title: KRp1-180

city: Houston

first: Jianfeng

address: one baylor plaza

institute: Baylor College of Medicine

data_processing:
For each plasma sample, after trimming adaptor and low-quality bases, we use BSMAP (2.90) to align bisulfite sequencing reads to hg19 human genome assembly. The methylation ratio of CpG site is calculated by the methratio.py script (from BSMAP package). The CpG methylation ratios supported by less than 4 reads are discarded before the downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: methratio output produced by using methratio.py of BSMAP

extract_protocol:
The plasma was transferred to 2-mL microcentrifuge tube and centrifuged at 16,000g for 10 minutes at 4°C to remove any cellular debris. Circulating cell-free DNA (10–50 ng) was extracted from 1-2 ml plasma using the QIAamp Circulating Nucleic Acid kit (Qiagen) and quantified using the Quant-iT high-sensitivity Picogreen double-stranded DNA Assay Kit (Invitrogen by Thermo Fisher Scientific) according to manufacturer instructions.
For targeted methylation sequencing, 10 ng plasma cell-free DNA was first bisulfite treated using the ZYMO Gold Kit per the manufacturer’s protocol. We adapted Swift Bioscience Methyl-Seq library preparation kit to generate individual libraries incorporating 13 PCR cycles and overnight ligation. Custom targeted CpG methylation probes were designed using Roche Nimblegen target capture kit, Custom SeqCap Epi Choice 30 MB. Libraries were quantified using Quant-iT high-sensitivity Picogreen double-stranded DNA Assay Kit before equimolarly pooling 10 individual libraries per capture consisting of 2 ug total DNA. Hybridization and capture were performed using VK SeqCap Epi Reagent Kit Plus and SeqCap EZ hybridization/wash kit from Roche Nimblegen following manufacturer recommendations. For blocking, we used universal blocker from IDT technologies. We sequenced the pooled libraries on Illumina NovaSeq S4 using paired-end 100-base-pair reads incorporating 150 individual libraries per lane.

tag: Stage


title: KRp1-179

status: Public on Aug 27 2021

type: SRA

last: Xu

state: Texas

country: USA

library_source: genomic

molecule: other

organism: Homo sapiens

source_name: ESCC

tag: tissue

value: ESCC

tag: age

value: #N/A

tag: alternate id

tag: assayed molecule

value: cell-free DNA


title: RNA-seq_D T-BET

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
Fastq files were aligned to human reference genome GRCh38 using STARv2.42 and gencode v25 as guide gtf
Counts were generated on the fly by STAR
QC of fastq files was done with FastQC
Genome_build: GRCh38
Supplementary_files_format_and_content: a tab separated raw count matrix file

molecule: polyA RNA

source_name: Hematopoietic stem cell

growth_protocol: HPC were obtained by isolating peripheral blood monocytes form umbilical cord blood by density gradient centrifugation and subsequently CD34+ HPC were enriched by magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours.

extract_protocol:
Total mRNA was extracted using the RNeasy micro kit (Qiagen). The concentration and quality of the total extracted RNA was checked by using the Quant-it ribogreen RNA assay (Life Technologies) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, U.S.A), respectively.
Illumina sequencing library preparation was performed using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR.

treatment_protocol: Pre-cultured CD34+ HPC were harvested, transferred to RetroNectin (Takara Bio, Saint-Germain-en-Laye, France)-coated plates and viral supernatant was added. Additional cytokines were added to keep the concentrations constant after virus addition. The plates were centrifuged at 950 g and 32°C during 90 min. Another 48 hours after transduction, lineage-(CD3/CD14/CD19/CD56) CD34+eGFP+ HPC were sorted using a BD FACSAria™ Fusion cell sorter (BD Biosciences).

value: umbilical cord blood

tag: cell type

value: Hematopoietic stem cell

tag: donor

value: Donor D

tag: treatment

value: Retroviral transduction


title: RNA-seq_B EOMES

value: Donor B


title: Sample2.Human.202897220084_R02C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Calibration species=Human

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Calibration

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from premixed DNA standards from EpigenDx Inc (products 80-8060H-PreMixHuman, 80-8060M-PreMixMouse, and Standard80-8060R-PreMixRat Premixed Calibration Standard)

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: dna source

value: premixed DNA standards from EpigenDx Inc (80-8060H-PreMixHuman)

tag: proportionmethylated


title: znf2Δ_12h_2_Strand_specific

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

country: China

institute: the institute of microbiology chinese academy of sciences

data_processing:
Basecalls performed using CASAVA version 1.4
Standard sequencing for samples contain wildtype at seven time points with 3 repeats and wildtype. Strand-specific sequencing for crz1Δ, mpk1Δ, znf2Δ at one time point with two repeats. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and then ~2 GB of clean data of each sample (representing over 100 × coverage) was mapped to the genome sequence of H99 using STATR_2.6.0c.  All unigenes were subsequently aligned against the well-annotated genome of H99.
The gene expression level was measured in TPM to determine unigenes by StringTie v1.3.3.
The differentially expressed genes (DEGs) were assessed using the DEseq2 v1.16.1 Bioconductor package and defined based on the fold change criterion.
Genome_build: H99
Supplementary_files_format_and_content: TPM values for each Sample

organism: Cryptococcus neoformans H99

growth_protocol: Strains were cultured in YPD liquid medium at 30°C for 12 hrs. The cells were collected, washed twice with ddH2O, and diluted to A600 = 5.0. The diluted cells were spotted on YPGlcN medium and incubated at 30°C

extract_protocol:
Total RNA was subsequently extracted from the cells collected at different time points. The RNA concentration of each sample was assessed using a Qubit RNA Assay Kit on a Qubit 2.0 Fluorometer (Life Technologies, CA, USA). The RNA integrity was evaluated using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The transcriptome libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) following the manufacturer’s instructions. Transcriptome library sequencing was performed by Annoroad Gene Technology Co., Ltd (Beijing, China). The samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced on an Illumina platform.

tag: strain background

tag: mating type

value: Mating type alpha

tag: genotype/variation

value: YPGlcN (2% GlcN) at 30°C, 12h


title: Sample4.Human.202897220084_R04C01


title: mpk1Δ_12h_1_Strand_specific


title: RNA-seq_B T-BET


title: Sample3.Human.202897220084_R03C01


title: KRp1-181


title: KRp1-176

source_name: GC

value: GC


title: KRp1-177

source_name: PDAC

value: PDAC


title: RNA-seq_NK_B Stage 4 T-BET

description: Sample 2

source_name: Natural Killer cells

growth_protocol: HPC were obtained by isolating peripheral blood monocytes form umbilical cord blood by density gradient centrifugation and subsequently CD34+ HPC were enriched by magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours. Sucessfully transduced HPC were sorted and co-cultured with mitomycin-inactivated EL08.1D2 cells in Dulbecco’s modified Eagle medium plus Ham’s F-12 medium (2:1 ratio), supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM glutamine, 10 mM sodium pyruvate (all from Life Technologies), 20% of heat-inactivated human AB serum (Biowest, Nuaillé, France), 24 μM β-mercaptoethanol, 20 μg/mL ascorbic acid and 50 ng/mL sodium selenite (all from Sigma-Aldrich). The following cytokines were added: IL-3 (5 ng/mL, first week only, R&D systems), IL-7 (20 ng/mL), IL-15 (10 ng/mL) (all from Miltenyi Biotec), SCF (20 ng/mL; Peprotech, London, UK.), and Flt3-L (10 ng/mL; R&D Systems, Minneapolis, MN, U.S.A.) . Culture medium was refreshed on day 7 by addition of the same volume of fresh medium with cytokines. At day 14 the non-adherent cells were harvested and transferred to new mitomycin-treated EL08.1D2 feeder cells.

treatment_protocol: CD34+ HPC underwent retroviral transduction with T-BET or EOMES overexpression vectors or the control vector. After 48 hours, eGFP+CD34+ HPC were sorted by FACS cell sorting.

value: Natural Killer cells

tag: day of culture

value: Day 21

value: retroviral transduction


title: RNA-seq_B Control


title: KRp1-175

source_name: HCC

value: HCC

value: II


title: KRp1-173

source_name: Normal

value: Normal

value: #N/A


title: KRp1-174

value: cell-free DNA


title: crz1Δ_12h_2_Strand_specific


title: KRp1-171


title: Sample1.Human.202897220084_R01C01


title: KRp1-169

value: ESCC


title: RNA-seq_A EOMES

value: umbilical cord blood

value: Hematopoietic stem cell

value: Donor A


title: znf2Δ_12h_1_Strand_specific


title: crz1Δ_12h_1_Strand_specific


title: KRp1-178


title: KRp1-164


title: KRp1-166

value: I


title: RNA-seq_EC3

city: Blenheim

first: Darrell

middle: Karl

last: Lizamore

state: Marlborough

address: 85 Budge St

country: New Zealand

institute: Bragato Research Institute

description: Vitis vinifera cv. 'Chardonnay' embryopgenic callus - rRNA depleted total RNA, replicate 3

data_processing:
Adapter and quality read trimming using fastq-mcf with default parameters except -l 36
Reads were mapped to tRNA & rRNA sequences from rfam (v 12.0) and reads that mapped were excluded.
Remaining read pairs were mapped to the 12X Vitis vinifera reference genome using HiSat2 with parameters --rna-strandness RF --dta -k 100
Gene and TE transcripts were counted simultaneously using TEtranscripts with the V2.1 gene annotation track.
Read counts for two genes demonstrating evidence of genome over-assembly (VIT_213s0019g0263 and VIT_207s0031g03000) were removed, prior to read analysis withg DeSeq2
Genome_build: GCA_000003745.2
Supplementary_files_format_and_content: Count tables are output from TETranscripts (not normalised)

molecule: total RNA

organism: Vitis vinifera

source_name: Vitis vinifera cv. 'Chardonnay' proliferating embryogenic callus

extract_protocol:
RNA was purified from 100mg tissue using the Spectrum Plant Total RNA kit (Sigma). Library construction was performed by Macrogen, including rRNA depletion with Illumina Ribo-Zero Plant (Leaf) kit and Illumina TruSeq RNA sample prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryogenic callus

tag: cultivar

value: Chardonnay


title: KRp1-162


title: WT_12h_2_Strand_specific

value: Mating type alpha

value: wild type

value: YPGlcN (2% GlcN) at 30°C, 12h


title: KRp1-163


title: KRp1-160


title: RNA-seq_EC2

description: Vitis vinifera cv. 'Chardonnay' embryopgenic callus - rRNA depleted total RNA, replicate 2


title: WT_12h_1_Strand_specific


title: RNA-seq_EC1

description: Vitis vinifera cv. 'Chardonnay' embryopgenic callus - rRNA depleted total RNA, replicate 1


title: KRp1-159


title: KRp1-161


title: KRp1-157

value: GC


title: WT_GlcN_60h_2

value: YPGlcN (2% GlcN) at 30°C, 60h


title: KRp1-167

value: PDAC

value: III


title: RNA-seq_Leaf3

description: Vitis vinifera cv. 'Chardonnay' young leaf tissue - rRNA depleted total RNA, replicate 3

value: Leaf


title: KRp1-158


title: KRp1-156

value: HCC


title: KRp1-154

value: cell-free DNA


title: WGBS_callus

data_processing:
Read pairs were mapped to the grapevine reference genome using Bs-Seeker2 with parameters -X 1000 -m 0.04
Methylation calling was performed with the ‘bam2cgmap’ tool from the cgmaptools programme package with the setting --rmOverlap
Methylation across features and methylation per feature were calculated using the ‘mfg’ and ‘mtr’ functions from the cgmaptools package, respectively
cgmaptools calculates methylation across all the features of a type, with the features themselves divided into 100 bins (R1   R100), as well as 2kb upstream (U1-U6) and downstream (D1-D6) regions.
Genome_build: GCA_000003745.2
https://urgi.versailles.inra.fr/Species/Vitis/Annotations
Supplementary_files_format_and_content: fragment files (*_mfg.txt) were produced using the mfg function from the cgmaptools package, with cytosine methylation call files from cgmaptools bam2cgmap and feature files as input. Gene features and TE features were analysed separately.
Supplementary_files_format_and_content: fragment files (*_filtered.tab) were produced using the mtr function from the cgmaptools package. First cytosine methylation call files from cgmaptools bam2cgmap were sorted by cytosine context and regions mapping to unscaffolded reference sequences (chrUn) were removed. The sorted methylation files were then used as input with TE feature annotation files. TE features overlapping genes (TEsInGenes*) and TE features not overlapping genes (TEsNotInGenes*) were produced using bedtools intersect based on TE and gene feature files. These were used as input for cgmaptools mtr separately, in order to analyse TE methylation my genic context.

