title: PHILO, MYC2, 2hJA, rep2

value: anti-H3K9ac (39137, Active Motif)


title: PHILO, TC, Col-0, H3K9ac, 2hJA, rep3

status: Public on Dec 02 2024

type: SRA

city: Piscataway

first: Mark

last: Zander

address: 190 Frelinghuysen Rd

country: USA

institute: Rutgers State University of New Jersey

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie2 (version 2.4.1).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and Col-0 IgG samples as controls.
MYC2 DNA binding peaks were identified with MACS2 (version 2.2.7.1) by comparing two biological replicates of untreated (ctrl) and 2 h JA-treated myc2 MYC2:MYC2-FLAG seedlings.
Assembly: TAIR10
Supplementary files format and content: bigwig, narrowPeak, domain.csv

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 10-day-old whole seedling

growth_protocol: Arabidopsis seedlings were grown for 10 days under long day conditions.

extract_protocol:
Seedlings were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'5' exo-) (New England Biolabs)), adapter ligation(1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).

treatment_protocol: Seedlings were either untreated or treated for the indicated hours with gaseous MeJA.

tag: tissue

value: 10-day-old whole seedling

tag: chip antibody

tag: genotype

tag: treatment

value: 2h JA


title: PHILO, TC, Col-0, H3K9ac, 2hJA, rep2


title: PHILO, MYC2, 2hJA, rep1

value: untreated


title: PHILO, Col-0, H3K4me3, rep3

value: anti-H3K4me3 (#04-475, Millipore Sigma)


title: PHILO, MYC2, ctrl, rep2


title: PHILO, Col-0, IgG, rep1


title: PHILO, MYC2, ctrl, rep1


title: PHILO, Col-0, H3K9ac, rep2


title: PHILO, Col-0, H3K9ac, rep1


title: PHILO, TC, Col-0, H3K9ac, 0.5hJA, rep2

value: 0.5h JA


title: PHILO, TC, Col-0, H3K9ac, ctrl, rep3

value: control


title: regular, Col-0, H3K9ac, rep2


title: PHILO, Col-0, H3K9ac, rep3


title: regular, Col-0, H3K9ac, rep1


title: P46

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2.
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: Rnor_6.0
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) were fed ad lib with a standard rat diet and ad lib tap water. All animal cages were housed in the same room and environment with gestating females and females with litters being housed individually within cages. Conditions were designed to minimize differences that would cause maternal effects. The breeding of unrelated males and females at 70 to 100 days of age within specific exposure lineages (interbreeding) was used to optimize the maternal and paternal lineage contributions to the phenotypes observed. No inbreeding within the colonies was performed. Sixteen unrelated breeding pairs made up the treated lineage F0 generation, so that offspring of subsequent generations could be bred at the F1, F2 F3 and F4 generations without inbreeding.

extract_protocol:
The epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. The tissue was then minced, the released sperm pelleted at 4ºC by centrifuging at 3,000 x g for 10 min, then resuspended in 250 µL NIM buffer and stored at -80ºC. For molecular analysis, an appropriate amount of rat sperm suspension (approximately 50 µL) was used for DNA extraction. Previous studies have shown mammalian sperm heads are resistant to sonication unlike somatic cells. Somatic cell contamination and debris were removed by brief sonication (Fisher Sonic Dismembrator, model 300, power level 25), which destroys the somatic cells, then centrifugation and washing 1-2 times in 1X PBS. The resulting purified sperm pellet was resuspended in 820 µL DNA extraction buffer and 80 µl 0.1M DTT added, then incubated at 65°C for 15 minutes. Proteinase K (80 µl of 20 mg/ml) was added and the sample was incubated at 55°C for 2-3 hours under constant rotation. Protein was removed by addition of protein precipitation solution (300 µl, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500  g for 30 minutes at 4°C. One ml of the supernatant was precipitated with 2 µl of GlycoBlue (Invitrogen, AM9516) and 1 ml of cold 100% isopropanol at -20° overnight. After incubation, the sample was spun at 13,500  g for 30 min at 4°C, then washed with 70% cold ethanol. The pellet was air-dried for about 5 minutes then resuspended in 100 µl of nuclease free water.  For all generations equal amounts of DNA from each individual’s sample was used to produce 6 different DNA pools per lineage and the pooled DNA used for methylated DNA immunoprecipitation (MeDIP).  Each pool containted 10-11 individual rat samples for each treatment group, with the exception of one control pool that only contained 5 individual samples. For the MeDIP procedure, genomic DNA was sonicated and run on 1.5% agarose gel for fragment size verification. The sonicated DNA was then diluted with 1X TE buffer to 400 μl, then heat-denatured for 10 min at 95˚C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100 μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight with rotation at 4˚C. The following day magnetic beads (Dynabeads M280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and for each sample 50 μl of beads were added to the 500 μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h with rotation at 4˚C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250 μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5 μl Proteinase K (20 mg/ml), and incubated for 2-3 hours on a rotator at 55˚C. DNA clean-up was performed using a Phenol-Chloroform-Isoamyl-Alcohol extraction, and the supernatant precipitated with 2 μl of GlycoBlue (20 mg/ml), 20 μl of 5M NaCl and 500 μl ethanol at -20˚C for one to several hours. The DNA precipitate was pelleted at 13,500  g for 30 minutes at 4°C, washed twice with 70% ethanol, then dried and resuspended in 20 μl H2O. DNA concentration was measured in a Qubit apparatus (Life Technologies) with the ssDNA analysis kit (Molecular Probes Q10212).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E770L, New England Biolabs, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Timed-pregnant F0 generation females were mated and on embryonic days 8 through 14 (E8-E14) of gestation were administered daily intraperitoneal injections of the treatment compound (vinclozolin 100mg/kg). Similarly, pregnant F1 females were treated with jet fuel hydrocarbons (250mg/kg JP8), and F2 females were treated with 25 mg/kg DDT (dichlorodiphenyltrichloroethane, Sigma-Aldrich). The F3 and F4 generations were bred without additional treatments during gestation. The F5 generation animals are considered transgenerational, as neither they nor the germ cells that produced them were directly exposed to these toxicants. For control lineage animals, F0 generation pregnant females were treated with vehicle dimethyl sulfoxide (DMSO, Sigma-Aldrich) from E8-E14, the F1 and F2 generations were not treated during pregnancy, and the F3 generation rats were considered to be the control lineage transgenerational generation. No sibling or cousin breeding was used to avoid any inbreeding artifacts. All animals were aged to 1 year for pathology and epigenetic analysis.

tag: cell type

value: Sperm

tag: generation

tag: lineage

value: toxicant exposed


title: P41


title: P42


title: PHILO, Col-0, H3K27me3, rep2

value: anti-H3K27me3 (#39155, Active Motif)


title: P47


title: P40


title: P39


title: P45


title: P43


title: PHILO, Col-0, H3K4me3, rep2


title: P38


title: P48


title: P37


title: P33


title: P34


title: P35


title: P36


title: P31


title: [S. pombe] [Input] [S18A S24A swi6 (851)] [replicate C]

city: San Francisco

first: Bassem

last: Al-Sady

state: CA

address: 513 Parnassus Ave HSW 1501

institute: UCSF

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.39.
first, the custom genome was indexed using the bowtie2-build function of Bowtie2 v2.5.1. Trimmed ChIP-seq reads were aligned to the genome using Bowtie2 v2.5.1.
ChIP-seq reads were then sorted and indexed following SAMtools "view", "sort" and "index" functions. The view function was used this the following flags to remove multi-mappers and PCR duplicates: -bh -F 3844 -f 3 -q 10 -@ 4.
deepTools v3.5.4  bamCoverage function was used to convert sorted, indexed BAM files to bigWig coverage tracks: -b "$bam_file" -o "$filename_without_extension.bw" --binSize 10 --normalizeUsing CPM --extendReads --exactScaling --samFlagInclude 64 --effectiveGenomeSize 13000000
The bigwigCompare tool (deepTools) was used to normalize bigWig files to input.
Normalized bigWig files were loaded into R v4.3.0 using rtracklayer v1.60.1. Bioconductor Gviz v1.44.2  DataTrack, AnnotationTrack, and GenomeAxisTrack functions were used to visualize ChIP -seq signal tracks from input normalized bigWig files.
Assembly: Genome Assembly ASM294v2 with custom chromosome II. The MAT locus was edited to our custom heterochromatin spreading sensor.
Supplementary files format and content: bigWig

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: YES media, 32degreesC, 225RPM shaking

extract_protocol:
Cells fixed in 1% formaldehyde for 15 minutes at 30degreesC in roller drums. Next glycine was added to a final concentration of 0.25M, incubated 5 minutes at 30degreesC in roller drum. Pellets washed twice with cold 1XTBS. Lysate was spun down, pellet was isolated and flash frozen in liquid nitrogen.
Libraries were prepared using Index Primer Set 1 (NEBNext Mulitplex Oligos for Illumina, E7335L, Lot 10172541) and Ultra II FS DNA Library Prep Kit for Illumina (E7805L, Lot 10202083) following the manufacturer’s protocol, “Protocol for FS DNA Library Prep Kit (E7805, E6177) with Inputs </=100 ng (NEB)”. 200 pg of input and IP DNA was used as starting material. Libraries were amplified using 11 cycles via PCR. NEBNext sample purification beads (E6178S, Lot 10185312) were used to clean up PCR-enriched adaptor-ligated DNA. DNA concentration was quantified using a Qubit4 Fluorometer and quality was checked by a 4200 TapeStation instrument (Agilent). Libraries were pooled to equimolar quantities for sequencing.

tag: genotypes

value: no antibody input

value: yeast


title: P32


title: P30


title: [S. pombe] [H3K9me2 ChIP] [S18A S24A swi6 (851)] [replicate C]


title: P29


title: P44


title: [S. pombe] [Input] [S18A S24A swi6 (851)] [replicate B]


title: P28


title: [S. pombe] [H3K9me2 ChIP] [S18A S24A swi6 (851)] [replicate B]


title: [S. pombe] [H3K9me3 ChIP] [S18A S24A swi6 (851)] [replicate B]

value: H3K9me3 (Diagenode, Cat. No. C15500003 Lot No. 003)


title: P27


title: P24


title: [S. pombe] [Input] [S18A S24A swi6 (851)] [replicate A]


title: [S. pombe] [input] [wt swi6 (814)] [replicate C]


title: [S. pombe] [H3K9me2 ChIP] [S18A S24A swi6 (851)] [replicate A]


title: P26


title: [S. pombe] [H3K9me3 ChIP] [S18A S24A swi6 (851)] [replicate A]


title: P25


title: P23


title: [S. pombe] [H3K9me3 ChIP] [wt swi6 (814)] [replicate C]


title: [S. pombe] [H3K9me2 ChIP] [wt swi6 (814)] [replicate C]


title: P20


title: [S. pombe] [H3K9me3 ChIP] [S18A S24A swi6 (851)] [replicate C]


title: P19


title: [S. pombe] [input] [wt swi6 (814)] [replicate B]


title: P18


title: [S. pombe] [H3K9me2 ChIP] [wt swi6 (814)] [replicate B]


title: P21


title: [S. pombe] [H3K9me3 ChIP] [wt swi6 (814)] [replicate B]


title: P16


title: [S. pombe] [H3K9me2 ChIP] [wt swi6 (814)] [replicate A]


title: [S. pombe] [input] [wt swi6 (814)] [replicate A]


title: P15


title: [S. pombe] [Input] [delta swi6 (807)] [replicate C]

value: delta swi6 (807)


title: [S. pombe] [H3K9me3 ChIP] [wt swi6 (814)] [replicate A]


