title: Model_Replicate1_H3K4me3

data_processing:
Quality control steps (Trimmomatic (version 0.32) = Leading:3 ; trailing:3 slidingwindow:4:15 ; minlen:32) were performed on the raw data files.
ChIP-seq and ATAC-seq reads were aligned to the GRCH37/hg19 genome assembly using BWA version 0.7.10 with the default parameters.
Duplicates were removed by Samtools (version 1.9). For ATAC-seq data, mitochondrial DNA were removed (samtools idxstats input.bam | cut -f 1 | grep -v MT | xargs samtools view -b input.bam > output.bam)
Peaks were called using MACSPeaks version 2.2.4 with the following setting: callpeak -g hs -q 0.05 --format BAMPE
Analysis of correlated gene expression and histone modifications was perfomed using EaSeq (version 1.04)
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: BigWig files were generated using Homer (default parameters).
"Merge" files with all replicates:
CD34_H3K4me3 (Replicate 1 + 2):
CD34_Merge_Replicates_H3K4me3.bigWig, CD34_Merge_Replicates_H3K4me3.narrowPeak
CD34_H3K27me3 (Replicate 1 + 2 + 3):
CD34_Merge_Replicates_H3K27me3.bigWig, CD34_Merge_Replicates_H3K27me3.narrowPeak
CD34_H3K79me2 (Replicate 1 + 2 + 3):
CD34_Merge_Replicates_H3K79me2.bigWig, CD34_Merge_Replicates_H3K79me2.narrowPeak
CD34_KM3_H3K4me3 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K4me3.bigWig, CD34_KM3_Merge_Replicates_H3K4me3.narrowPeak
CD34_KM3_H3K27me3 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K27me3.bigWig, CD34_KM3_Merge_Replicates_H3K27me3.narrowPeak
CD34_KM3_H3K79me2 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K79me2.bigWig, CD34_KM3_Merge_Replicates_H3K79me2.narrowPeak
CD34_KM3_ATAC-seq (Replicate 1 + 2 + 3):
CD34_KM3_Merge_ATAC-seq.bigWig, CD34_KM3_Merge_ATAC-seq.narrowPeak
Model_H3K4me3 (Replicate 1 + 2 + 3):
Model_Merge_H3K4me3.bigWig, Model_Merge_H3K4me3.narrowPeak
Model_H3K27me3 (Replicate 1 + 2 + 3 + 4):
Model_Merge_H3K27me3.bigWig, Model_Merge_H3K27me3.narrowPeak
Model_H3K79me2 (Replicate 1 + 2 + 3):
Model_Merge_H3K79me2.bigWig, Model_Merge_H3K79me2.narrowPeak
Model_ATAC-seq (Replicate 1 + 2 + 3 + 4):
Model_Merge_ATAC-seq.bigWig, Model_Merge_ATAC-seq.narrowPeak


title: m1_Young1_D5

status: Public on Jul 01 2020

type: SRA

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

country: USA

institute: Stanford

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table

molecule: total RNA

organism: Mus musculus

source_name: three-mo mouse BEC

growth_protocol: Mice 3 (young)

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: primary murine brain endothelial cells


title: miR-200b/a KD-1

city: Baoding

first: Dong

last: Yang

state: Hebei

address: No. 180, Wusi Road

country: China

institute: Hebei university

data_processing:
The libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
The steps to generate the cleandata are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed );
2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads);
3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads);
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample. FPKM could eliminate the effect of sequencing depth and gene length on gene expression levels.
DEGseq was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs). DESeq2 was designed for differential gene expression analysis between two samples with biological replicates under the theoretical basis obeys the hypothesis of negative binomial distribution for the value of count. Differing from DESeq, DESeq2 estimates the depth parameters of samples and gene-specific, as well as uses "linear regression" for dispersion to "shrink", which was mainly considering genes of the same expression level may share the similarity deviations or own their the expression characteristics. DESeq2 estimates the expression level of each gene in per sample by the linear regression, then calculates the p-value with Wald test. Finally the p-value was corrected by the BH method. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs).
Genome_build: Mus_musculus.GRCm38.89
Supplementary_files_format_and_content: tab-delimited text files include gene, readcount, baseMean, log2Foldchange, pval, and gene name for each Sample.