extract_protocol:
Genomic DNA was purified from 100mg tissue using the NucleoMag® Plant DNA kit (Machery-Nagel). Library construction was performed by Macrogen, using the TruSeq DNA Methylation kit.
Bisulfite-seq libraries were prepared for sequencing using standard Illumina protocols


title: RNA-seq_Leaf1

description: Vitis vinifera cv. 'Chardonnay' young leaf tissue - rRNA depleted total RNA, replicate 1


title: WT_GlcN_60h_3


title: RNA-seq_Leaf2

description: Vitis vinifera cv. 'Chardonnay' young leaf tissue - rRNA depleted total RNA, replicate 2


title: WT_GlcN_60h_1


title: KRp1-152

value: Normal

value: #N/A


title: WGBS_leaf

source_name: Vitis vinifera cv. 'Chardonnay' young leaf tissue


title: WT_GlcN_48h_2

value: YPGlcN (2% GlcN) at 30°C, 48h


title: KRp1-153


title: KRp1-155

value: II


title: KRp1-151

value: ESCC


title: KRp1-15


title: WT_GlcN_48h_1


title: KRp1-147


title: WT_GlcN_36h_3

value: YPGlcN (2% GlcN) at 30°C, 36h


title: KRp1-144


title: KRp1-145


title: KRp1-143


title: KRp1-142


title: KRp1-141

value: IIA


title: WT_GlcN_36h_2

value: Mating type alpha


title: WT_GlcN_36h_1

value: wild type


title: KRp1-140

value: IV


title: WT_GlcN_48h_3


title: KRp1-138


title: WT_GlcN_24h_3

value: YPGlcN (2% GlcN) at 30°C, 24h


title: KRp1-136


title: RNA-seq_A T-BET

value: umbilical cord blood

value: Hematopoietic stem cell

value: Donor A

value: Retroviral transduction


title: WT_GlcN_24h_1


title: KRp1-139

source_name: EAC

value: EAC


title: KRp1-149

value: cell-free DNA


title: WT_GlcN_24h_2


title: KRp1-135

value: Normal


title: KRp1-134

value: #N/A


title: RNA-seq_A Control


title: ATAC-seq_C Stage 5 EOMES

description: Sample 60

data_processing:
QC on fastq files was performed using FastQC
fastq files were aligned to GRCh38 using STAR_2.4.2a with settings --outFilterMultimapNmax 1 --alignIntronMax 1 --alignMatesGapMax 1000
MACS2 was used for peak calling with BAMPE setting and peakfiles were subsequently merged to create a bed file containing all possible ATAC sites
featureCounts from the Subreadv2.0.0 package was used to create a count matrix based on the merged bed file
Genome_build: GRCh38
Supplementary_files_format_and_content: bed file with ATAC sites
Supplementary_files_format_and_content: count matrix on ATAC sites

extract_protocol:
Genomic DNA was extracted according to the Fast-ATAC protocol as previously described by Corses, M.R., et al. 2016. Nat Genet, 48(10): p. 1193-203 (DOI:10.1038/ng.3646)
Library preparation was performed according to the Fast-ATAC protocol as previously described by Corses, M.R., et al. 2016. Nat Genet, 48(10): p. 1193-203 (DOI:10.1038/ng.3646). Libraries underwent size selection (120-1000 bp) and quality control before sequencing.

value: Natural Killer cells

value: Donor C

value: day 21

value: retroviral transduction


title: ATAC-seq_C Stage 5 T-BET

description: Sample 59


title: KRp1-132

value: PDAC

value: IIA


title: WT_GlcN_12h_1

value: Mating type alpha

value: wild type

value: YPGlcN (2% GlcN) at 30°C, 12h


title: KRp1-133

value: ESCC


title: WT_GlcN_12h_2


title: WT_GlcN_6h_3

value: YPGlcN (2% GlcN) at 30°C, 6h


title: KRp1-131


title: KRp1-130


title: WT_GlcN_12h_3


title: WT_GlcN_6h_2


title: LK0863 cell line grown in hypoxia

type: RNA

city: Linköping

first: Emilia

last: Wiechec

address: Sandbäcksgatan 7

department: Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

description: Gene expression data; RMA expression value

hyb_protocol: Hybridization was done according to the GeneChip® WT Plus Reagent Kit manufacturer's instructions. A total of 5.5 µg of sscDNA was fragmented and hybridized on a Human Transcriptome 2.0 Array.

scan_protocol: Hybridized arrays were scanned with an Affymetrix GeneChip® 3000 fluorescent scanner.

data_processing: Raw intensity CEL files generated by the GeneChip Command Console were imported into R and CHP files were generated for gene level analysis using the RMA summarization method.

label: biotin

source_name: HNSCC cell line

label_protocol: Labeling was done according to the GeneChip® WT Plus Reagent Kit manufacturer’s instructions The starting amount of total RNA was 150 ng. 15 µg of cRNA was used for single-stranded cDNA-synthesis (sscDNA).

growth_protocol: Tumor cells cultured in cell culture flasks in keratinocyte-SFM supplemented with antibiotics and 1% FBS.

extract_protocol: Total RNA extraction from cells grown n normoxia and hypoxia was performed using the RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Tumor cells were grown in normoxic (21% O2) and hypoxic (1% O2).

value: HNSCC cell line (larynx)

tag: cell line

tag: protocol

value: hypoxic


title: KRp1-13

tag: Stage


title: ATAC-seq_C Stage 5 Ctrl

description: Sample 58


title: WT_GlcN_6h_1


title: ATAC-seq_B Stage 5 T-BET

description: Sample 56

value: Donor B


title: ATAC-seq_B Stage 5 EOMES

description: Sample 57


title: WT_GlcN_0h_3

value: YPD liquid medium at 30°C, 12h


title: UT-SCC-14 cell line grown in hypoxia

tag: tissue

value: HNSCC cell line (tongue)


title: KRp1-129

value: GC

tag: age

value: #N/A

value: cell-free DNA


title: KRp1-128

tag: alternate id


title: ATAC-seq_B Stage 5 Ctrl

description: Sample 55

value: Natural Killer cells

value: day 21


title: WT_GlcN_0h_2


title: WT_GlcN_0h_1


title: KRp1-127

value: Normal

tag: assayed molecule


title: LK0863 cell line grown in normoxia

value: normoxic


title: ATAC-seq_C Stage 4 EOMES

description: Sample 52

tag: cell type

value: Donor C

value: retroviral transduction


title: LK0858 cell line grown in normoxia


title: ATAC-seq_C Stage 4 Ctrl

description: Sample 54

tag: donor


title: Leaf_smallRNA

description:
18-35 nt small RNA
Vitis vinifera cv. 'Chardonnay' young leaf tissue - 18-35 nt size-selected small RNA

data_processing:
Adapter trimming and size filtering (18-35 nt) of sequence reads was performed in the UEA small RNA Workbench package
Reads were mapped to rRNA and tRNA sequences from rfam (v 12.0) using PatMaN, and reads that mapped were excluded from further analysis
Remaining reads were mapped to the 12X Vitis vinifera reference genome using ShortStack which included siRNA cluster discovery and annotation
Enrichment of 20 to 24 nt cluster sizes across three genomic feature types: genes, promoters (defined as regions 2kb upstream of genes) and Tes, was assessed using gat
Genome_build: GCA_000003745.2
Supplementary_files_format_and_content: DicerCall files are siRNA clusters identified and annotated by ShortStack

extract_protocol:
Small RNA (<200 nt) was purified from 50 mg each of embryogenic cell cultures and young leaf tissue, using the Plant microRNA Purification Kit (Norgen BioTek). Library construction was performed by New Zealand Genomics limited, including isolation of 18-35 nt RNA fragments by polyacrylamide gel electrophoresis followed by standard preparation with the Illumina TruSeq Small RNA Library Preparation kit
Small RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf

value: Chardonnay


title: LK0858 cell line grown in hypoxia


title: ATAC-seq_B Stage 4 EOMES

description: Sample 51

tag: treatment


title: KRp1-124


title: ATAC-seq_C Stage 4 T-BET

description: Sample 53


title: UT-SCC-14 cell line grown in normoxia


title: KRp1-123


title: Control Media - D42B

city: Bronx

first: Stephen

last: Redenti

state: NY

address: Biology Dept. , 250 Bedford Park Blvd.

institute: Lehman College, CUNY

data_processing:
The pooled smalRNA library was sequenced on Illumina Miseq using v3 reagrents by Norgen biotek Corp
A small RNA expression profile was generated from the resulting FASTQ files using the exceRpt small RNA-seq pipeline
RNA sequencing was done using Ion PI Hi-Q OT2 200 Kit, with Ion PI Chip Kit v3
Basecalling in Proton runs used Torrent Suite with filtering for subthreshold reads and adapter sequence trimming
subopimal sequences were removed from FASTQ data by FASTX-Toolkit
Total transcriptome reads were aligned to human genome reference with Proton RNAseq Analysis Plugin tool v5.2.0.5
Genome_build: hg19(RNAseq)  hg38(smallRNAseq)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: blank sample

source_name: control media

growth_protocol:
hiPSC-derived 3D retinal organoids were generated and maintained in culture as previously described [10].
human retinal progenitor cells were culutre expanded at 37C

extract_protocol:
Exosomal RNA was isolated from samples 1-3, 9-11 using the RNA Isolation Midi Kit (Cat# 60800)
Total RNA was isolated for RNA seq using a RNeasy Mini Kit (Cat# 74104, Qiagen) according to the supplier’s protocol.
Barcoded total transcriptome RNA libraries were prepared by Ion Total RNA-Seq kit v2 (cat#4475936, Ion Torrent, ThermoFisher Scientific) according to manufacturer’s protocols.

treatment_protocol: Retinal organoid EVs from D42 were added to 6-well plates (78ug/well) containing (1.2*105 hRPCs/well) and incubated at 37°C. A second EV concentration (78ug/well) was added to each well at 48hrs and the experiment continued to 96hrs.

value: Control Media - D42B


title: Control Media - D63/D90B

extract_protocol:
Exosomal RNA was isolated from samples 4,5, 12,13 using the RNA Isolation Maxi Kit (Cat#60900)
Total RNA was isolated for RNA seq using a RNeasy Mini Kit (Cat# 74104, Qiagen) according to the supplier’s protocol.
Barcoded total transcriptome RNA libraries were prepared by Ion Total RNA-Seq kit v2 (cat#4475936, Ion Torrent, ThermoFisher Scientific) according to manufacturer’s protocols.

value: Control Media - D63/D90B


title: WMCL.1_ctr_rep1

city: Brescia

first: Aldo

middle: Maria

last: Roccaro

state: BS

address: P.le Spedali Civili di Brescia, n. 1

country: Italy

institute: ASST Spedali Civili di Brescia

description: Human Waldenström’s Macroglobulinemia cell line WMCL.1_untreated_rep1

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: All the following analyses were performed in R Bioconductor (version 3.5.1). Robust Multichip Average (RMA) processing was applied on raw data, based on the platform design (pd.clariom.d.human), allowing background subtraction, quantile normalization and median-polish summarization on core probe sets, by using oligo package.Global expression levels of 138.745 total transcripts were extracted from the ExpressionSet. Following Affymetrix Human Clariom D annotation (clariomdhumantranscriptcluster.db, version 8.7.0, org.Hs.eg.db, version 3.7.0 ) and filtering based on Entrez Gene Identifier and the exclusion of non-coding or uncharacterized protein transcripts (by subtracting microRNA, long non-coding RNA, long intergenic non-coding RNA, small nucleolar RNA, antisense, intronic, uncharachterized protein transcripts), 20.558 total features were further considered.

