reads. Next, sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0 (Wingett et al., 2015) (no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) for short read mapping. The trimming of sequencing adapters in the first step would not have been necessary, because potentially remaining sequencing adapter in reads from valid ligation products should also be removed by the truncation after ligation sites implemented in the HiCUP pipeline. In case replicates were available, they were combined after the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 (Durand et al., 2016) was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing (Durand et al., 2016; Knight and Ruiz, 2013; Rao et al., 2014). For binning and normalization, only the genomic region chr5:27,800,001- 30,600,000 enriched in the DNA-capturing step was considered. Therefore, only reads pairs mapping to this region were kept, shifted by the offset of 27,800,000 bp and imported with Juicer tools using a custom chrom.sizes file which contained only the length of the enriched region (2.8 Mb). Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb and 10kb resolution and coordinates were shifted back to their original values. Subtraction maps were generated from KR normalized maps, which were normalized in a pair-wise manner before subtraction. To account for differences between two maps in their distance-dependent signal decay, maps were scaled jointly across their sub-diagonals. Therefore, the values of each sub-diagonal of one map were divided by the sum of this sub-diagonal and multiplied by the average of these sums from both maps. Afterwards, the maps were scaled by 10^6 / total sum. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 97-th  percentile were truncated for visualization purposes.
In order to obtain more fine-grained interaction profiles for selected loci, we defined 10kb viewpoint regions and generated virtual Capture-C-like profiles based on the filtered, unique read-pairs that were also used for the cHiC maps. A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region, while the other read mapped outside of it. The reads outside of the viewpoint were counted per restriction fragment and read counts were binned afterwards to 1 kb bins. In case a fragment was overlapping more than one bin, the read count was distributed proportionally. Afterwards, the each binned profiles wasere smoothed by averaging over a running window of 5 bins and scaled by 10^3 / sum of all its counts on chr5. The viewpoint and a window ± 5kb around it were not considered for the computation of the scaling factor. The profiles were generated with custom Java code using htsjdk v2.12.0  (https://samtools.github.io/htsjdk/). Virtual Capture-C viepoint: Shh promoter (chr5:28,789,001-28,799,000)

source_name: Embryonic Limb Bud

tag: development stage

value: delta-CTCF i4i5ZRSreg


title: Day12-12 replicate B

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

data_processing:
Sequences were mapped to the mm10 genome using the align function in the Rsubread package (Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (Ritchie et al. Nucleic Acids Research, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: AML246 RNAseq Dox addition/withdrawal

growth_protocol: AML246 cells were cultured in standard medium (10% FCS in IMDM) supplemented with IL-3

extract_protocol:
FACS sorted cell pellets were lysed and RNA prepared on same day using QIAGEN RNeasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols and sequenced on an Illumina NextSeq500.

treatment_protocol: 0.1 ug/mL Doxycycline was administered at day 0, and withdrawn at day 12

value: 12 days off Dox

tag: sort parameters

value: total viable cells


title: HASMC3

source_name: aortic smooth muscle cells


title: HCASMC1


title: Day12-12 replicate A


title: Day12-8 replicate B

value: 8 days off Dox


title: HASMC2


title: FLHL-i4i5_L12946-2

description:
ΔCTCF i4i5
FLHL-i4i5_L12946_L12946-2_merged_MAPQ30_KR_10kb.WashU.txt
vC_i4i5_FLHL_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

data_processing:
Library strategy: Capture Hi-C
Raw sequencing reads were preprocessed with cutadapt v1.15 (Martin, 2011) to trim potential low quality bases (-q 20 -m 25) and Illumina sequencing adapters (-a and -A option with Illumina TruSeq adapter sequences according to the cutadapt documentation) at the 3’ end of reads. Next, sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0 (Wingett et al., 2015) (no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) for short read mapping. The trimming of sequencing adapters in the first step would not have been necessary, because potentially remaining sequencing adapter in reads from valid ligation products should also be removed by the truncation after ligation sites implemented in the HiCUP pipeline. In case replicates were available, they were combined after the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 (Durand et al., 2016) was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing (Durand et al., 2016; Knight and Ruiz, 2013; Rao et al., 2014). For binning and normalization, only the genomic region chr5:27,800,001- 30,600,000 enriched in the DNA-capturing step was considered. Therefore, only reads pairs mapping to this region were kept, shifted by the offset of 27,800,000 bp and imported with Juicer tools using a custom chrom.sizes file which contained only the length of the enriched region (2.8 Mb). Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb and 10kb resolution and coordinates were shifted back to their original values. Subtraction maps were generated from KR normalized maps, which were normalized in a pair-wise manner before subtraction. To account for differences between two maps in their distance-dependent signal decay, maps were scaled jointly across their sub-diagonals. Therefore, the values of each sub-diagonal of one map were divided by the sum of this sub-diagonal and multiplied by the average of these sums from both maps. Afterwards, the maps were scaled by 106 / total sum. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 97-th  percentile were truncated for visualization purposes.
In order to obtain more fine-grained interaction profiles for selected loci, we defined 10kb viewpoint regions and generated virtual Capture-C-like profiles based on the filtered, unique read-pairs that were also used for the cHiC maps. A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region, while the other read mapped outside of it. The reads outside of the viewpoint were counted per restriction fragment and read counts were binned afterwards to 1 kb bins. In case a fragment was overlapping more than one bin, the read count was distributed proportionally. Afterwards, the each binned profiles wasere smoothed by averaging over a running window of 5 bins and scaled by 103 / sum of all its counts in the enriched region on chr5. The viewpoint and a window ± 5kb around it were not considered for the computation of the scaling factor. The profiles were generated with custom Java code using htsjdk v2.12.0  (https://samtools.github.io/htsjdk/). Virtual Capture-C viepoint: Shh promoter (chr5:28,789,001-28,799,000)
Supplementary_files_format_and_content: bedgraph, txt

