title: Green Onion_Neg_Ctrl

description: eukaryotice cell RNA

organism: Allium fistulosum

source_name: negative control RNA

value: carrier cDNA control


title: Hep-VDR/VitD-E2

status: Public on Apr 01 2020

type: RNA

city: Valencia

first: RAMIRO

last: JOVER

address: Avenida Fernando Abril Martorell, 106.

department: Experimental Hepatology Unit

country: Spain

institute: IIS Hospital La Fe

description: 48 h transfection + 4 h VitD in DMSO

hyb_protocol: The hybridization cocktail was heated at 99° for 5 minutes followed by 45° for 5 minutes and then centrifuged at max speed for 1 minute. 80µL were transferred to each array. Genechip array was incubated overnight at 45°C while rotating in a Hybridization Oven 645 (Affymetrix). After 16h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the FS450_0007 protocol.

scan_protocol: The distribution of fluorescent signals on the array was obtained using GeneChip Scanner 3000 7G (Affymetrix). GeneChip Operating Software (Affymetrix) was used to generate the CEL files.

data_processing: The data were normalized using the RMA method, and probes were summarized using the revised entrez-based probe annotation. A probe-filtering step excluding those probes that show a lower coefficient of variation, low intensity levels in all observations or that are non-informative (not annotated) was employed. Differential expression analysis was assessed using linear models for microarray data based on empirical Bayes moderated t-statistics for all filtered probe sets. To correct for multiple testing, the false discovery rate was estimated from p-values derived from the moderated t-statistics using the method of Benjamini and Hochberg. The data were also analyzed with Transcriptome Analysis Console version 4.0.2 (TAC 4.0.2) using Affymetrix default analysis settings.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: The fragmented biotinylated cRNA, using WT Terminal Labeling Kit (Affymetrix), derived from 300 ng of total RNA

growth_protocol: HepG2 cells were cultured in Ham’s F-12/Leibovitz L-15 (1:1, v/v) medium supplemented with 7% newborn calf serum, 2 mmol/L L-glutamine, 50 U/mL penicillin, and 50 mg/mL streptomycin

extract_protocol: Total cellular RNA was extracted with the RNeasy Plus minikit (Qiagen), which removes contaminating genomic DNA. RNA concentration was measured by absorbance at 260 nm with a capillary spectrophotometer (GeneQuant Pro, GE Healthcare Biosciences). Purity was examined by OD260/230 and OD260/280 ratios. RNA integrity was assessed with a 2100 Bioanalyzer with Eukaryote total RNA Nano Assay (Agilent Technologies). RNA Integrity Numbers were all above 9.3.

treatment_protocol: HepG2 cells were infected with adenoviral vectors (Ad-VDR, encoding human VDR, or Ad-C, an insertless adenovirus) and 48 h latter cells were shifted to adenovirus-free medium and cultured for 4 h in the presence of 10 nM VitD (1a,25-dihydroxyvitamin D3 / calcitriol)

tag: treatment

value: Ad-VDR + 10nMVitD

tag: cell type

value: hepatocellular carcinoma

tag: cell line


title: Celery_NoV_R

city: Laurel

first: Christine

middle: Fang

last: Yu

state: MD

address: 8301 Muirkirk Rd.

department: Center for Food Safety and Applied Nutrition

country: USA

institute: US Food and Drug Administration

description: ultracentrifugation: viral RNA

hyb_protocol: Samples were prepared and hybridized to FDA-EVIR GeneChip Tiling Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip scanner with a scanning resolution of 1.56 µm pixelsize according to manufacturer's instruction.

data_processing: The probe intensities were extracted with Affymetrix PowerTools software (APT 2.10.2.2), and then exported to Excel for further processing.

organism: Apium graveolens

source_name: NoV-spiked celery, RNeasy kit extraction

growth_protocol: Confluent culture of FRhK-4 cells in 75 cm2 flasks (5 x 106 cells) were infected with 5-10 pfu/cell of HAV/18f in 1.5 ml of MEM containing 1% heat inactivated FBS.  After 1 hr of adsorption, 13.5 ml of the same medium was added to each flask and Incubation continued for 5-6 days.

extract_protocol: HAV/18f was spiked onto tomatoes, and the samples were shaked in TGBE buffer and homogenized.  The eluate was collected and clarified by centrifugation to remove food particulates.  The supernatant was recovered, and RNA was precipitated with 70% ice cold isopropanol.  The RNA pellet was collected by centrifugation and re-suspended in the lysis buffer following the instructions of RNAqueous Kit.  Potassium acetate was added to precipitate any remaining polysaccharides.  The extracted RNA samples were further treated with DNase and Dynabeads mRNA Purification Kit.   For virus-spiked green onions and celery, material was eluted using either Glycine Buffer or TGBE buffer supplemented with pectinase, respectively, then virus particles were concentrated by ultracentrifugation and RNA was extracted with commercial kits.

treatment_protocol: HAV/18f culture supernatant was collected and used for inoculation.  NoV GII.4 Minerva stool sample was suspended in 10% phosphate-buffered saline (PBS), centrifuged at 9000 ×g for 3 min, and the supernatant was collected and used for inoculation.

tag: treatment(s)

value: Celery + NoV + RNeasy kit

tag: infection

value: human norovirus

tag: virus strain

value: Minerva

tag: virus genotype


title: Rat2

type: SRA

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

description:
rat_barcodes.tsv
rat_features.tsv
rat_matrix.mtx.gz
2

library_source: transcriptomic

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.0.2)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
The cellranger aggr pipeline was employed, to generate a single cell-barcode matrix containing all the samples without normalization
Genome_build: mm10, Rattus_norvegicus.Rnor_6.0.dna.toplevel
Supplementary_files_format_and_content: Standard cellranger output format

organism: Rattus norvegicus

source_name: PNS

extract_protocol:
Sciatic nerves and the brachial nerve plexus were dissected from intracardial PBS perfused the mice. Nerves were first mechanically dissociated. Cells were then isolated by combining enzymatic digestion (Trypsin, Collagenase II, Hyaluronidase and Pronase) with myelin depletion and flow cytometry-based cell sorting (Calcein-AM, Zombi NIR, DAPI). Rats sciatic nerves were isolated and enzymatically digested in Collagenase/Dispase and DNase I. Cells were centrifuged on a 30%/70% Percoll gradient and the mononuclear interphase was collected. No sorting was performed.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (both from 10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell
ScRNA-seq

tag: genetic background

value: Naive Lewis rat


title: VC_2_2

city: Tochigi

first: shota

last: Nakagawa

address: 2606, Akabane, Ichikai-Machi, Haga-Gun

country: Japan

institute: Kao Corporation

description:
Gene expression after 24hr exposure of control (DMSO)
sample name:
SAMPLE 5

hyb_protocol: The labeled samples were hybridized to the SurePrint G3 GE 8×60K Ver 2.0 Microarray (Agilent Technologies, Palo Alto, CA, USA) with rotation at 10 rpm for 17 h at 65°C.

scan_protocol: After hybridization, the microarray chips were washed with the Gene Expression Wash Pack (Agilent Technologies, Palo Alto, CA, USA) and scanned with a DNA microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing:
All microarray data were processed using Genespring GX 14.5 (Agilent Technologies, Palo Alto, CA, USA). These data were normalized and modified using quality control flags.
processed data matrices include normalized signal intensity

source_name: hepatocytes, 24h, DMSO

label_protocol: RNA was converted to cDNA and then the labeled cRNA were produced from the cDNA using the Low Input Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA, USA).