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA).

growth_protocol: The Human WM cell lines BCWM.1 and MWCL-1 were kindly gifted to us from Dr. Steven Treon (Dana Farber Cancer Institute, Harvard, Boston, MA, USA) and Dr. Steven Ansell (Mayo Clinic, Rochester, MN, USA). Cell lines were cultured in RPMI-1640 medium and IMDM (1x)+GlutaMax containing 10% fetal bovine serum, 2 μM l-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin, respectively.

extract_protocol: RNA was extracted from MM cell lines using RNeasy Mini kit (Qiagen).

treatment_protocol: BCWM.1 and MWCL.1 cell lines were treated with NSC12 (6µM) for 12 hours.

value: Waldenström’s Macroglobulinemia


title: WMCL.1_NSC12_treat_rep3

description: Human Waldenström’s Macroglobulinemia cell line WMCL.1_NSC12 treated_rep3


title: ATAC-seq_B Stage 4 Ctrl

description: Sample 49

value: Donor B


title: Col-0_Sub-3

city: DAEJEON

first: Hyo-Jun

last: Lee

state: DAEJEON

address: 125 GWAHAK-RO YUSEONG-GU

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Sequencing adapters and low quality bases were trimmed by CLC Genomics Workbench software
High quality reads were mapped to the reference genome by CLC Genomics Workbench software
To quantify the mapped reads on the reference genome, CLC Genomics Workbench software was used
Genome_build: TAIR10
Supplementary_files_format_and_content: An excel file containing read counts and differentially expressed genes

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Seedlings were grown on MS-agar plates for 14 d under long-day conditions at light intensity of 100 mmol m-2 s-1

extract_protocol:
Total RNA was extracted using Trizol
Library construction was performed according to the protocol of Seeders, an RNA-sequencing company in South Korea

treatment_protocol: Seedlings were submerged or left in air for 1 h and then whole seedlings were harvested.

value: Submerged in distilled water for 1h

tag: developmental stage

value: 14 days after germination

tag: ecotype


title: EC_smallRNA

description:
18-35 nt small RNA
Vitis vinifera cv. 'Chardonnay' embryopgenic callus -18-35 nt size-selected small RNA

value: Embryogenic callus


title: WMCL.1_NSC12_treat_rep1

description: Human Waldenström’s Macroglobulinemia cell line WMCL.1_NSC12 treated_rep1


title: ATAC-seq_B Stage 4 T-BET

description: Sample 50


title: Control Media - D63/D90A

extract_protocol:
Small RNA Libraries were generated using a NEBNext® Multiplex Small RNA Library Prep Set for Illumina
Exosomal RNA was isolated from samples 4,5, 12,13 using the RNA Isolation Maxi Kit (Cat#60900)
Total RNA was isolated for RNA seq using a RNeasy Mini Kit (Cat# 74104, Qiagen) according to the supplier’s protocol.
Barcoded total transcriptome RNA libraries were prepared by Ion Total RNA-Seq kit v2 (cat#4475936, Ion Torrent, ThermoFisher Scientific) according to manufacturer’s protocols.

value: Control Media - D63/D90A


title: KRp1-122

value: #N/A

value: cell-free DNA


title: BMCWM.1_ctr_rep2

description: Human Waldenström’s Macroglobulinemia cell line BMCWM.1_untreated_rep2


title: WMCL.1_ctr_rep3

description: Human Waldenström’s Macroglobulinemia cell line WMCL.1_untreated_rep3


title: Col-0_Sub-1


title: WMCL.1_NSC12_treat_rep2

description: Human Waldenström’s Macroglobulinemia cell line WMCL.1_NSC12 treated_rep2


title: KRp1-12


title: BMCWM.1_NSC12_treat_rep2

description: Human Waldenström’s Macroglobulinemia cell line BMCWM.1_NSC12 treated_rep2


title: ATAC-seq_D EOMES

description: Sample 48

source_name: Hematopoietic progenitor cells

growth_protocol: HPC were obtained by removal of peripheral blood monocytes from umbilical cord blood by density gradient centrifugation and subsequently CD34+ HPC were enriched by magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours.

extract_protocol:
Genomic DNA was extracted according to the Fast-ATAC protocol as previously described by Corses, M.R., et al. 2016. Nat Genet, 48(10): p. 1193-203 (DOI:10.1038/ng.3646).
Library preparation was performed according to the Fast-ATAC protocol as previously described by Corses, M.R., et al. 2016. Nat Genet, 48(10): p. 1193-203 (DOI:10.1038/ng.3646). Libraries underwent size selection (120-1000 bp) and quality control before sequencing.

value: umbilical cord blood

value: Hematopoietic progenitor cells

value: Donor D

value: retroviral transfection


title: ATAC-seq_D T-BET

description: Sample 47


title: WMCL.1_ctr_rep2

description: Human Waldenström’s Macroglobulinemia cell line WMCL.1_untreated_rep2


title: Control Media - D42A

extract_protocol:
Small RNA Libraries were generated using a NEBNext® Multiplex Small RNA Library Prep Set for Illumina
Exosomal RNA was isolated from samples 1-3, 9-11 using the RNA Isolation Midi Kit (Cat# 60800)
Total RNA was isolated for RNA seq using a RNeasy Mini Kit (Cat# 74104, Qiagen) according to the supplier’s protocol.
Barcoded total transcriptome RNA libraries were prepared by Ion Total RNA-Seq kit v2 (cat#4475936, Ion Torrent, ThermoFisher Scientific) according to manufacturer’s protocols.

value: Control Media - D42A


title: Col-0_Air-3

value: Left in air for 1h


title: BMCWM.1_NSC12_treat_rep3

description: Human Waldenström’s Macroglobulinemia cell line BMCWM.1_NSC12 treated_rep3


title: ATAC-seq_D Ctrl

description: Sample 46


title: Col-0_Sub-2


title: BMCWM.1_NSC12_treat_rep1

description: Human Waldenström’s Macroglobulinemia cell line BMCWM.1_NSC12 treated_rep1


title: KRp1-118

value: PDAC


title: Col-0_Air-2


title: BMCWM.1_ctr_rep3

description: Human Waldenström’s Macroglobulinemia cell line BMCWM.1_untreated_rep3


title: ATAC-seq_C EOMES

description: Sample 45

value: Donor C


title: Col-0_Air-1


title: KRp1-117


title: BMCWM.1_ctr_rep1

description: Human Waldenström’s Macroglobulinemia cell line BMCWM.1_untreated_rep1


title: KRp1-115

value: HCC

value: I


title: 17dpp PAC Igsf11 control 2

city: Beijing

first: Jing

last: He

state: Beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

department: School of Medicine

institute: Tsinghua University

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
17dpp_PAC_Igsf11_control_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with fastp 0.20.0
RNA-seq data were mapped to mm9 whole genome using hisat2 v2.1.0 with default parameters, and expression value raw counts were calculated using htseq-count v0.11.2
Paired end Hi-C sequencing reads were processed using HiC-Pro v2.11.1
The unmapped reads, multiple mapped reads and uninformative reads pairs from self-circle ligation, dangling ends, undigested DNA fragments, PCR artifacts were discarded, only the valid read pairs from two different restriction fragments were retained
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: interaction validpairs for each Hi-C sample

organism: Mus musculus

source_name: spermatocyte

extract_protocol: Total RNAs were purified with TRIzol reagent (Life Technologies, 15596) from each of 3×105 sorted cells. mRNA libraries were constructed by Smart-seq2 method with a library preparation kit (Vazyme, TD502) and an index kit (Vazyme, TD202) according to the manufacturer's protocol.

value: Pachytene spermatocyte

value: 17 dpp

value: wildtype

tag: strain


title: 17dpp PAC Igsf11 KO 2

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
17dpp_PAC_Igsf11_KO_rep2

value: Igsf11 KO


title: 17dpp PAC Igsf11 control 1

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
17dpp_PAC_Igsf11_control_rep1


title: ATAC-seq_C Ctrl

description: Sample 43


title: KRp1-119

extract_protocol:
The plasma was transferred to 2-mL microcentrifuge tube and centrifuged at 16,000g for 10 minutes at 4°C to remove any cellular debris. Circulating cell-free DNA (10–50 ng) was extracted from 1-2 ml plasma using the QIAamp Circulating Nucleic Acid kit (Qiagen) and quantified using the Quant-iT high-sensitivity Picogreen double-stranded DNA Assay Kit (Invitrogen by Thermo Fisher Scientific) according to manufacturer instructions.
For targeted methylation sequencing, 10 ng plasma cell-free DNA was first bisulfite treated using the ZYMO Gold Kit per the manufacturer’s protocol. We adapted Swift Bioscience Methyl-Seq library preparation kit to generate individual libraries incorporating 13 PCR cycles and overnight ligation. Custom targeted CpG methylation probes were designed using Roche Nimblegen target capture kit, Custom SeqCap Epi Choice 30 MB. Libraries were quantified using Quant-iT high-sensitivity Picogreen double-stranded DNA Assay Kit before equimolarly pooling 10 individual libraries per capture consisting of 2 ug total DNA. Hybridization and capture were performed using VK SeqCap Epi Reagent Kit Plus and SeqCap EZ hybridization/wash kit from Roche Nimblegen following manufacturer recommendations. For blocking, we used universal blocker from IDT technologies. We sequenced the pooled libraries on Illumina NovaSeq S4 using paired-end 100-base-pair reads incorporating 150 individual libraries per lane.


title: ATAC-seq_C T-BET

description: Sample 44


title: 17dpp PAC Igsf11 KO 1

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
17dpp_PAC_Igsf11_KO_rep1


title: KRp1-114

value: ESCC


title: 9dpp LEP Igsf11 KO 2

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
9dpp_LEP_Igsf11_KO_rep2

value: Leptotene spermatocyte

value: 9 dpp


title: ATAC-seq_B T-BET

description: Sample 41

value: umbilical cord blood

value: Donor B


title: ATAC-seq_B EOMES

description: Sample 42

value: Hematopoietic progenitor cells


title: GRID_DC3000_rep2

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

description: ~210 nt DNA

data_processing:
Library strategy: GRID-seq
GRID-seq: Raw reads from each library were de-duplicated and barcode sequences were removed using FASTX-Toolkit (v0.0.13). All processed read mates were aligned to TAIR10 using Bowtie (version 1.0.0) with -m 0 to keep unique mapped reads.
HiC:  Raw reads were first scanned for the presence of bridge-linker with ChIA-PET2 (v0.9.7). The bridge-linker sequence was then trimmed off and the left and right flanking sequences were mapped to TAIR10 with BWA (v0.7.17-1188).
RNA-seq: Low quality reads were removed and adapters were trimmed using Trimmomatic (v0.36). Clean RNA reads were then mapped to TAIR 10 with default parameters using TopHat v2.0.9. The expression level of each gene was normalized to Fragments Per Kilobase of transcript per Million mapped reads (FPKM). Differential gene expression analysis was performed using Cuffdiff. Genes with a ≥ 1.5-fold change and an FDR ≤ 0.05 were identified as differentially expressed genes.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Bedpe
Supplementary_files_format_and_content: FPKM    FPKM_conf_lo    FPKM_conf_hi    FPKM_status

source_name: 24-day-old leaves

growth_protocol: Arabidopsis seeds were sterilized with 5% NaClO containing 0.05% Tween-20 for 15 min and then stratified for 2 days at 4°C in dark. After that, the seeds were plated on half-strength MS medium with the supplementation of 1% sucrose, 0.4% agar and grown for 12 days at 22°C with a 16 h light/8 h dark photoperiod. For 24-day-old seedlings, the plate-grown seedlings were transferred to soil and grown in greenhouse under a 16h light/8h dark photoperiod for additional 12 days.