source_name: miR-200b/a KD_main olfactory epithelium

extract_protocol:
MOE were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 2 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

tag: strain background

tag: genotype/variation

value: miR-200b/a KD

tag: age

value: 5 month-old

tag: Sex

value: male

tag: tissue

value: main olfactory epithelium


title: Model_Replicate1_H3K79me2

city: Montreal

first: Thomas

last: Milan

state: Quebec

address: 2950 Chemin de Polytechnique

country: Canada

institute: IRIC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: human HSPCs

extract_protocol:
[ChIP-seq]  After crosslinking cells by using formaldehyde 1% (final concentration) for 7 minutes at room temperature, glycine 0.125nM (final concentration) was added for 5 minutes at room temperature to stop the reaction. Fixed cells were washed with PBS, resuspended in 1mL of a first lysis buffer (Triton 0.25%, Tris pH 8.0 10mM, EDTA 10mM, EGTA 0.5mM, protease inhibitor 1X) for 5 minutes, and in 1 mL of a second buffer for 30 minutes (NaCl 200mM, Tris pH 8.0 10mM, EDTA 1mM, EGTA 0.5mM, protease inhibitor 1X). Lysate was resuspended in another buffer (0.5% SDS, 0.5% Triton, Tris pH 8.0 10mM, NaCl 140mM, EDTA 1mM, EGTA 0.5mM, protease inhibitor 1X) and then sonicated by using a Covaris S2 sonicator. The parameters used were as follows: duty Factor 10%, 200 cycles per burst, 105W, 4 minutes. The supernatant collected after the spinning at 13000 rpm for 5 minutes was used for future experiments.  Beads (Protein G Dynabeads™ ; resuspension buffer : Triton 1%, Tris pH 8.0 10mM, NaCl 150mM, EDTA 2mM) were incubated overnight on a rotator at 4°C with 3μg of antibodies recognizing histone marks (H3 : #ab1791, H3K4me3 : #ab8580-100, H3K27me3 : Millipore 07-449, H3K79me2 : #ab3594, H3K27ac : Millipore 07-360). Sonicated chromatin was incubated with 250μL of beads during 4 hours on a rotator at 4°C. The beads were washed sequentially with different buffers: ‘Low Salt’ Buffer (0.5% NP40, 15mM KCl, 10mM Tris pH 8.0, 1mM EDTA), 3 different ‘High Salt’ buffers (0.5% Triton, 10mM Tris pH 8.0, 100mM (2) or 400mM (3) or 500mM (4) NaCl), twice in LiCl Buffer (0.5% NP40, 250mM LiCl, 10mM Tris pH 8.0, 1mM EDTA). ChIPed material was then eluted a classic elution buffer (10mM Tris pH8.0, 1mM EDTA) and incubated overnight at 65°C with shaking (1200rpm). An RNase and proteinase K digestion was performed in order to reverse crosslink. DNA was extracted and purified by a classic phenol-chloroform protocol.
[ATAC-seq]  ATAC-seq experiment was based on method published by Buenrostro et al. (PMID: 24097267)
TruSeq ChIP Library Preparation Kit by Illumina (#IP-202-9001) was used to construct DNA libraries as described in the manufacturer’s instructions with a PCR for a total of 12 cycles using the Illumina indexed library primers. NextSeq 500 was used to sequence samples (75pb paired-end) according to standard Illumina protocols.

treatment_protocol: 1-10x10e6 cells CD34-KM3 were injected into multiple immunodeficient mice (NSG-SGM3; NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ-IL-3/GM/SF). After a few weeks, animals were sacrificed and bone marrow was harvested.

value: HSPCs

tag: chip antibody

tag: development stage

value: model leukemia cells from xenograft


title: Model_Replicate1_H3K27me3

value: H3K27me3 :#Millipore 07-449


title: Model_Replicate1_H3


title: miR-200b/a KD-2


title: Brg1KO1

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Reads were mapped to Mouse Genome Assembly GRCm38.p5 by STAR v2.5.
Gene and isoform expression quantification was called by RSEM v1.2 with default parameters on GENCODE mouse M16 gene annotation file.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Csv file indicates fpkm values for detected genes in duplicates of Brg1-deficient ILC3s and WT-ILC3s.