growth_protocol: Cryopreserved male Sprague Dawley primary rat hepatocytes (KaLy-Cell, Plobsheim, France) were used for in vitro assay. The cells were cultured at 37°C with 5% CO2 in the supplied medium (Kurabo, Osaka, Japan).

extract_protocol: After the 24 hours exposure with each chemical, total RNAs were extracted from rat primary hepatocytes using the mRNAeasy kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. For elucidating the gene expression profile, 100 ng of RNA in total were used for microarray analysis.

treatment_protocol: After 24 h pre-culture, the cells were exposed to each compound at 300 µM for 24 h.

value: primary hepatocytes

tag: strain

value: SD

tag: gender

value: Male


title: Tomato_Neg_Ctrl3

description: total RNA: polyA enrichment

organism: Solanum lycopersicum

source_name: non-spiked tomato RNA

label_protocol: Samples were prepared and hybridized to FDA-EVIR GeneChip Tiling Array according to Affymetrix specifications.

value: no virus spiked tomato


title: Hep-C-E3

description: 48 h transfection + 4 h treatment (Veh=DMSO)

value: control Ad-C + Vehicle


title: VC_1_1

description:
Gene expression after 24hr exposure of control (DMSO)
sample name:
SAMPLE 1


title: Celery_Neg_Ctrl1

description: eukaryotice cell RNA


title: Rat1

description:
rat_barcodes.tsv
rat_features.tsv
rat_matrix.mtx.gz
1


title: Tomato_HAV_Expt3

description: total RNA: polyA enrichment

source_name: HAV-spiked tomato

value: tomato + HAV

value: hepatitis A virus

value: IB


title: Hep-C-E2


title: Hep-VDR-E2

value: Ad-VDR + Vehicle


title: Hep-VDR/VitD-E1

description: 48 h transfection + 4 h VitD in DMSO


title: Tomato_Neg_Ctrl2

description: total RNA: polyA enrichment


title: Hep-VDR-E1


title: Green Onion_HAV

description: ultracentrifugation: viral RNA

source_name: HAV-spiked green onion

value: green onion + HAV


title: Tomato_HAV_Expt2

description: total RNA: polyA enrichment


title: Tomato_Neg_Ctrl1

description: total RNA: polyA enrichment


title: Tomato_HAV_Expt1

description: total RNA: polyA enrichment


title: Whole-CLIP rep.4

status: Public on Mar 31 2020

city: Fujisawa

first: Masato

last: Yugami

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Research

institute: Takeda Pharmaceutical Company

data_processing:
collapsing of exact sequences
stripping of degenerate linker (barcode:First 5nt; ends with a C and next 9nt degenerate linker ends with a C)
alignment with  Novalign
to have Bed
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by CIMS tools. Bed files contain HNRNPU binding RNA regions (peak height: 5th column).

source_name: HeLa cell whole lysate

growth_protocol: HeLa cells were  stimulated by PMA/Ca2+ ionophore, UV irradiated and subjected to MY-CLIP

extract_protocol:
HNRNPU fragments were ligated to a degenerate a 3'linker to discriminate derivateive tags from stimulated HeLa cells
MY-CLIP

treatment_protocol: Cytoplasmic fractionation, Partial RNase digestion, RNA linker ligation, IP with anti-HNRNPU Ab (sc-32315, Santa Cruz), Reverse transcription with BrdU label, cDNA purification with anti-BrdU Ab (MAB3222, Millipore) and PCR amplificiation.

value: HeLa

tag: antibody

value: anti-hnRNPU

tag: rna fraction

value: whole cell lysate

tag: protocol

value: MY-CLIP


title: Whole-CLIP rep.2


title: Whole-CLIP rep.5


title: Cyto-CLIP rep.5

source_name: HeLa cell cytoplasmic fraction

value: cytoplasm


title: Whole-CLIP rep.3


title: Cyto-CLIP rep.3


title: Cyto-CLIP rep.2


title: Whole-CLIP rep.1


title: Cyto-CLIP rep.4


title: Cyto-CLIP rep.1


title: HNRNPC rep.3

data_processing:
collapsing of exact sequences
stripping of degenerate linker (barcode:First 5nt; ends with a C and next 9nt degenerate linker ends with a C)
alignment with  Novalign
to have Bed
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by CIMS tools

growth_protocol: HeLa cells were UV irradiated and subjected to  BrdU-CLIP or MY-CLIP

extract_protocol:
HNRNPU or HNRNPC bound fragments were ligated to a degenerate a 3'linker to discriminate derivateive tags from HeLa cells
HNRNPU or HNRNPC and RNA complex is purified by immunoprecipitation from UV-irradiated HeLa cells, and then separated by PAGE and isolated from the gel with proteinase K treatment. The isolated RNA is attached with 3'-linker and reverse transcribed with BrdUTP labeling. cDNA is immunoprecipitated by anti-BrdU antibody, and circularized and digested for forming 5'- and 3'-adaptors. CLIP cDNA library is produced by the cDNA amplification by PCR and purification.

treatment_protocol: Partial RNase digestion, RNA linker ligation, Reverse transcription, cDNA purification and PCR amplificiation.

value: anti-hnRNPC


title: HNRNPC rep.1


title: HNRNPC rep.2


title: CLIP cDNA library is produced by the cDNA amplification by PCR and purification.  rep.2


title: CLIP cDNA library is produced by the cDNA amplification by PCR and purification.  rep.1


title: BrdU-CLIP rep.2


title: β-naphthoflavone  treatment  48 hours

city: LONGJUMEAU

first: Angela

last: PATATIAN

address: 1CHEMIN DE SAULXIER

department: ESSONNE

country: France

institute: GENEX

description: Homo sapiens

hyb_protocol: All cRNAs were hybridized to human whole genome oligo microarrays (Agilent Technologies V2  AMADID039494) which contains 60.000 probes, derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner G2505C (Agilent Technologies)

data_processing:
Microarray data were quantified (GeneExtraction Feature V11.0,1) and normalized with R tools (Bioconductor).
Fold-changes (FC) were deduced from the calculated ratios: normalized intensity of treated samples by pollutant mix versus normalized intensity of control samples treated by solvent. Upregulated genes were selected for a FC≥1.5 and downregulated genes for a FC≤0.6.

source_name: HEK treated by BNF

label_protocol: RNAs of each sample were used for reverse transcription, amplification and Cy3 labeling, using the Low Input Labeling kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Neonatal human epidermal keratinocytes (HEKn) are primary cells derived from neonatal foreskins.  These cells were cultured in a specific medium (Epilife, Life Technologies) supplemented with a plant-derived supplement (HKSdaFREE and HKGE, AvantBio) that replaces the sera of animal origin more commonly used in cell culture. The cells were cultured at 37 ° C in an incubator (5% CO2 / 95% air).

extract_protocol: Total RNA was extracted from keratinocyte using RNeasy Mini Plus Kits (Qiagen).

treatment_protocol: Keratinocytes were exposed to the test inducer in a systemic way; the molecule was diluted in the culture medium. βNF being poorly water-soluble, stock solutions in a compatible solvent had to be prepared. Dimethyl sulfoxide (DMSO, Sigma-Aldrich) was used to prepare intermediate solutions before final dilution in the culture medium. Its final concentration does not exceed 0.2% in order to avoid cytotoxicity.

tag: tissue

value: skin

tag: age

value: keratinocytes


title: BrdU-CLIP rep.1


title: solvant  treatment 24 hours

description: Homo sapiens

source_name: HEK treated by solvant

value: primary cells derived from neonatal foreskins


title: solvant  treatment 48 hours

description: Homo sapiens


title: β-naphthoflavone  treatment  24 hours

description: Homo sapiens


title: β-naphthoflavone  treatment  6 hours

description: Homo sapiens


title: solvant  treatment 6 hours

description: Homo sapiens


title: Brain microvessels, diabetic, biological rep6

city: Groningen

first: Youhai

last: Li

state: Groningen

address: Hanzeplein 1

department: Dept. Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen (UMCG)