extract_protocol:
Libraries for GRID-seq were constructed as previously described (Li et al, 2017) with minor modifications. Briefly, after end repair and adenylation of the 3’ ends, the 84-bp DNA fragments were ligated with adaptors using T4 DNA ligase (NEB, M0202M). After PCR amplification, the 210-bp products were purified by using AMPure XP beads. Libraries were paired-end sequenced on an Illumina HiSeqX-Ten platform.
Total RNA was extracted using RNeazy Plant Mini Kit (QIAGEN, 74904). The RNA sequencing (RNA-seq) libraries were generated using NEXTFLEX ®Rapid Directional qRNA-SeqTM Kit (Bioo Scientific, NOVA-5130-01D) according to the manufacturer’s instructions.

treatment_protocol: For heat treatment, 12-day-old wild-type Col-0 seedlings were transferred to a growth chamber set at 37°C and incubated for 30 min. For mock treatment, the seedlings were kept at the growth chamber set at 22°C and incubated for 30 min. For DC3000 treatment, whole leaves of 24-day-old soil-grown plants were syringe-infiltrated with suspensions of DC3000 at OD600 = 0.001. For mock treatment, the leaves were syringe-infiltrated with 10 mM MgSO4. The treated leaves were harvested 24 h after infiltration.

tag: genotype

value: Columbia

value: 24 hour post DC3000 (OD=0.001) treatment


title: 9dpp LEP Igsf11 control 2

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
9dpp_LEP_Igsf11_control_rep2

tag: genotype/variation


title: HiC_Wt_rep1

description: 300-600 nt DNA

data_processing:
GRID-seq: Raw reads from each library were de-duplicated and barcode sequences were removed using FASTX-Toolkit (v0.0.13). All processed read mates were aligned to TAIR10 using Bowtie (version 1.0.0) with -m 0 to keep unique mapped reads.
HiC:  Raw reads were first scanned for the presence of bridge-linker with ChIA-PET2 (v0.9.7). The bridge-linker sequence was then trimmed off and the left and right flanking sequences were mapped to TAIR10 with BWA (v0.7.17-1188).
RNA-seq: Low quality reads were removed and adapters were trimmed using Trimmomatic (v0.36). Clean RNA reads were then mapped to TAIR 10 with default parameters using TopHat v2.0.9. The expression level of each gene was normalized to Fragments Per Kilobase of transcript per Million mapped reads (FPKM). Differential gene expression analysis was performed using Cuffdiff. Genes with a ≥ 1.5-fold change and an FDR ≤ 0.05 were identified as differentially expressed genes.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Bedpe
Supplementary_files_format_and_content: FPKM    FPKM_conf_lo    FPKM_conf_hi    FPKM_status

source_name: 12-day-old seedling

extract_protocol:
Libraries for BL-Hi-C were constructed essentially the same as previously described (Liang et al, 2017), except that the restriction endonuclease AluI was used to digest genomic DNA.
Total RNA was extracted using RNeazy Plant Mini Kit (QIAGEN, 74904). The RNA sequencing (RNA-seq) libraries were generated using NEXTFLEX ®Rapid Directional qRNA-SeqTM Kit (Bioo Scientific, NOVA-5130-01D) according to the manufacturer’s instructions.


title: KRp1-110

value: Normal

value: #N/A

value: cell-free DNA


title: KRp1-111


title: HiC_Wt_rep2

description: 300-600 nt DNA


title: 9dpp LEP Igsf11 KO 1

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
9dpp_LEP_Igsf11_KO_rep1


title: ATAC-seq_B Ctrl

description: Sample 40

value: retroviral transfection


title: GRID_DC3000_rep1

description: ~210 nt DNA


title: 9dpp LEP Igsf11 control 1

description:
LEP_PAC_Igsf11_control_and_KO_rnaseq.counts.txt
9dpp_LEP_Igsf11_control_rep1


title: KRp1-11


title: human retinal progenitor cells, control 2

source_name: retina

growth_protocol: human retinal progenitor cells were culutre expanded at 37C

extract_protocol:
Total RNA was isolated for RNA seq using a RNeasy Mini Kit (Cat# 74104, Qiagen) according to the supplier’s protocol.
Barcoded total transcriptome RNA libraries were prepared by Ion Total RNA-Seq kit v2 (cat#4475936, Ion Torrent, ThermoFisher Scientific) according to manufacturer’s protocols.

value: EV treated


title: KRp1-120


title: KRp1-109

value: GC


title: GRID_Mock_for_DC3000_rep1

description: ~210 nt DNA

value: 24 hour post 10 mM MgSO4 treatment


title: GRID_Mock_for_DC3000_rep2

description: ~210 nt DNA


title: human retinal progenitor cells, control 1


title: KRp1-108


title: KRp1-107

value: HCC

value: I


title: GRID_Heat_rep2

description: ~210 nt DNA

value: 0.5 hour post heat (37℃) treatment


title: 23dpp Igsf11 WT Hi-C repeat1

extract_protocol: sisHi-C libraries were produced as following. Briefly, samples were cross-linked with 1% formaldehyde at room temperature (RT) for 10min. Formaldehyde was quenched with glycine at RT for 10min. The cells were lysed on ice for 50min and the chromatin was solubilized with 0.5% SDS. The nuclei were digested with MboI at 37°C overnight. After fill-in with biotin-14-dCTP, the fragments were ligated at RT for 5.5h. These was followed by reversal of cross-linking, DNA purification, and sonication. Then the biotin-labeled DNA was pulled down with 10?l Dynabeads MyOne Streptavidin C1 (Life Technology). The fragments that included a ligation junction were subjected to Illumina library preparation, which including end repair, dATP tailing and adaptor ligation. 12-15 cycles of PCR amplification were performed with TransStart Fastpfu (Transgene), and the products were purified and size-selected with AMPure XP beads. Fragments ranging from 200 bp to 500 bp were selected.

value: Diplotene spermatocyte

value: 23 dpp

value: wildtype


title: human retinal progenitor cells, experimantal 1


title: KRp1-105

value: PDAC

value: IIA


title: human retinal progentior cells, experimental 2


title: 23dpp Igsf11 KO Hi-C repeat1

value: Abnormal diplotene spermatocyte

value: Igsf11 KO


title: 23dpp Igsf11 KO Hi-C repeat2


title: GRID_Mock_for_heat_rep1

description: ~210 nt DNA

value: Columbia


title: GRID_Mock_for_heat_rep2

description: ~210 nt DNA


title: rpb1-CTD-S2A_rep2

status: Public on Aug 26 2021

city: Oxford

first: Krzysztof

last: Kus

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Libraries were sequenced by Illumina NextSeq 500.
Reads trimmed with fastp (0.20.0)
Reads aligned to concatenated rRNA and tRNA with STAR (2.7.3a)
rRNA and tRNA further filtered with sortmerna (4.2.0)
Unmapped reads were aligned to concatenated genome of S.pombe and S. cerevisiae
Reads were split to each of the organisms keeping unique alignments with samtools and bash command line
Reads which had too distant pairs were further filtered using a custom script
Aligned, filtered files were sorted and indexed using samtools
Bigwig files were prepared and separated by strand with deeptools (bamCoverage  3.5.0, --samFlagInclude 64, -bs 1 with appropriate scaleFactors). A signal from - strand was multiplied by -1.
Genome_build: ASM294v2 from pombase.org
Supplementary_files_format_and_content: bigwig with normalised coverage using spiked-in reads

organism: Schizosaccharomyces pombe

growth_protocol: S. pombe strains were grown in YES media(0.5% yeast extract, 3% glucose, 0.0225% supplements (Histidine, Adenine, Uracil, Leucine, Lysine) to exponential phase at 30°C. Meantime S. cerevisiae cells were grown YPD(1% yeast extract, 2% peptone, and 2% glucose). RNA of S. cerevisiae cells was spiked-in to S. pombe cells.

extract_protocol:
Total RNAs were extracted by a standard hot phenol method.
NEBNext ultra II directional RNA library prep kit for Illumina

value: All Ser2 in CTD of Rpb1 was replaced by alanine


title: 23dpp Igsf11 WT Hi-C repeat2


title: GRID_Wt_rep1

description: ~210 nt DNA


title: Naked DNA UV Replicate 1 resequencing

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
Library strategy: CPD-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences and the final base in the sequencing read were trimmed, using a custom perl script. The resulting fastq files were uploaded as the raw sequencing data for each experiment.
Fastq files were aligned to the human genome (hg19 or hg19+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine (dipy; i.e., TT, TC, CT, CC) were retained in BED files using custom perl script
BED files were converted to WIG file using COUNT function of IGVTools
Genome_build: hg19
Supplementary_files_format_and_content: WIG files containing counts of CPD damage reads filtered for only dipyrimidine mapping sequences (dipy files). Inbetween WIG files use half-integer values to indicate the precise location of the CPD

source_name: NHF1 genomic DNA

growth_protocol: Telomerase-immortalized normal human fibroblast (NHF1) cells were grown in 10 cm plates to confluence in Dulbecco's  modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) at 37 C and 5% CO2.

extract_protocol:
NHF1 genomic DNA was isolated with Puregene Cell and Tissue kits (158388, Qiagen) or GenElute Mammalian Genomic DNA Miniprep kits (G1N70, Sigma), following the manufacturer’s manual.
CPD-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433-1444) and our own CPD-seq publication in yeast (Mao et al, PNAS 2016,113, 9057-9062). Briefly, DNA fragments were ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP.  CPD lesions were cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE1, to generage new 3'-OHs. DNA was then ligated to one of six different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4:ATCGCGAT; A5: TACTGGA; and A6: GAACTGAT) were used to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for ~5 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: For UV treatment of naked DNA, genomic DNA was first isolated from untreated NHF1 cells. The purified DNA was spotted on a clean microscope cover glass, 10 ul in each spot, and the glass with DNA spots was irradiated with UV light. The irradiated DNA was collected and used for CPD-seq library preparation.