source_name: lamina proprial lymphocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen).Total RNA sample is digested by DNaseІ (NEB), and purified by oligo-dT beads (Dynabeads   mRNA purification kit, Invitrogen)
Construction of the cDNA library and transcriptome sequencing were performed by BGI Genomics, BGI-Shenzhen, as following. First-strand cDNA was generated by SuperScript III reverse transcriptase (Thermo Fisher Scientific). Free primers were removed using Exonuclease I (New England Biolabs). 3’ poly (A) tailing was done by adding terminal deoxynucleotidyl transferase (Thermo Fisher Scientific). Then, the second-strand cDNA was synthesized and the cDNA was amplified by PCR. PCR products were purified with Ampure XP Beads (Beckman Coulter). After that, second round of PCR was performed and PCR products were fragmented by a sonicator (Covaris). End repaired was performed and A-tailing was added. Adaptor ligation was done and the cDNA was further amplified by PCR and purified with Ampure XP Beads. Fragment sizes were checked using Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents) and the library was quantified by real-time quantitative PCR (QPCR) (TaqMan Probe). The qualified libraries were amplified on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3–cBot–HS，Illumina). And the amplified flowcell was sequenced single end on the HiSeq 2000 System (TruSeq SBS KIT-HS V3，Illumina) with reading length of 90bp.

value: lamina proprial lymphocytes

tag: treatment

value: Brg1-deficient ILC3s


title: Brg1KO2


title: Spt6 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 HA-SPT6
ChIP library from Spt6 ChIP-seq with Spn1 non-depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (ATATAGGA) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 1 mg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding an HA-tagged protein (FWP568) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. For immunoprecipitation, 10 μg anti-HA (Abcam, ab9110) was used. Immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (~16-18 hr). Protein G Sepharose beads (GE Healthcare, 4 Fast Flow) were washed with WB140, and a 50% slurry was subsequently made in WB140. Fifty-μL aliquots of slurry were transferred into new Eppendorf tubes, and the WB140 was removed. The immunoprecipitation reactions were added directly to the beads and incubated at 4°C with end-over-end rotation for 4 hr. Bead-washing and elution were done are previously described (doi:10.1093/nar/gkz119). The 200 μL of eluate was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.

treatment_protocol: Cells were grown in YPD at 30°C to OD600 ≈ 0.65, diluted back to OD600 ≈ 0.3-0.4 in pre-warmed YPD, treated with DMSO, and allowed to grow for 90 minutes.

tag: strain

tag: genotype

value: MATa leu2delta1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 HA-SPT6

value: DMSO

tag: antibody


title: m1_Young1_K9


title: Model_Replicate1_Input


title: Spt6 ChIP-seq, input DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 HA-SPT6
Input library from Spt6 ChIP-seq with Spn1 non-depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GATCAG) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 1 mg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding an HA-tagged protein (FWP568) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. Five percent (40 μL) was set aside as input and stored for later processing. The saved input was thawed from storage, and 60 μL LB140 and 100 μL TES were added. The 200 μL of input was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: m1_AY_Y3_L16


title: Spt6 ChIP-seq, ChIP DNA: Spn1-AID + IAA 1

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 HA-SPT6
ChIP library from Spt6 ChIP-seq with Spn1 depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GCCAAT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

treatment_protocol: Cells were grown in YPD at 30°C to OD600 ≈ 0.65, diluted back to OD600 ≈ 0.3-0.4 in pre-warmed YPD, treated with IAA at a final concentration of 25 μM, and allowed to grow for 90 minutes.

value: 25 microM IAA


title: Brg1WT2


title: Spt6 ChIP-seq, input DNA: Spn1-AID + DMSO 1

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (ATCACG) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol: Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: CD34_KM3_ATAC-seq_Replicate3

treatment_protocol: Human hematopoietic stem cell CD34+ cells from cord blood were transduced with a retrovirus containing GFP and the human KM3 fusion gene and were subsequently cultured in vitro under myeloid promoting conditions (15% FSC + IL3 + SCF) for ~30 days.