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at  on the Genechip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChips were scanned using the Genechip Scanner 7G (Affymetrix)

data_processing: These raw CEL files were normalized using the Affymetrix® Expression Console Software (version 4.0, Affymetrix) and the adjusted intensity values were transformed to log2 format

source_name: Brain microvessels

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 20 ug total RNA

growth_protocol: The retinae and brain hemisphere from individual rat was cryosectioned.

extract_protocol: Total RNA was obtained with RNeasy Plus Micro kit (Qiagen, Hilden, Germany)

treatment_protocol: Diabetes was induced with tail vein injection of Streptozotocin. These retinal and brain crysections were homogenated and centrifuged. The microvessels samples were captured by filtering the homogenate with nylon mesh.

tag: diagnosis

value: diabetic

value: Brain

tag: tissue compartment

value: Brain microvessels

tag: Sex

value: male

value: Wistar


title: Brain microvessels, nondiabetic, biological rep6

value: non-diabetic


title: Brain microvessels, diabetic, biological rep2


title: Brain microvessels, nondiabetic, biological rep4


title: Brain microvessels, diabetic, biological rep3


title: Retinal microvessels, diabetic, biological rep4

source_name: Retinal microvessels

value: Retina

value: Retinal microvessels


title: Brain microvessels, diabetic, biological rep4


title: Brain microvessels, diabetic, biological rep5


title: Brain microvessels, nondiabetic, biological rep2


title: Retinal microvessels, diabetic, biological rep6


title: Brain microvessels, diabetic, biological rep1


title: CLIP cDNA library is produced by the cDNA amplification by PCR and purification.  rep.3

value: HeLa


title: Retinal microvessels, nondiabetic, biological rep6


title: Hep-C-E1

tag: treatment

value: control Ad-C + Vehicle

tag: cell type

value: hepatocellular carcinoma


title: Retinal microvessels, diabetic, biological rep2


title: Brain microvessels, nondiabetic, biological rep1


title: RPTEC 2

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Sequencing reads were mapped to the UCSC human transcriptome (genome build hg19) using Bowtie 2 and expression levels of all genes were quantified using RSEM
RSEM yielded an expression matrix of inferred gene counts. Differential expression analysis was performed using R package DESeq2 using default parameters.
Reported are p-values from a negative binomial Wald-test.
Genome_build: hg19
Supplementary_files_format_and_content: .txt; raw counts

source_name: Isolated Primary human primary proximal tubule epithelial cells

growth_protocol: E6/E7-transformed human proximal tubular cell line HK-2 (CRL-2190) was obtained from the ATCC (Gaithersburg, MD) and cultured in DMEM/F-12 medium (Sigma-Aldrich, USA) supplemented with 5 ng ml-1 epidermal growth factor (EGF, Peprotech, USA), 10% fetal bovine serum, 2 mM L-Alanyl-L-Glutamine, and 100 U ml−1 penicillin and streptomycin (Biological Industries, Israel).    Primary human primary proximal tubule epithelial cells (hPTC) were purchased from Lonza (Basel, Switzerland) and Upcyte Technologies GmbH (Hamburg, Germany). Cells were cultured in MCDB 153 basal medium (Sigma-Aldrich, USA) supplemented with 0.5% fetal bovine serum (Biological Industries, Israel), ITS supplement (Gibco, USA), 0.1 µM dexamethasone (Sigma-Aldrich, USA), 10 ng ml-1  EGF (Peprotech, USA), 5 pM Triiodothyronine (Sigma-Aldrich, USA), 0.5 µg ml-1 Epinephrin (Sigma-Aldrich, USA), and 100 U ml−1 penicillin and streptomycin. Primary cells were cultured up to 8 population doublings.    Microvascular endothelial cells (Vec Technologies, USA) were cultured on gelatin-coated flasks using Endothelial Cell Growth Medium-2MV (Lonza, Switzerland) according to manufacturer directions. All cells were cultured under standard conditions in a humidified incubator at 37°C under 5% CO2.

extract_protocol:
RNA extraction was performed using RNeasy Micro kit (Qiagen, Valencia, CA) according to manufacturer’s direction.
Library preparation and RNA sequencing was performed by the Hebrew University Center for Genomic Technologies. Library construction was conducted using Illumina TruSeq RNA Library Prep V2 Kit (Illumina, San Diego, CA) according to manufacturer's protocol and sequenced on Illumina NextSeq500 with single-end, 86 bp reads using the High Output V2 Kit.

value: Kidney; Proximal Tubule

value: Isolated Primary cells

tag: passages


title: RPTEC 1


title: Brain microvessels, nondiabetic, biological rep5


title: Brain microvessels, nondiabetic, biological rep3


title: Retinal microvessels, nondiabetic, biological rep3


title: Retinal microvessels, nondiabetic, biological rep4


title: Retinal microvessels, diabetic, biological rep3


title: Retinal microvessels, diabetic, biological rep1


title: Retinal microvessels, diabetic, biological rep5


title: Retinal microvessels, nondiabetic, biological rep2


title: hPTC 2

source_name: Cultured Primary human primary proximal tubule epithelial cells

value: Primary cells cultured on treated plastic


title: Retinal microvessels, nondiabetic, biological rep1


title: Retinal microvessels, nondiabetic, biological rep5


title: HK2 cells 1

source_name: E6/E7-transformed human proximal tubular cell line

value: Cell line

value: UNKOWN


title: HK2 cells 2


title: Kidney Orgnaoid 2

source_name: hPTC and rMEC organoids formed spontaneously in matrigel

value: Primary cultured cells in 3D matrix


title: DDMB_2

description:
Gene expression after 24hr exposure of DDMB (300 µM)
sample name:
SAMPLE 8

source_name: hepatocytes, 24h, DDMB, 300 µM

value: primary hepatocytes

value: SD

value: Male


title: ZBTB1 KO + ZBTB1 cDNA ATF4

city: New York

first: Robert

middle: T

last: Williams

state: NY

address: 1230 York Avenue

institute: Rockefeller University

library_source: genomic

data_processing:
Reads were aligned using Rsubread's align method and predicted fragment lengths calculated by the ChIPQC package.
Normalised, fragment extended signal bigWigs are created using the rtracklayer package.
Peak calls are made in HOMER software and their peak summits used in MEME-ChIP software for known and de novo motif discovery.
Read counts in peaks are calculated using the featureCounts method in the Rsubread library.
Differential ChIP-seq signal is identified using the binomTest from the edgeR package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq and ATAC-Seq: bigWig files
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text file (mergedDF.txt)  includes RPKM values for each sample.

molecule: genomic DNA

source_name: Jurkat cells

extract_protocol:
RNA: Cells were harvested and RNA was isolated by Qiagen RNeasy kit. 1ug of total RNA was used for construction of sequencing libraries.
ChIP: Cells were cross-linked with 1% paraformaldehyde for 10 minutes at 37C. Cross-linking was quenched with 125 mM glycine. Cells were pelleted and flash-frozen in liquid nitrogen. Nuclei were isolated and sonicated using a Covaris sonicator. Protein A/G beads were added to 2-4 ug of appropriate antibodies and bound at room temperature for 1.5 hours. Samples were immunoprecipitated with appropriate protein A/G-antibody complexes overnight at 4C. Immunoprecipitates were collected and washed twice each with low salt, high salt, and lithium chloride wash buffers. DNA was eluted, reverse-crosslinked and treated with RNase and proteinase K before being isolated with a PCR purification kit (Zymogen).
ATAC: Cells were treated in the presence or absence of asparagine for 24 hours. Nuclear extracts were prepared from 100,000 cells for each cell line and condition, and incubated with 2.5 μl of transposase (Illumina) in a 50 μl reaction for 30 min at 37 °C. Transposase-fragmented DNA was purified, and the library was amplified by PCR.
RNA, ATAC and ChIP libraries were prepared using standard Illumina protocols.