value: UV irradiated 80 J/m2

tag: repair time


title: KRp1-10

data_processing:
For each plasma sample, after trimming adaptor and low-quality bases, we use BSMAP (2.90) to align bisulfite sequencing reads to hg19 human genome assembly. The methylation ratio of CpG site is calculated by the methratio.py script (from BSMAP package). The CpG methylation ratios supported by less than 4 reads are discarded before the downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: methratio output produced by using methratio.py of BSMAP

value: cell-free DNA


title: ATACseq_VTA2_DN

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

data_processing:
For bulk mESC ATAC-seq, paired-end reads were mapped to the mouse genome (mm10) using Bowtie with the following parameters: --minins 25 --maxins 2000 --no-discordant --dovetail --soft-clipped-unmapped-tlen. Low quality mapped reads (MQ < 30) and mitochondrial reads were removed. Duplicated reads were removed with Sambamba115 (version 0.6.8). Reads passing quality checks were converted to BAM format for further analyses. Next, dimensionality reduction was performed using the Latent semantic indexing (LSI) dimensionality reduction method from ArchR, with default parameters (except: iterations = 10, resolution =0.2, varFeatures = 60000). The ArchR addHarmony function was ysed to run the Harmony algorithm for batch correction with default parameters, followed by clusters calling. Gene scores were determined as specified by ArchR116. DNs were identified as the cluster with higher gene scores for Th, a well-known DN marker, and confirmed by additional DN marker expression (e.g. Lmx1b, Foxa2, Foxa1, Slc6a3). The DN cluster is composed of 216 cells in total (113 from VTA-1 and 103 from the VTA-2). UMI duplicates were collapsed to one fragment. To visualize an approximation for gene expression, gene scores were calculated using the createArrowFiles (addGeneScoreMat = TRUE) function in ArchR.
For VTA snATAC-seq, paired-end reads were demultiplexed and mapped to the mouse genome (mm10) using the 10X Genomics Cellranger software. The two VTA snATAC-seq libraries were analyzed using ArchR software116. Doublets were removed following default parameters in ArchR. Next, low-quality cells (identified as TSS enrichment score < 4 and < 2500 unique fragments per cell) were removed for further analyses. Next, dimensionality reduction was performed using the Latent semantic indexing (LSI) dimensionality reduction method from ArchR, with default parameters (except: iterations = 10, resolution =0.2, varFeatures = 60000). The ArchR addHarmony function was ysed to run the Harmony algorithm for batch correction with default parameters, followed by clusters calling. Gene scores were determined as specified by ArchR116. DNs were identified as the cluster with higher gene scores for Th, a well-known DN marker, and confirmed by additional DN marker expression (e.g. Lmx1b, Foxa2, Foxa1, Slc6a3). The DN cluster is composed of 216 cells in total (113 from VTA-1 and 103 from the VTA-2). UMI duplicates were collapsed to one fragment. To visualize an approximation for gene expression, gene scores were calculated using the createArrowFiles (addGeneScoreMat = TRUE) function in ArchR.
Genome_build: mm10

source_name: dopaminergic neurons

extract_protocol: For collection of single-nucleus ATAC-seq (snATAC-seq), male C57Bl/6Nl (RRID: IMSR_CR:027; WT) mice, ages 9 weeks, was sacrificed by cervical disolation. Brain was removed and the tissue containing the midbrain VTA was dissected from each hemisphere at room temperature and rapidly frozen on dry ice. Frozen midbrain was kept at -80C until further processing. 10x Genomics scATAC-seq library was generated from midbrain VTA according to the 10X Genomics manual “Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Rev B” for flash frozen tissue with minor adjustments. Briefly, 500 uL 0.1X lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% Nonidet P40 Substitute 0.001% Digitonin) was added to the frozen samples and immediately homogenized using a pellet pestle (15x), followed by 5 min incubation on ice. The lysate was pipette mixed 10x, then incubated 10 min on ice. Finally, 500 uL of chilled wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 2 mM MgCl2, 1% BSA, 0.1% Tween-20) was added to the lysed cells, and the suspension was passed through 30 uM CellTrics strainers (Th Geyer, cat# 7648779) The final ~500 l nuclei suspension was stained with DAPI (final concentration 0.03 ug/mL) for ~5 min.   Around 200,000 DAPI positive events were sorted using a BD FACSAria III Flow Cytometer with 70µm nozzle configuration with sample and sort collection device cooling set to 4°C into 300 l Diluted Nuclei buffer (commercial buffer from 10X Genomics) in a 1,5mL Eppendorf tube. A first gate excluded debris in a FSC/SSC-plot and a consecutive, second gate in a DAPI-A/DAPI-H-plot was used to exclude doublets and nuclei with incomplete DNA content. The collected nuclei were centrifuged at 500g for 5 min at 4°C and resuspended in 20µl Diluted Nuclei Buffer. The nuclei concentration was determined using a Countess II FL Automated Cell Counter in DAPI fluorescence mode. snATACseq libraries were prepared following the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 User Guide. Briefly, nuclei were loaded on a microfluidics chip together with RT reagents, beads with oligo-dT tags and oil to create an emulsion. Afterwards the reverse transcription reaction takes place inside the droplets. The barcoded cDNA is recovered from the emulsion, amplified and cleaned using a bead purification process. The cDNA is then using for library construction including enzymatic fragmentation, adapter ligation and sample index PCR. Libraries were sequenced with either an Illumina NextSeq 500 machine using paired-end 75 bp reads (for VTA-1, 150 cycles), or by NovaSeq 6000 using paired-end 75 bp reads (for VTA-2, 100 cycles).

value: 9 w

tag: Sex

value: M

value: midbrain ventral tegmental area

value: dopaminergic neurons


title: NHF1 No UV

data_processing:
library strategy: UVDE-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A4 and A5 barcodes, and the barcode sequences and the final base in the sequencing read were trimmed, using a custom perl script. The resulting fastq files were uploaded as the raw sequencing data for each experiment.
Fastq files were aligned to the human genome (hg19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine (dipy; i.e., TT, TC, CT, CC) were retained in BED files using custom perl script
BED files were converted to WIG file using COUNT function of IGVTools or custom perl scripts
Genome_build: hg19
Supplementary_files_format_and_content: WIG files containing counts of 6-4PP damage reads filtered for only dipyrimidine mapping sequences (dipy files). Inbetween WIG files use half-integer values to indicate the precise location of the 6-4PP

source_name: NHF1 cells

extract_protocol:
NHF1 genomic DNA was isolated with GenElute Mammalian Genomic DNA Miniprep kits (G1N70, Sigma), following the manufacturer’s manual.
6-4PP-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433-1444) and our own UVDE-seq publication in yeast (Laughery et al, Cell Reports 2020,33, 108401). Briefly, DNA fragments were ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-GTP.  CPD lesions were cleaved with CPD photolyase, afterwhich 6-4PP lesions were cleaved with UVDE. DNA was then ligated to different barcoded A adaptors ( A4:ATCGCGAT; A5: TACTGGA) to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for ~8 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Once confluent, 2mL PBS was pipetted onto cells and cells were exposed to 500J/m^2 UVC light. Cells were then treated with trypsin to digest cell adhesions,neutralized with DMEM+10% FBS, and transferred to a 15mL conical tube and pelleted at 400xg for 4 minutes.

value: human skin fibroblasts (NHF1) cells


title: WT_rep1

source_name: WT

value: Wild-type strain


title: human retinal progenitor cells, experimental 3

value: EV treated


title: GRID_Heat_rep1

description: ~210 nt DNA

value: 0.5 hour post heat (37℃) treatment


title: GRID_Wt_rep2

description: ~210 nt DNA


title: KRp1-106

value: EAC

value: #N/A


title: cerevisiae_freeMNase_rep1B

city: Seattle

first: Eric

middle: Jan

last: Foss

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
S. cerevisiae, wildtype (no MCM-ChEC construct)
factor-agnostic DNA binding S. cerevisiae protein footprints identified by exogenously added MNase

data_processing:
align using bwa with -n option set to 1; reads that map to more than one location are arbitrarily assigned to one of those locations; in case of mouse, align to both the standard mm10 genome build and to mm10 genome with single nucleotide substitutions from spretus genome (provided here as a fasta file)
picard CleanSam
picard SortSam
picard FixMateInformation
picard AddOrReplaceReadGroups
picard ValidateSamFile
choose only (1) perfect matches to mm10 that do not have perfect matches to mm10musculusSNPStospretusSNPs (musculus); or (2) perfect matches to mm10musculusSNPStospretusSNPs that do not have perfect matches to mm10 (spretus); or (3) restrict fragment length (TLEN designation in sam file format) to appropriate size range, if called for
calculate per-base-pair coverage with BedTools' genomecov with -d and -split options
Genome_build: mm10 (musculus); sacCer3 (S. cerevisiae); mm10 with single nucleotide substitutions from spretus SPRET_EiJ (spretus); Schizosaccharomyces_pombe_ASM294v2 (S. pombe); hg38 (human)
Supplementary_files_format_and_content: bedgraph files or txt files with coverage for single base pairs or intervals, as indicated; 1 fasta format file with musculus genome, except with single nucleotide substitution differences replaced with spretus sequence

organism: Saccharomyces cerevisiae

source_name: Antonio Bedalov

growth_protocol:
Yeast: All S. cerevisiae strains were in S288C background. S. cerevisiae experiments were carried out using standard YPD (yeast peptone dextrose) medium [2% (wt/vol) glucose, 1% yeast extract, 2% (wt/vol) peptone]. S. pombe experiments were carried out in Yeast Extract Dextrose (YES); logarithmically growing cells were arrested in early S-phase by adding 15 mM hydroxyurea and incubating for 3 hours.
Mammalian: Cells were transduced with lentiviral supernatant containing plx302-MCM2-FL-MNase, infected cells were selected out on Puromycin (2.5μg/ml) and expanded for further experiments. The expression of tagged MCM2 in HeLa and Patski cells was confirmed by Western blot using anti- MCM2 rabbit polyclonal antibody (HPA031495 Sigma) at 1:1,000 dilution.

extract_protocol: as described:  Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108(45):18318-23. Epub 2011/10/26. doi: 1110731108 [pii]10.1073/pnas.1110731108. PubMed PMID: 22025700; PubMed Central PMCID: PMC3215028.

treatment_protocol:
Yeast MNase-seq: Cells grown to log phase in rich medium, Yeast Peptone Agar with 2% glucose (YEPD) for S. Cerevisiae or Yeast Extract with Supplements with 3% glucose (YES), from an overnight 25 mL culture were synchronized with 3 μM alpha-factor for 1.5 hrs. at 30° C (S. cerevisiae) or with 15 mM hydroxyurea for 2 hours in S. pombe, which are the same conditions we used to prepare cells for ChEC. Arrested cells were crosslinked with 1% formaldehyde for 30 min at room temperature water bath with shaking. Formaldehyde was quenched with 125 mM glycine and cells were centrifuged at 3000 rpm for 5 min. Cells were washed twice with water and resuspended in 1.5 mL Buffer Z (1 M sorbitol, 50 mM Tris-HCl pH 7.4) with 1 mM beta-mercaptoethanol (1.1 μL of 14.3 M beta-mercaptoethanol diluted 1:10 in Buffer Z) per 25 mL culture. Cells were treated with 100 μL 20 mg/mL zymolyase at 30° C for 20–30 min depending on cell density. Spheroplasts were centrifuged at 5000 rpm for 10 min and resuspended in 5 mL NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) supplemented with 500 μM spermidine, 1 mM beta-mercaptoethanol and 0.075% NP-40. Nuclei were aliquoted in tubes with varying concentrations of micrococcal nuclease (Worthington), mixed via tube inversion, and incubated at room temperature for 20 mins. Chromatin digested with 1.9 U– 7.5 U micrococcal nuclease per 1/5th of spheroplasts from a 25 mL culture yielded appropriate mono-, di-, tri- nucleosome protected fragments for next-generation sequencing. Digestion was stopped with freshly made 5x stop buffer (5% SDS, 50 mM EDTA) and proteinase K was added (0.2 mg/ml final concentration) for an overnight incubation at 65° C to reverse crosslinking. DNA was extracted with phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation.
Yeast MCM-MNase: In budding yeast, ChEC-seq was carried out as previously described [33]. Fission yeast with MNases-tagged MCM2 were transferred from log phase to 15 mM HU for 3 hours, and then processed as in budding yeast. Two biological replicas were prepared for each genotype.
Mammalian MCM-MNase: Cells were grown in 6 well plates until >100% confluent, trypsinized and washed with a Wash Buffer (20mM HEPES, 110mM Potassium Acetate, 5mM Sodium Acetate, pH to 7.3 with NaOH). Cells were permeabilized with 0.02% digitonin in the Wash Buffer along with protease inhibitors (Roche # 04693159001) for 5 mins at RT. CaCl2 was added to a final concentration of 2.5mM for differing amounts of time, as indicated. The MNase activity was stopped by adding equal volume of a 2X Stop Buffer (400mM NaCl, 20mM EDTA, 4mM EGTA, 2% SDS). Proteinase K was added to a final concentration of 0.4mg/ml and samples incubated for 1 hr at 50° C. DNA was isolated using standard Phenol:Chloroform extraction and air dried DNA pellets resuspended in 0.1X TE (pH 8). All samples were treated with RNase A (0.3 μg/ml) before being processed for library preparation. Two biological replicas were prepared for both human and mouse cells.
Mouse replication: Patski cells were stained with propidium iodine and sorted according to DNA content into G1 and S-cells using flow cytometry. DNA was extracted from each cell fraction, fragmented by sonication and sequenced.