tag: embryonic stage

value: deltaCTCF i4i5


title: Day12-8 replicate A


title: Day12-4 replicate B

value: 4 days off Dox


title: HASMC1


title: Day12-4 replicate A


title: CTCF-FLHL-E105-i4i5ZRS-Mm-Rep1-L13977

description: ΔCTCF i4i5ZRS

data_processing:
Single-end reads from ChIP-seq experiments were mapped with Bowtie-2.2.6 (Langmead and Salzberg, 2012) to reference genome mm9. Mapped reads were filtered for mapping quality ≥10, and duplicates were removed using samtools (https://github.com/samtools/samtools).
Reads were extended (chromatin modifications: 300bp, transcription factors: 200bp) and scaled (one million / total of unique reads) to produce coverage tracks. For figure display purposes, ChIP-seq BigWig files were merged using the bigWigMerge from UCSC tools. BigWig files were visualized in the UCSC browser.
Genome_build: mm9
Supplementary_files_format_and_content: bw

source_name: Limb

value: deltaCTCF i4i5ZRS

value: Embryonic day 10.5

value: CTCF (Diagenode:C15410210)


title: EPISMC4

value: hPSC-epi-derived smooth muscle cells


title: Day12M replicate B

value: 12 days Dox

value: Cd11b-high viable cells


title: EPISMC3


title: Day12M replicate A


title: EPISMC1


title: EPI4

source_name: engineered epicardial cells

value: hPSC-derived epicardium


title: Day12 replicate B


title: Day8 replicate A

value: 8 days Dox


title: EPI3


title: EPI1


title: CF4

source_name: engineered cardiac fibroblasts

value: hPSC-epi-derived cardiac fibroblasts


title: Day12 replicate A


title: CF3


title: chronic lymphocytic leukemia 7

value: chronic lymphocytic leukemia (CLL)

value: B-lymphocytes

value: Peripheral blood


title: Day4 replicate A

value: 4 days Dox


title: SJG5-C16

value: glioma tumor


title: Day0 replicate B

value: untreated

value: total viable cells


title: CF1


title: Day0 replicate A


title: PU.1 ChIP

data_processing:
Sequences were mapped to the mm10 genome using the align function in the Rsubread package (Liao et al. Nucleic Acids Research, 2013) with default parameters.
Peaks were called using MACS version 2 with the following settings: callpeak (call peaks from alignment), qvalue cutoff 0.05 and fold enrichment cutoff 10.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using macs2 and contain all peaks that pass the specified q-value and fold enrichment cut-offs.

source_name: AML246 ChIPseq Dox addition/withdrawal

extract_protocol:
Cells were isolated by FACS and ChIP was performed
ChIP-seq libraries were prepared using Truseq ChIP seq DNA sample prep kit from Illumina and sequenced on an Illumina NextSeq500.

value: 12 days off Dox


title: PU.1 ChIP knockdown Day 12- 4


title: PU.1 ChIP knockdown Day 12- 8

value: 4 days off Dox


title: PU.1 ChIP knockdown Day 12- 12

value: 8 days off Dox


title: PU.1 ChIP restoration Day 12


title: Day8 replicate B


title: Day4 replicate B


title: PU.1 ChIP restoration Day 4


title: PU.1 ChIP restoration Day 0


title: Old_28_RNA

first: Maria

last: Figueroa

address: 1501 NW 10th Avenue

department: Biochemistry

institute: University of Miami

data_processing:
Using Cutadapt (version 1.12), all reads were trimmed to 48 basepairs and adapters were removed.
Reads were aligned to the hg19 gencode v19 reference genome using the STAR aligner (version 2.5.2b), specifying the following parameters: outFilterType= BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1 , outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, alignEndsType=EndToEnd12.
Gene counts were calculated using QoRTs. QoRTs was run in secondstranded mode using the hg19 gencode annotation file without entries for ribosomal RNA.
Regularized log (rlog) normalized counts were generated using DESeq2. A multifactor design was used in order to control for sex of the donor as well as any batch effect during library preparation.
Genome_build: hg19
Supplementary_files_format_and_content: The HSCe_Normalized_Counts.txt file contains the regularized log-counts matrix generated by the DESeq2 rlog function. Prior to rlog transformation, a ddsHTSeq object was created with DESeq2 using a multifactor design controlling for donor sex and batch of library preparation. For each sample, a text file is also included that contains the raw counts generated by QoRTs.