tag: cell line

value: Jurkat

tag: genotype/variation

value: ZBTB1 KO expressing FLAG-ZBTB1 cDNA

value: Normal media conditions

tag: chip antibody


title: ZBTB1 KO + ZBTB1 cDNA H3K4me3


title: Input DNA ZBTB1 KO + ZBTB1 cDNA No Asparagine

value: Asparagine deprivation


title: ZBTB1 KO + ZBTB1 cDNA FLAG

value: Flag


title: ZBTB1 KO + ZBTB1 cDNA FLAG No Asparagine


title: hPTC 1


title: ZBTB1 KO H3K27Ac

value: ZBTB1 KO


title: ZBTB1 KO H3K4me3


title: ZBTB1 KO + ZBTB1 cDNA ATF4 No Asparagine


title: ZBTB1 KO FLAG


title: ZBTB1 KO + ZBTB1 cDNA H3K27Ac


title: ZBTB1 KO H3K4me3 No Asparagine


title: ZBTB1 KO H3K27Ac No Asparagine


title: ZBTB1 KO ATF4


title: ZBTB1 KO FLAG No Asparagine


title: 4163-003 (prostate cancer)

city: Burley-in-Wharfedale

first: David

middle: Edwin

last: Iles

state: West Yorkshire

address: 50 Hall Drive

country: United Kingdom

institute: Omics Ltd.

data_processing:
Basecalling and demultiplexing were performed using the bcl2fastq Conversion Software from Illumina.
Reads were processed to remove adapter sequence and reads shorter than 18 nt using TrimGalore!
Reads were aligned to the hg38 genome using subread-align (v1.4.6) with the options -B 1 -d 16 -M 1 -H.
Count tables of reads mapping to features in the NCBI RefSeq, piRNA, miRNA and NCBI repeatmasker databases were generated using the Rsubread function featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files were generated from alignment files using the BedTools function genomeCoverageBed.

source_name: cell-free semen

extract_protocol:
Control semen samples (n = 5) were obtained from healthy donors and from post-vasectomy semen samples (n = 5) from patients undergoing procedural checks for sperm clearance at the histopathology Unit, Seacroft Hospital in Leeds (UK). Semen samples (n = 4) from patients with or suspected of having prostate cancer were also obtained.
Libraries were prepared from size-fractionated (18-23 nt and 30-34 nt) RNAs using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit and sequenced on a Illumina NextSeq 500.

treatment_protocol: For total RNA isolation, spermatozoa, round cells and cell debris were cleared from liquefied semen samples by 10 min centrifugation at 1000 g to remove debris, followed by 16000 g for 30 min at 4°C to remove all cells (including spermatozoa). Cell-free seminal plasma was frozen at - 80°C for storage and/or shipping. Samples of frozen seminal plasma (0.5 ml) were first thawed at 37°C and mixed with 0.8 ml of Trizol and incubated for 5 min at room temperature. Chloroform (VWR, 200 μL) was added and the mix re-incubated for 3 min at room temperature. The mixture was centrifuged in a benchtop microfuge at 13200 g at maximum speed for 15 min at 4°C. The upper layer was transferred to a fresh tube and mixed thoroughly with an equal volume of isopropanol (Sigma, UK). After a 10 min incubation at room temperature, the mixture was centrifuged at full speed on a bench-top microfuge for 15 min at 4°C. Isopropanol was removed and the RNA pellet was washed twice with 70% ethanol. Finally, RNA was dissolved in 50 μl of RNAse-free H2O. The purity and quality of the RNA was checked using an Agilent 2100 bioanalyzer with the high sensitivity 6000 RNA Pico Kit (Agilent), following the manufacturer’s instructions.

tag: status

value: prostate cancer

tag: sample type

value: cell-free semen


title: Input DNA ZBTB1 KO No Asparagine


title: Input DNA ZBTB1 KO + ZBTB1 cDNA

value: ZBTB1 KO expressing ZBTB1 cDNA


title: Kidney Orgnaoid 1

value: Kidney; Proximal Tubule


title: ZBTB1 KO + ZBTB1 cDNA H3K4me3 No Asparagine


title: ZBTB1 KO + ZBTB1 cDNA H3K27Ac No Asparagine


title: 4163-001 (prostate cancer)


title: 4163-002 (prostate cancer)


title: 4163-005 (prostate cancer)


title: Input DNA ZBTB1 KO


title: ZBTB1 KO ATF4 No Asparagine


title: 2803_S5 (non-vasectomized)

value: fertile


title: 2803_S7 (vasectomized)

value: sterile


title: 2803_S9 (non-vasectomized)


title: 2803_S6 (vasectomized)


title: 2803_S3 (vasectomized)


title: 2803_S4 (non-vasectomized)


title: 2803_S2 (vasectomized)


title: 2803_S10 (non-vasectomized)


title: SiTFEBWnt3aCM2

city: Seoul

first: Eek-hoon

last: Jho

address: 163 Seoulsiripdae-ro, Dongdaemoon-gu

department: Department of Life Science

country: South Korea

institute: University of Seoul

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cervical cancer cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s Medium (DMEM, Lonza) supplemented with 10% FBS and 1% antibiotics.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA) standard protocols.

value: HeLa


title: SiGFPWnt3aCM1


title: SiGFPWnt3aCM2


title: 2803_S8 (vasectomized)


title: 2803_S1 (non-vasectomized)


title: SiGFPLCM2


title: RNA-Seq_deltaSTAG2_Bio3

city: Belfast

first: Ken

last: Mills

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

description: Ribodepleted RNA

data_processing:
ChIP-Seq reads were aligned with Bowtie2 and peaks called using MACS2.
RNA-Seq reads were aligned with STAR aligner with reads per gene output
HiChIP was processed through the Juicer pipeline to align to hg19, mate interaction pairs and generate contact matrix
Genome_build: hg19
Supplementary_files_format_and_content: ChIP bigWig files generated using Deeptools bamCoverage, normalised to 1x Human Genome. RNA bigWig files normalised to FPKM. HiChIP files are in .hic format for viewing in Juicebox

growth_protocol: Cultured in RPMI/1640 with 10% FBS and 1% P/S

extract_protocol:
RNA was isolated using the Qiagen RNAEasy Kit before processessing using the KAPA Stranded RNA-seq kit with ribodepletion
KAPA Stranded RNA-seq

value: Early Monocycte/Macrophages

tag: stag2 status


title: WIL2-NS_CytoScanHD_array

type: genomic

city: Ibaraki

first: Fumio

last: Kasai

state: Osaka

address: Saito-Asagi 7-6-8

department: JCRB Cell Bank

institute: National Institute of Biomedical Innovation

description: Hybridized to CytoScan™ HD Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The data analysis was performed based on the GRCh37 (hg19) reference using the Chromosome Analysis Suite software, ChAS 4.0.