value: CD34+ cells transformed with KMT2A-MLLT3 fusion (CD34-KM3)


title: Spt6 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 1

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (ACAGTG) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: m1_Young1_D11


title: m1_AY_Y3_K4


title: CD34_KM3_ATAC-seq_Replicate2


title: Brg1WT1


title: CD34_KM3_ATAC-seq_Replicate1


title: Rpb1 CTD Ser2-P ChIP-seq, ChIP DNA: Spn1-AID + IAA 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Rpb1 CTD Ser2-P ChIP-seq with Spn1 depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (CTCTGTCT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding a V5-tagged protein (FWP485) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. For immunoprecipitation, 10 μg anti-Ser2-P (Active Motif, 3E10) (Active Motif, 3E8) was used. Immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (~16-18 hr). Protein G Sepharose beads (GE Healthcare, 4 Fast Flow) were washed with WB140, and a 50% slurry was subsequently made in WB140. Fifty-μL aliquots of slurry were transferred into new Eppendorf tubes, and the WB140 was removed. The immunoprecipitation reactions were added directly to the beads and incubated at 4°C with end-over-end rotation for 4 hr. Bead-washing and elution were done are previously described (doi:10.1093/nar/gkz119). The 200 μL of eluate was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.

value: MATa leu2delta1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6


title: scRNA_seq_P0_skin

city: Qingdao

first: Wei

last: Ge

state: Shandong Province

address: Changcheng Road

department: College of life sciences

institute: Qingdao Agricultural University

description:
The group information is prefixed with 0dpp in the column of processed data file
scRNA_seq_skin.txt

data_processing:
We used CellRanger count pipeline 2.2.0 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=7000 \’.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

source_name: P0 XY skin

extract_protocol:
All skin tissues were obtained from male fetuses prior to digestion. To prepare dorsal skin single cell suspension for single-cell RNA sequencing, the fetus back skin tissues were isolated via microdissection and 0.25% trypsin/EDTA solution was used to digest E13.5 and E16.5 fetus dorsal skin tissues at 37 °C for 5 min. For P0 mice dorsal skin tissues, 2 mg/ml collagenase IV (Sigma, St Louis, MO, USA, Cat#C5138) was used to digest skin tissues at 37 °C for 30 min. After trypsinization, the skin tissues were mechanically dissociated into single cell suspension by pipetting, the cell suspensions were then filtered through a 40 μm nylon cell strainer (BD Falcon, BD Biosciences, San Jose, CA, USA, Cat#352340) prior to single cell library construction. The single-cell Gel-Bead in Emulsions (GEMs) were then generated with Chromium 10x Genomics single-cell system by using single-cell 3’ Library and Gel Bead Kit V2 (10x Genomics Inc., Pleasanton, CA, USA, Cat#120237). Captured cells were then lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics Inc., Pleasanton, CA, USA, Cat#120237) following the manufacture’s introduction.

value: skin

tag: developmental stage


title: Rpb1 CTD Ser2-P ChIP-seq, ChIP DNA: Spn1-AID + IAA 1

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (AACCGTGT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: m1_AY_Y3_L4


title: scRNA_seq_E16.5_skin

description:
The group information is prefixed with E16.5 in the column of processed data file
scRNA_seq_skin.txt

source_name: E16.5 XY skin


title: m1_Young1_C7


title: CD34_KM3_Replicate2_H3K79me2


title: m1_AY_Y3_F1


title: m1_Young2_N5


title: scRNA_seq_E13.5_skin

description:
The group information is prefixed with E13.5 in the column of processed data file
scRNA_seq_skin.txt

source_name: E13.5 XY skin


title: CD34_KM3_Replicate2_H3K4me3


title: WT rep1

city: Shenzhen

first: Qing

last: Li

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences,

data_processing:
Illumina RTA software used for basecalling.
rRNA sequences were filtered out by SortMeRNA v2.0
Clean reads were obtained from the raw data by removing adapter-containing reads, poly-N-containing reads and low-quality reads using Trimmomatic (version 0.36)
Clean reads was mapped to mm9 whole genome using TopHat v2.0.12 with parameters -N 5 --read-edit-dist 5 --read-realign-edit-dist 6 -r 150 --library-type fr-firststrand
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated by cufflinks(2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: E14 (obtained from the American Type Culture Collection) mouse ES cells were cultured on 0.1% gelatin-coated plates in ES medium (Knockout-DMEM containing 15% FBS, 100 U/mL Penicillin, 100 ug/mL Streptomycin, 0.1 mM MEM nonessential amino acids, 1 mM sodium pyruvate, 2 mM GlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/mL LIF, 3 mM CHIR99021 [GSK3b inhibitor, selleck], 1 mM PD0325901 [MEK inhibitor, selleck]) and maintained in a pluripotent state in the absence of a feeder layer.