source_name: Bone marrow

extract_protocol:
HSCe RNA was extracted following the manufactures’ protocol for the Qiagen Allprep Micro Kit (#80284). Samples were eluted in 14 µL RNAse free water. An ethanol precipitation was then used to concentrate samples.
Samples with a RIN>8.5 were used for library preparation. Ribosomal RNA was removed using RiboGone (Clontech, #634846). Stranded libraries were prepared by the University of Michigan Sequencing Core using the SMARTer Stranded RNA-seq Kit (Clontech, #634836). Libraries were sequenced on the HiSeq-2500 with 50 bp pair-end sequencing.

treatment_protocol: Miltenyi MACS magnetic bead purification was used to enrich frozen bone marrow MNC for CD34+ cells. The CD34+ fraction was then stained with CD2-TC, CD3-TC, CD4-TC, CD7-TC, CD8-TC, CD10-TC, CD11b-TC, CD14-TC, CD19-TC, CD20-TC, CD56-TC, and Glycophorin A-TC, followed by CD34-APC, CD38-PE-Cy7, CD123-PE,  CD45RA-FITC and DAPI. Using a BD FACSAria I, HSCe (DAPI-, Lineage-, CD34+, CD38-) were FACS sorted into RLT+ from the Qiagen Allprep Micro Kit (#80284).

value: HSCe (CD34+, CD38-,Lineage-)

tag: donor age

tag: donor sex

value: F


title: Old_25_RNA


title: Old_22_RNA


title: Old_19_RNA


title: Old_21_RNA

value: M


title: Old_23_RNA


title: Old_4_RNA


title: Old_20_RNA


title: ESC_WT_G4_L13736-2

description: ESC-WT-G4_L13065-2-L13736-2_merged_MAPQ30.KR_10kb.WashU.txt

source_name: Embryonic Stem Cells

value: wild type


title: PU.1 ChIP restoration Day 8


title: PU.1  knockdown Day 12- 12

data_processing:
Sequences were mapped to the mm10 genome using the align function in the Rsubread package (Liao et al. Nucleic Acids Research, 2013) with default parameters.
ATAC-seq reads were aligned to the mm10 genome assembly using Rsubread
Duplicates were filtered out using MarkDuplicate function in Picard (version 2.14.0).
Peaks were called using MACS version 2 with the following setting: callpeak (call peaks from alignment), qvalue 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using macs2 and contain all peaks that pass the specified q-value cut-off.

source_name: AML246 ATACseq Dox addition/withdrawal

extract_protocol:
Cells were isolated by FACS and ChIP was performed
Libraries were prepared using the Nextera Kit from 50,000 cells per standard ATACseq protocols described in Buenrostro et al, Nature Methods 10:1213 (2013). Libraries were size selected from 200-700bps on a PippenPrep and sequenced on an Illumina NextSeq500 with 75bp PE reads.


title: Old_18_RNA


title: DIPGVI-P15

data_processing:
The ATAC-seq libraries were sequenced with 125 bp paired-end reads and trimmed for Nextera sequencing adaptors using trimgalore with default settings. The trimmed reads were then mapped to hg19. Reads were filtered to remove duplicates, unmapped or poor quality (phred33<30) reads, mitochondrial reads, and those overlapping the ENCODE blacklist (Carroll et al., 2014).
Following alignment, accessible chromatin regions/peaks were called using MACS2. Default parameters were used, except for the following: --keep-dup all -B --nomodel --SPMR -q 0.05 --slocal 6250 --llocal 6250. The signal intensity was calculated as the fold enrichment of the signal per million reads in a sample over a modelled local background using the bdgcmp function in MACS2 (Zhang et al., 2008). Custom scripts along with the bedtools suite were used to identify chromatin accessibility peaks unique to specific groups of samples and to identify overlaps with H3K27ac peaks. ENCODE’s Genome Structure Correction tool (Bickel et al., 2011) was used to calculate the significance of the change in agreement between the H3K27ac and ATAC-seq signal.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: H3.3K27M patient-derived cell line

tag: cell line background

value: DIPGVI

value: Tumor-derived cell-line

value: H3.3K27M patient-derived cell line


title: G477-C6

source_name: Tumor-derived cell-line

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy mini kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2000, 2500 and 4000 platforms.