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cultured cells using the Qiagen AllPrep DNA/RNA Mini Kit. DNA quality and quantity was assessed using the NanoDrop.

value: Human lymphoblast


title: RNA-Seq_WT_Bio3

description: Ribodepleted RNA


title: RNA-Seq_deltaSTAG2_Bio1

description: Ribodepleted RNA


title: RNA-Seq_WT_Bio1

description: Ribodepleted RNA


title: Diseased_hTERT_biological replicate 4

city: Darlinghurst

first: Andrian

last: Yang

state: NSW

address: 405 Liverpool Street

country: Australia

institute: Victor Chang Cardiac Research Institute

data_processing:
RNA-seq reads were processed using the Falco framework (Yang et al, Bioinformatics 2016 btw732)
Trimmomatic was used to remove TruSeq3 adapter sequence as well as to remove low quality reads using the following parameters: ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
STAR was then used for aligning reads to the hg38 genome, followed by running featureCount to perform read quantification using GTF from Gencode with parameters -s 2 -t exon -g gene_name.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file containing counts values for each gene per sample

molecule: polyA RNA

source_name: Cardiac mesenchymal stem cells

growth_protocol: Human cardiac mesenchymal stem cells were isolated by explant culture and purified by fluorescence-activated cell sorting (PDGFRα+/CD90+/CD31-) as per previously described (Le et al., Stem Cells Dev. 2018 Feb 1;27(3):184-198.)

extract_protocol:
Total RNA from NT, EV and hTERT+ cells was isolated using Isolate II RNA mini kit (Bioline) according to manufacturer’s protocol. RNA purity and quality was confirmed using a Bioanalyser.
RNA-seq libraries were prepared for sequencing on Illumina HiSeq 2500 using the Illumina TruSeq Stranded mRNA sample preparation kit Set A (Illumina, CA, USA). Samples were indexed and run twelve per lane, generating ~ 10 million 50 bp reads per sample.

treatment_protocol: Human cardiac mesenchymal stem cells from young, adult and diseased samples were transduced with hTERT lentivirus in media containing polybrene (8 µg/ml) overnight and then selected with Blasticidin (10 µg/ml) for 5-7 days. Non-transduced (NT) and empty vector (EV)-tranduced cells are included as controls.

tag: disease state

value: diseased (idiopathic dilated cardiomyopathy)

value: hTERT+

value: 54-64 years

tag: gender

value: male

value: left ventricular

value: Cardiac mesenchymal stem cells


title: Diseased_EV_biological replicate 4

value: empty vector control


title: Diseased_NT_biological replicate 4

value: non-transduced control


title: RNA-Seq_WT_Bio2

description: Ribodepleted RNA


title: Diseased_hTERT_biological replicate 3


title: RNA-Seq_deltaSTAG2_Bio2

description: Ribodepleted RNA


title: Diseased_EV_biological replicate 3


title: ChIP-Seq_deltaSTAG2_Input

description: Chromatin

extract_protocol:
Lysates were clarified from sonicated nuclei and target-DNA complexes were isolated with antibody.
Diagenode Microplex V1


title: SiTFEBWnt3aCM1


title: ChIP-Seq_deltaSTAG2_H3K27me3

description: Chromatin

value: Diagenode H3K27me3 polyclonal antibody - Premium (Lot A1811-001P)


title: ChIP-Seq_deltaSTAG2_STAG2

description: Chromatin

value: CST STAG2 (D25A4) XP® Rabbit mAb #5882 (Lot 1)


title: SiGFPLCM1


title: ChIP-Seq_deltaSTAG2_H3K27ac

description: Chromatin

value: Diagenode H3K27ac polyclonal antibody - Premium (Lot A1723-0041D)


title: Diseased_NT_biological replicate 3


title: TK6_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array


title: Diseased_EV_biological replicate 2


title: Diseased_hTERT_biological replicate 2


title: ChIP-Seq_deltaSTAG2_STAG1

description: Chromatin

value: Abcam Anti-SA1 antibody - ChIP Grade (ab4457)


title: ChIP-Seq_WT_Input

description: Chromatin


title: ChIP-Seq_deltaSTAG2_CTCF

description: Chromatin

value: Diagenode CTCF polyclonal antibody - Classic (Lot A2359-00234P)


title: Diseased_hTERT_biological replicate 1


title: Diseased_EV_biological replicate 1


title: Diseased_NT_biological replicate 2


title: ChIP-Seq_WT_H3K27me3

description: Chromatin


title: ChIP-Seq_WT_STAG2

description: Chromatin


title: Adult_hTERT_biological replicate 4

value: non-diseased


title: Adult_EV_biological replicate 4


title: ChIP-Seq_WT_CTCF

description: Chromatin


title: ChIP-Seq_WT_STAG1

description: Chromatin


title: ChIP-Seq_WT_H3K27ac

description: Chromatin


title: Adult_NT_biological replicate 3


title: Adult_hTERT_biological replicate 3


title: Adult_EV_biological replicate 3


title: HiChIP_deltaSTAG2_CTCF_Bio1_Tech1

description: Chromatin

data_processing:
Library strategy: Tn5 Tagmentation
ChIP-Seq reads were aligned with Bowtie2 and peaks called using MACS2.
RNA-Seq reads were aligned with STAR aligner with reads per gene output
HiChIP was processed through the Juicer pipeline to align to hg19, mate interaction pairs and generate contact matrix
Genome_build: hg19
Supplementary_files_format_and_content: ChIP bigWig files generated using Deeptools bamCoverage, normalised to 1x Human Genome. RNA bigWig files normalised to FPKM. HiChIP files are in .hic format for viewing in Juicebox

extract_protocol:
Lysates were digested with MboI, filled in with dNTP's, (Biotin dATP), Ligated and CTCF bound junctions isolated
Nextera DNA library


title: HiChIP_WT_CTCF_Bio2

description: Chromatin


title: HiChIP_WT_CTCF_Bio1

description: Chromatin


title: Adult_hTERT_biological replicate 1


title: Adult_EV_biological replicate 2


title: Adult_NT_biological replicate 2


title: Adult_hTERT_biological replicate 2


title: Adult_EV_biological replicate 1


title: Diseased_NT_biological replicate 1


title: Adult_NT_biological replicate 1


title: AGO2fl/fl;KRASG12D;p48Cre replicate 1

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 E. Medical Center Drive

department: Pathology

institute: University of Michigan

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using STAR v2.7.0f
readcounts were calculated using a protocol from Liao Y et al., Bioinformatics, 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes read counts for each Sample

organism: Mus musculus

source_name: pancreas

growth_protocol: Different genotypes with different lifespans compared

extract_protocol:
Pancreas were excised, RNA extraction was perfomed using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were untreated

tag: strain

value: LSL KRAS mixed

value: pancreas

value: 500 day survival

tag: genotype


title: AGO2fl/fl;KRASG12D;p48Cre replicate 2

tag: tissue

tag: age


title: AGO2+/+;KRASG12D;p48Cre replicate 1

value: 349 day survival


title: Young_hTERT_biological replicate 4

value: hTERT+

value: 2-10 years


title: Adult_NT_biological replicate 4

value: 54-64 years

value: male


title: Young_NT_biological replicate 4

value: left ventricular

value: Cardiac mesenchymal stem cells


title: HiChIP_deltaSTAG2_CTCF_Bio2_Tech1

description: Chromatin

value: Early Monocycte/Macrophages


title: Young_hTERT_biological replicate 3


title: Young_EV_biological replicate 3

value: empty vector control


title: Young_NT_biological replicate 3

value: non-transduced control


title: Young_hTERT_biological replicate 2


title: Young_EV_biological replicate 2


title: GC033954_TCCTGAGC-TAGATCGC

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

data_processing:
Basecalls performed using BCL2Fastq
Fastq  reads were aligned to the mm10 genome assembly using Tophat v2
The minimal score of alignment quality to be included in count analysis was 10.
Resulting SAM and BAM  alignment files were handled with Samtools v0.1.19.24
Genome_build: mm10
Supplementary_files_format_and_content: Quantification of reads per gene was performed with HT-Seq count v0.5.3p3 using Ensembl annotation version 78