title: P14


title: P13


title: [S. pombe] [H3K9me2 ChIP] [delta swi6 (807)] [replicate C]


title: P22


title: P12


title: P10


title: [S. pombe] [H3K9me3 ChIP] [delta swi6 (807)] [replicate C]


title: [S. pombe] [Input] [delta swi6 (807)] [replicate B]


title: [S. pombe] [H3K9me3 ChIP] [delta swi6 (807)] [replicate B]


title: P8


title: P9


title: [S. pombe] [H3K9me2 ChIP] [delta swi6 (807)] [replicate A]


title: P7


title: P6


title: P17


title: [S. pombe] [H3K9me3 ChIP] [delta swi6 (807)] [replicate A]


title: P4


title: P5


title: Protein_Sah73_S8

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Fresh frozen spatial transcriptome sequencing

library_source: other

data_processing:
Raw sequencing files processed using 10X Genomics Space Ranger to produce fastq files
Fastq files aligned to hg38 reference assembly
Gene and protein expression quantified using spaceranger count with Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv and feature reference Visium_Human_Immune_Cell_Profiling_Panel_v1.0.csv
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: raw_feature_bc_matrix.h5.gz: raw feature barcode matrix in hdf5 format
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene/protein IDs
Supplementary files format and content: matrix.mtx.gz: gene/protein expression count data
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: aligned_tissue_image.jpg.gz:
Supplementary files format and content: cytassist_image.tiff.gz: single field of view image of the tissue section
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv.gz: spatial enrichment of features
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

molecule: protein

organism: Homo sapiens

source_name: liver

extract_protocol:
RNA was extracted from an adjacent 3μm tissue section utilizing the Quick-RNA FFPE kit (Zymo Research, R1008).
Visium CytAssist Spatial Gene Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking. (10X Genomics, User Guide #CG000520,Rev B); Visium CytAssist Spatial Gene and Protein Expression Reagent Kits, (10X Genomics, User Guide #CG000494, Rev B); KAPA Library Quantification Kit, Illumina® Platforms. KK4824 – 07960140001; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome,6.5mm, 4rxns (10X Genomics, PN-1000520); Visium Human Immune Cell Profiling Panel (10X Genomics, PN-1000607)

value: liver

value: AH


title: Protein_Sah80_S4


title: P3


title: Protein_N126_S7

value: non-ALD


title: P2


title: P1


title: Gene_Sah80_S2

library_source: transcriptomic

molecule: polyA RNA


title: P11


title: Protein_N123_S3


title: Tm-2

city: hangzhou

first: xiao

middle: chen

last: wen

address: desheng_road NO.298

country: China

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: ABySS_70bp_45k_152cov_v1（https://www.ncbi.nlm.nih.gov/genome/?term=txid523103[orgn]）
Supplementary_files_format_and_content: tab-delimited text file includes count and FPKM values for each Sample

molecule: total RNA

organism: Trichophyton mentagrophytes

source_name: mycelium

extract_protocol:
For extraction of total RNA, TRIzol Reagent (Invitrogen) was used per manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: SDA drug sensitive plates with Trichoderma concentrations of 0, 10 and 100 UG / ml were prepared respectively. The fungi were inoculated on the medium and cultured for 6 days.

value: mycelium


title: Gene_Sah73_S6


title: Gene_N123_S1


title: Tm-1


title: Tm-10uL-3

value: Trichoderma, 10ug/ml


title: Tm-10uL-2


title: Human_Fibroblast_CTCF

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Barcode adapter sequences removed
Paired-end fastq files were trimmed to 25 bp and mapped to the mm10 or hg38 genome with bowtie2 (options -q -N 1 -X 1000)
Mapped reads were duplicate-filtered using Picard and filtered for mapping quality (MAPQ ≥ 10) using SAMtools.
Reads were converted to bigWig files using deepTools. Heatmaps were generated using deepTools computeMatrix (options -a 2000 -b 2000 -bs 20 --missingDataAsZero) and plotHeatmap
Assembly: mm10/hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Skin

growth_protocol: Human Fibroblasts - Human primary fibroblasts were derived from forearm skin punches and cells were grown in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 4.5 g/L glucose, and 1% Penicillin-Streptomycin solution in a humidified incubator at 37C and 5% CO2. Cells were passaged every 48-72 hours using trypsin and split at a rate of 1:4 with fresh medium. Mouse Oligodendrocytes - Oligodendrocytes (OLs)were derived from Oligodendrcoyte Precursor Cells (OPCs) isolated from 6-7 day old mouse pups by immunopanning. OPCs were grown in DMEM Sato, supplemented with 2% B27, 2 mM-Glutamine, 16 μg/mL putrescine, 6.2 ng/mL progesterone, 5 ng/mL sodium selenite, 100 μg/mL bovine serum albumin, 5 μg/mL insulin, 50 μg/mL Apo-transferrin (Sigma) and 4.2 ng/mL Forskolin in DMEM. For proliferation OPCs were also supplemented with PDGF-AA (10 ng/mL), NT-3 (1 ng/mL) and CNTF (10 ng/mL). OPCs were For differentiation into OLs, cells were transferred to fresh DMEM Sato plus T3 4ng/ml, NT-3 (1 ng/mL) and CNTF (10 ng/mL) and maintained in differentiation medium for four days.

extract_protocol:
Nuclei were isolated from cell populations by incubating cell pellets with a nuclear extraction hypotonic buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5mM spermidine, 0.1% Triton X-100, 20% glycerol, freshly added protease inhibitors) for 10 minutes on ice. Samples were centrifuged and nuclei were flash frozen.
CUT&RUN enriched fragments isolated were used as input for a library build consisting of end repair and adenylation, NEBNext stem-loop adapter ligation, and subsequent purification with AMPure XP beads (Agencourt). Barcoded fragments were then amplified by 17 cycles of high-fidelity PCR and purified using AMPure XP.

treatment_protocol: Not applicable

value: Skin

tag: cell line

value: Primary Fibroblast

value: Oligodendrocyte

value: Wild type

tag: antibody

value: CTCF:Millipore 07-729 (Lot 3429114)


title: [S. pombe] [Input] [delta swi6 (807)] [replicate A]


title: Tm-10uL-1


title: Gene_N126_S5


title: [S. pombe] [H3K9me2 ChIP] [delta swi6 (807)] [replicate B]


title: Human_Fibroblast_IgG

value: IgG


title: RDH42, stim, Vd2

city: Brisbane

first: Zuleima

last: Pava Imitola

state: Queensland

address: 300 Herston road

country: Australia

institute: QIMR Berghofer

data_processing:
Transcriptomic data was processed using STAR aligner, samtools, and HTSeq
Assembly: GRCh38
Supplementary files format and content: data files contain the raw counts obtained by Htseq. Columns are libraries rows are genenames

source_name: Tcells Vd2

extract_protocol:
RNA was extracted from isolated cell population lysates using the QIAGEN PicoPureTM RNA isolation kit (Applied Biosystems™, KIT0204)
RNA sequencing libraries were constructed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (E6420S) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (E6440S).

value: Tcells Vd2

value: stim


title: Tm-3

value: control


title: Tm-100uL-3

value: Trichoderma, 100ug/ml


title: RDH42, unstim, Vd2

value: unstim


title: Tm-100uL-2


title: RDH41, stim, Vd2


title: RDH41, unstim, Vd2


title: Tm-100uL-1


title: Jurkat E6.1, biorep 2

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
The read pairs were firstly quality trimmed by cutadapt (-m 32 -j 4 -q 20 -e 0.25 -a AGATCGGAAGAGCACACGTC -A ATATN{11}AGATCGGAAGAGCGTCGTG).
Then the UMI along with the fixed ATAT spacer sequences were extracted by umi_tools.
In silico converted read pairs (read1 A-to-G, read2 T-to-C) were aligned by HISAT2 against A-to-G converted (for positive strand) and T-to-C converted (for negative strand) reference genome and transcriptome first (key options: -k 5 –fr –rna-strandness FR –no-temp-splicesite –no-mixed). Then the unique alignments were extracted and the in silico converted reads were inverse-transformed to the original format.
The 5’ most ends of read1 were called and the ReCappable-seq pipeline was performed to find out the enriched transcription start nucleotides. Non-conversion rates of the transcription start nucleotides were calculated by A counts over A and G counts.
Assembly: GRCh38
Supplementary files format and content: CSV. For csv output, the columns are chromosone id, 1-based position, strand, numer of A, T, C, G started readas
Library strategy: CROWN-seq