title: Old_11_RNA


title: PU.1 restoration Day 12- MAC1

value: 12 days Dox

value: Cd11b-high viable cells


title: pCGBM2-C7


title: DIPGXIII-C14_H3K27ac

data_processing:
Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (Bolger et al., 2014) (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple quality control metrics were obtained using FASTQC (v0.11.2), samtools (Li et al., 2009) (v0.1.19), BEDtools (Quinlan and Hall, 2010) (v2.17.0) and custom scripts.   Reads were processed as described for RNAseq, and then aligned using the human repeat genome as reference, as previously described (Solovyov et al., Cell Reports 2018). Repbase reference genome was used (Bao et al., 2015) (v23.03) (http://www.girinst.org/repbase). Since Repbase largely consists of family consensus sequences, reads are assigned to these sequences regardless of where and how many times they are present in the genome, mitigating mapping uncertainty. We combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus elements, and counted the number of reads mapping into each of these elements using featureCounts (MAPQ>3). Differential enrichment of H3K27ac at the consensus sequences were then calculated using DESeq2 (Love et al., 2014). The inverse of ChIP-Rx spike-in scaling factors (i.e. 1/rx) were supplied to DESeq2 as normalization factors (i.e. size factors).
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

source_name: H3.3K27M_Tumor-derived cell-line

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction ~5% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below). ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 6ug of H3K27ac antibody (Diagenode, C15410196), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail (Life Technologies) at 65°C for 30 min followed by 2ul Proteinase K (Thermo Fisher Scientific) at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: sample type

value: H3K27ac antibody (Diagenode, C15410196)


title: PU.1  knockdown Day 12- 4


title: PU.1  restoration Day 12


title: Young_7_RNA


title: PU.1  restoration Day 8

value: 8 days Dox


title: Young_6_RNA


title: PU.1  restoration Day 4

value: 4 days Dox


title: Young_5_RNA


title: PU.1  restoration Day 0

value: untreated


title: Young_4_RNA


title: Young_25_RNA


title: PU.1  knockdown Day 12- 8

value: total viable cells


title: mo-NSK-iPS

city: Stanford

first: Thach

last: Mai

address: 269 Campus Dr

institute: Stanford University

data_processing:
Basecalls performed using Illunima HiSeq 2000 or Nextseq 500
RNA-seq reads were mapped to a concatenated genome sequence of human GRCh38/hg38 and mouse GRCm38/mm10 annotations using STAR/2.4.2a.
Following mapping, human and mouse transcript abundance were individually quantified using rsem/1.2.21.
Expression levels were normalized by transcripts per million (TPM).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: text file with expected count, TPM and FPKM.

source_name: mouse iPS

extract_protocol:
RNA was obtained using Rneasy purification kit
Libraries were prepared according to Illumina's instructions accompanying the Tru-Seq V2 kit (RS-122-2001). Briefly, Poly-A+ RNA was isolated from total RNA using oligo-dT magnetic beads (Illumina TruSeq V2). Following first (Superscript III, Life Technologies) and second strand synthesis, cDNA libraries were constructed according to standard Illumina protocols. RNA and DNA integrity and quality was measured using an Agilent Bioanalyzer 2100.

value: iPS-derived from MEFs


title: Young_16_RNA


title: Young_17_RNA


title: Young_12_RNA


title: Young_9_RNA


title: Old_21_mC

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Adapter sequences were filtered out using the FAR software (Dodt, M, Ahmed R, Dieterich C. FAR -- flexible adapter remover. FAR project website (2011)) (http://sourceforge.net/projects/theflexibleadap/)
Reads were aligned to the hg19 genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool.
Genome_build: hg19
Supplementary_files_format_and_content: The myCpG.txt is a tab-delimited text file that contains the location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The column headers are: chrBase, chr, base, strand, coverage, freqC, freqT.

extract_protocol:
HSCe DNA was extracted following the manufactures’ protocol for the Qiagen Allprep Micro Kit (#80284).
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012) with modified size selection to accommodate the low amount of input DNA (see materials and methods).


title: DNMT1_siRNA_rep3_cardiomyocyte

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

data_processing:
The fastq files generated from RNA-Seq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. The remaining high quality RNA-Seq reads were mapped to the mouse genome (mm10) with the Tophat2 tool. Counting of RNA-Seq reads were performed with HTSeq, with Ensembl Mus_GRCm38.79.gtf as the reference annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each gene annotated to Ensembl Mus_GRCm38.79.gtf.

source_name: Embryonic cardiomyocyte

growth_protocol: Primary cardiomyocytes were isolated from mouse E13.5 embryonic ventricles. Briefly, hearts were dissected from embryos, and the ventricular tissue from each litter of embryos was pooled and digested with papain solution that contained 4 mg/ml papain, 1.1 mM EDTA, 5.5 mM L-cystein, and 67 mM b-mercaptoethanol dissolved in the Earle’s Balanced Salt Solution. Digestion was terminated with 1 mg/ml soybean trypsin inhibitor solution. Cells were suspended in DMEM supplemented with 10% inactivated fetal bovine serum, 2 mM L-glutamine, and antibiotic/antimycotic solution. Cells were placed in non-coated flasks for 1 h to allow differential attachment to occur. The non-attached cells, which are predominantly cardiomyocytes, were transferred to new flasks or plates coated with 2% gelatin (for plastic) or 10 mg/ml fibronectin (for glass surface).