tag: sample type

value: MNase-seq

value: free MNase (MNase-seq)


title: rpb1-CTD-S2A_rep1


title: cerevisiae_MCM6ChEC_rep1

description:
S. cerevisiae with MCM6-ChEC construct
MCM6 binding sites in S. cerevisiae determined by MCM6-ChEC in cells arrested in G1 with alpha  factor

value: MCM6-ChEC, rep1

value: calcium-treated DNA (ChEC)


title: cerevisiae_MCM4ChEC_rep1

description:
S. cerevisiae with MCM4-ChEC construct
MCM4 binding sites in S. cerevisiae determined by MCM4-ChEC in cells arrested in G1 with alpha  factor

value: MCM4-ChEC, rep1


title: KRp1-100

source_name: PDAC

value: PDAC


title: NHF1 UV 0hr

value: UV irradiated 500 J/m2


title: cerevisiae_MCM2ChEC_rep1

description:
S. cerevisiae with MCM2-ChEC construct
MCM2 binding sites in S. cerevisiae determined by MCM2-ChEC in cells arrested in G1 with alpha  factor

value: MCM2-ChEC, rep1


title: WT_rep2


title: cerevisiae_MCM2ChEC_rep2

value: MCM2-ChEC, rep2


title: Surf1-/- injured, rep 3

city: Dallas

first: Peter

middle: M

last: Douglas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

description:
Collected 2 hour post treatment
KO_3_I2h

data_processing:
Basecalling and trimming were performed using CLC Genomics Workbench ver. 9.5
Sequences were mapped to the whole Mus musculus genome using CLC ver. 9.5.
Expression values and Reads per kilobase million (RPKM) were calculated according to default CLC settings.
Genome_build: mm39
Supplementary_files_format_and_content: excel file contains RPKM values for each transcript

source_name: Brain

extract_protocol:
Whole brains were harvested and flash frozen in liquid nitrogen. RNA was extracted using Trizol with freeze/thawing and vortexing. RNA was later enriched for mRNA using oligo(dt) beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice received closed head traumatic brain injury with a weight drop device.

value: brain

value: 10 weeks old

value: Closed head TBI


title: Surf1-/- injured, rep 1

description:
Collected 2 hour post treatment
KO_1_I2h


title: WT grown  in phosphate enriched media, replicate 1

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

country: India

institute: Bose Institute

description: Sample 2_3

hyb_protocol: hybridization was done using Agilent's In situ Hybridization kit 5188-5242 on Agilent SureScan Microarray Scanner G2600D.

scan_protocol: not provided

data_processing: Normalization has been done using GeneSpring GX 12.0 Software.  Data analysis was carried out by Genotypic Technology, Bangalore, India.

organism: Mycobacterium tuberculosis

label_protocol: 500ng RNA was labeled with Agilent's Quick-Amp labelling kit (p/n5190-0442).T7 promoter based-linear amplification was performed  to generate labeled complementary RNA (one - color Microarray-based gene expression analysis)

growth_protocol: Mtb strains (H37Rv or its isogenic  DregX3) was initially grown to log phase in MiddleBrook 7H9 broth containing 10% ADC

extract_protocol: RNA was extracted by homogenising in a bead beater  and purified with Qiagen RNeasy kit

treatment_protocol: Log phase cells were  further grown in phosphate limited or   phosphate enriched  MB7H9 for 72 hours at 37◦C under shaking

value: WT

tag: media

value: phosphate enriched media


title: DregX3 grown in phosphate enriched media, replicate 1

description: Sample  2_1


title: cerevisiae_freeMNase_rep1A


title: Surf1-/- uninjured, rep 3

description:
Collected 2 hour post treatment
KO_3_C2h


title: Surf1-/- uninjured, rep 2

description:
Collected 2 hour post treatment
KO_2_C2h


title: DregX3 grown in phosphate enriched media, replicate 2

description: Sample  2_2


title: Surf1+/+ injured, rep 4

description:
Collected 2 hour post treatment
WT_4_I2h


title: Surf1+/+ injured, rep 2

description:
Collected 2 hour post treatment
WT_2_I2h


title: Surf1-/- injured, rep 2

description:
Collected 2 hour post treatment
KO_2_I2h


title: Surf1-/- uninjured, rep 1

description:
Collected 2 hour post treatment
KO_1_C2h


title: Surf1+/+ injured, rep 3

description:
Collected 2 hour post treatment
WT_3_I2h


title: Surf1-/- injured, rep 4

description:
Collected 2 hour post treatment
KO_4_I2h


title: regX3-inactivated Mtb (DregX3) grown in phosphate limited media, replicate 1

description: Sample  1_3

value: phosphate limited media


title: WT grown  in phosphate limited media, replicate 2

description: Sample 1_2


title: cerevisiae_MCM2ChEC_HU_rep1

description:
S. cerevisiae with MCM2-ChEC construct
MCM2 binding sites in S. cerevisiae determined by MCM2-ChEC in cells arrested hydroxyurea (HU)

value: MCM2-ChEC, HU, rep1


title: Surf1+/+ uninjured, rep 3

description:
Collected 2 hour post treatment
WT_3_C2h


title: Surf1+/+ injured, rep 1

description:
Collected 2 hour post treatment
WT_1_I2h


title: 45_16B_AS970_Kidney

first: Megan

last: Maurano

state: Washington

address: 750 Republican St, Building E

department: Immunology

institute: University of Washington

data_processing:
trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30, using Galaxy FASTQ Trimmer tool v1.0.0
remaining adaptor sequence was trimmed using  FastqMcf (v1.1.2)
trimmed reads aligned with STAR aligner (v2.4.2a) to GRCm38 reference genome with gene annotations from ensembl release 91
Gene counts were generated using HTSeq-count (v0.4.1)
Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney

extract_protocol:
Liver, Kidney, and Cerebellum were removed, and frozen in TRIzol reagant. RNA was extracted using a doubleprimed Directzol RNA extraction kit, with Dnase digestion.
Libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.

value: Kidney

value: post natal day 23


title: Mtb wild type (WT) grown  in phosphate limited media, replicate 1

description: Sample  1_1


title: 43_15C_AS969_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: Surf1-/- uninjured, rep 4

description:
Collected 2 hour post treatment
KO_4_C2h


title: 46_16C_AS970_Cerebellum


title: DregX3 grown in phosphate limited media, replicate 2

description: Sample  1_4


title: WT grown  in phosphate enriched media, replicate 2

description: Sample  2_4


title: 42_15B_AS969_Kidney


title: 40_14C_AA460_Cerebellum


title: 41_15A_AS969_Liver

source_name: Liver

value: Liver


title: 39_14A_AA460_Liver


title: 36_13A_AA458_Liver


title: 34_12B_AC530_Kidney


title: 37_13B_AA458_Kidney


title: Surf1+/+ uninjured, rep 2

description:
Collected 2 hour post treatment
WT_2_C2h


title: Surf1+/+ uninjured, rep 1

description:
Collected 2 hour post treatment
WT_1_C2h


title: 29_10C_AC407_Cerebellum


title: 35_12C_AC530_Cerebellum


title: 32_11C_AC533_Cerebellum


title: 44_16A_AS970_Liver


title: 28_10B_AC407_Kidney


title: 33_12A_AC530_Liver


title: 25_9B_AC405_Kidney


title: 23_8C_AC404_Cerebellum


title: 22_8B_AC404_Kidney


title: 24_9A_AC405_Liver


title: 30_11A_AC533_Liver


title: 20_7C_AC403_Cerebellum


title: 26_9C_AC405_Cerebellum


title: 21_8A_AC404_Liver


title: 18_7A_AC403_Liver


title: 19_7B_AC403_Kidney


title: 38_13C_AA458_Cerebellum


title: 17_6C_P094-6_Cerebellum


title: 27_10A_AC407_Liver


title: 16_6B_P094-6_Kidney


title: 12_4C_P094-4_Cerebellum


title: 15_6A_P094-6_Liver


title: 13_5B_P094-5_Kidney


title: 10_4A_P094-4_Liver


title: 31_11B_AC533_Kidney


title: 9_3C_P094-3_Cerebellum


title: 2_1B_P094-1_Kidney


title: 14_5C_P094-5_Cerebellum


title: 11_4B_P094-4_Kidney


title: 7_3A_P094-3_Liver


title: 8_3B_P094-3_Kidney


title: 6_2C_P094-2_Cerebellum


title: 4_2A_P094-2_Liver


title: 5_2B_P094-2_Kidney


title: ACE2 63-3 [AVP_63_3]

city: Hangzhou

first: Bocheng

last: Xu

state: China

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

institute: Zhejiang University

data_processing:
The raw data were further processed to remove the low-quality reads.
The miRNA was screened based on the length of the transcripts.
The interval between 18 and 26 nt was selected based on the miRbase and mirdeep2.
Biological function of differentially expressed (DE)-miRNAs was predicted with the target gene through GO and KEGG analyses.
For an intuitive representation of the relation network between gene and miRNA, the regulation pattern was constructed with cytoscape2.
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: 293T_antiviral peptide

extract_protocol:
RNA extracted from 293T cells using Trizol reagent. Total amount and integrity of RNA were accurately detected with an Agilent RNA 6000 Nano Kit of the Bioanalyzer 2100 system.
miRNA Libraries were constructed by NEBNext Multiplex small RNA Library Prep Set, followed by sequencing on Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA).

tag: cell line

value: human embryonic kidney (HEK) 301T cells

value: antiviral peptide


title: ACE2 62-1 [AVP_62_1]

value: human embryonic kidney (HEK) 296T cells


title: Liver Vehicle_1

city: Yangzhou

first: Demin

last: Cai

address: Daxue South Road 88

institute: Yangzhou University

data_processing:
The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow. Sequence reads were mapped to mm9 assembly with BWA and Bowtie software. The Cufflinks package was used for transcript assembly, quantification of normalized gene and isoform expression, and analysis of differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed a normal chow diet for one week for acclimation and were then randomized into four groups (n = 6): the first group received a chow diet with linoleic acid supplementation (LA, 1.5% w/w) as control/Veh (vehicle injections were applied when appropriate), the second group received a diet with CLA (1.5% w/w), the third group received the LA diet with i.p. injection of the PPARα antagonist GW6471 (G5045, Sigma, 20 mg kg-1 body weight) daily, and the last group received the CLA dietary treatment (1.5% w/w) for 28 days with i.p. injection of GW6471.