extract_protocol:
RNA was isolated using Trizol (Invitrogen) from WT and enhancer KO ES cells.
The 8 libraries (two biological duplicates in four groups) were constructed by VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, China) prior to multiplexed massively parallel sequencing (paired-end 150 base pairs [bp]) using the Illumina platform.

treatment_protocol: Three enhancer knockout cells were constructed via CRISPR/Cas9 system with mESCs.

value: mouse embryonic stem cell

tag: passages


title: WT rep2


title: Rpb1 CTD Ser5-P ChIP-seq, ChIP DNA: Spn1-AID + IAA 1

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Rpb1 CTD Ser5-P ChIP-seq with Spn1 depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (CGCATTAA) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding a V5-tagged protein (FWP485) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. For immunoprecipitation, 10 μg anti-Ser5-P (Active Motif, 3E8) was used. Immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (~16-18 hr). Protein G Sepharose beads (GE Healthcare, 4 Fast Flow) were washed with WB140, and a 50% slurry was subsequently made in WB140. Fifty-μL aliquots of slurry were transferred into new Eppendorf tubes, and the WB140 was removed. The immunoprecipitation reactions were added directly to the beads and incubated at 4°C with end-over-end rotation for 4 hr. Bead-washing and elution were done are previously described (doi:10.1093/nar/gkz119). The 200 μL of eluate was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: m1_AY_Y3_M1

value: primary murine brain endothelial cells


title: Rpb1 CTD Ser2-P ChIP-seq, ChIP DNA: Spn1-AID + DMSO 1

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Rpb1 CTD Ser2-P ChIP-seq with Spn1 non-depleted.


title: Rpb1 CTD Ser5-P ChIP-seq, ChIP DNA: Spn1-AID + IAA 2

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GTCTACAT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: CD34_KM3_Replicate2_H3K27me3


title: Rpb1 CTD Ser5-P ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Rpb1 CTD Ser5-P ChIP-seq with Spn1 non-depleted.


title: CD34_KM3_Replicate2_H3


title: CD34_KM3_Replicate2_Input


title: E3-KO rep1


title: m1_Young2_N16


title: CD34_KM3_Replicate1_H3K79me2


title: Rpb1 CTD Ser5-P ChIP-seq, ChIP DNA: Spn1-AID + DMSO 1

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (CCATACAC) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: ChIP-seq input DNA: Spn1-AID + IAA 4

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
Input library from Rpb1 ChIP-seq with Spn1 depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (TGACCA) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

source_name: ChIP-seq input DNA: Spn1-AID + IAA 4

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding a V5-tagged protein (FWP485) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. Five percent (40 μL) was set aside as input and stored for later processing. The saved input was thawed from storage, and 60 μL LB140 and 100 μL TES were added. The 200 μL of input was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: E2-KO rep2


title: m1_AY_Y3_A10


title: m1_Young2_A4


title: Rpb1 CTD Ser2-P ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (AGGTCAGT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: CD34_KM3_Replicate1_H3K27me3