extract_protocol:
At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA) and magnetically sorted using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). Total RNA was isolated from the sorted cardiomyocytes with the RNAqueous®-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA). mRNA was isolated from total RNA using NEXTflex™ Poly(A) Beads (Bioo Scientific, Austin, TX). The mRNA was quantitated using the Qubit RNA assay and Qubit 2.0 Flourometer (Thermo Fisher Scientific), as well as a 2200 TapeStation (Pico mRNA; Agilent Technologies).
Sequencing libraries were prepared with the NEBNext® mRNA Library Prep Master Mix Set for Illumina (NEB, Ipswich, MA). Briefly, purified mRNA (50-250 ng) was fragmented to ~200 nucleotide mRNA prior to generating first and second strand cDNA. The resulting cDNA was prepared for sequencing by blunt end repair, dA-tailing, adaptor ligation using the NEBNext Multiplex Oligos for Illumina (NEB), size selection using Agencourt AMPure XP Beads (Beckman Coulter, Brea, CA), and PCR enrichment of adaptor ligated cDNA. Library quality was assessed using the Agilent 2200 TapeStation (high sensitivity DNA assay). The concentration of each library was quantitated by a KAPA Library Quantification kit (Illumina platforms; Kapa Biosystems, Woburn, MA) on a GeneAmp 7300 Real Time PCR (Thermo Fisher Scientific).

treatment_protocol: Cardiomyocytes were cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT1 siRNA (#GS13433) or AllStars negative control siRNA (#1027281) at 12 nM using lipofectamine RNAiMAX (n=3 per treatment).

value: heart ventricle

value: cardiomyocyte

tag: developmental stage

value: embryonic day 13.5

value: DNMT3a siRNA


title: negative_siRNA_rep2_cardiomyocyte

value: negative siRNA


title: DNMT1_siRNA_rep1_cardiomyocyte


title: negative_siRNA_rep3_cardiomyocyte


title: Old_17_mC

value: HSCe (CD34+, CD38-,Lineage-)

value: F


title: DNMT1_siRNA_rep2_cardiomyocyte


title: Old_12_mC


title: negative_siRNA_rep1_cardiomyocyte


title: Old_5_mC

value: M


title: T10: chronic lymphocytic leukemia 10 (HTA-2_Array)

type: RNA

hyb_protocol: Affymetrix GeneChip® HTA 2.0 protocol

scan_protocol: Affymetrix GeneChip® HTA 2.0

data_processing: Transcriptome Analysis Console

source_name: peripheral blood

label_protocol: Affymetrix GeneChip® HTA 2.0 kit

extract_protocol: TriReagent with isopropanol precipitation, DNase treatment

tag: gender

value: peripheral blood

tag: diagnosis

value: chronic lymphocytic leukemia


title: Young_27_mC


title: Old_1_mC


title: T8: chronic lymphocytic leukemia 8 (HTA-2_Array)

tag: tissue


title: Arabidopsis_root_Drop-seq_replicate_C

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

state: CA

address: 1, Cyclotron Road

institute: DOE-Joint Genome Institute

data_processing:
Illumina CASAVA bcl2fastq v2.17 used for basecalling.
Sequenced reads were trimmed for adaptor sequence and polyA, then mapped to a combined GRCh38-TAIR10 or mm10-TAIR10 genome mega-reference using STAR v. 2.5.2b for Drop-seq data, or mapped to TAIR10 using HISAT for RNA-seq data.
Digital gene expression matrices were created by following the Drop-seq Core Computational Protocol version 1.0.1 (http://mccarrolllab.com/dropseq/) for Drop-seq data. For mRNA-seq data, library counts were generated use featureCounts.
Genome_build: GRCh38; mm10; TAIR10
Supplementary_files_format_and_content: digital gene expression matrices and library counts are provided as txt files

organism: Arabidopsis thaliana

source_name: whole root

growth_protocol: Seeds were sown at a density of ~125 seeds per row on sterile nylon mesh filters placed on top of plant growth media consisting of 1X Murashige and Skoog Basal Medium (Sigma-Aldrich, St. Louis, MO) supplemented with 1% sucrose (Sigma-Aldrich), 1% agar (Sigma-Aldrich), 2.6 mM 2-(N-Morpholino)ethanesulfonic acid (MES; Sigma-Aldrich), and adjusted to pH 5.7. Petri dishes were positioned vertically in an incubator (Percival Scientific, Perry, IA) under a long-day photoperiod (16 h of light) at 22°C.

extract_protocol:
Cells were used at their starting concentration after protoplasting. 2.5% human cells were added to each suspension. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads as previously described (PMID: 26000488).
The library was prepared according to Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/) using Illumina's Nextera XT DNA Library Preparation Kit. The library was uniquely indexed and then sequenced on a single lane of a HiSeq 2500.

treatment_protocol: Protoplast suspensions were prepared from 7-day-old Arabidopsis seedlings using previously described methods (PMID: 16170893).