value: Kunming

value: Vehicle

tag: tissue


title: 3_1C_P094-1_Cerebellum

tag: age


title: 1_1A_P094-1_Liver


title: ACE2 62-3 [AVP_62_3]

value: human embryonic kidney (HEK) 298T cells


title: Glioma stem cells - MK1

city: Cleveland

first: Kui

last: Zhai

state: Ohio

address: 9620 Carnegie Ave n building, Cleveland, OH 44106

department: Cancer Biology

institute: CCF

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.FASTQ format described by four lines:@HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGTNAAGAACACGTTCGGTCACCTCAGCACACTTGTGAATGTCATGGGATCCAT+#55???BBBBB?BA@DEEFFCFFHHFFCFFHHHHHHHFAE0ECFFD/AEHHLine 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).Line 2 is the raw sequence letters.Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.The details of Sequencing identifier of Illumina are as follows:(1) HWI-ST1276:71 HWI-ST1276,Instrument – unique identifier of the sequencer; 71,run number – Run number on instrument(2) C1162ACXX:1:1101:1208:2458 means the coordinate of read on C1162ACXX(Flowcell ID)flowcell,line 1, 1101 tile is(x=1208,y=2458)(3) 1:N:0:CGATGT the first number is 1 or 2, 1 means single reads or the first read of paired ends, 2 means the second of paired ends; the second letter means whether reads is adjusted(Y means yes, N means no); the third number represent the number of Control Bits in sequence; six bases on the fourth place is Illumina index sequence. For RNA-seq technology, sequencing error rate distribution has two features. Error rate grows with sequenced reads extension for the consumption of sequencing reagent. The phenomenon is common in the Illumina high-throughput sequencing platform (Erlich Y, Mitra PP et al.2008; Jiang L, Schlesinger F et al.2011.). The first six bases have a relatively high error rate. The reason is incomplete binding of the random hex-primers and RNA template in cDNA synthesis (Jiang et al.). In general, a single base error rate should be lower than 1%.GC-content is used to detect potential AT/GC separation.The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. In order to avoid this, it's necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows:(1) Remove reads containing adaptors;(2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.RNA-seq Adapter information:NEBNext® UltraTM RNA Library Prep KitRNA 5' Adapter(5'Adaptor)5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTRNA 3' Adapter(3'Adaptor,The underlined 6bp bases is Index)5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG  Genome_build: hg19 Supplementary_files_format_and_content: MS Excel format containing raw counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count and  FPKM values for each Sample

source_name: Glioma stem cells_MK8931-treated

growth_protocol: GSCs were cultured in GSC medium contaning 1% penicillin/streptomycin in a humidified chamber under 5% CO2 at 37 °C.

extract_protocol:
Total RNA samples were extracted from GSCs by using the PureLinkTM RNA Kit (ThermoFisher, 12183020)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GSCs were treated by MK-8931 or vehicle for 3 dyas

value: GBM

value: Glioma stem cells


title: ACE2 63-2 [AVP_63_2]

value: human embryonic kidney (HEK) 300T cells


title: ACE2 62-2 [AVP_62_2]

value: human embryonic kidney (HEK) 297T cells


title: ACE2 63-1 [AVP_63_1]

value: human embryonic kidney (HEK) 299T cells


title: GM-Hypo01x-R1

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2 and the iterative mapping approach described in Imakaev et al. 2012
Filtering was carried out using the dekkerlab-cMapping pipeline available on github https://github.com/dekkerlab/cMapping
All sequencing runs from each replicate were mapped separately, then combined for iterative correction and binning performed using method described by Imakaev et al. and implemented in https://github.com/dekkerlab/cMapping
Genome_build: hg19
Supplementary_files_format_and_content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 10 kb, 20 kb, 40 kb, 100 kb, 250 kb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 2.5 Mb bin size

source_name: GM12878 cells

growth_protocol: GM12878 cells were maintained and split according to Coriell SOPs.

extract_protocol:
Hi-C experiments were performed on 10-20 million cells for each condition.  Crosslinking was performed with 1% formaldehyde pre-mixed with the corresponding appropriate buffer (1x HBSS, or 1 mM EDTA + 10 mM HEPES) immediately before addition to the plates of nuclei.  After 10 minutes, crosslinking was quenched with glycine, and plates of crosslinked nuclei were washed in the same buffer corresponding to their expansion or contraction condition.  It was not possible to harvest and collect nuclei by scraping and centrifugation due to the fragility of the nuclei, particularly in the expanded case, so nuclei were lysed directly in plates by aspirating all liquid and then adding 1.8 mL of 0.3% SDS in 1x NEB2 buffer (New England Biolabs) per 10 cm dish. Dishes were incubated with gentle agitation at 37oC for 30 min.  Crosslinked material was then removed the plate by scraping. If more than one plate was to be combined to obtain enough cells, the SDS-cell mixture scraped from the first plate was transferred to the second plate for another round of incubation, so that cells from all plates were combined into a final volume of less than 3 mL.  SDS was sequestered by addition of 1.8% Triton (final concentration).  Crosslinked complexes were then divided into aliquots of 560 uL each to match other Hi-C protocols, and were then subjected to digestion with HindIII overnight (500 U per 560 uL aliquot), biotin fill-in, and dilute ligation as previously described (Belton et al. 2012).
After streptavidin enrichment of biotinylated ligation junctions,  Illumina paired-end adapters were ligated onto the DNA ends and then the fragments were PCR amplified.

treatment_protocol: GM12878 nuclei were isolated with the following approach:  1x10^8 cells were collected by centrifugation (200xg, 5 minutes, room temperature) and then washed twice with 10 mL ice-cold 1X dPBS and then twice with 5 mL ice cold Nuclei Buffer (NB) (10 mM PIPES pH 7.4, 2 mM MgCl2, 10 mM KCl, 1mM DTT, H2O pH 7.4) containing protease inhibitors (Thermo Scientific).  After final wash and spin, the cell pellet was resuspended in 10 mL NB + 0.06% NP-40, vortexed gently, and then allowed to equilibrate on ice for 10 minutes. Cells were then homogenized on ice using a Dounce homogenizer (Pestle A) with 10 slow strokes.  To remove excess cellular material, 5 mL of lysed cell mixture was layered on top of a 20 mL sucrose cushion: 30% sucrose in NB and centrifuged for 10 minutes at 730xg. The supernatant and interface was carefully removed and the pellet containing nuclei was resuspended in either 1x Hank’s Balanced Salt Solution (HBSS: 1.26 mM CaCl2, 0.49 mM MgCl2, 0.41 mM MgSO4, 5 mM KCl, 0.44 mM KH2PO4, 4.17 mM NaHCO3, 137.9 mM NaCl, 0.34 mM Na2HPO4, 5.56 mM D-Glucose) and were allowed to settle and attach to poly-D-lysine coated dishes at 4 C for several hours or overnight.

tag: condition

value: Isolated nuclei expanded by incubation in 0.1x HBSS for 1 hour, 4 degrees C

value: RPMI, 15 percentFBS, 100 micrograms/mL penicillin-streptomycin


title: GM-1xHBSS-R1

value: Isolated nuclei in 1xHBSS


title: ACE2 CON-2 [H2O_2]

value: human embryonic kidney (HEK) 294T cells

value: control


title: GM-HBSSpostEDTA-R1

value: Isolated nuclei after expansion in 1 mM EDTA for 1 hour, returned to 1xHBSS for 20 minutes


title: ACE2 CON-1 [H2O_1]

value: human embryonic kidney (HEK) 293T cells


title: Glioma stem cells - CTL1

source_name: Glioma stem cells_control


title: GM-1xHBSS-R2


title: GM-EDTA-R1

value: Isolated nuclei expanded by incubation in 10 mM HEPES pH 7.4 + 1 mM EDTA for 1 hour, 4 degrees C


title: GM-Ret1x-R1

value: Isolated nuclei after expansion in 0.1x HBSS for 1 hour, returned to 1xHBSS for 20 minutes


title: Relapse sample 3 months after unsuccessful re-exposure to nivolumab

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Single Cell V(D)J R2-only

data_processing:
demultiplexing of illumina BCL files with cellranger mkfastq version 3.1
alignment of sequencing reads to hg38 reference genome using cellranger count version 3.1
calling of single cells using the default parameters in cellranger
identification of TCR and BCR sequences using cellranger vdj version 3.1
Genome_build: hg38
Supplementary_files_format_and_content: filtered feature matrix with gene expression and antibody capture; TCR and BCR sequences in csv file format

source_name: Peripheral blood

extract_protocol:
Ficoll density centrifugation and bead-based dead cell removal
droplet-based scRNA-seq (5' scRNA-seq) using the chromium platform (10x Genomics); surface marker staining using Total-seq C antibodies

value: blood

tag: disease state

value: AML active disease

tag: wbc

value: Progression


title: Glioma stem cells - CTL2

value: GBM

tag: cell type


title: Relapse sample after 1 cycle of nivolumab re-exposure

description: Single Cell V(D)J R2-only


title: ACE2 CON-3 [H2O_3]

value: human embryonic kidney (HEK) 295T cells

tag: treatment


title: Relapse sample 5 months after response

description: Single Cell V(D)J R2-only

value: Relapse


title: AML5.BCR Relapse sample after 1 cycle of nivolumab re-exposure

description: Single Cell V(D)J R2-only


title: Glioma stem cells - MK2

value: Glioma stem cells


title: AML4.BCR Relapse sample 5 months after response

description: Single Cell V(D)J R2-only


title: Baseline sample 6 months before nivolumab

description: Single Cell V(D)J R2-only

value: Baseline


title: AML6.BCR Relapse sample 3 months after unsuccessful re-exposure to nivolumab

description: Single Cell V(D)J R2-only


title: Response sample after 1 cycle of nivolumab

description: Single Cell V(D)J R2-only


title: Response sample after 3 cycles of nivolumab

description: Single Cell V(D)J R2-only


title: AML5.CITE Relapse sample after 1 cycle of nivolumab re-exposure

description: Single Cell 5' R2-only


title: AML6.CITE Relapse sample 3 months after unsuccessful re-exposure to nivolumab

description: Single Cell 5' R2-only


title: AML3.BCR Response sample after 3 cycles of nivolumab

description: Single Cell V(D)J R2-only


title: AML4.CITE Relapse sample 5 months after response

description: Single Cell 5' R2-only


title: AML2.CITE Response sample after 1 cycle of nivolumab

description: Single Cell 5' R2-only


title: AML1.BCR Baseline sample 6 months before nivolumab

description: Single Cell V(D)J R2-only


title: AML5.RNA Relapse sample after 1 cycle of nivolumab re-exposure

description:
Relapse sample after 1 cycle of nivolumab re-exposure
Single Cell 5' R2-only


title: AML2.BCR Response sample after 1 cycle of nivolumab

description: Single Cell V(D)J R2-only


title: AML2.ATAC Response sample after 1 cycle of nivolumab

data_processing:
demultiplexing of illumina BCL files with cellranger-atac mkfastq version 1.2
alignment of sequencing reads to hg38 reference using cellranger-atac count version 1.2
calling of single cells using the default parameters in cellranger-atac
Genome_build: hg38
Supplementary_files_format_and_content: processed fragment files from cellranger-atac count

extract_protocol:
Ficoll density centrifugation, bead-based dead cell removal
scATAC-seq on 10x Chromium platform


title: AML3.CITE Response sample after 3 cycles of nivolumab

description: Single Cell 5' R2-only


title: AML1.RNA Baseline sample 6 months before nivolumab

description:
Baseline sample 6 months before nivolumab
Single Cell 5' R2-only


title: AML1.ATAC Baseline sample 6 months before nivolumab


title: AML4.ATAC Relapse sample 5 months after response


title: AML1.CITE Baseline sample 6 months before nivolumab

description: Single Cell 5' R2-only


title: AML6.ATAC Relapse sample 3 months after unsuccessful re-exposure to nivolumab


title: AML6.RNA Relapse sample 3 months after unsuccessful re-exposure to nivolumab

description:
Relapse sample 3 months after unsuccessful re-exposure to nivolumab
Single Cell 5' R2-only


title: AML5.ATAC Relapse sample after 1 cycle of nivolumab re-exposure


title: AML2.RNA Response sample after 1 cycle of nivolumab

description:
Response sample after 1 cycle of nivolumab
Single Cell 5' R2-only


title: N70-Input

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

description: Input for N70-H3K27ac

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to mouse reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files; Scores represent the RPM value.