data_processing:
Quality control steps (Trimmomatic (version 0.32) = Leading:3 ; trailing:3 slidingwindow:4:15 ; minlen:32) were performed on the raw data files.
ChIP-seq and ATAC-seq reads were aligned to the GRCH37/hg19 genome assembly using BWA version 0.7.10 with the default parameters.
Duplicates were removed by Samtools (version 1.9). For ATAC-seq data, mitochondrial DNA were removed (samtools idxstats input.bam | cut -f 1 | grep -v MT | xargs samtools view -b input.bam > output.bam)
Peaks were called using MACSPeaks version 2.2.4 with the following setting: callpeak -g hs -q 0.05 --format BAMPE
Analysis of correlated gene expression and histone modifications was perfomed using EaSeq (version 1.04)
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: BigWig files were generated using Homer (default parameters).
"Merge" files with all replicates:
CD34_H3K4me3 (Replicate 1 + 2):
CD34_Merge_Replicates_H3K4me3.bigWig, CD34_Merge_Replicates_H3K4me3.narrowPeak
CD34_H3K27me3 (Replicate 1 + 2 + 3):
CD34_Merge_Replicates_H3K27me3.bigWig, CD34_Merge_Replicates_H3K27me3.narrowPeak
CD34_H3K79me2 (Replicate 1 + 2 + 3):
CD34_Merge_Replicates_H3K79me2.bigWig, CD34_Merge_Replicates_H3K79me2.narrowPeak
CD34_KM3_H3K4me3 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K4me3.bigWig, CD34_KM3_Merge_Replicates_H3K4me3.narrowPeak
CD34_KM3_H3K27me3 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K27me3.bigWig, CD34_KM3_Merge_Replicates_H3K27me3.narrowPeak
CD34_KM3_H3K79me2 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K79me2.bigWig, CD34_KM3_Merge_Replicates_H3K79me2.narrowPeak
CD34_KM3_ATAC-seq (Replicate 1 + 2 + 3):
CD34_KM3_Merge_ATAC-seq.bigWig, CD34_KM3_Merge_ATAC-seq.narrowPeak
Model_H3K4me3 (Replicate 1 + 2 + 3):
Model_Merge_H3K4me3.bigWig, Model_Merge_H3K4me3.narrowPeak
Model_H3K27me3 (Replicate 1 + 2 + 3 + 4):
Model_Merge_H3K27me3.bigWig, Model_Merge_H3K27me3.narrowPeak
Model_H3K79me2 (Replicate 1 + 2 + 3):
Model_Merge_H3K79me2.bigWig, Model_Merge_H3K79me2.narrowPeak
Model_ATAC-seq (Replicate 1 + 2 + 3 + 4):
Model_Merge_ATAC-seq.bigWig, Model_Merge_ATAC-seq.narrowPeak


title: E2-KO rep1


title: ChIP-seq input DNA: Spn1-AID + IAA 2

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (CCTTTACAG) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

source_name: ChIP-seq input DNA: Spn1-AID + IAA 2

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding an HA-tagged protein (FWP568) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. Five percent (40 μL) was set aside as input and stored for later processing. The saved input was thawed from storage, and 60 μL LB140 and 100 μL TES were added. The 200 μL of input was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: E1-KO rep2


title: ChIP-seq input DNA: Spn1-AID + DMSO 4

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
Input library from Rpb1 ChIP-seq with Spn1 non-depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (TTAGGC) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

source_name: ChIP-seq input DNA: Spn1-AID + DMSO 4


title: E3-KO rep2


title: m1_AY_Y3_M3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table


title: m1_AY_Y3_I11


title: ChIP-seq input DNA: Spn1-AID + IAA 1

source_name: ChIP-seq input DNA: Spn1-AID + IAA 1


title: E1-KO rep1


title: ChIP-seq input DNA: Spn1-AID + IAA 3

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (CGATGT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

source_name: ChIP-seq input DNA: Spn1-AID + IAA 3


title: ChIP-Seq BV2 siPL4-3 α c-Jun

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description: Transfected with a second siRNA for Piwil4 LPS-treated

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the genome assembly mm9 using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Supplementary_files_format_and_content: bigWig

growth_protocol: BV-2 cells, murine microglial cells, cultured in DMEM, 5% heat-inacivated FBS

extract_protocol:
For ChIP-seq, samples were fixed for 10 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Chromatin DNA was sheared to 200–500 bp size by sonication. Soluble sheared chromatin was immunoprecipitated with specific antibodies overnight at 4°C. Next day, lysates were incubated in prewashed protein G dynabeads (Invitrogen). After washing and elution, the protein–DNA complex was decross-linked by heating at 65°C for 4 hours. Immunoprecipitated DNA was purified by using QIAquick PCR purificaion kit.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: BV-2 cells were treated with 1mg/ml LPS for 2 hours before collection for experiment