source_name: Jurkat E6.1

extract_protocol:
Cellular total RNA in TRIzol LS (ThermoFisher 10296028) was extracted by Direct-zol RNA Miniprep kit (Zymo #R2070). mRNA was purified by NEBNext Oligo d(T)25 Beads (NEB #E7499) based on mRNA purification from total RNA protocol of Dynabeads Oligo (dT)25 (Ambion #61002).
1.5-5 μg oligo(dT) selected RNA was used as input. RNA was first diluted in 14 μl water. To perform glyoxal protection, 6 µl 8.8 M glyoxal and 20 μl DMSO were then added to the diluted RNA and well mixed. The 40 µl mix was first incubated at 50 ºC for 30 minutes, then 10 μl boric acid was added to the mix. The 50 µl mix was then incubated for an additional 30 minutes at 50 ºC. After protection, the 50 μl protected RNA was mixed with 50 μl deamination buffer (25 μl 1500 mM NaNO2, 4 μl 500 mM MES, pH 6.0, 10 μl 8.8 M glyoxal, and 11 μl water). The deamination reaction was performed at 16 ºC for 8 hours. After deamination, the RNA was recovered by ethanol precipitation. To remove the glyoxal adduct from the RNA, the RNA pallet was dissolved in 50 μl deprotection buffer (500 mM TEAA pH=8.6, 47.5% deionized formamide) and was incubated at 95 ºC for 10 minutes. After incubation, the reaction was brought to 250 μl with water. Converted RNA was purified by ethanol precipitation and eluted in 39 μl water for 5’ end enrichment. The converted RNA was stored at -80 ºC before 5’ end enrichment. To eliminate the contamination of RNA with 5’-triphosphate and 5’-monophosphate, 5 µl 10X CutSmart buffer, 5 µl Quick CIP (5 U/µl) (NEB #M0525L), and 1 µl Superase*IN RNase inhibitor (ThermoFisher #AM2696) were added to the 39 μl converted RNA to set up a dephosphorylation reaction. The dephosphorylation reaction was performed at 37 °C for 30 minutes. The reaction was cleaned up using Zymo RCC-5 column and the RNA was eluted in 42 µl water. To de-cap the m7G capped RNA, a 50 µl decapping reaction was set up by adding 5 µl 10X yDcpS buffer, 2 µl (200 U) yDcpS (NEB #M0463S), and 1 µl Superase*IN to the 42 µl dephosphorylated RNA. The decapping reaction was performed at 37 ºC for 1 hour. This unique decapping enzyme liberates m7GMP, resulting in mRNAs with a 5’-diphosphate. Reaction was cleaned and eluted as before. The reaction was cleaned up using Zymo RCC-5 column and the RNA was eluted in 33.5 µl water. The 5’-diphosphorylated mRNAs were recapped with desthiobiotin-GTP (DTB-GTP, NEB #N0761S) using vaccinia capping enzyme (5 μL VCE buffer, 0.5 μL inorganic pyrophosphatase (NEB #M0361S), 5 μL DTB-GTP (5 mM; NEB N0761S), 50 U VCE, 1 µl Superase*IN) at 37 °C for 4 hour. The reaction was cleaned up using Zymo RCC-5 column and the RNA was eluted in 30 µl water. Now the RNA is ready for streptavidin enrichment. Streptavidin beads (NEB #S1421S) were washed in a high salt wash buffer (10 mM Tris-HCl pH 7.5, 2 M NaCl, 1 mM EDTA) and resuspended in the high salt buffer at 4 mg/mL. To enrich the RNA and tag the 5’ and 3’ end by the specific adapter, the 30 µl recapped RNA was first mixed with 30 µl streptavidin beads and incubated at room temperature for 45 minutes with agitation. Beads were washed twice in high salt buffer, twice in a lower salt buffer (10 mM Tris-HCl pH 7.5, 250 mM NaCl, 1 mM EDTA), and twice in PNK wash buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2, 0.2% Tween). To remove 3’ phosphates resulting from fragmentation during conversion, beads were resuspended in 50 µl PNK reaction without ATP (5 µl 10X PNK buffer, 1 µl T4 PNK (#M0201S), 1 µl Superase*IN, 43 µl water), and incubate at 37 °C for 30 minutes with agitation. The beads were then washed once in PNK wash buffer, once in 2 M NaCl wash, and twice in PNK wash. Next, RNA was ligated to a 74 nt-long 3’ adapter (/5’rApp/AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAAAAAAAAAAAAACCCCCCCCCCAAAAAAAAAAAAAAA/3AmMO/) in the following 40 μl 3’ ligation mix: 4 μL T4 RNA ligase buffer, 2 μl T4 RNA ligase 2 truncated KQ (NEB #M0373L), 1 µl Superase*IN, 2 μl extended-L7 adapter (20 μM stock, see Key Resource table), 16 μl of 50% PEG-8000) and incubated at 25 °C for 2 hours. After incubation, the reaction buffer was removed by washing once with high salt buffer and twice with PNK wash buffer. To remove the exceeded adapter, the beads were incubated in 50 μl adapter digestion reaction (40 μl waater, 5 µl 10X RNA ligase buffer, 1 µl RecJf (NEB #M0264S), 1 5’ Deadenylase (NEB #M0331S), 1 µl Superase*IN) at 30 °C for 15 minutes then at 37 °C for 15 minutes. The beads were washed once with PNK wash, once with high salt buffer and twice with low salt buffer. To elute the DTB labeled RNA, beads were then suspended 30 µl low salt wash buffer containing 1 mM free D-biotin (ThermoFisher #B20656) and incubate at room temperature for 1 hour. The DTB labeled RNA were purified with ethanol-AMPure XP (RNA:beads:ethanol=1:2:3) and elute in 30 µl water. To increase stringency, the streptavidin bead enrichment was repeated omitting enzymatic steps and instead washing three times with high salt and then three times with lower salt wash, and the eluate cleaned again by ethanol-AMPure XP. The DTB-GTP cap was removed using 0.5 U/µl RppH in 1X ThermoPol buffer (NEB #M0356S) and incubating at 37 °C for 1 hour. The resulting 5’-monophosphate RNA fragments were purified by ethanol-AMPure XP and eluted in 10 μl water. 1 μl (10 pmol) reverse transcription primer (AGACGTGTGCTCTTCCGATCT) was pre-annealed to the templates by heating up to 90 °C for 30 seconds, then 65 °C for 5 minutes, and chilled at 4 °C for over 30 seconds. 30 pmol of a 5’ adapter was ligated for 3 hours at 25 °C with 2 U/μl T4 RNA ligase 1 (NEB #M0437M). This RNA adapter contains an 11 nt UMI followed by a fixed sequence (AUAU) at its 3’ end. The UMI allows robust duplicate removal, and the fixed sequence provides an anchor point to correctly identify the first nucleotide of the mRNA. 40 μl ligation product was used. Reverse transcription was carried out at 50 °C for 45 minutes in a 50 μl reaction containing 0.5 mM dNTPs, 5 mM DTT, 20 U RNaseOUT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, and 300 U SuperScript III. To perform indexing PCR, 40 μl Phusion master mix (NEB # M0532L) was added to the reverse transcription product, along with 5 μl i5 indexing primer and 5 μl i7 indexing primer (NEB #E7600S). Cycling conditions were typically 98 °C 2 minutes, then 16 cycles of 98 °C 15 seconds, 65 °C 30 seconds, 72 °C 30 seconds, with a final 5 minute 72 °C extension. Two rounds of 0.9X AMPureXP beads purifications were performed to remove primers.

value: Jurkat E6.1

value: wildtype


title: Jurkat E6.1, biorep 1


title: 3-79 2 DPA epidermis and fiber protoplasts

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Library name: Gb-2DPA

library_source: transcriptomic single cell

data_processing:
Initial mapping and processing was carried out using the Cellranger pipeline. Detailed analysis was carried out in R using the Seurat package. Cells were filtered to include only those with a minimum of 200 distinct features, with >80% of features mapping to the parent genome.
Assembly: Gossypium hirsutum v2.1 VKGJ00000000
Assembly: Gossypium barbadense v1.1 VKDL01000000
Supplementary files format and content: Processed ouput from the 10x cellranger pipeline  with default setting for each sample with the peaks.bed barcodes.tsv and matrix.mtx files readable by Seurat packge in R.

organism: Gossypium barbadense

source_name: Cotton Ovule

growth_protocol: All plants were grown under a natural sunlight a greenhouse at The University of Texas at Austin

extract_protocol:
Ovules were digested in a enzyme mix of cellulase and macerase in 450 mM mannitol for 15 minutes to release protoplasts from the epidermal layers. The ovules were then strained out and the protoplasts were allowed to continue digesting for an additional hour to remove any remaining cell wall debris. To recover the protoplasts, we used density gradient flotation: samples were centrifuged for 2 minutes at 200 g at 4°C to gently pellet the protoplasts, after which all but ~100 ul of the protoplasting buffer was removed, which was mixed with 0.25 volumes chilled Iodixanol (OptiPrep, Sigma-Aldritch, St. Louis, MO) and used to gently resuspend the pellet. 100 ul of chilled 450 mM mannitol was layered atop the denser layer containing iodixanol, and the samples were centrifuged at 200g and 4°C, followed by collecting protoplasts from the top layer.
Libraries were constructed acording to the manufacturer's instructions using the single cell 3' v2 kit (10x Genomics) the the Genome Sequencing and Analysis Facility at UT Austin.

value: Cotton Ovule

tag: age

value: 2 DPA


title: RDH39, unstim, Vd2


title: RDH39, stim, Vd2


title: HepG2, biorep 2


title: RDH26, unstim, Vd2


title: RDH18, stim, Vd2


title: RDH18, unstim, Vd2


title: RDH12, stim, Vd2


title: Huh-7, biorep 2


title: Huh-7, biorep 1


title: HepG2, biorep 1


title: RDH12, unstim, Vd2


title: HCT-116, biorep 1


title: HCT-29, biorep 1


title: HCT-116, biorep 2


title: RDH11, stim, Vd2


title: RDH11, unstim, Vd2


title: HCT-29, biorep 2


title: RDH07, unstim, Vd2


title: K562, biorep 3


title: RDH03, stim, Vd2


title: K562, biorep 2


title: CCD841 CoN, biorep 2

source_name: CCD841 CoN

value: CCD841 CoN


title: RDH03, unstim, Vd2


title: RDH01, stim, Vd2


title: CCD841 CoN, biorep1


title: RDH26, stim, Vd2


title: K562, biorep 1


title: A549 wildtype, biorep 3, techrep 1


title: RDH01, unstim, Vd2


title: RDH42, stim, Monocytes

source_name: Monocytes

value: Monocytes


title: HEK293T PCIF1 knockout, biorep 2, techrep 1

value: PCIF1 KO


title: RDH41, stim, Monocytes


title: HEK293T wildtype, biorep 2, techrep 2


title: RDH42, unstim, Monocytes


title: RDH07, stim, Vd2


title: RDH39, stim, Monocytes


title: HEK293T wildtype, biorep 2, techrep 1


title: RDH41, unstim, Monocytes


title: AR21 Input

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

description: Input for AR21 ICeChIP-seq.

data_processing:
To align reads, a reference genome was first created, consisting of the human genome (GRCh38/hg38) appended by the sequences of each of the nucleosome standard barcodes. Reads were then mapped to this reference genome using Bowtie2 using the sensitive preset and end-to-end alignment options.
Using SAMTools, any reads which were not paired, not mapped in a proper pair, or mapped with a map quality below 20 were then discarded to prevent low-quality mapping or sequencing reads from impacting downstream analyses. Reads were then flattened to create a single mapping from each matched pair of reads, and any mappings with lengths greater than 200bp were also discarded to ensure only mononucleosomes were being analyzed.
Bedgraphs of genome coverage were then generated using BEDTools, and IP and input genome coverage bedgraphs were merged using BEDTools7. The sum of reads across ladder members for each nucleosomal standard was computed for each sample and HMD bedgraphs were then generated from the merged bedgraphs using awk to apply the following formula: HMD (%) = 100% * (IPlocus/INlocus) / (IPbarcode/INbarcode). Error and 95% confidence intervals were computed with Poisson statistics and error propagation from the merged bedgraphs using awk to apply the following formula: 95CI Error (%) = 1.96 * HMD (%) * sqrt(1/IPlocus + 1/INlocus). Bigwig files were generated for visualization using the bedGraphToBigWig tool.
Assembly: hg38_bar_Ca1-17
Supplementary files format and content: Supplementary_files_format_and_content: Bedgraph files all have the form <chromosome> <start> <end> <value>, where the fourth field represents the value of the measurement. Bigwig files are bedgraph files in binary format, appropriate for viewing on a genome browser. Bed files all have the form <chromosome> <start> <end> and represent a list of intervals. Fasta file (with extension .fa) represents the reference genome used in this study, with the human genome (GRCh38/hg38) appended by the DNA barcode sequences used for the semisynthetic nucleosome standards.

growth_protocol: K562 cells were grown in DMEM (Invitrogen) containing 10% (v/v) HyClone FBS Characterized U.S. and 1x Penicillin/Streptomycin. Cells were grown in supplemented medium in suspension in 25 cm-squared vented flasks. The cells were seeded at 100,000 to 200,000 cells per mL and were grown until they reached a density of 1 million cells per mL, at which point they were passaged 1:10. Cells used in ChIP experiments were harvested at a concentration of approximately 1 million cells per mL.