tag: ecotype

tag: age

value: 7 day

tag: genotype

value: WT

value: whole root


title: T7: chronic lymphocytic leukemia 7 (HTA-2_Array)


title: mo-OSK-iPS

tag: cell type


title: Young_23_mC


title: T6: chronic lymphocytic leukemia 6 (HTA-2_Array)


title: Young_1_RNA


title: Young_21_mC

value: Unknown


title: T5: chronic lymphocytic leukemia 5 (HTA-2_Array)


title: Young_20_mC


title: T4: chronic lymphocytic leukemia 4 (HTA-2_Array)


title: Young_13_mC


title: T3: chronic lymphocytic leukemia 3 (HTA-2_Array)


title: T9: chronic lymphocytic leukemia 9 (HTA-2_Array)


title: T2: chronic lymphocytic leukemia 2 (HTA-2_Array)


title: T1: chronic lymphocytic leukemia 1 (HTA-2_Array)


title: Old_31_Input

data_processing:
FastQC was run all samples. Samples with a sequencing duplication rate of >90% were discarded.
Adapters and reads of less than 25 basepairs were removed using cutadapt (version 1.12).
Reads were aligned to the hg19 genome using bowtie2 (version 2.0.5).
Reads were filtered to retain only those that were aligned and had one alignment (!XS:i:N) samtools (version 1.2)
Unique mapped reads for each IP type for each age group were pooled using samtools merge (version 1.2)
Peak calling using the pooled IP and its pooled corresponding Input was performed using macs2 (version 2.0.10.20131216) with the --nomodel option. For H3K4me1, H3K4me3, and H3K27ac, a q-value cutoff of 0.0001 with the narrow peak option was used. Broad peak calling with a q-value cutoff  of 0.1 was used for H3K27me3.
Bigwig files of the fold-enrichment(IP/Input) were generated using macs2 SPMR peak calling, followed by macs2 bdgcmp with the -m FE option.
Bigwig files of the log2(IP/Input) were generated using Deeptools2, with the following command: bamCompare --bamfile1 ip --bamfile2 input --outFileName name_log2.bw --ratio log2  -p 30 --verbose --outFileFormat bigwig --scaleFactorsMethod readCount.
Genome_build: hg19
Supplementary_files_format_and_content: One of the processed files is the bedgraph file containing the tag chromosome coordinates and score produced from macs2 peak calling on the pooled IPs and Inputs. For Input samples, the control_lamda.bdg file was uploaded, and for IPs, the treat_pileup.bdg was uploaded. If a donor was used for multiple IP types, then multiple bedgraph files (corresponding to each IP type) are included for the Input. The "_FE.bw" is a bigwig file that contains the fold-enrichment of the IP/Input. The "_log2.bw" is a bigwig file that contains the read-normalized log2(IP/Input) enrichment.

extract_protocol:
Micro-ChIPseq was performed using the True MicroChIP (Diagenode, #C01010130) kit and antibodies that had been validated for specificity and reactivity using the MODified Histone Peptide Array (Active Motif, #13001). The following antibodies were used, 1 g H3K27me3 (Millipore, #07-449, Lot: 21494165), 1 g H3K4me3 (Abcam, #ab8580, Lot: GR164207-1), 0.5 g H3K4me1 (Diagenode, #C15410194, Lot: A1862D), or 0.5 g H3K27ac (Abcam, #ab4729, Lot: GR155970-2).
ChIP-seq libraries were prepared using the V1 MicroPlex Library Preparation kit (Diagenode, #C05010011). For the PCR amplification, a total of 16 amplification cycles was used. Libraries were purified using a 1:1 Ampure bead cleanup and eluted in 16 uL of Tris-HCl ph 8.0. Only libraries with enrichment at targeted sites by QPCR were used for sequencing. Libraries were multiplexed and sequenced using an Illumina Hi-Seq-2500 with 50bp single end sequencing.

treatment_protocol: Miltenyi MACS magnetic bead purification was used to enrich frozen bone marrow MNC for CD34+ cells. The CD34+ fraction was then stained with CD2-TC, CD3-TC, CD4-TC, CD7-TC, CD8-TC, CD10-TC, CD11b-TC, CD14-TC, CD19-TC, CD20-TC, CD56-TC, and Glycophorin A-TC followed by CD34-APC, CD38-PE-Cy7, CD123-PE,  CD45RA-FITC and DAPI. Using a BD FACSAria I, HSCe (DAPI-,Lin-, CD34+, CD38-) were FACS sorted. HSCe were sorted into 1mL IMDM 20% FBS. For H3K4me1, H3K4me3, and H3K27me3, 14,000-20,000 HSCe were used per immunoprecipitation; for H3K27ac, 15,000-35,000 cells were used per immunoprecipitation.

tag: chip antibody


title: Old_27_Input


title: Old_24_Input

description:
O_Pooled_H3K4me3_control_lambda.bdg
O_Pooled_H3K27me3_control_lambda.bdg


title: Old_29_Input

description:
O_Pooled_H3K4me1_control_lambda.bdg
O_Pooled_H3K4me3_control_lambda.bdg
O_Pooled_H3K27me3_control_lambda.bdg


title: EV_B4

data_processing:
Using Cutadapt (version 1.12), all reads were trimmed to 72 basepairs and adapters were removed.
Reads were aligned to the hg19 gencode v19 reference genome using the STAR aligner (version 2.5.2b), specifying the following parameters: outFilterType= BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1 , outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, alignEndsType=EndToEnd.
Gene counts were calculated using QoRTs. QoRTs was run in stranded mode using the hg19 gencode annotation file that included ERCC spike-in information, but did not include entries for ribosomal RNA, mitochondrial RNA, or tRNA.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: The processed data files are tab-delimited text files that contain the raw counts generated by QoRTs.

