title: LLC_CON_1

city: Fuzhou

first: Fei

last: Huang

address: No 20 Chazhong Road

institute: First Affiliated Hospital, Fujian Medical University

data_processing:
Raw sequences were mapped to mouse genome mm10 by STAR (v2.5.4b) with key parameters setting of --readMatesLengthsIn Equal --outFilterMultimapNmax 20 --alignEndsType Local --al ignSJDBoverhangMin 10 --alignMatesGapMax 10000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3.  The expression level FPKM values were obtained from Cuffnorm in Cufflinks package (v2.2.1), further, significant differential expressed genes (BM vs Parent, LM vs Parent and BM vs LM) were called by Cuffdiff in Cufflinks packages, requiring p-value < =0.01 and fold change >= 1, all significant differential expressed genes were compiled together.
Supplementary_files_format_and_content: cuffdiff output gene_exp.diff
Genome_build: mm10

source_name: Lewis lung cells

growth_protocol: We injected the Lewis lung carcinoma cells (LLCs) into tail veins of C57/BL6 mice, resulting in lung metastases and bone metastases. And then lung metastases and bone metastases tissues were harvested.Mice Lewis lung cell (LLC) was maintained in RIPM-1640 medium (Gibco) containing 10% fetal calf serum (Gibco), 100 U/mL penicillin and 100μg/mL streptomycin (Milipore). The cultured cells were maintained at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from mice tissues with TRIzol (Invitrogen).
RNA library preparation was performed as described in the QIAseq Stranded RNA Library Kits (QIAGEN). The mRNA was fragmented to an average insert size of 200–400 bp. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase (Thermo Fisher Scientific) and random primers. The first-strand cDNA was converted into double-stranded DNA in the presence of dUTP. These cDNA fragments were subjected to the addition of a single ’A’ base and subsequent ligation of the adapter. The products were purified and enriched via PCR to generate the final library. After testing quality using Qubit2.0 Fluorometer and Agilent 2100 Bioanalyzer (Agilent Technologies), the libraries were sequenced on the Illumina HiSeq platform (Illumina Inc., San Diego, CA, USA).

treatment_protocol: With vehicle or 20ng/mL BMP2 treatment.

tag: cell line source

value: Lewis lung carcinoma cells (LLCs)

tag: host strain

tag: cell/tissue type

value: parental Lewis lung cells

value: with vehicle treatment


title: parent_1

status: Public on Jul 01 2020

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: treatment


title: LLC_B_1

value: with BMP2 treatment


title: L1_1

source_name: Lewis lung lung metastasis tissues

value: lung metastasis tissue


title: m1_AY_Y3_J1

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

country: USA

institute: Stanford

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

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: B1_1

source_name: Lewis lung  bone metastasis tissues

value: bone metastasis tissue


title: Human iPSC-Endothelial Cells [EC_1_1]

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

description:
EC_1_1
small RNA
processed data file: transcript_count_matrix.csv

data_processing:
Indexing GRCh38 for 75nt single end using STAR v.2.7.3a.
Alignment to indexed genome using STAR v.2.7.3a (--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --clip3pAdapterSeq TGGAATTCTCGGGTGCCAAGG --clip3pAdapterMMp 0.1).
Remove 5' genomically trimmed reads, convert to sorted bam using samtools v.1.10.
Quantify transcripts using StringTie v.2.11 against miRBase v.22.1 annotations (-e -b).
Genome_build: GRCh38
Supplementary_files_format_and_content: transcript_count_matrix.csv: Comma-separated text file output by Stringtie containing transcript counts mapped to miRBase v22.1.

organism: Homo sapiens

source_name: Induced pluripotent stem cells

growth_protocol: Human induced pluripotent stem cells were passaged using standard protocols then differentiated into cardiomyocytes, endothelial cells, and fibroblasts in vitro using published protocols from the Wu lab.