source_name: Zeb2-null MyoD

value: myogenic


title: GC033954_TAGGCATG-TAGATCGC


title: GC033954_TAAGGCGA-TAGATCGC

source_name: CTR MyoD


title: GC033954_GGACTCCT-TAGATCGC


title: GC033954_GTAGAGGA-TAGATCGC


title: AGO2+/+;KRASG12D;p48Cre replicate 2

value: 328 day survival


title: GC033954_TAGGCATG-CTCTCTAT


title: GC033954_GCTACGCT-TAGATCGC

source_name: R26_Zeb2 MyoD


title: GC033954_GGACTCCT-CTCTCTAT

source_name: CTR


title: GC033954_TCCTGAGC-CTCTCTAT


title: GC033954_TAAGGCGA-CTCTCTAT


title: Young_EV_biological replicate 1


title: Young_hTERT_biological replicate 1


title: GC033954_CTCTCTAC-TAGATCGC


title: GC033954_CGTACTAG-TAGATCGC


title: GC033954_CGTACTAG-CTCTCTAT


title: GC033954_CTCTCTAC-CTCTCTAT


title: Young_NT_biological replicate 1


title: GC033954_CGAGGCTG-TAGATCGC


title: GC033954_GCTACGCT-CTCTCTAT


title: GC033954_AGGCAGAA-TAGATCGC


title: GC033954_CGAGGCTG-CTCTCTAT


title: GC033954_AGGCAGAA-CTCTCTAT


title: Young_EV_biological replicate 4


title: GC033954_AAGAGGCA-CTCTCTAT


title: GC033954_CAGAGAGG-TAGATCGC


title: GC033954_CAGAGAGG-CTCTCTAT


title: GC033954_AAGAGGCA-TAGATCGC


title: WT-13wk-ctrl-female

city: Philadelphia

first: Peng

last: Hu

state: PA

address: 415 Curie Blvd, 545 CRB

department: Genetics

institute: University of Pennsylvanian

data_processing:
For Drop-seq data sets, paired-end sequencing reads of Single cell RNA-seq were processed using publicly available the Drop-Seq Tools v1.12 software. Briefly, each mRNA read (read2) was tagged with the cell barcode (bases 1 to 12 of read 1) and unique molecular identifier (UMI, bases 13 to 20 of read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned using STAR v 2.5.2a to the mouse (mm10, Gencode release vM13). Cell barcodes were corrected for possible bead synthesis errors, using the DetectBeadSynthesisErrors program from the Drop-Seq Tools v1.12 software. To generate digital expression matrix, a list of UMIs in each gene (as rows), within each cell (as columns), was assembled, and UMIs within ED = 1 were merged together. The total number of unique UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given cell. For 10x Genomics data sets, cellranger was used to generate the digital expression matrix.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression matrix containing read counts for each gene (rows) in each cell (columns)

source_name: Pituitary

extract_protocol:
Single cell pituitary suspensions were prepared by non-enzymatic methods as previously descripted (Ho et al., 2011) with minor modifications to adapt to the Drop-seq protocol (Macosko et al., 2015). Briefly, the pituitaries were isolated and washed with cold PBS, incubated with 1 ml of enzyme-free cell dissociation buffer (Life technologies, Carlsbad, CA) for 1 minute, passed through a 40 μm cell strainer, and then re-suspend in 10 ml of PBS.
For Drop-Seq, single cell, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (uFluidix). Cells in droplets were lysed and hybridized to beads. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by tagmentation of cDNA (Illumina), and amplified by PCR and purified by SPRI beads. For 10x Genomics, single cell suspension of mouse pituitary was loaded onto a well on a 10x Chromium Single Cell instrument (10x Genomics). Library preparation was performed according to the manufacturer’s instructions (Chromium Single Cell 3’ Library & Gel Bead Kit v2).

tag: developmental stage

value: 13 weeks

value: WT

value: female

tag: physiological condition

value: Virgin

tag: datatype

value: Drop-Seq


title: WT-13wk-lac1-female

tag: Sex

value: Lactation


title: WT-13wk-lac2-female


title: WT-8wk-0511-female

value: 8 weeks

value: Undertermined


title: transgenic-8wk-female

value: mt/hGRF


title: WT-8wk-0324-female


title: WT-8wk-0324-male

value: male


title: IgG_2

city: Worcester

first: Sneha

last: Shah

state: Massachusetts

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

institute: UMASS CHAN MEDICAL SCHOOL

data_processing:
The broad peaks for H3K36me3 ChIP-Seq were called using the SICER v1.1 package (Xu et al., 2014)
ChIP-seq read alignments were performed with Bowtie2 (2.1.0) using the mm10 genome, duplicates were removed with Picard and TDF files for IGV viewing were generated using a ChIP-seq pipeline from DolphinNext (Yukselen et al., 2019)
H3K36me3 enriched islands were identified using the parameters set to a window size of 200bp, gap size 600bp and FDR cutoff of 1 × 10-3, and the default value for the redundant rate cutoff. Significantly enriched islands for each genotype were identified using the sicer-df.sh script with an FDR cutoff of 1 × 10-3.
Genome_build: mm10

source_name: Hippocampus tissue

growth_protocol: Hippocampal tissue was isolated from 4 adult mice (P35) per genotype and minced into tissue < 0.5mm3 in 250ul of ice-cold PBS with protease inhibitors. Tissue was cross-linked with 1% formaldehyde and rotated at room temperature for 15 min at 50 rpm and quenched with 150mm glycine for 10 min in a total volume of 1ml PBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For library preparation, purified input and IP DNA was end repaired using T4 DNA polymerase, Klenow polymerase and T4 Polynucleotide kinase. DNA was extracted using Agencourt Ampure XP beads and ‘A’ bases were added to the 3’ end using Klenow exonuclease (3’ to 5’ exo minus) from NEB. DNA was purified using Agencourt Ampure XP beads and Illumina adapter sequences were ligated to the DNA fragments using the Quick Ligase (NEB). The library was size-selected using Agencourt Ampure XP beads. Using the multiplexing barcoded primers, the library was PCR amplified and purified and analyzed using a Fragment Analyzer (Advanced Analytical, performed by Molecular Biology Core Labs at UMMS). Libraries were pooled with equal molar ratios, denatured, diluted, and sequenced with NextSeq 500/550 High Output Kit v2.5 (Illumina, 75bp paired-end runs,) on a Nextseq500 sequencer (Illumina).