source_name: Peripheral blood

growth_protocol: Pre-stim type II

extract_protocol:
Samples were extracted using Trizol, following the manufacturer's instructions.
Stranded paired-end libraries were prepared using the Illumina TruSeq Stranded Total RNA kit by the University of Miami Human Genomics Sequencing Core. ERCC spike-ins were included prior to ribo-depletion. Libraries were sequenced on the NextSeq 500 with 75 bp-reads.

treatment_protocol: shRNA-mediated knockdown of LMNA was performed.

value: CD34+ HSCe

tag: shRNA

value: empty vector control


title: Old_22_Input


title: sh_3495

extract_protocol:
Samples were extracted using the Qiagen RNeasy Plus Micro kit (#74034), following the manufacturer's instructions.
Stranded paired-end libraries were prepared using the Illumina TruSeq Stranded Total RNA kit by the University of Miami Human Genomics Sequencing Core. ERCC spike-ins were included prior to ribo-depletion. Libraries were sequenced on the NextSeq 500 with 75 bp-reads.

value: LMNA


title: sh_B4


title: EV_3495


title: Old_16_Input


title: Young_25_mC


title: Old_15_Input


title: sh_3435


title: EV_3364


title: Old_13_Input


title: sh_3364


title: Old_12_Input


title: EV_3330


title: Young_3_mC


title: Old_10_Input


title: Old_9_Input


title: sh_3330


title: Old_8_Input


title: sh_3469

growth_protocol: Pre-stim


title: EV_3506


title: Old_26_Input


title: Old_7_Input

description:
O_Pooled_H3K4me1_control_lambda.bdg
O_Pooled_H3K4me3_control_lambda.bdg


title: Old_6_Input


title: Old_5_Input


title: EV_3435


title: Old_3_Input


title: EV_A1E4


title: Old_2_Input


title: Yng_29_Input

description:
Input
Y2_H3_FE.bw

data_processing:
FastQC was run all samples. Samples with a sequencing duplication rate of >90% were discarded.
Adapters and reads of less than 25 basepairs were removed using cutadapt (version 1.12).
Reads were aligned to the hg19 genome using bowtie2 (version 2.0.5).
Reads were filtered to retain only those that were aligned and had one alignment (!XS:i:N) samtools (version 1.2)
Unique mapped reads for each IP type for each age group were pooled using samtools merge (version 1.2)
Deeptools bamCompare with --scaleFactorsMethod readCount and --ratio log2 was used to generate a bigwig file containing the log2 enrichment of H3 compared to Input
Genome_build: hg19
Supplementary_files_format_and_content: The processed file is a bigwig file containing the log2(H3/Input), normalized by read count.

extract_protocol:
Micro-ChIPseq was performed using the True MicroChIP (Diagenode, #C01010130) kit and 0.5 ug H3 (Abcam ab10799, lot #GR275925-1) per immunoprecipitation
ChIP-seq libraries were prepared using the V1 MicroPlex Library Preparation kit (Diagenode, #C05010011). For the PCR amplification, a total of 16 amplification cycles was used. Libraries were purified using a 1:1 Ampure bead cleanup and eluted in 16 uL of Tris-HCl ph 8.0. Libraries were multiplexed and sequenced using a NextSeq 500 with 75bp single end sequencing.

treatment_protocol: Miltenyi MACS magnetic bead purification was used to enrich frozen bone marrow MNC for CD34+ cells. The CD34+ fraction was then stained with CD2-TC, CD3-TC, CD4-TC, CD7-TC, CD8-TC, CD10-TC, CD11b-TC, CD14-TC, CD19-TC, CD20-TC, CD56-TC, and Glycophorin A-TC followed by CD34-APC, CD38-PE-Cy7, CD123-PE,  CD45RA-FITC and DAPI. Using a BD FACS SORP Aria-Ilu HSCe (DAPI-,Lin-, CD34+, CD38-) were FACS sorted. HSCe were sorted into 1mL IMDM 20% FBS. 10,000-15,000 HSCe were used per immunoprecipitation.

tag: antibody


title: Yng_28_H3

description:
H3 pulldown
Y1_H3_FE.bw


title: sh_A1E4


title: Yng_29_H3

description:
H3 pulldown
Y2_H3_FE.bw


title: Yng_28_Input

description:
Input
Y1_H3_FE.bw


title: Yng_24_Input


title: Old_33_H3

description:
H3 pulldown
O3_H3_FE.bw


title: Yng_18_Input

description:
Y_Pooled_H3K4me1_control_lambda.bdg
Y_Pooled_H3K4me3_control_lambda.bdg
Y_Pooled_H3K27me3_control_lambda.bdg