extract_protocol:
K562 cell pellets were washed twice with 5 mL of PBS, then washed twice with 5 mL of Buffer N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 8.5% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized), with each wash consisting of complete resuspension of the pellet, centrifugation at 500 g for 5 minutes at 4°C, and removal of supernatant. The washed pellet was then resuspended in at least 2 packed cell volumes (PCV) of Buffer N and mixed with 1 volume of Lysis Buffer (Buffer N supplemented with 0.6% NP-40 Substitute) and incubated on ice for 10 minutes to lyse cells. The crude nuclei were spun down at 500 g for 5 minutes at 4°C before being resuspended in at least 6 packed nuclear volumes (PNV) of Buffer N and applied to the top of 7.5 mL of Sucrose Cushion N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 30% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized) in a 15 mL centrifuge tube, then spun down at 500 g for 12 minutes at 4°C in a swinging-bucket rotor. The supernatant was discarded after centrifugation, and the pellet was resuspended in approximately 2 PNV of Buffer N. The nuclei were then quantified by diluting 2 uL of nuclei suspension into 48 uL of 2 M NaCl, water-bath sonicating to solubilize DNA, and spectroscopically measuring DNA concentration by Nanodrop measurement, where 1 A280nm¬ = 50 ng/uL chromatin in the measurement sample. After accounting for the 25-fold dilution of the measurement sample, the concentration of the nuclei was adjusted down to 1ug/uL of chromatin. Nuclei were aliquoted into 100 uL aliquots, flash frozen, and stored at -80°C until use. When nuclei aliquots were used, they were first thawed and spiked approximately 1 uL of each barcoded nucleosome standard per 50 ug of chromatin to be used. The nuclei suspension with spiked calibrants was then mixed with a pipette and transferred to a new tube, then warmed to 37°C for 2 minutes. After warming, 1 unit of micrococcal nuclease (MNase) per 4.375 ug of chromatin was added to the nuclei suspension and incubated at 37°C while shaking at 900 rpm for 12 minutes. After incubation, the digestion was stopped by adding 1/9 volume of 10x MNase Stop Buffer (100 mM EDTA, 100 mM EGTA, Filter Sterilized) while slowly vortexing, and nuclei were lysed by adding 5 M NaCl to a final concentration of 600 mM NaCl while slowly vortexing. 66 mg of HAP resin (BioRad, CHTTM Ceramic Hydroxyapatite, Type I, 20 um) per 100 ug of chromatin digested was rehydrated with 200 uL of HAP Buffer 1 (5 mM Sodium Phosphate pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) per 100 ug of chromatin digested. The lysed nuclei were then spun down at 18,000 g for 1 minute to pellet insoluble nuclear debris, and the soluble fraction was added to the rehydrated HAP resin and incubated for 10 minutes on a rotator at 4°C. After incubation, the HAP resin slurry was added to a centrifugal filter unit (Millipore Ultrafree MC–HV Centrifugal Filter 0.45 um) and spun at 1000 g for 30 seconds at 4°C. The HAP resin left on the filter unit was then washed 4 times with 200 uL HAP Buffer 1 and 4 times with 200 uL HAP Buffer 2 (5 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) by spinning at 1000 g for 30 seconds at 4°C. Into a clean tube, the HAP resin was eluted with three elutions of 100 uL HAP Elution Buffer (500 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized). The DNA content of the elution was then quantified spectroscopically with a Nanodrop, and the chromatin concentration was adjusted to 20 ng/uL with ChIP Buffer 1 (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) with 100 ug/mL of BSA. Antibody-bead conjugates were then prepared. 150 uL of the diluted chromatin elution was added to each antibody-bead conjugate and incubated for 15 minutes on a rotator at 4°C. After this incubation, the beads were washed twice with ChIP Buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) and once with ChIP Buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% Sodium Deoxycholate, 0.5% v/v NP-40 Substitute, Filter Sterilized), with a wash consisting of removal of the existing supernatant by use of a magnetic rack, resuspension into 150 uL of buffer, transfer to a new siliconized tube, and incubation on the rotator for 10 minutes at 4°C. After these washes, the supernatant was removed, and the beads were resuspended in ChIP Buffer 1, transferred to a new siliconized tube, then rinsed once with 200 uL of TE before being resuspended in 50 uL of ChIP Elution Buffer and incubated at 55°C for 5 minutes. After incubation, the supernatant was transferred to a new set of siliconized tubes, and the beads were discarded. To each supernatant was then added 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. 15 uL of Input DNA was also diluted to 50 uL with 35 uL of ChIP Elution Buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% w/v SDS, Filter Sterilized) and was supplemented with 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. The IP elutions and diluted input were then incubated at 55°C for 2 hours for a Proteinase K digestion. After digestion, the DNA was purified by adding 1.5 volumes of Serapure HD (1:50 dilution of Sera-Mag SpeedBeads [Fisher], 20% PEG-8000, 2.5 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.05% Tween-20, Filter Sterilized prior to addition of SpeedBeads), incubating at room temperature for 15 minutes, then collecting the beads on a magnetic rack, washing twice with 150 uL of 70% ethanol, and eluting into 50 uL of water, which was then recovered and stored at -20°C.
NEBNext Ultra II DNA Library Prep Kit was used per manufacturer instructions.


title: AR21 H3K27me3 3C2-H2

description: ICeChIP-seq conducted on K562 cells against H3K27me3 using 3C2-H2 clasping Fab.


title: AR21 H3K27me3 CST C36B11

description: ICeChIP-seq conducted on K562 cells against H3K27me3 using CST C36B11 antibody.


title: Tumor_219

city: Houston

first: Sung Wook

last: Kang

address: one plaza

department: Surgery

institute: Baylor college of medicine

description: Library name: Tumor_219

data_processing:
The raw sequence reads were mapped to GRCh38 using STAR (V2.5.3a).
The alignmented bam file were performed using markduplicated.
The FPRM value extract were performed using cufflinks.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.

value: Tumor

tag: subject id

tag: predominant histology

value: acinar

tag: Sex

value: F

tag: age at_surgery

tag: Stage

value: IIIA

tag: smoking status

value: N


title: RDH11, stim, Monocytes


title: RDH11, unstim, Monocytes


title: RDH12, unstim, Monocytes


title: RDH26, unstim, Monocytes


title: RDH39, unstim, Monocytes


title: RDH18, stim, Monocytes


title: Tumor_221

description: Library name: Tumor_221

tag: tissue

value: IB


title: Normal_221

description: Library name: Normal_221

source_name: Tumor (adjacent normal)

value: Tumor (adjacent normal)


title: RDH12, stim, Monocytes

value: stim


title: RDH18, unstim, Monocytes


title: Normal_219

description: Library name: Normal_219


title: RDH07, unstim, Monocytes


title: Tumor_216

description: Library name: Tumor_216

value: solid

value: Y


title: Normal_216

description: Library name: Normal_216


title: RDH07, stim, Monocytes


title: RDH26, stim, Monocytes


title: RDH03, stim, Monocytes


title: Tumor_215

description: Library name: Tumor_215

value: M


title: Normal_215

description: Library name: Normal_215


title: HEK293T FTO knockout, biorep 2, techrep 1

value: FTO KO


title: Tumor_214

description: Library name: Tumor_214


title: Tumor_207

description: Library name: Tumor_207


title: RDH01, stim, Monocytes


title: Normal_214

description: Library name: Normal_214


title: RDH03, unstim, Monocytes

value: unstim


title: Normal_207

description: Library name: Normal_207


title: RDH01, unstim, Monocytes


title: Mouse_Oligodendrocyte_SUZ12

data_processing:
Barcode adapter sequences removed
Paired-end fastq files were trimmed to 25 bp and mapped to the mm10 genome with bowtie2 (options -q -N 1 -X 1000)
Mapped reads were duplicate-filtered using Picard and filtered for mapping quality (MAPQ ≥ 10) using SAMtools.
Reads were converted to bigWig files using deepTools. Heatmaps were generated using deepTools computeMatrix (options -a 2000 -b 2000 -bs 20 --missingDataAsZero) and plotHeatmap
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

organism: Mus musculus

source_name: Brain

growth_protocol: Oligodendrocytes (OLs)were derived from Oligodendrcoyte Precursor Cells (OPCs) isolated from 6-7 day old mouse pups by immunopanning. OPCs were grown in DMEM Sato, supplemented with 2% B27, 2 mM-Glutamine, 16 μg/mL putrescine, 6.2 ng/mL progesterone, 5 ng/mL sodium selenite, 100 μg/mL bovine serum albumin, 5 μg/mL insulin, 50 μg/mL Apo-transferrin (Sigma) and 4.2 ng/mL Forskolin in DMEM. For proliferation OPCs were also supplemented with PDGF-AA (10 ng/mL), NT-3 (1 ng/mL) and CNTF (10 ng/mL). OPCs were For differentiation into OLs, cells were transferred to fresh DMEM Sato plus T3 4ng/ml, NT-3 (1 ng/mL) and CNTF (10 ng/mL) and maintained in differentiation medium for four days.

extract_protocol:
Nuclei were isolated from cell populations by incubating cell pellets with a nuclear extraction hypotonic buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5mM spermidine, 0.1% Triton X-100, 20% glycerol, freshly added protease inhibitors) for 10 minutes on ice. Samples were centrifuged and nuclei were flash frozen.
CUT&RUN enriched fragments isolated were used as input for a library build consisting of end repair and adenylation, NEBNext stem-loop adapter ligation, and subsequent purification with AMPure XP beads (Agencourt). Barcoded fragments were then amplified by 15 cycles of high-fidelity PCR and purified using AMPure XP.

value: Brain

value: Primary Oligodendrocyte

value: Oligodendrocyte

value: Wild type

value: No treatment

value: Suz12:Cell signaling 3737S, Lot 8


title: Tumor_199

description: Library name: Tumor_199

value: Tumor

value: mucinous


title: Normal_199

description: Library name: Normal_199


title: Tumor_194

description: Library name: Tumor_194

value: acinar

value: F


title: Mouse_Oligodendrocyte_IgG

value: IgG


title: Tumor_195

description: Library name: Tumor_195

value: IB


title: Normal_197

description: Library name: Normal_197

value: Tumor (adjacent normal)

value: lepidic


title: Mouse_Oligodendrocyte_CTCF

value: CTCF:Millipore 07-729 (Lot 3429114)


title: Normal_194

description: Library name: Normal_194

value: Y


title: Tumor_188

description: Library name: Tumor_188

value: M

value: N


title: Normal_195

description: Library name: Normal_195


title: Human adipose tissue from group PD, 267

type: RNA

city: Coimbra

first: Daniela

middle: Rosendo

last: Silva

address: Azinhaga de Santa Comba, Celas

country: Portugal

institute: Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra

data_processing:
Raw data was collected from the Fluidigm Real-Time PCR Analysis software. Target gene signals normalized to housekeepng gene - ACTB;
2^-deltaCt was calculated, where deltaCt = (Ct_Target − Ct_HKG)

label: SYBR Green

source_name: Omental adipose tissue

label_protocol: Each RNA sample was diluted to the same concentration (25 ng/μL). 1μl of Reverse transcriptase enzyme  [qScript cDNA super mix (Quanta BioSciences)] was added to 4μl of each RNA sample to obtain cDNA. Each cDNA sample was pre-amplified (PA). Briefly, 1.25μl of each cDNA sample was mixed with 0.5μl of a mix of pooled primers (500nM final concentration each), 2.25μl water and 1μl of PreAmp Master Mix enzyme (Fluidigm). Thermal cycling was performed according to the enzyme manufacturer for 12 cycles. The samples were then treated with Exonuclease I (New England Biolabs) to remove unincorporated primers. After Exonuclease treatment the samples were diluted 5x in TE buffer (10mM Tris-HCl, 1mM EDTA). For each sample (2.25μl) a Pre-Mix was prepared with 2.5μl SsoFast Eva Green Supermix (BioRad), 0,25μl of 20x DNA binding dye sample reagent (Fluidigm). 5μl of each sample was pipetted into the respective inlet of a Fluidigm® 96.96 Gene expression integrated fluidic circuit (IFC). For each assay (gene) a mix of 12μl was individually prepared: 6μl of 2x Assay loading reagent (Fluidigm), 5.4μl of TE buffer, 1.2 μl from a stock of 50μM each mixed forward and reverse primers. 5μl of each assay was pipetted into their respective assay inlets on the chip. The assay and sample mixes were loaded with the Load mix (136x) script of the HX controller (HD Biomark). After loading, the chip qRT-PCR was carried out using the BioMark HDTM, accordingly to the cycling parameters recommended by Fluidigm® for 96.96 Gene expression IFC. Data were collected with Data Collection Software and were analyzed using Fluidigm® Real Time PCR Analysis v2.1 software. Genes with melting curves displaying more of one peak (amplification of non-specific products) were not included in the analysis. The data were normalized for the reference gene ATCB and ddCt was calculated.The oligos were designed for human transcripts and were synthesized by Sigma-Aldrich and reconstituted to a final concentration of 100 µM in water.