value: C57BL/6N (wild-type)

value: Male

value: Hippocampus

value: IgG (Sigma 12-371, 5 μg per ChIP)


title: WT-8wk-0511-male


title: IgG_3

value: B6.129P2-Fmr1tm1Cgr/J (Fmr1 KO)


title: WT-8wk-male

value: 10x Genomics


title: IgG_4


title: WT-8wk-female


title: Young_NT_biological replicate 2

value: non-diseased

tag: treatment

value: non-transduced control

value: 2-10 years

value: left ventricular

tag: cell type

value: Cardiac mesenchymal stem cells


title: Input_4


title: Input_1


title: H3K36me3_3

value: H3K36me3 (Abcam ab9050, 5μg per ChIP)


title: Input_3


title: H3K36me3_4


title: ATAC_DZp.2

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw reads were be aligned to reference genome mm9 using BWA MEM (Li, 2013). Apparent PCR duplicates were removed using Picard MarkDuplicates (Wysoker, et al., 2013). Read alignments were adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. Open chromatin peaks were called using Macs2 (Zhang, et al., 2008) with --nomodel set and no background provided; peaks with a score >5 were retained.
genome build: mm9
Supplementary_files_format_and_content: peak bed file: peak calls from Macs2 in bed format

source_name: Germinal center B cells

extract_protocol: To prepare Nuclei, respective flow sorted mouse GC B cell subsets (100,000) were centrifuged at 500g for 5 min, which was followed by a wash with ice-cold PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min at 4oC and supernatant removed. The nuclei pellet was resuspended in the transposase reaction mix (25 μL 2X Tagment buffer, 2.5 μL Tagment DNA enzyme (Illumina, FC-121-1030) and 22.5 μL nuclease-free water). The transposition reaction was carried out at 37 °C for 30 min. Directly following transposition the sample was purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10-12 cycles. The libraries were then purified using a Qiagen PCR cleanup kit. The amplified, adapter ligated libraries were size selected using Life Technologies' E-Gel® SizeSelect™ gel system in the 150-650bp range. The size-selected libraries were quantified using the Agilent Bioanalyzer and via q-PCR in triplicate using the KAPA Library Quantification Kit on the Life Technologies Step One System. Libraries were sequenced on the Illumina NextSeq 500 system to generate 75-100M, 42bp paired end reads.

treatment_protocol: Mice were immunized intraperitoneally with 10^9 sheep red blood cells in PBS, then boosted with 10^9 SRBC 5 days later. On day 14, germinal center B cells were isolated from spleens for downstream applications.

value: Germinal center B cells

tag: sorting strategy

value: GC B cells FACS isolated by the new three population strategy were defined as follows. Total GC B cells were defined as B220+GL7+CD95+, then subsets were defined based on CXCR4 and CD83 expression. Proliferative DZ B cells (DZp) were defined as CXCR4+CD83+ (also described as gray zone [GZ] B cells), differentiating DZ B cells were CXCR4+CD83-, and LZ cells were defined as CXCR4-CD83+ GC B cells.


title: ATAC_LZ.1


title: H3K36me3_2

tag: chip antibody


title: ATAC_DZp.1


title: ATAC_LZ.2


title: Input_2


title: IgG_1


title: H3K36me3_1


title: ATAC_DZd.2


title: ATAC_DZd.1


title: ATAC_Classic_GC_DZ.1

value: Classic GC DZ and LZ B cells were sorted using FACS. Classic GC DZ B cells were defined as B220+GL7+CD95+CXCR4+CD83lo, and classic GC LZ B cells were defined as B220+GL7+CD95+CXCR4loCD83+.


title: ATAC_Classic_GC_LZ.1


title: ATAC_Classic_GC_DZ.2


title: ATAC_Classic_GC_LZ.2


title: ChIP_Classic_GC_LZ_H3K4me1.2

data_processing:
Raw reads were be aligned to reference genome mm9 using BWA MEM (Li, 2013). Apparent PCR duplicates were removed using Picard MarkDuplicates (Wysoker, et al., 2013). Peaks were called against inputs using Macs2 (Zhang, et al., 2008). Peaks with a score >5 were retained.
genome build: mm9
Supplementary_files_format_and_content: peak bed file: peak calls from Macs2 in bed format

extract_protocol: Chromatin from the indicated flow sorted GC B cell population (1-2 million cells) was used for each ChIP experiment with anti-H3K4me1 (Millipore 07-436) or anti-H3K27Ac (Abcam ab4729) antibody. DNA libraries were prepared by tagmentation from the sheared chromatin (200–600 bp). Libraries were sequenced on the Illumina Hiseq4000.


title: ChIP_Classic_GC_LZ_H3K27Ac.2


title: JSC153CD44v9Minus

city: Tokyo

first: Tetsuo

last: Mashima

address: Koto-ku, Ariake 3-8-31

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: Human Gastric Cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The cell line was cultured in vitro in 10cm dishes until 80-90% confluency and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: no treatment

tag: cell line

tag: sorted cell


title: TFEB-tg ECM-Rep_3-2

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: Gene expression of bone marrow-derived macrophages from LysM-Double-Cre x TFEB transgene+ mice treated with EO771 tumor-conditioned medium and lyste in DMEM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.5 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 14.8 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

source_name: BMDMs from LysM-Double-Cre x TFEB transgene+ mice treated with EO771 tumor-conditioned medium and tumor lysate in DMEM

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: Legs from eight week-old female LysM-Double-Cre x TFEB transgene+ and LysM-Double-Cre x TFEB transgene- mice were obtained from Babak Razani (Washington University in St. Louis).

extract_protocol: Total RNAs were isolated from bone marrow-derived macrophages using RNeasy Mini kit (Qiagen, Germantown, MD) following the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer.

treatment_protocol: Bone marrow was differentiated into macrophages using recombinant M-CSF. After one week of differentiation, macrophages were replated and treated with either DMEM only or DMEM supplemented with tumor-conditioned medium (serum-free DMEM supernatant exposed to EO771 tumor cells) and tumor lysate for 24 hours.

tag: strain background

tag: genotype/variation

value: LysM-Double-Cre x TFEB transgene+

value: 8 weeks

value: female

value: bone marrow-derived macrophage (BMDM)


title: TFEB-wt ECM-Rep_3

description: Gene expression of bone marrow-derived macrophages from LysM-Double-Cre x TFEB transgene- mice treated with EO771 tumor-conditioned medium and lyste in DMEM

source_name: BMDMs from LysM-Double-Cre x TFEB transgene- mice treated with EO771 tumor-conditioned medium and tumor lysate in DMEM

value: LysM-Double-Cre x TFEB transgene- mice


title: ChIP_Classic_GC_LZ_H3K4me1.1


title: JSC153CD44v9Plus


title: TFEB-tg Control-Rep_1

description: Gene expression of bone marrow-derived macrophages from LysM-Double-Cre x TFEB transgene+ mice treated with DMEM only

source_name: BMDMs from LysM-Double-Cre x TFEB transgene+ mice treated with DMEM only

value: DMEM only


title: TFEB-tg Control-Rep_3


title: TFEB-tg ECM-Rep_3

value: EO771 tumor-conditioned medium and lyste in DMEM


title: TFEB-tg Control-Rep_2


title: ChIP_Classic_GC_LZ_H3K27Ac.1


title: TFEB-wt ECM-Rep_3-2


title: TFEB-wt ECM-Rep_1


title: TFEB-tg ECM-Rep_2


title: ChIP_Classic_GC_DZ_H3K4me1.2


title: TFEB-wt Control-Rep_1

description: Gene expression of bone marrow-derived macrophages from LysM-Double-Cre x TFEB transgene- mice treated with DMEM only

source_name: BMDMs from LysM-Double-Cre x TFEB transgene- mice treated with DMEM only


title: ChIP_Classic_GC_DZ_H3K4me1.1


title: TFEB-wt ECM-Rep_2


title: TFEB-wt Control-Rep_3-2


title: G0 cell at 48 hours in suspension with Wnt3A, biological rep2

city: SAN ANTONIO

first: PRETHISH

last: SREENIVAS

state: TX

address: 8403 Floyd Curl Dr

department: GCCRI

institute: UTHSCSA

hyb_protocol: Purified Labelled cDNA was incubated on the Affymetrix 430A_2 Chip according to manufacturers protocol

scan_protocol: Scanned using Affymetric microarray scanner

data_processing:
Gene Chip operating software (GCOS) of Affymetrix followed by AvadisTM software version 4.3 (an Affymetrix approved software manufactured by Strand Life Sciences, Bangalore, India
The data normalization was performed using PLIER algorithm and genes with differential expression of ≥ 1.5 fold, either upregulated or downregulated with p ≤ 0.05 were processed for further analysis