source_name: Native tissue from colorectal cancer patient

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606).

value: tumor

tag: chip antibody

value: colorectal cancer


title: N79-Input

description: Input for N79-H3K27ac


title: N77-Input

description: Input for N77-H3K27ac


title: N74-Input

description: Input for N74-H3K27ac


title: N68-Input

description: Input for N68-H3K27ac


title: N75-Input

description: Input for N75-H3K27ac


title: N76-Input

description: Input for N76-H3K27ac


title: N73-Input

description: Input for N73-H3K27ac


title: N78-Input

description: Input for N78-H3K27ac


title: AML4.RNA Relapse sample 5 months after response

description:
Relapse sample 5 months after response
Single Cell 5' R2-only


title: AML3.RNA Response sample after 3 cycles of nivolumab

description:
Response sample after 3 cycles of nivolumab
Single Cell 5' R2-only


title: N65-Input

description: Input for N65-H3K27ac


title: N67-Input

description: Input for N67-H3K27ac


title: N72-Input

description: Input for N72-H3K27ac


title: N60-Input

description: Input for N60-H3K27ac


title: N59-Input

description: Input for N59-H3K27ac


title: N57-Input

description: Input for N57-H3K27ac


title: N62-Input

description: Input for N62-H3K27ac


title: N69-Input

description: Input for N69-H3K27ac


title: N80-Input

description: Input for N80-H3K27ac


title: N63-Input

description: Input for N63-H3K27ac


title: N56-Input

description: Input for N56-H3K27ac


title: N58-Input

description: Input for N58-H3K27ac


title: AML3.ATAC Response sample after 3 cycles of nivolumab


title: N53-Input

description: Input for N53-H3K27ac


title: N66-Input

description: Input for N66-H3K27ac


title: N51-Input

description: Input for N51-H3K27ac


title: N48-Input

description: Input for N48-H3K27ac and N48-H3K4me3


title: N61-Input

description: Input for N61-H3K27ac


title: N45-Input

description: Input for N45-H3K27ac and N45-H3K4me3


title: N49-Input

description: Input for N49-H3K27ac and N49-H3K4me3


title: N55-Input

description: Input for N55-H3K27ac


title: N39-Input

description: Input for N39-H3K27ac and N39-H3K4me3


title: N47-Input

description: Input for N47-H3K27ac and N47-H3K4me3


title: N37-Input

description: Input for N37-H3K27ac and N37-H3K4me3


title: N54-Input

description: Input for N54-H3K27ac


title: N50-Input

description: Input for N50-H3K27ac


title: N42-Input

description: Input for N42-H3K27ac and N42-H3K4me3


title: N46-Input

description: Input for N46-H3K27ac and N46-H3K4me3


title: N35-Input

description: Input for N35-H3K27ac and N35-H3K4me3


title: N36-Input

description: Input for N36-H3K27ac and N36-H3K4me3


title: N44-Input

description: Input for N44-H3K27ac and N44-H3K4me3


title: N33-Input

description: Input for N33-H3K27ac and N33-H3K4me3


title: N31-Input

description: Input for N31-H3K27ac and N31-H3K4me3


title: N43-Input

description: Input for N43-H3K27ac and N43-H3K4me3


title: N52-Input

description: Input for N52-H3K27ac


title: N40-Input

description: Input for N40-H3K27ac and N40-H3K4me3


title: N41-Input

description: Input for N41-H3K27ac and N41-H3K4me3


title: N49-H3K4me3

value: H3K4me3 (Millipore, 04-745)


title: N38-Input

description: Input for N38-H3K27ac and N38-H3K4me3


title: N48-H3K4me3


title: N45-H3K4me3


title: N30-Input

description: Input for N30-H3K27ac and N30-H3K4me3


title: N64-Input

description: Input for N64-H3K27ac


title: N42-H3K4me3


title: N34-Input

description: Input for N34-H3K27ac and N34-H3K4me3


title: N35-H3K4me3


title: N37-H3K4me3


title: N32-Input

description: Input for N32-H3K27ac and N32-H3K4me3


title: N34-H3K4me3


title: N30-H3K4me3


title: N31-H3K4me3


title: N44-H3K4me3


title: T77-Input

description: Input for T77-H3K27ac

source_name: Tumor from colorectal cancer patient


title: T76-Input

description: Input for T76-H3K27ac


title: T73-Input

description: Input for T73-H3K27ac


title: T69-Input

description: Input for T69-H3K27ac


title: N47-H3K4me3


title: N40-H3K4me3


title: N39-H3K4me3


title: T68-Input

description: Input for T68-H3K27ac


title: N36-H3K4me3


title: N38-H3K4me3


title: N33-H3K4me3


title: T64-Input

description: Input for T64-H3K27ac


title: N43-H3K4me3


title: T78-Input

description: Input for T78-H3K27ac


title: T63-Input

description: Input for T63-H3K27ac


title: T80-Input

description: Input for T80-H3K27ac


title: N46-H3K4me3


title: T61-Input

description: Input for T61-H3K27ac


title: T74-Input

description: Input for T74-H3K27ac


title: T79-Input

description: Input for T79-H3K27ac


title: T75-Input

description: Input for T75-H3K27ac


title: T59-Input

description: Input for T59-H3K27ac


title: T62-Input

description: Input for T62-H3K27ac


title: N41-H3K4me3


title: T70-Input

description: Input for T70-H3K27ac


title: T57-Input

description: Input for T57-H3K27ac


title: T71-Input

description: Input for T71-H3K27ac


title: T72-Input

description: Input for T72-H3K27ac


title: N32-H3K4me3


title: T67-Input

description: Input for T67-H3K27ac


title: T65-Input

description: Input for T65-H3K27ac


title: T45-Input

description: Input for T45-H3K27ac and T45-H3K4me3


title: T40-Input

description: Input for T40-H3K27ac and T40-H3K4me3


title: T38-Input

description: Input for T38-H3K27ac and T38-H3K4me3


title: T39-Input

description: Input for T39-H3K27ac and T39-H3K4me3


title: T35-Input

description: Input for T35-H3K27ac and T35-H3K4me3


title: T60-Input

description: Input for T60-H3K27ac


title: T66-Input

description: Input for T66-H3K27ac


title: T56-Input

description: Input for T56-H3K27ac


title: T55-Input

description: Input for T55-H3K27ac


title: T58-Input

description: Input for T58-H3K27ac


title: T32-Input

description: Input for T32-H3K27ac and T32-H3K4me3


title: T30-Input

description: Input for T30-H3K27ac and T30-H3K4me3


title: T48-Input

description: Input for T48-H3K27ac and T48-H3K4me3


title: T54-Input

description: Input for T54-H3K27ac


title: T49-H3K4me3


title: T53-Input

description: Input for T53-H3K27ac


title: T48-H3K4me3


title: T44-Input

description: Input for T44-H3K27ac and T44-H3K4me3


title: T47-H3K4me3


title: T46-Input

description: Input for T46-H3K27ac and T46-H3K4me3


title: T42-Input

description: Input for T42-H3K27ac and T42-H3K4me3


title: T50-Input

description: Input for T50-H3K27ac


title: T47-Input

description: Input for T47-H3K27ac and T47-H3K4me3


title: T36-Input

description: Input for T36-H3K27ac and T36-H3K4me3


title: T37-Input

description: Input for T37-H3K27ac and T37-H3K4me3


title: T39-H3K4me3


title: T41-Input

description: Input for T41-H3K27ac and T41-H3K4me3


title: T37-H3K4me3


title: T45-H3K4me3


title: T34-Input

description: Input for T34-H3K27ac and T34-H3K4me3


title: T31-H3K4me3


title: N29-Input

description: Input for N29-H3K27ac and N29-H3K4me3

value: Colorectal cancer

value: Native tissue


title: N28-Input

description: Input for N28-H3K27ac and N28-H3K4me3


title: T43-Input

description: Input for T43-H3K27ac and T43-H3K4me3


title: T52-Input

description: Input for T52-H3K27ac


title: N26-Input

description: Input for N26-H3K27ac and N26-H3K4me3


title: T33-Input

description: Input for T33-H3K27ac and T33-H3K4me3


title: N27-Input

description: Input for N27-H3K27ac and N27-H3K4me3


title: N24-Input

description: Input for N24-H3K27ac and N24-H3K4me3


title: T34-H3K4me3


title: T31-Input

description: Input for T31-H3K27ac and T31-H3K4me3


title: T49-Input

description: Input for T49-H3K27ac and T49-H3K4me3


title: T38-H3K4me3


title: T41-H3K4me3


title: T46-H3K4me3


title: T42-H3K4me3


title: T43-H3K4me3


title: T35-H3K4me3


title: T30-H3K4me3


title: T32-H3K4me3


title: T44-H3K4me3


title: T33-H3K4me3


title: T40-H3K4me3


title: T51-Input

description: Input for T51-H3K27ac


title: T36-H3K4me3


title: N20-Input

description: Input for N20-H3K27ac and N20-H3K4me3


title: N3-Input

description: Input for N3-H3K27ac and N3-H3K4me3


title: N10-Input

description: Input for N10-H3K27ac and N10-H3K4me3


title: N2-Input

description: Input for N2-H3K27ac and N2-H3K4me3


title: N17-Input

description: Input for N17-H3K27ac and N17-H3K4me3


title: N6-Input

description: Input for N6-H3K27ac and N6-H3K4me3


title: N9-Input

description: Input for N9-H3K27ac and N9-H3K4me3


title: N19-Input

description: Input for N19-H3K27ac and N19-H3K4me3


title: N22-Input

description: Input for N22-H3K27ac and N22-H3K4me3


title: N18-Input

description: Input for N18-H3K27ac and N18-H3K4me3


title: N4-Input

description: Input for N4-H3K27ac and N4-H3K4me3


title: N16-Input

description: Input for N16-H3K27ac and N16-H3K4me3


title: N7-Input

description: Input for N7-H3K27ac and N7-H3K4me3


title: N5-Input

description: Input for N5-H3K27ac and N5-H3K4me3


title: N21-Input

description: Input for N21-H3K27ac and N21-H3K4me3


title: N8-Input

description: Input for N8-H3K27ac and N8-H3K4me3


title: N23-Input

description: Input for N23-H3K27ac and N23-H3K4me3


title: N28-H3K4me3


title: N26-H3K4me3


title: N1-Input

description: Input for N1-H3K27ac and N1-H3K4me3


title: N29-H3K4me3


title: N27-H3K4me3


title: N4-H3K4me3


title: N9-H3K4me3


title: N8-H3K4me3


title: N5-H3K4me3


title: N17-H3K4me3


title: N24-H3K4me3


title: N23-H3K4me3


title: N19-H3K4me3


title: N22-H3K4me3


title: N6-H3K4me3


title: N21-H3K4me3


title: N10-H3K4me3


title: N20-H3K4me3


title: N7-H3K4me3


title: N18-H3K4me3


title: N16-H3K4me3


title: N1-H3K4me3


title: N2-H3K4me3


title: N3-H3K4me3


title: T28-Input

description: Input for T28-H3K27ac and T28-H3K4me3

value: Tumor


title: T21-Input

description: Input for T21-H3K27ac and T21-H3K4me3


title: T19-Input

description: Input for T19-H3K27ac and T19-H3K4me3


title: T26-Input

description: Input for T26-H3K27ac and T26-H3K4me3


title: T16-Input

description: Input for T16-H3K27ac and T16-H3K4me3


title: T24-Input

description: Input for T24-H3K27ac and T24-H3K4me3


title: T8-Input

description: Input for T8-H3K27ac and T8-H3K4me3