extract_protocol: Samples of visceral adipose tissue were collected from the greater omentum while undergoing metabolic surgery, which was always performed by the same appointed surgeon. Adipose tissue biopsies were collected from the patients and kept in liquid nitrogen during transportation to our facilities, to be stored at -80 ºC. Total RNA was isolated from human visceral adipose tissue biopsies (100 mg of tissue) with a RNeasy Lipid Tissue Mini Kit (Qiagen, Germany), according to manufacturer instructions.

value: adipose tissue

tag: group

value: PD


title: Human adipose tissue from group IS NG, 268

value: IS NG


title: Tumor_187

description: Library name: Tumor_187


title: Normal_187

description: Library name: Normal_187


title: Normal_188

description: Library name: Normal_188


title: Human adipose tissue from group PD, 263


title: Human adipose tissue from group IR NG, 265

value: IR NG


title: Tumor_197

description: Library name: Tumor_197


title: Mouse_Oligodendrocyte_IgG2

value: Brain

value: Primary Oligodendrocyte

value: Oligodendrocyte

tag: genotype

value: Wild type


title: Human adipose tissue from group IR NG, 259


title: Tumor_183

description: Library name: Tumor_183

value: Tumor

value: acinar

value: F


title: Tumor_180

description: Library name: Tumor_180

value: IB


title: Mouse_Oligodendrocyte_H3K27me3


title: Human adipose tissue from group T2D, 250


title: Normal_183

description: Library name: Normal_183

value: Tumor (adjacent normal)


title: Human adipose tissue from group PD, 249


title: Human adipose tissue from group T2D, 247


title: Human adipose tissue from group PD, 248


title: Normal_179

description: Library name: Normal_179

value: lepidic


title: Tumor_179

description: Library name: Tumor_179

value: Y


title: Tumor_178

description: Library name: Tumor_178

value: M


title: Human adipose tissue from group IR NG, 257


title: Tumor_175

description: Library name: Tumor_175

value: papillary


title: Normal_180

description: Library name: Normal_180


title: Human adipose tissue from group T2D, 245

value: adipose tissue


title: Tumor_173

description: Library name: Tumor_173


title: Human adipose tissue from group T2D, 251


title: Human adipose tissue from group IR NG, 242


title: Human adipose tissue from group IR NG, 239


title: Human adipose tissue from group T2D, 234


title: Human adipose tissue from group T2D, 232


title: Human adipose tissue from group T2D, 233


title: Tumor_168

description: Library name: Tumor_168

value: IIA


title: Human adipose tissue from group IS NG, 227

value: IS NG


title: Human adipose tissue from group T2D, 228


title: Tumor_167

description: Library name: Tumor_167


title: Normal_173

description: Library name: Normal_173


title: Normal_178

description: Library name: Normal_178


title: Normal_170

description: Library name: Normal_170


title: Tumor_170

description: Library name: Tumor_170


title: Human adipose tissue from group IS NG, 224


title: Human adipose tissue from group PD, 231

value: PD


title: Tumor_163

description: Library name: Tumor_163


title: Human adipose tissue from group PD, 230


title: Tumor_169

description: Library name: Tumor_169


title: Human adipose tissue from group PD, 218


title: Normal_163

description: Library name: Normal_163


title: Normal_169

description: Library name: Normal_169


title: Human adipose tissue from group PD, 226


title: Human adipose tissue from group PD, 225


title: Normal_167

description: Library name: Normal_167


title: Tumor_165

description: Library name: Tumor_165


title: Human adipose tissue from group IS NG, 223


title: Human adipose tissue from group IR NG, 221

value: IR NG


title: Normal_168

description: Library name: Normal_168


title: Normal_175

description: Library name: Normal_175


title: Human adipose tissue from group PD, 220


title: Normal_165

description: Library name: Normal_165


title: Human adipose tissue from group T2D, 210


title: Normal_153

description: Library name: Normal_153

value: IIB


title: Normal_151

description: Library name: Normal_151


title: Human adipose tissue from group IR NG, 212


title: Human adipose tissue from group T2D, 211


title: Tumor_151

description: Library name: Tumor_151


title: Tumor_155

description: Library name: Tumor_155

value: solid


title: Human adipose tissue from group PD, 207


title: Human adipose tissue from group PD, 206


title: Normal_150

description: Library name: Normal_150


title: Human adipose tissue from group PD, 219


title: Tumor_153

description: Library name: Tumor_153


title: Human adipose tissue from group T2D, 123


title: Human adipose tissue from group T2D, 201


title: Human adipose tissue from group PD, 205


title: Normal_155

description: Library name: Normal_155


title: Normal_148

description: Library name: Normal_148

value: N


title: Human adipose tissue from group PD, 200


title: Tumor_150

description: Library name: Tumor_150

value: Tumor


title: Human adipose tissue from group PD, 120


title: Human adipose tissue from group IS NG, 122


title: Tumor_144

description: Library name: Tumor_144


title: Tumor_140

description: Library name: Tumor_140


title: Tumor_148

description: Library name: Tumor_148

value: acinar


title: Human adipose tissue from group T2D, 121


title: Normal_144

description: Library name: Normal_144

value: F


title: Human adipose tissue from group IS NG, 119


title: Tumor_136

description: Library name: Tumor_136


title: Normal_140

description: Library name: Normal_140


title: Normal_134

description: Library name: Normal_134


title: Normal_136

description: Library name: Normal_136


title: Human adipose tissue from group IS NG, 116


title: Normal_130

description: Library name: Normal_130


title: Human adipose tissue from group IS NG, 101


title: Human adipose tissue from group PD, 117


title: Human adipose tissue from group PD, 118


title: Human adipose tissue from group PD, 115


title: Human adipose tissue from group IS NG, 93


title: Human adipose tissue from group IS NG, 96


title: Human adipose tissue from group PD, 111


title: Tumor_127

description: Library name: Tumor_127


title: Tumor_130

description: Library name: Tumor_130


title: Normal_127

description: Library name: Normal_127


title: Human adipose tissue from group IS NG, 89


title: Tumor_126

description: Library name: Tumor_126


title: Normal_126

description: Library name: Normal_126


title: Human adipose tissue from group PD, 98


title: Normal_125

description: Library name: Normal_125

value: mucinous

value: IIIA


title: Tumor_125

description: Library name: Tumor_125


title: Tumor_123

description: Library name: Tumor_123

value: IB


title: Human adipose tissue from group T2D, 81


title: Human adipose tissue from group PD, 85


title: Human adipose tissue from group IR NG, 74


title: Human adipose tissue from group IS NG, 80


title: Normal_123

description: Library name: Normal_123

value: Tumor (adjacent normal)

value: Y


title: Tumor_122

description: Library name: Tumor_122

value: M


title: Human adipose tissue from group PD, 71

value: adipose tissue


title: Human adipose tissue from group IR NG, 70


title: Human adipose tissue from group IR NG, 72


title: Normal_115

description: Library name: Normal_115


title: Tumor_115

description: Library name: Tumor_115


title: Tumor_134

description: Library name: Tumor_134

value: lepidic


title: Human adipose tissue from group IS NG, 65

value: IS NG


title: Human adipose tissue from group IR NG, 66


title: Human adipose tissue from group IR NG, 64


title: Tumor_106

description: Library name: Tumor_106


title: Tumor_109

description: Library name: Tumor_109


title: Human adipose tissue from group IR NG, 61


title: Human adipose tissue from group PD, 62

value: PD


title: Normal_122

description: Library name: Normal_122


title: Normal_106

description: Library name: Normal_106


title: Tumor_104

description: Library name: Tumor_104

value: papillary


title: Normal_104

description: Library name: Normal_104


title: Human adipose tissue from group IR NG, 60

value: IR NG


title: Human adipose tissue from group IS NG, 58


title: Normal_100

description: Library name: Normal_100


title: Tumor_100

description: Library name: Tumor_100


title: Tumor_099

description: Library name: Tumor_099


title: Human adipose tissue from group PD, 54


title: Normal_099

description: Library name: Normal_099


title: Tumor_098

description: Library name: Tumor_098


title: Normal_098

description: Library name: Normal_098


title: Normal_109

description: Library name: Normal_109


title: Human adipose tissue from group PD, 46


title: Tumor_097

description: Library name: Tumor_097

value: solid

value: IIB


title: Human adipose tissue from group IR NG, 47


title: Human adipose tissue from group PD, 44


title: Human adipose tissue from group IR NG, 45


title: Human adipose tissue from group IR NG, 42


title: Human adipose tissue from group PD, 38


title: Tumor_096

description: Library name: Tumor_096

value: Tumor


title: Normal_096

description: Library name: Normal_096

value: acinar


title: Human adipose tissue from group IR NG, 37


title: Human adipose tissue from group IR NG, 53


title: Tumor_088

description: Library name: Tumor_088


title: Human adipose tissue from group IR NG, 56


title: Human adipose tissue from group IR NG, 57


title: Human adipose tissue from group PD, 36


title: Human adipose tissue from group IR NG, 35


title: Normal_088

description: Library name: Normal_088


title: Tumor_086

description: Library name: Tumor_086

value: F


title: Tumor_082

description: Library name: Tumor_082


title: Human adipose tissue from group IR NG, 33


title: Normal_097

description: Library name: Normal_097


title: Human adipose tissue from group IR NG, 34


title: Normal_086

description: Library name: Normal_086


title: Normal_082

description: Library name: Normal_082


title: Tumor_075

description: Library name: Tumor_075

value: IIA


title: Human adipose tissue from group PD, 27


title: Human adipose tissue from group T2D, 14


title: Human adipose tissue from group PD, 32


title: Normal_075

description: Library name: Normal_075


title: Human adipose tissue from group T2D, 13


title: Tumor_071

description: Library name: Tumor_071


title: Human adipose tissue from group IS NG, 11


title: Normal_071

description: Library name: Normal_071


title: Human adipose tissue from group T2D, 8


title: Human adipose tissue from group T2D, 10


title: Normal_063

description: Library name: Normal_063


title: Tumor_057

description: Library name: Tumor_057


title: Normal_057

description: Library name: Normal_057


title: Human adipose tissue from group IS NG, 6


title: Human adipose tissue from group PD, 5


title: 05 , skin, porous, iKTN, 16 weeks

city: Salt Lake City

first: Sujee

last: Jeyapalina

state: Utah

address: 500 Foothill Dr

institute: Department of Veteran Affairs

data_processing:
Sequences were aligned to the Sus Scrofa v11.1 reference genome using STAR via twopassMode.
Feature quantification was performed using featureCounts with Ensembl Sus Scrofa annotations v104.
Assembly: Sus scrofa v11.1
Supplementary files format and content: raw_counts.txt provide the count matrix generated from featureCounts for all samples.

organism: Sus scrofa

source_name: granulation tissue

extract_protocol:
RNeasey Fibrous Tissue Mini Kit
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold (human, mouse, rat, etc.)