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: anti-cJun (9165, Cell Signaling)


title: m1_AY_Y3_I4


title: CD34_KM3_Replicate1_Input


title: ChIP-Seq BV2 siPL4-3 α p65

value: anti-p65 (6956, Cell Signaling)


title: CD34_Replicate3_H3K79me2

treatment_protocol: Isolated cells from fresh umbilical cord blood (< 30 hours)

value: Fresh purified CD34+ cells


title: ChIP-seq input DNA: Spn1-AID + DMSO 3

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (ATCACG) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

source_name: ChIP-seq input DNA: Spn1-AID + DMSO 3


title: m1_Young1_H4


title: ChIP-seq input DNA: Spn1-AID + DMSO 2

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (AACACCTAC) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

source_name: ChIP-seq input DNA: Spn1-AID + DMSO 2


title: CD34_KM3_Replicate1_H3


title: m1_Young1_O7


title: CD34_Replicate3_H3


title: CD34_KM3_Replicate1_H3K4me3


title: m1_Young2_N11


title: ChIP-seq input DNA: Spn1-AID + DMSO 1

source_name: ChIP-seq input DNA: Spn1-AID + DMSO 1


title: CD34_Replicate3_Input


title: m1_Young2_N7


title: ChIP-Seq BV2 ctrl α c-Jun

description: Control cells


title: CD34_Replicate2_H3K79me2


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + IAA 3

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Rpb1 ChIP-seq with Spn1 depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (TAGCTT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding a V5-tagged protein (FWP485) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. For immunoprecipitation, 10 μL anti-Rpb1 (Millipore, 8WG16) was used. Immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (~16-18 hr). Protein G Sepharose beads (GE Healthcare, 4 Fast Flow) were washed with WB140, and a 50% slurry was subsequently made in WB140. Fifty-μL aliquots of slurry were transferred into new Eppendorf tubes, and the WB140 was removed. The immunoprecipitation reactions were added directly to the beads and incubated at 4°C with end-over-end rotation for 4 hr. Bead-washing and elution were done are previously described (doi:10.1093/nar/gkz119). The 200 μL of eluate was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + IAA 4

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (CTTGTA) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: m1_Young1_H14


title: CD34_Replicate2_H3K27me3


title: CD34_Replicate2_H3K4me3


title: ChIP-Seq BV2 ctrl α p65

description: Control cells


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + IAA 2

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (TTGAGTGT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding an HA-tagged protein (FWP568) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. For immunoprecipitation, 10 μL anti-Rpb1 (Millipore, 8WG16) was used. Immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (~16-18 hr). Protein G Sepharose beads (GE Healthcare, 4 Fast Flow) were washed with WB140, and a 50% slurry was subsequently made in WB140. Fifty-μL aliquots of slurry were transferred into new Eppendorf tubes, and the WB140 was removed. The immunoprecipitation reactions were added directly to the beads and incubated at 4°C with end-over-end rotation for 4 hr. Bead-washing and elution were done are previously described (doi:10.1093/nar/gkz119). The 200 μL of eluate was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + IAA 1

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GAGTTAAC) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: ChIP-Seq BV2 LPS α c-Jun

description: LPS-treated


title: CD34_Replicate3_H3K27me3


title: m1_Young2_B16


title: m1_Young1_H10


title: ChIP-Seq BV2 LPS α p65

description: LPS-treated


title: CD34_Replicate2_H3


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 4

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Rpb1 ChIP-seq with Spn1 non-depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GGCTAC) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: CD34_Replicate2_Input


title: m1_Young2_F4


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 3

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GATCAG) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: m1_Young1_D16


title: m1_AY_Y3_H2


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GGTCCTTGA) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: CD34_Replicate1_H3K27me3


title: m1_Young2_L12


title: CD34_Replicate1_H3K4me3


title: 9_base_array

type: RNA

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description:
9_base_252800422025_1_1.txt
disease

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Agilent scanner

data_processing:
Images were quantified using Feature Extraction Software, log10 Green over Red.  Raw, individual array files need log2 adjusted and reversed for Red over Green.
Log(base2) of R/G Lowess Normalized Ratio (Mean), NONmedian centered data were multiplied by -3.321928 to convert to Log2(Cy3/Cy5) ratios, probes with > 20% data were removed

source_name: Sample: Human PBMC

label_protocol: 50ng of total RNA was reversed transcribed using Agilent Low Input Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted from PBMC following manufacturer's protocol. UHR is Stratagene, Universal Human Reference RNA Catalog #740000

treatment_protocol: Collection of PBMC in PAXgene

tag: diagnosis

value: SSc

value: Cyclophosphamide

tag: timepoint

value: base

tag: response

value: Responder

value: PMBC

source_name: Universal Human Reference

tag: sample type

value: Universal Human Reference (UHR)


title: m1_AY_Y3_P12

source_name: three-mo mouse BEC

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type