title: Yng_23_Input


title: Old_33_Input

description:
Input
O3_H3_FE.bw


title: Yng_22_Input


title: sh_3506


title: Old_32_H3

description:
H3 pulldown
O1_H3_FE.bw


title: Yng_17_Input


title: Old_32_Input

description:
Input
O1_H3_FE.bw


title: EV_3469


title: Yng_11_Input


title: Yng_12_Input


title: Yng_26_Input


title: Yng_27_Input


title: 3hr_rep1

data_processing:
Basecalls performed using Illunima Nextseq 500
Reads were mapped to a concatenated human plus mouse genome with Bowtie 2.0
Reads originating from the mitochondria and those with low mapping quality scores (below 10) were removed
For motif enrichment, regions of increased accessibility at 3 hours versus fibroblast were identified with bdgdiff command in the MACS 2.0 package, and then were used as input into Homer 4.7 with human fibroblast peaks as background.
MACS 2.0 was used to call peaks; DESEQ2 used tag counts per peak genome-wide to identify regions of increased accessibility at 3 hours, and Homer 4.7 software was used with the findMotifsGenome.pl software to peaks containing the NKX3-1 motif (CisBP).
The 18-state map was condensed in the following way: States 1-4 were merged as TSS Active, states 7 and 8 were merged as Enhancer Genic, states 9 and 10 were Enhancer Distal, states 14 and 15 were Bivalent, states 16 and 17 were Polycomb Repressed. States 6, 11, and 12 were removed for simplicity.
The starting cell type for the transition matrix was IMR90 and the ending was H1 ES cell. DESEQ2 was used to generate log2fold change of ATAC-seq signal at each time point relative to time 0 (unfused MRC-5 fibroblasts).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: Peaks_log2fold.bed, IMR90_to_H1ESC_Transitions.bed

source_name: human fibroblast/mouse ES cells

extract_protocol:
To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed-angle centrifuge and carefully pipetted away from the pellet after centrifugations. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.
Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.

value: human fibroblast/mouse ES cells


title: 48hr_rep2


title: 48hr_rep1


title: Yng_8_Input

description:
Y_Pooled_H3K4me3_control_lambda.bdg
Y_Pooled_H3K27ac_control_lambda.bdg


title: CC_rep2


title: 3hr_rep2


title: Yng_10_Input

description:
Y_Pooled_H3K4me1_control_lambda.bdg
Y_Pooled_H3K27ac_control_lambda.bdg


title: Arabidopsis_root_Drop-seq_replicate_I

growth_protocol: Seeds were sown at a density of ~125 seeds per row on sterile nylon mesh filters placed on top of plant growth media consisting of 1X Murashige and Skoog Basal Medium (Sigma-Aldrich, St. Louis, MO), 1% agar (Sigma-Aldrich), 2.6 mM 2-(N-Morpholino)ethanesulfonic acid (MES; Sigma-Aldrich), with no sucrose added, and adjusted to pH 5.7. Petri dishes were positioned vertically in an incubator (Percival Scientific, Perry, IA) under a long-day photoperiod (16 h of light) at 22°C.

extract_protocol:
Cells were diluted in Solution A (PMID: 16170893) to 100 cells/ul. 10% mouse embryonic cells were added to each suspension. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads as previously described (PMID: 26000488).
The library was prepared according to Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/) using Illumina's Nextera XT DNA Library Preparation Kit. The library was uniquely indexed and then pooled and sequenced on a single lane of a NextSeq instrument (Illumina)

treatment_protocol: Protoplast suspensions were prepared from 5-day-old Arabidopsis seedlings using previously described methods (PMID: 16170893).

value: 5 day


title: Arabidopsis_root_Drop-seq_replicate_H


title: Yng_2_Input


title: CC_rep1


title: Old_26_H3K27ac

description:
O_Pooled_H3K27ac_treat_pileup.bdg
none


title: Arabidopsis_root_Drop-seq_replicate_F


title: Arabidopsis_root_Drop-seq_replicate_G


title: Old_22_H3K27ac


title: Arabidopsis_root_Drop-seq_replicate_J


title: Fib

source_name: human fibroblast

value: human lung fibroblast


title: hu-NSK-iPS

source_name: human iPS

value: iPS-derived from human fibroblast


title: Arabidopsis_root_Drop-seq_replicate_E


title: Old_9_H3K27ac


title: Arabidopsis_root_Drop-seq_replicate_D


title: Yng_14_Input


title: T10: chronic lymphocytic leukemia 10 (CytoScanHD_Array)

hyb_protocol: CytoScan HD CytoScan HD/Cytogenetic Array 2.7M

data_processing: Chromosome Analysis Suite

extract_protocol: DNA blood & tissue isolation kit, Qiagen


title: hu-OSK-iPS


title: Old_13_H3K27ac


title: T9: chronic lymphocytic leukemia 9 (CytoScanHD_Array)

scan_protocol: CytoScan HD CytoScan HD/Cytogenetic Array 2.7M


title: T8: chronic lymphocytic leukemia 8 (CytoScanHD_Array)

label_protocol:
CytoScan HD
CytoScan HD/Cytogenetic Array 2.7M


title: T6: chronic lymphocytic leukemia 6 (CytoScanHD_Array)


title: Old_3_H3K27ac