value: granulation tissue

tag: animal id

tag: device

value: 2 GT

tag: necropsy

value: 16 weeks

tag: implant

value: porous

tag: coating

value: iKTN


title: Normal_054

description: Library name: Normal_054

value: Tumor (adjacent normal)

value: M

value: Y


title: Normal_051

description: Library name: Normal_051

value: IB


title: 05 , skin, smooth, control, 16 weeks

value: 3 GT

value: smooth

value: control


title: 05 , skin, smooth, iKTN, 16 weeks

value: 4 GT


title: Tumor_051

description: Library name: Tumor_051

value: Tumor

value: solid


title: 05 , skin, smooth, gKOS, 16 weeks

value: 5 GT

value: gKOS


title: Tumor_049

description: Library name: Tumor_049

value: acinar

value: F

value: IIB

value: N


title: Human adipose tissue from group IS NG, 3

value: adipose tissue

value: IS NG


title: 05 , skin, porous, control, 16 weeks

value: granulation tissue

value: 6 GT

value: 16 weeks

value: porous


title: 05 , skin, porous, gKOS, 16 weeks

value: 1 GT


title: 04 , skin, porous, control, 16 weeks

value: control


title: Tumor_046

description: Library name: Tumor_046

value: Y


title: Normal_046

description: Library name: Normal_046

value: Tumor (adjacent normal)


title: Tumor_063

description: Library name: Tumor_063

value: Tumor

value: IB


title: 04 , skin, smooth, gKOS, 16 weeks

value: 5 GT

value: smooth

value: gKOS


title: Normal_049

description: Library name: Normal_049

value: acinar

value: F

value: IIB


title: 04 , skin, smooth, control, 16 weeks

value: 3 GT


title: Tumor_039

description: Library name: Tumor_039

value: N


title: 04 , skin, porous, iKTN, 16 weeks

value: granulation tissue

value: 2 GT

value: iKTN


title: 04 , skin, smooth, iKTN, 16 weeks

value: 4 GT

value: 16 weeks


title: Normal_040

description: Library name: Normal_040

value: mucinous

value: IA

value: Y


title: Tumor_040

description: Library name: Tumor_040

value: Tumor


title: Tumor_054

description: Library name: Tumor_054

value: M


title: Normal_039

description: Library name: Normal_039

value: Tumor (adjacent normal)


title: 81 , skin, porous, control, 16 weeks

value: 6 GT

value: porous

value: control


title: 04 , skin, porous, gKOS, 16 weeks

value: 1 GT

value: gKOS


title: Human adipose tissue from group PD, 4

value: adipose tissue

value: PD


title: Tumor_038

description: Library name: Tumor_038

value: F

value: IIB


title: 81 , skin, smooth, gKOS, 16 weeks

value: granulation tissue

value: 5 GT

value: smooth


title: 81 , skin, porous, iKTN, 16 weeks

value: 2 GT

value: 16 weeks

value: iKTN


title: 81 , skin, smooth, control, 16 weeks

value: 3 GT


title: Tumor_037

description: Library name: Tumor_037

value: Tumor

value: acinar

value: IA

value: N


title: 81 , skin, porous, gKOS, 16 weeks

value: 1 GT

value: porous


title: 81 , skin, smooth, iKTN, 16 weeks

value: 4 GT


title: 08 , skin, porous, control, 8 weeks

value: 6 GT

value: 8 weeks

value: control


title: donor3 biol rep 1

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

institute: National Jewish Health

description: Library name: donor3 biol rep 1

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the bbduk tool from the BBMap Suite (v. 38.73) with arguments ‘ref=adapters.fa ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=20 ftr=36’
Trimmed reads were mapped to the human genome (hg38; downloaded from the UCSC genome browser on September 16, 2019, with corresponding hisat2 index files) using hisat2 (v. 2.1.0)
Resulting SAM files were converted to BAM format using samtools view (v. 1.9) with arguments ‘-S -b’, duplicates were removed using picard tools MarkDuplicates (v. 2.26.6) and then resulting BAM files were sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.29.2) with arguments ‘-bg -ibam -g hg38 -strand +’.
Assembly: hg38
Supplementary files format and content: BedGraph files are non-normalized coverage files.

source_name: proximal airway epithelium

growth_protocol: De-identified live airway epithelial cells were obtained from research bronchoscopy on healthy never smoking donors. Cells were collected from cytology brushes, manually dissociated and stored in cold saline until ATAC-seq processing (< 2 hrs).

extract_protocol:
Cells were washed once with 1X PBS and dissociated from cytology brushes prior to counting. Approximately 50K cells were pelleted and processed in duplicate or quadruplicate as described in the Omni-ATAC-seq protocol published by Corces et al (Nature Methods, 2017).
Uniquely indexed sequencing adapters from the Nextera DNA CD Indexes Kit were added to both ends of transposed fragment libraries by PCR. Following final purification and size selection for 100-1000 bp fragments, libraries were pooled and sequenced on an Illumina NextSeq instrument using 150 bp paired-end reads.

treatment_protocol: No treatment was applied to cells obtained from bronchoscopy. The research subjects were healthy controls not undergoing any treatment or intervention.

value: proximal airway epithelium


title: donor3 biol rep 2

description: Library name: donor3 biol rep 2


title: donor2 biol rep 4

description: Library name: donor2 biol rep 4


title: Normal_038

description: Library name: Normal_038

value: Tumor (adjacent normal)

value: mucinous

value: F

value: IIB

value: Y


title: donor2 biol rep 3

description: Library name: donor2 biol rep 3


title: donor2 biol rep 2

description: Library name: donor2 biol rep 2


title: 08 , skin, smooth, control, 8 weeks

value: granulation tissue

value: 3 GT

value: smooth


title: donor1 biol rep 2

description: Library name: donor1 biol rep 2


title: 08 , skin, porous, gKOS, 8 weeks

value: gKOS


title: 08 , skin, porous, iKTN, 8 weeks

value: 2 GT

value: iKTN


title: donor1 biol rep 1

description: Library name: donor1 biol rep 1


title: 07 , skin, porous, control, 8 weeks

value: porous


title: 07 , skin, smooth, gKOS, 8 weeks

value: 5 GT


title: pDC,C274+KI696,Donor413,Female

first: David

last: Oliver

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

description:
Library name: C274.KI696_PDC413
NRF2_Counts.txt

data_processing:
fastp -q 15 -n 10 -l 20  -i target_R1.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - > target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Assembly: hg38
Supplementary files format and content: Tab delimited file containing reads per gene across samples

source_name: Blood

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Plus Mini Kit. All samples were examined for RNA quality by Agilent Bioanalyzer 2100. Illumina libraries were constructed using NEB low input library preparation kit.
Illumina libraries were constructed using NEB low input library preparation kit. Multiplexed libraries were generated and pooled at equimolar concentration, and pair-end reads were sequenced on an Illumina NOVASeq 6000 in the Weill Cornell Epigenomics Core Facility at the depth of 21-37 million fragments per sample.

treatment_protocol: Enriched leukocytes were obtained from the New York Blood Center (Long Island City, NY) under internal Institutional Review Board–approved protocols and all experiments were approved by the Institutional Biosafety Committee (IBC #: 19-0231) from Weill Cornell Medicine. PBMCs were prepared using Ficoll-Paque density gradient and pDCs were isolated using BDCA4+ positive selection (Miltenyi Biotec: 130-090-532) as previously described (Guiducci et al., 2006). pDCs were cultured at 40,000 cells (for HDs)

value: Blood

tag: cell type

value: pDC

tag: donor id

value: Female


title: pDC,C274,Donor413,Female

description:
Library name: C274_PDC413
NRF2_Counts.txt


title: pDC,Medium,Donor413,Female

description:
Library name: Med_PDC413
NRF2_Counts.txt

value: Medium


title: 07 , skin, smooth, iKTN, 8 weeks

value: 4 GT

value: 8 weeks


title: 08 , skin, smooth, iKTN, 8 weeks


title: Normal_037

description: Library name: Normal_037

value: Tumor (adjacent normal)

value: acinar

value: F

value: IA

value: N


title: pDC,C274+KI696,Donor409,Male

description:
Library name: C274.KI696_PDC409
NRF2_Counts.txt

value: Male


title: 07 , skin, porous, iKTN, 8 weeks

value: granulation tissue


title: 07 , skin, smooth, control, 8 weeks

value: 3 GT

value: smooth

value: control


title: 06 , skin, porous, control, 8 weeks

value: 6 GT

value: porous


title: pDC,Medium,Donor409,Male

description:
Library name: Med_PDC409
NRF2_Counts.txt

value: Blood

value: pDC


title: 07 , skin, porous, gKOS, 8 weeks

value: 1 GT

value: gKOS


title: 08 , skin, smooth, gKOS, 8 weeks

value: 5 GT

value: 8 weeks


title: 06 , skin, smooth, gKOS, 8 weeks


title: pDC,C274,Donor404,Female

description:
Library name: C274_PDC404
NRF2_Counts.txt

value: Female


title: pDC,C274+KI696,Donor404,Female

description:
Library name: C274.KI696_PDC404
NRF2_Counts.txt


title: donor2 biol rep 1

description: Library name: donor2 biol rep 1

value: proximal airway epithelium


title: 06 , skin, smooth, iKTN, 8 weeks

value: 4 GT

value: iKTN


title: 06 , skin, smooth, control, 8 weeks


title: pDC,Low.kPA,Ctrl,Donor84,Female

description:
Library name: lowKPA_Donor84
KPA_Counts.txt

tag: treatment

value: Ctrl


title: 06 , skin, porous, gKOS, 8 weeks

value: granulation tissue


title: pDC,Medium,Donor404,Female

description:
Library name: Med_PDC404
NRF2_Counts.txt

value: Medium


title: 06 , skin, porous, iKTN, 8 weeks

value: 2 GT


title: pDC,Low.kPA,Ctrl,Donor83,Male

description:
Library name: lowKPA_Donor83
KPA_Counts.txt

value: Male


title: pDC,Low.kPA,Ctrl,Donor82,Female

description:
Library name: lowKPA_Donor82
KPA_Counts.txt


title: 18 , skin, smooth, gKOS, 4 weeks

value: 4 weeks

value: smooth


title: 18 , skin, smooth, iKTN, 4 weeks


title: pDC,High.kPA,Ctrl,Donor88,Female

description:
Library name: hiKPA_Donor88
KPA_Counts.txt

value: Blood


title: 18 , skin, porous, control, 4 weeks

value: 6 GT

value: porous

value: control


title: pDC,High.kPA,Ctrl,Donor83,Male

description:
Library name: hiKPA_Donor83
KPA_Counts.txt

value: pDC


title: 18 , skin, porous, iKTN, 4 weeks


title: 18 , skin, smooth, control, 4 weeks

value: 3 GT


title: pDC,High.kPA,Ctrl,Donor82,Female

description:
Library name: hiKPA_Donor82
KPA_Counts.txt

value: Female


title: pDC,C274,Donor409,Male

description:
Library name: C274_PDC409
NRF2_Counts.txt


title: pDC,High.kPA,Ctrl,Donor84,Female

description:
Library name: hiKPA_Donor84
KPA_Counts.txt


title: pDC,High.kPA,Tlr9,Donor23,Male

description:
Library name: VC8497_8
KPA_Counts.txt


title: 17 , skin, porous, control, 4 weeks


title: pDC,Low.kPA,Tlr9,Donor23,Male

description:
Library name: VC8497_7
KPA_Counts.txt


title: 18 , skin, porous, gKOS, 4 weeks

value: 1 GT

value: gKOS


title: 17 , skin, smooth, gKOS, 4 weeks

value: 5 GT


title: pDC,High.kPA,Tlr9,Donor21,Male

description:
Library name: VC8497_6
KPA_Counts.txt


title: pDC,Low.kPA,Tlr9,Donor21,Male

description:
Library name: VC8497_5
KPA_Counts.txt


title: 17 , skin, smooth, control, 4 weeks


title: 17 , skin, smooth, iKTN, 4 weeks

value: 4 GT

value: iKTN


title: pDC,High.kPA,Tlr9,Donor22,Female

description:
Library name: VC8497_4
KPA_Counts.txt


title: 17 , skin, porous, iKTN, 4 weeks

value: granulation tissue


title: pDC,Low.kPA,Tlr9,Donor22,Male

description:
Library name: VC8497_3
KPA_Counts.txt


title: pDC,Low.kPA,Ctrl,Donor88,Female

description:
Library name: lowKPA_Donor88
KPA_Counts.txt

value: Ctrl


title: 16 , skin, porous, control, 4 weeks


title: pDC,High.kPA,Tlr9,Donor20,Female

description:
Library name: VC8497_2
KPA_Counts.txt


title: pDC,Low.kPA,Tlr9,Donor20,Male

description:
Library name: VC8497_1
KPA_Counts.txt

value: Male


title: 16 , skin, smooth, gKOS, 4 weeks

value: 4 weeks


title: BT-549 cells, UCM, rep3

city: Atlanta

first: Karmella

middle: A

last: Haynes

state: GA

address: 1760 Haygood Dr NE

department: Wallace H. Coulter Department of Biomedical Engineering

institute: Emory University

data_processing:
Raw reads were trimmed with Trim Galore and aligned via seed searching using STAR with the most recent human genome (GRCh38/hg38). mRNA levels were calculated with RSEM.
Assembly: hg38
Supplementary files format and content: txt, raw counts (TPM and FPKM) for each Sample
Supplementary files format and content: txt, ACM over UCM log2 fold change and p values for 32199 Ensembl annotated genes