extract_protocol:
Exosomes were extracted from culture medium supernatant, followed by Qiagen miRNeasy isolation of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq small RNA).

treatment_protocol: Untreated

value: iPSC-derived endothelial cells exosomes

tag: biological replicate


title: Human iPSC-Cardiomyocytes [CM_2_2]

description:
CM_2_2
small RNA
processed data file: transcript_count_matrix.csv

value: iPSC-derived cardiomyocytes exosomes


title: m1_AY_Y3_G17


title: m1_Young2_J6


title: Human iPSC-Endothelial Cells [EC_2_2]

description:
EC_2_2
small RNA
processed data file: transcript_count_matrix.csv


title: m1_Young2_J1


title: RNA-seq: wild type + IAA 1

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
RNA-seq of a wild type strain treated with IAA.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). The random hexamer molecular barcode on the 5′ end of each read was removed and processed using a custom Python script. Cutadapt was then used to remove adapter sequences and low-quality base calls from the 3′ end of the read, as well as poly-A sequences from the 5′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using TopHat2 without a reference transcriptome, and uniquely mapping alignments were selected using SAMtools. Alignments mapping to the same location as another alignment with the same molecular barcode were identified as PCR duplicates and removed using a custom Python script. Coverage corresponding to the 3′-most base of the RNA fragment sequenced as well as the entire interval for each alignment was extracted using BEDTools genomecov and normalized to the total number of alignments uniquely mapping to the S. pombe genome.
"Minus" and "plus" bigWig files are spike-in normalized coverage of entire RNA-seq alignments mapping to the minus and plus strands, respectively.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

source_name: RNA-seq: wild type + IAA 1

extract_protocol:
Total RNA was prepared by hot acid phenol extraction, and a portion of each sample was treated with RQ1 DNase and used for subsequent steps (Promega, M6101). Ribosomal RNA was depleted using a Ribo-Zero kit for yeast (Illumina, MRZY1324) as per manufacturer instructions, except all volumes were halved.
Library preparation was carried out according to a previously published method (doi:10.1002/0471142727.mb0414s98), except fragmentation was performed prior to linker ligation for RNA-seq. Briefly, alkaline fragmentation (2x fragmentation buffer: 100 mM NaCO3 pH 9.2, 2 mM EDTA pH 8.0) was performed to obtain 40-70-nucleotide fragments that were subsequently size-selected and dephosphorylated with T4 PNK (NEB, M0201S) for ligation of a 3’ DNA linker containing a random hexamer molecular barcode to allow detection of PCR duplicates. First-strand cDNA was synthesized with SuperScriptIII (Invitrogen, #56575) using a primer with sequence complimentary to the 3’ linker and with an additional adapter sequence. cDNA was circularized with CircLigase (Epicentre, CL4111K). DNA libraries were amplified by PCR for 6-10 cycles with Phusion HF DNA Polymerase (NEB, M0530) using Illumina TruSeq indexing primers for multiplexing. Libraries were gel-purified and run on Agilent Bioanalyzer and/or TapeStation to assess size distribution, quality, and concentration.

treatment_protocol: Cells were grown in YPD at 30°C to ~ 3.5 x 107 cells/mL, diluted back to OD600 ≈ 0.3 in pre-warmed YPD, treated with IAA at a final concentration of 25 μM, and grown for an additional 90 minutes.

tag: strain

tag: genotype

value: MATa leu2delta1 ura3-52

value: 25 microM IAA


title: Human iPSC-Cardiomyocytes [CM_2_1]

description:
CM_2_1
small RNA
processed data file: transcript_count_matrix.csv


title: m1_Young1_N1


title: Human iPSC-Cardiomyocytes [CM_1_2]

description:
CM_1_2
small RNA
processed data file: transcript_count_matrix.csv


title: CT26 tumor, antiPD1-non-responder, 32R (RNA-Seq)

first: Xiaole

last: Liu

address: 3 Blackfan Circle

institute: Dana-Farber Cancer Institute

description:
32R_combined_R1
RNA-seq of CT26 tumor with no response to antiPD1 treatment

data_processing:
Sequenced reads were mapped to mm10 using STAR
Gene quantification was done using RSEM to obtain Transcripts Per Million (TPM) and Fragments Per Killobase of transcript per Millon (FPKM)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM and FPKM values for each sample.