source_name: Breast mammary gland

growth_protocol: BT-549 cells (ATCC #HTB122) were maintained in RPMI-1640 (ATCC #30-2001) with 10% tetracycline system approved fetal bovine serum (tsFBS, Thermo #A4736401), and 0.8 ug/mL insulin (Thermo #12585014) in humidified atmosphere with 5% CO2 at 37˚C

extract_protocol:
RNA was extracted and purified as instructed by the RNeasy Mini kit (Qiagen #74104).
Frozen RNA (-80°C) was submitted to Novogene for library preparation (polyA-enriched) and next generation sequencing with the following parameters: paired-end, 150 bp, Q30 ≥85%.

treatment_protocol: BT-549 cells were seeded at 1x106 cells/mL in a 6-well plate and grown in UCM or 50% ACM, with 3 replicates per condition, for 24 hours.

value: Breast mammary gland

tag: cell line

value: epithelial

value: WT

value: unconditioned media


title: BT-549 cells, UCM, rep2


title: 16 , skin, smooth, control, 4 weeks

value: smooth

value: control


title: BT-549 cells, UCM, rep1


title: BT-549 cells, ACM, rep3

value: adipocyte-conditioned media


title: 16 , skin, porous, iKTN, 4 weeks

value: 2 GT

value: porous


title: 16 , skin, porous, gKOS, 4 weeks

value: 1 GT

value: gKOS


title: BT-549 cells, ACM, rep2


title: BT-549 cells, ACM, rep1


title: S0, replicate 1, scRNAseq

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl Street, Wolfson Building 321

department: Immunology and Regenerative Biology

country: Israel

institute: Weizmann Institute Of Science

description:
Library name: sample 1
MARSseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation is done with scMARSseq pipeline reported in https://doi.org/10.1038/s41596-019-0164-4
Assembly: mm9
Supplementary files format and content: comma-seperated values format

extract_protocol:
Mice were anesthetized with Pental (1:1 in PBS) and perfused with cold PBS. Whole mouse brains were isolated in intact condition and incubated for 40 min at 37 °C with gentle shaking in the digestion solution (3 ml HBSS /per brain containing 2% BSA, 5 mM EDTA, and 0.2 mg/ml Collagenase type 2 (Worthington)). After the incubation leptomeningeal cells were washed out from the surface of mouse brains with pipetting of digestion solution on the surface and collected in tubes with cold PBS after passing a 100-µm mesh filter. Collected cells were centrifuged at 400 g at 4 °C for 5 min and re-suspended with cold FACS buffer containing 2% FBS and 1 mM EDTA based on PBS w/o Ca2+ and Mg2+ for antibody staining. Intact brains were further digested for parenchymal cell isolation. Brains were dissected in 1 ml of digestion solution containing 2% BSA, 1 mg/ml collagenase D (Sigma) and 1 mg/ml DNase1 (Sigma), and incubated for 20 min at 37 °C. In the middle of incubation, brains were homogenized by pipetting. After the incubation, the homogenate was filtered through a 100-µm mesh and centrifuged at 970 g at 4 °C for 5 min. To enrich brain cells, the cell pellet was re-suspended with 3 ml of 40% Percoll solution and centrifuged at 970 g, w/o acceleration and brake, at room temperature for 15 min. After the centrifugation, the myelin layer was removed, and the rest of the supernatant and cell pellets were washed in cold PBS. Cells were re-suspended with cold FACS buffer for antibody staining for sorting. Cells were kept on ice during all steps, except for the enzymatic digestion and cells for bulk-RNAseq and scRNAseq were processed always with actinomycin D (ActD) to prevent transcriptomic changes, as reported.
A derivation of MARSseq protocol was used to prepare libraries for RNAseq. For the single-cell RNA sequencing (scRNAseq) library preparation, cells were isolated from five one-year-old Ms4a3cre: R26-TdTomfl/fl: Cx3cr1gfp  mice and sorted in a 384-well plate with lysis buffer and poly-T barcoded primers and placed at -80C for future processing. When thawed, they are heated to bind the primer to the mRNA and the first strand mix is added for the cDNA-mRNA hybrid. ExoI is added to remove excess primers and all samples are then pooled followed by second-strand synthesis. Pooled samples are amplified overnight using IVT, followed by RNA fragmentation and ligation of the adapter for pooled sample identification. Finally, first strand synthesis and PCR for final sample amplification. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument. RNaseq libraries were sequenced using the Illumina NextSeq 500 with 90 reads, 75 for read 1, which contained the ligation adapter sequence and mRNA sequence, and 15 for read 2, which contained the single sample or single cell barcode and UMI sequences.

value: Brain

value: microglia and macrophages


title: Mutant_leptohostMac_2

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Crep_GFPp_2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation is done with MARSseq pipeline and UTAP analysis reported in https://doi.org/10.1186/s12859-019-2728-2.
Assembly: mm10
Supplementary files format and content: comma seperated values file includes raw count and RPKM for each sample

source_name: brain

extract_protocol:
Mice were anesthetized with Pental (1:1 in PBS) and perfused with cold PBS. Whole mouse brains were isolated in intact condition and incubated for 40 min at 37 °C with gentle shaking in the digestion solution (3 ml HBSS /per brain containing 2% BSA, 5 mM EDTA, and 0.2 mg/ml Collagenase type 2 (Worthington)). After the incubation leptomeningeal cells were washed out from the surface of mouse brains with pipetting of digestion solution on the surface and collected in tubes with cold PBS after passing a 100-µm mesh filter. Collected cells were centrifuged at 400 g at 4 °C for 5 min and re-suspended with cold FACS buffer containing 2% FBS and 1 mM EDTA based on PBS w/o Ca2+ and Mg2+ for antibody staining. Intact brains were further digested for parenchymal cell isolation. Brains were dissected in 1 ml of digestion solution containing 2% BSA, 1 mg/ml collagenase D (Sigma) and 1 mg/ml DNase1 (Sigma), and incubated for 20 min at 37 °C. In the middle of incubation, brains were homogenized by pipetting. After the incubation, the homogenate was filtered through a 100-µm mesh and centrifuged at 970 g at 4 °C for 5 min. To enrich brain cells, the cell pellet was re-suspended with 3 ml of 40% Percoll solution and centrifuged at 970 g, w/o acceleration and brake, at room temperature for 15 min. After the centrifugation, the myelin layer was removed, and the rest of the supernatant and cell pellets were washed in cold PBS. Cells were re-suspended with cold FACS buffer for antibody staining for sorting. Cells were kept on ice during all steps, except for the enzymatic digestion and cells for bulk-RNAseq and scRNAseq were processed always with actinomycin D (ActD) to prevent transcriptomic changes, as reported.
100000 or less (when isolated cell number was insufficient) microglia and leptomeningeal macrophages were sorted into 40 µL of lysis/binding buffer (Life Technologies) and stored at -80 C degree  until mRNA isolation. mRNA was captured with Dynabeads oligo(dT) (Life Technologies) according to the manufacturer’s guidelines. A derivation of MARSseq protocol was used to prepare libraries for RNAseq reported in https://doi.org/10.1038/s41596-019-0164-4.

value: brain

value: leptomeningeal macrophages

value: BMT 16w


title: Mutant_leptohostMac_1

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Crep_GFPp_1


title: Mutant_leptoMoMac_4

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Crep_GFPn_4


title: Untransduced T cells donor 1

city: Los Angeles

first: Babak

last: Moghimi

address: 4650 sunset blvd

institute: CHLA

data_processing:
Quality Control: Assessed raw FASTQ file quality using FastQC
Trimming: Removed adapters and low-quality bases with Trimmomatic
Alignment: Mapped reads to the reference genome with HISAT2
Post-Alignment QC: Checked BAM file quality with Samtools
Read Quantification: Counted reads per gene with HTSeq-count to create a raw counts matrix.
Assembly: hg38
Supplementary files format and content: Raw Counts Matrix: Text file with raw read counts per gene across samples.

source_name: T cells

extract_protocol:
RNA was isolated from T cells following their elimination of target AML cells using the Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T cells

value: primary immune cell

value: Untransduced


title: Untransduced T cells donor 3


title: Mutant_leptoMoMac_2

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Crep_GFPn_2


title: Untransduced T cells donor 2


title: Constituitive CD123 CAR-T donor2

value: Constituitive CD123 CAR


title: Constituitive CD123 CAR-T donor3


title: Mutant_leptoMoMac_1

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Crep_GFPn_1


title: gated CD33-CD123 CAR-T donor3

value: CD33-CD123 gated CAR


title: Constituitive CD123 CAR-T donor1


title: gated CD33-CD123 CAR-T donor2


title: Control_leptohostMac_1

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Cren_GFPp_1


title: 16 , skin, smooth, iKTN, 4 weeks

value: granulation tissue

value: 4 GT

value: 4 weeks

value: smooth

value: iKTN


title: gated CD33-CD123 CAR-T donor1


title: 17 , skin, porous, gKOS, 4 weeks

value: 1 GT

value: porous


title: Control_leptoMoMac_3

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Cren_GFPn_3


title: Control_leptoMoMac_1

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Cren_GFPn_1


title: PRO_dTAG-3h_HEXIM2-29-32D-OE_PNUTS-dTAG_DLD-1_Rep2

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

description: HEXIM2-29-32D overexpressed and treated with dTAG13 for 3h

data_processing:
The paired PRO-seq reads were subjected to trimming using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a read length threshold of >15 bp.
After removal of molecular barcode (UMI) with fastp v0.21.0,100 ribosomal RNA reads were discarded using Bowtie v2.3.5.1 with ‘‘--un-conc-gz’’.
Then the remaining reads were aligned to the hg19 or mm10 genome using Bowtie v2.3.5.1 with ‘‘--local --sensitive-local’’.
The mapped data were next deduplicated with UMI-tools to remove PCR duplicates based on the UMI sequences.
The normalization factor was generated following the approach used in ChIP-Rx, and strand-specific coverage tracks were created using deeptools v3.5.0.
Assembly: hg19
Supplementary files format and content: bigWig files
Library strategy: PRO-Seq

molecule: nuclear RNA

growth_protocol: Human DLD-1 cells were grown in DMEM (Gibco) supplemented with 10% FBS (Yeasen) and 1 × Penicillin-Streptomycin (Thermo) at 37 °C, 5% CO2.

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.  Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG13 for corresponding time.