source_name: CT26 tumor

growth_protocol: Tumors were directly harvested from mice

extract_protocol:
RNA extraction was performed using the Qiagen AllPrep DNA/RNA Mini Kit
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Tumors were treated by control IgG or anti-PD-1 prior to harvesting

tag: cell line

value: BALBc

tag: tissue

value: CT26 tumor

tag: response

value: non-responder


title: CT26 tumor, antiPD1-responder, 35L (RNA-Seq)

description:
35L_combined_R1
RNA-seq of CT26 tumor with response to antiPD1 treatment

value: responder


title: CT26 tumor, antiPD1-non-responder, 33R (RNA-Seq)

description:
33R_combined_R1
RNA-seq of CT26 tumor with no response to antiPD1 treatment


title: CT26 tumor, antiPD1-non-responder, 33L (RNA-Seq)

description:
33L_combined_R1
RNA-seq of CT26 tumor with no response to antiPD1 treatment


title: m1_AY_Y3_L12


title: H3K36me3 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3K36me3 ChIP-seq with Spn1 non-depleted.

library_source: genomic

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 (GTTGTCCCA) 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

molecule: genomic DNA

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, 6 μganti-H3K36me3 (Abcam, ab9050) 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.

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

value: DMSO

tag: antibody


title: H3K36me2 ChIP-seq, ChIP DNA: Spn1-AID + IAA 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3K36me2 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 (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 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, 6 μganti-H3K36me2 (Abcam, ab9050) 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 IAA at a final concentration of 25 μM, and allowed to grow for 90 minutes.


title: H3K36me3 ChIP-seq, ChIP DNA: Spn1-AID + IAA 1

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3K36me3 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 (TGCGGTTA) 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: H3K36me3 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 (TATACCGT) 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_Young2_J4


title: CT26 tumor, antiPD1-responder, 30R (RNA-Seq)

description:
30R_combined_R1
RNA-seq of CT26 tumor with response to antiPD1 treatment


title: Human iPSC-Cardiomyocytes [CM_1_1]

description:
CM_1_1
small RNA
processed data file: transcript_count_matrix.csv


title: H3K36me3 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 (TGACGCAT) 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: H3K36me2 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 (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


title: m1_Young1_I11


title: CT26 tumor, antiPD1-responder, 30L (RNA-Seq)

description:
30L_combined_R1
RNA-seq of CT26 tumor with response to antiPD1 treatment


title: CT26 tumor, antiPD1-non-responder, 29L (RNA-Seq)

description:
29L_combined_R1
RNA-seq of CT26 tumor with no response to antiPD1 treatment


title: m1_AY_Y3_D17


title: JX39_DMSO_6

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

data_processing:
adapter trimming using trimgalore v0.4.1
fastqc v0.10.1 for quality score assessment
star version v2.5.2b for alignment
ht-seq-gene v0.5.3 to consoldiate reads to features
Genome_build: hg38
Supplementary_files_format_and_content: raw count table at the gene level for all 9 samples

source_name: JX39 GBM xenograft cells

growth_protocol: GBM patient derived xenografts (PDX) D456 (Duke University)and JX39 (parental and TMZ resistant; Mayo Clinic)were propagated subcutaneously in athymic nude mice with assistance from the UAB Brain Tumor Bank or in the Hjelmeland laboratory in accordance with IACUC approval.