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG


title: PRO_dTAG-3h_HEXIM2-29-32A-OE_PNUTS-dTAG_DLD-1_Rep2

description: HEXIM2-29-32A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HEXIM2-29-32A-OE_PNUTS-dTAG_DLD-1_Rep1

value: HEXIM2-29-32A overexpressed and treated with dTAG13 for 3h


title: Control_leptoMoMac_2

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Cren_GFPn_2

value: brain

value: leptomeningeal macrophages


title: Mutant_hostMg_3

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPp_3

value: microglia

value: BMT 16w


title: Mutant_hostMg_4

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPp_4


title: PRO_dTAG-3h_HEXIM2-29-32D-OE_PNUTS-dTAG_DLD-1_Rep1

value: HEXIM2-29-32D overexpressed and treated with dTAG13 for 3h


title: Mutant_leptoMoMac_3

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Crep_GFPn_3


title: PRO_dTAG-3h_CPSF7-203D-OE_PNUTS-dTAG_DLD-1_Rep1

description: CPSF7-203D overexpressed and treated with dTAG13 for 3h


title: Mutant_hostMg_2

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPp_2


title: Mutant_hostMg_1

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPp_1


title: Control_leptohostMac_2

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Cren_GFPp_2


title: PRO_dTAG-3h_CPSF7-203A-OE_PNUTS-dTAG_DLD-1_Rep2

description: CPSF7-203A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_CPSF7-203D-OE_PNUTS-dTAG_DLD-1_Rep2

value: CPSF7-203D overexpressed and treated with dTAG13 for 3h


title: Mutant_MoMg_3

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPn_3


title: PRO_dTAG-3h_CPSF7-203A-OE_PNUTS-dTAG_DLD-1_Rep1

value: CPSF7-203A overexpressed and treated with dTAG13 for 3h


title: Mutant_MoMg_2

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPn_2


title: PRO_dTAG-3h_MEPCE-152D-OE_PNUTS-dTAG_DLD-1

description: MEPCE-152D overexpressed and treated with dTAG13 for 3h


title: Control_leptoMoMac_4

description:
MARSseq
JS_hDNMT3A_BMT_Lepto_Cren_GFPn_4


title: Mutant_MoMg_1

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPn_1


title: Control_hostMg_3

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPp_3


title: Control_hostMg_4

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPp_4


title: PRO_dTAG-3h_HNRNPA2B1-225D-OE_PNUTS-dTAG_DLD-1_Rep1

description: HNRNPA2B1-225D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_MEPCE-152A-OE_PNUTS-dTAG_DLD-1_Rep1

description: MEPCE-152A overexpressed and treated with dTAG13 for 3h


title: Control_hostMg_2

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPp_2


title: Control_hostMg_1

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPp_1


title: Control_MoMg_4

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPn_4


title: PRO_dTAG-3h_RPRD2-758D-OE_PNUTS-dTAG_DLD-1_Rep2

description: RPRD2-758D overexpressed and treated with dTAG13 for 3h


title: Control_MoMg_3

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPn_3


title: PRO_dTAG-3h_RPRD2-758D-OE_PNUTS-dTAG_DLD-1_Rep1

value: RPRD2-758D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPA2B1-225A-OE_PNUTS-dTAG_DLD-1_Rep1

description: HNRNPA2B1-225A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_RPRD2-758A-OE_PNUTS-dTAG_DLD-1_Rep2

description: RPRD2-758A overexpressed and treated with dTAG13 for 3h


title: Control_MoMg_1

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPn_1


title: DR_BMT_HSC_BAM_2

description:
MARSseq
JS_NHS_DR_BMT_GFP_BAM_2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation is done with MARSseq pipeline and UTAP analysis reported in https://doi.org/10.1186/s12859-019-2728-2.
Assembly: mm10
Supplementary files format and content: comma separated values file includes raw count and RPKM for each sample

value: BMT 32w


title: PRO_dTAG-3h_RPRD2-758A-OE_PNUTS-dTAG_DLD-1_Rep1

value: RPRD2-758A overexpressed and treated with dTAG13 for 3h


title: Mutant_MoMg_4

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Crep_GFPn_4


title: DR_BMT_HSC_BAM_1

description:
MARSseq
JS_NHS_DR_BMT_GFP_BAM_1


title: PRO_dTAG-3h_RPRD2-723D-OE_PNUTS-dTAG_DLD-1_Rep1

description: RPRD2-723D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_MEPCE-152A-OE_PNUTS-dTAG_DLD-1_Rep2

value: MEPCE-152A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_RPRD2-723D-OE_PNUTS-dTAG_DLD-1_Rep2

value: RPRD2-723D overexpressed and treated with dTAG13 for 3h


title: DR_BMT_moBAM_4

description:
MARSseq
JS_NHS_DR_BMT_DP_BAM_4


title: PRO_dTAG-3h_ZSCAN5A-340D-OE_PNUTS-dTAG_DLD-1_Rep2

description: ZSCAN5A-340D overexpressed and treated with dTAG13 for 3h


title: DR_BMT_moBAM_2

description:
MARSseq
JS_NHS_DR_BMT_DP_BAM_2


title: DR_BMT_moBAM_3

description:
MARSseq
JS_NHS_DR_BMT_DP_BAM_3


title: DR_BMT_moBAM_1

description:
MARSseq
JS_NHS_DR_BMT_DP_BAM_1


title: PRO_dTAG-3h_RPRD2-723A-OE_PNUTS-dTAG_DLD-1_Rep1

description: RPRD2-723A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_HNRNPA2B1-225A-OE_PNUTS-dTAG_DLD-1_Rep2

value: HNRNPA2B1-225A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ZSCAN5A-340D-OE_PNUTS-dTAG_DLD-1_Rep1

value: ZSCAN5A-340D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ZSCAN5A-340A-OE_PNUTS-dTAG_DLD-1_Rep2

description: ZSCAN5A-340A overexpressed and treated with dTAG13 for 3h

value: colorectal adenocarcinoma cell line


title: PRO_dTAG-3h_HNRNPA2B1-225D-OE_PNUTS-dTAG_DLD-1_Rep2

value: PNUTS-dTAG

value: HNRNPA2B1-225D overexpressed and treated with dTAG13 for 3h


title: DR_BMT_HSC_Microglia_3

description:
MARSseq
JS_NHS_DR_BMT_GFP_Microglia_3

value: brain


title: PRO_dTAG-3h_ZSCAN5A-340A-OE_PNUTS-dTAG_DLD-1_Rep1

value: ZSCAN5A-340A overexpressed and treated with dTAG13 for 3h


title: DR_BMT_HSC_Microglia_4

description:
MARSseq
JS_NHS_DR_BMT_GFP_Microglia_4

value: microglia


title: Control_MoMg_2

description:
MARSseq
JS_hDNMT3A_BMT_Paren_Cren_GFPn_2

value: BMT 16w


title: DR_BMT_HSC_Microglia_2

description:
MARSseq
JS_NHS_DR_BMT_GFP_Microglia_2


title: DR_BMT_moMicroglia_4

description:
MARSseq
JS_NHS_DR_BMT_DP_Microglia_4


title: DR_BMT_moMicroglia_3

description:
MARSseq
JS_NHS_DR_BMT_DP_Microglia_3


title: PRO_dTAG-3h_SRSF1-201D-OE_PNUTS-dTAG_DLD-1_Rep2

description: SRSF1-201D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ELP1-867D-OE_PNUTS-dTAG_DLD-1_Rep2

description: ELP1-867D overexpressed and treated with dTAG13 for 3h


title: DR_BMT_moMicroglia_2

description:
MARSseq
JS_NHS_DR_BMT_DP_Microglia_2


title: PRO_dTAG-3h_RPRD2-723A-OE_PNUTS-dTAG_DLD-1_Rep2

value: RPRD2-723A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_ELP1-867D-OE_PNUTS-dTAG_DLD-1_Rep1

value: ELP1-867D overexpressed and treated with dTAG13 for 3h


title: DR_BMT_moMicroglia_1

description:
MARSseq
JS_NHS_DR_BMT_DP_Microglia_1


title: PRO_dTAG-3h_ELP1-867A-OE_PNUTS-dTAG_DLD-1_Rep2

description: ELP1-867A overexpressed and treated with dTAG13 for 3h


title: DR_BMT_host_Microglia_4

description:
MARSseq
JS_NHS_DR_BMT_DN_Microglia_4


title: DR_BMT_host_Microglia_1

description:
MARSseq
JS_NHS_DR_BMT_DN_Microglia_1


title: PRO_dTAG-3h_ELP1-867A-OE_PNUTS-dTAG_DLD-1_Rep1

value: ELP1-867A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_CC2D1A-120D-OE_PNUTS-dTAG_DLD-1_Rep2

description: CC2D1A-120D overexpressed and treated with dTAG13 for 3h


title: DR_BMT_host_Microglia_2

description:
MARSseq
JS_NHS_DR_BMT_DN_Microglia_2


title: PRO_dTAG-3h_CC2D1A-120A-OE_PNUTS-dTAG_DLD-1_Rep2

description: CC2D1A-120A overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_MYBL1-5D-OE_PNUTS-dTAG_DLD-1_Rep2

description: MYBL1-5D overexpressed and treated with dTAG13 for 3h


title: PRO_dTAG-3h_CC2D1A-120A-OE_PNUTS-dTAG_DLD-1_Rep1

value: CC2D1A-120A overexpressed and treated with dTAG13 for 3h


title: DR_BMT_HSC_Microglia_1

description:
MARSseq
JS_NHS_DR_BMT_GFP_Microglia_1

value: BMT 32w


title: Episomal_MPRA_RNA6

city: Indianapolis

first: Nathan

last: VanDusen

state: IN

department: Pediatrics

institute: Indiana University School of Medicine

description:
RNA
RNA6_GEN00141107_S09
Episomal_MPRA_readcounts.csv

data_processing:
Reads were trimmed down to the barcode-containing region using Trimmomatic
The shell tool Grep was used to count the number of reads containing each barcode.
Supplementary files format and content: HDR_MPRA_readcounts.csv: Table containing the raw number of reads for each enhancer, for the Tnni1 integrated MPRA.
Supplementary files format and content: Episomal_MPRA_readcounts.csv: Table containing the raw number of reads for each enhancer-promoter pair, for the episomal MPRA.

source_name: P28 ventricles

growth_protocol: Mouse in vivo

extract_protocol:
DNA: Proteinase K digestion followed by isopropanol precipitation. RNA: extracted by Trizol and purified by Zymo RNA Clean and Concentrator column with DNAse digestion.
RNA was reverse transcribed with Oligo-dT, reporter transcripts were selectively amplfied, and NGS adapters added during two rounds of PCR.
NGS adapter addition by two sequential rounds of PCR

treatment_protocol: AAV injection at birth

value: P28 ventricles

value: wildtype

value: AAV


title: Episomal_MPRA_RNA2

description:
RNA
RNA2_GEN00141103_S05
Episomal_MPRA_readcounts.csv


title: PRO_dTAG-3h_SRSF1-201D-OE_PNUTS-dTAG_DLD-1_Rep1

value: SRSF1-201D overexpressed and treated with dTAG13 for 3h


title: Episomal_MPRA_RNA5

description:
RNA
RNA5_GEN00141106_S08
Episomal_MPRA_readcounts.csv


title: Episomal_MPRA_RNA4

description:
RNA
RNA4_GEN00141105_S07
Episomal_MPRA_readcounts.csv


title: PRO_dTAG-3h_MYBL1-5A-OE_PNUTS-dTAG_DLD-1_Rep2

description: MYBL1-5A overexpressed and treated with dTAG13 for 3h