extract_protocol:
RNA was extracted using Norgen Total RNA Purification Kit with DNAse treatment
NEBNext Ultra RNA Library Prep Kit for Illumina with polyA selection

treatment_protocol: Each cell line was treated with SRI-21979 at their respective IC-50, 2.5um for JX39 and 5um for D456, for 24 hours

value: JX39 GBM xenograft cells

tag: replicate #


title: CT26 tumor, antiPD1-responder, 26R (RNA-Seq)

description:
26R_combined_R1
RNA-seq of CT26 tumor with response to antiPD1 treatment


title: H3K36me2 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3K36me2 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 (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: m1_Young2_O6


title: CT26 tumor, antiPD1-responder, 24L (RNA-Seq)

description:
24L_combined_R1
RNA-seq of CT26 tumor with response to antiPD1 treatment


title: JX39_SRI_4


title: H3K4me3 ChIP-seq, ChIP DNA: Spn1-AID + IAA 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3K4me3 ChIP-seq with Spn1 depleted.

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, 6 μganti-H3K4me3 (Abcam, ab8580) 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: H3K4me3 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 (CAGGAGGCG) 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_F16


title: CT26 tumor, ctrl-IgG, 20R (RNA-Seq)

description:
20R_combined_R1
RNA-seq of CT26 tumor with IgG treatment

value: ctrl


title: JX39_DMSO_7


title: m1_AY_Y3_N8


title: D456_SRI_2

source_name: D456 GBM xenograft cells

value: D456 GBM xenograft cells


title: D456_DMSO_3


title: H3K4me3 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3K4me3 ChIP-seq with Spn1 non-depleted.


title: H3K36me2 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 (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


title: JX39_SRI_5


title: histone H3 ChIP-seq, ChIP DNA: Spn1-AID + IAA 3

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3 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 (TCGCGTAC) 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, 8 μganti-H3 (Abcam, ab1791) 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: CT26 tumor, ctrl-IgG, 17R (RNA-Seq)

description:
17R_combined_R1
RNA-seq of CT26 tumor with IgG treatment


title: m1_Young2_B18


title: histone H3 ChIP-seq, ChIP DNA: Spn1-AID + IAA 4


title: CT26 tumor, ctrl-IgG, 16R (RNA-Seq)

description:
16R_combined_R1
RNA-seq of CT26 tumor with IgG treatment


title: histone H3 ChIP-seq, ChIP 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. For immunoprecipitation, 8 μganti-H3 (Abcam, ab1791) 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: D456_SRI_1


title: Model_ATAC-seq_Replicate4

city: Montreal

first: Thomas

last: Milan

state: Quebec

address: 2950 Chemin de Polytechnique

country: Canada

institute: IRIC

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

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: CT26 tumor, ctrl-IgG, 14R (RNA-Seq)

description:
14R_combined_R1
RNA-seq of CT26 tumor with IgG treatment


title: m1_Young1_L10

value: primary murine brain endothelial cells


title: Tumor derived from resistant CT26 clone-B64_B (RNA-seq)

growth_protocol: Cells were grown in RPMI full media

extract_protocol:
RNA extraction was performed using the Qiagen miRNeasy Plus Mini Kit
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: tumor derived from anPD1-resistant clone B64 of CT26


title: Model_ATAC-seq_Replicate3


title: CT26 tumor, ctrl-IgG, 14L (RNA-Seq)

description:
14L_combined_R1
RNA-seq of CT26 tumor with IgG treatment


title: histone H3 ChIP-seq, ChIP DNA: Spn1-AID + IAA 1


title: Tumor derived from resistant CT26 clone-B64_A (RNA-seq)


title: Model_ATAC-seq_Replicate2


title: m1_AY_Y3_C17


title: m1_AY_Y3_N16


title: histone H3 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 4

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from H3 ChIP-seq with Spn1 non-depleted.


title: Model_ATAC-seq_Replicate1


title: m1_Young2_J8


title: D456_DMSO_4


title: Tumor derived from resistant CT26 clone-B04_B (RNA-seq)

value: tumor derived from anPD1-resistant clone B04 of CT26


title: histone H3 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 (GCAGCCTC) 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_Young2_L7

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_Young2_A7


title: Tumor derived from resistant CT26 clone-B04_A (RNA-seq)


title: Model_Replicate4_Input


title: Model_Replicate4_H3


title: histone H3 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 1


title: Tumor derived from parental line CT26_B (RNA-seq)

value: tumor derived from parental CT26


title: Set2 ChIP-seq, input DNA: Spn1-AID + IAA 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 SET2-3xHA
Input library from Set2 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 (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

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.

value: MATa leu2delta1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 SET2-3xHA


title: Tumor derived from parental line CT26_A (RNA-seq)


title: Tumor derived from resistant CT26 clone-B64_B (ATAC-seq)

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA mem
Unique reads were deduplicated using Picard Markduplicates
Peaks were called using MACS with FDR 0.01 (The "*treat_pileup.bw” file is the actual key signal track, while the “control_lambda.bw” can be viewed as the estimated background.  We used MACS (--SPMR -B) to call peaks and also output the computationally estimated local background as “control”. )
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files of ATAC-seq peaks

extract_protocol:
Extraction was performed accoring to the standard omni-ATAC protocol
Libraries were prepared according to Nextera DNA Flex Library Prep Kit

value: post

value: tumor derived from antiPD1-resistant clone B64 of CT26


title: histone H3 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 (ACTAACTGC) 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: Model_Replicate3_H3K79me2


title: Model_Replicate4_H3K27me3

value: H3K27me3 :#Millipore 07-449


title: Model_Replicate3_H3K27me3


title: m1_AY_Y3_B12


title: m1_AY_Y3_L3


title: Model_Replicate3_H3K4me3


title: Tumor derived from resistant CT26 clone-B64_A (ATAC-seq)

value: BALBc


title: Tumor derived from resistant CT26 clone-B04_B (ATAC-seq)

value: tumor derived from antiPD1-resistant clone B04 of CT26


title: Set2 ChIP-seq, input 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 (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

value: 25 microM IAA


title: Set2 ChIP-seq, ChIP DNA: Spn1-AID + IAA 1

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 SET2-3xHA
ChIP library from Set2 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 (ACTTGA) 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. 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.


title: H3K4me3 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 1

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

value: DMSO


title: m1_Young2_B8


title: m1_AY_Y3_P18


title: Set2 ChIP-seq, input DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 SET2-3xHA
Input library from Set2 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: Model_Replicate3_H3


title: Model_Replicate3_Input


title: Tumor derived from resistant CT26 clone-B04_A (ATAC-seq)


title: Set2 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 (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


title: Tumor derived from parental line CT26_A (ATAC-seq)


title: Tumor derived from parental line CT26_B (ATAC-seq)


title: Set2 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 SET2-3xHA
ChIP library from Set2 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 (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: m1_AY_Y3_A1


title: Model_Replicate2_H3K79me2


title: Set2 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 (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


title: NC-3

city: Baoding

first: Dong

last: Yang

state: Hebei

address: No. 180, Wusi Road

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: NC_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: NC

tag: age

value: 5 month-old

tag: Sex

value: male

value: main olfactory epithelium


title: m1_Young2_M5

value: primary murine brain endothelial cells


title: m1_AY_Y3_P1


title: m1_AY_Y3_B13


title: Model_Replicate2_H3K4me3

value: HSPCs

value: model leukemia cells from xenograft


title: Model_Replicate2_H3K27me3


title: NC-2


title: Set2 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 (CAGATC) 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_Young2_B13


title: Model_Replicate2_H3


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

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6 HA-SPT6
Input 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 (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

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


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

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 (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: NC-1


title: Model_Replicate2_Input


title: miR-200b/a KD-3

source_name: miR-200b/a KD_main olfactory epithelium

value: miR-200b/a KD


title: m1_Young2_G17


title: m1_Young1_K7


title: m1_Young1_G1


title: Spt6 ChIP-seq, input 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 (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