label: bitoin

source_name: C2C12 Cell line in methyl cellulose suspension treated with Wnt3A

label_protocol: 20 micrograms of RNA is taken for labelling with affymetrix protocol

growth_protocol: Grown in Dulbecco's modified Eagle medium supplemented with 20% Fetal calf serum

extract_protocol: RNA was isolated using Trizol Invitrogen)

treatment_protocol: Synchronized cells in G0 by culturing in semi solid methyl cellulose and treated with 50 ng/ml of purified Wnt3A for 48 hours


title: G0 cell at 48 hours in suspension, biological rep2

source_name: C2C12 Cell line in methyl cellulose suspension

value: control


title: ChIP_Classic_GC_DZ_H3K27Ac.2


title: G0 cell at 48 hours in suspension with Wnt3A, biological rep1


title: ChIP_Classic_GC_DZ_H3K27Ac.1


title: sham_hippocampus

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: sham hippocampus

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

value: ICR

tag: cell

value: hippocampus


title: TFEB-wt Control-Rep_3


title: TFEB-wt Control-Rep_2


title: G0 cell at 48 hours in suspension, biological rep1


title: Leukemia 2

first: Hideaki

last: Mizuno

address: HongoSanchome 7-3-1

institute: Unviersity of Tokyo

data_processing:
Illumina CASAVA ver 1.8.2 was used for basecalling.
Sequence reads were mapped to reference sequence using CLC Genomics Workbench software with standard parameters.
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) also using CLC Genomics Workbench software.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files including RPKM for each sample.

source_name: bone marrow

extract_protocol:
GFP+Lin-c-kit+ cells were isolated using flow cytometry cell sorting. Total RNA was extracted using Nucleospin RNA.
RNA library was prepared using NEB Next Ultra RNA Library Prep Kit for Illumina.

tag: strain

value: GFP+ Lin- c-kit+ bone marrow cells

tag: variation


title: Leukemia 1


title: Preleukemia 1


title: mock2

value: GFP


title: mock1


title: 5_6_hippocampus

source_name: 5/6 hippocampus


title: Capsella grandiflora 10 day old seedlings 1

city: Uppsala

first: Adrien

last: Sicard

address: Almas Allé 5

department: Uppsala BioCenter

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
RNA545 Seq data were processed using Trimmomatic (Bolger et al., 2014) to remove adapter sequences.
Reads for all samples were mapped against the C. rubella reference genome (Cru_183 from phytozome.org).
Quantification for C. rubella predicted genes was done using HTSeq-count (Anders et al., 2015).
Genome_build: Cru_183 (phytozome.org).
Supplementary_files_format_and_content: Raw read counts.

organism: Capsella grandiflora

source_name: 10 day old seedlings

extract_protocol:
Total RNA was extractedusing RNeasy Plant Mini Kit (Qiagen).
TruSeq RNA libraries were generated according to the manufacturer’s instructions (Illumina) and sequenced using the Illumina HiSeq2000 instrument (1 × 50 cycles).

value: 10 day old seedlings


title: Capsella grandiflora 10 day old seedlings 2


title: Capsella grandiflora 10 day old seedlings 3


title: Capsella grandiflora dividing flower buds 3

source_name: dividing flower buds

value: dividing flower buds


title: ZBTB1 KO + ZBTB1 cDNA No Asparagine ATAC

first: Robert

last: Williams

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Reads were aligned using Rsubread's align method and predicted fragment lengths calculated by the ChIPQC package.
Normalised, fragment extended signal bigWigs are created using the rtracklayer package.
Peak calls are made in HOMER software and their peak summits used in MEME-ChIP software for known and de novo motif discovery.
Read counts in peaks are calculated using the featureCounts method in the Rsubread library.
Differential ChIP-seq signal is identified using the binomTest from the edgeR package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq and ATAC-Seq: bigWig files
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text file (mergedDF.txt)  includes RPKM values for each sample.

source_name: Jurkat cells

extract_protocol:
RNA: Cells were harvested and RNA was isolated by Qiagen RNeasy kit. 1ug of total RNA was used for construction of sequencing libraries.
ChIP: Cells were cross-linked with 1% paraformaldehyde for 10 minutes at 37C. Cross-linking was quenched with 125 mM glycine. Cells were pelleted and flash-frozen in liquid nitrogen. Nuclei were isolated and sonicated using a Covaris sonicator. Protein A/G beads were added to 2-4 ug of appropriate antibodies and bound at room temperature for 1.5 hours. Samples were immunoprecipitated with appropriate protein A/G-antibody complexes overnight at 4C. Immunoprecipitates were collected and washed twice each with low salt, high salt, and lithium chloride wash buffers. DNA was eluted, reverse-crosslinked and treated with RNase and proteinase K before being isolated with a PCR purification kit (Zymogen).
ATAC: Cells were treated in the presence or absence of asparagine for 24 hours. Nuclear extracts were prepared from 100,000 cells for each cell line and condition, and incubated with 2.5 μl of transposase (Illumina) in a 50 μl reaction for 30 min at 37 °C. Transposase-fragmented DNA was purified, and the library was amplified by PCR.
RNA, ATAC and ChIP libraries were prepared using standard Illumina protocols.

value: Jurkat

value: ZBTB1 KO expressing ZBTB1 cDNA

value: Asparagine deprivation


title: Preleukemia 2


title: ZBTB1 KO + ZBTB1 cDNA Untreated ATAC

value: Normal media conditions


title: Heart, WT, HFD, RT18

city: SEATTLE

first: Rong

last: Tian

state: WA

address: 850 Republican Street, Room N130

institute: University of Washington

data_processing:
The low quality reads, reads with adaptors and reads with unknown bases were filtered with the software SOAPnuke to get the clean reads
Clean reads were mapped to the reference using Bowtie 2 and calculate gene expression level using RSEM
Differential gene expression analysis was conducted with R packages DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: comma-separated values (CSV) files include RPKM values for each Sample

source_name: Heart

growth_protocol: At 8 weeks of age, both ACC2f/f−MCM+ and ACC2f/f mice received an intraperitoneal injection of tamoxifen (20mg/kg) for 5 days, which was sufficient to cause ACC2 deletion in ACC2f/f−MCM+.

extract_protocol:
Total RNA was extracted from frozen LV tissue using the RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA samples (RNA integrity number (RIN) >8) were submitted to Northwest Genome Center for library preparation and sequencing. Poly(A)- enriched cDNA libraries were prepared using the Illumina TruSeq RNA Library Preparation kit according to the manufacturer’s instructions. Samples were run on Illumina HiSeq 2000 at a read length of 100nt single end, and a depth of about 50 million per sample. Five mice per genotype or diet condition are used for subsequent analysis
Poly(A)- enriched cDNA libraries were prepared using the Illumina TruSeq RNA Library Preparation kit according to the manufacturer’s instructions

treatment_protocol: Four weeks after the last injection of tamoxifen, ACC2f/f (designated as Con) and ACC2f/f−MCM+ (designated as iKO) mice were subjected to high fat diet (Research Diets, D12492) feeding for 16 weeks

tag: genotype

value: WT

tag: diet

value: HFD

tag: tissue

value: Heart


title: Heart, ACC2 iKO, HFD, RT20

value: ACC2 iKO


title: Heart, ACC2 iKO, HFD, RT17


title: Heart, WT, HFD, RT19


title: ZBTB1 KO No Asparagine ATAC

city: New York

value: ZBTB1 KO


title: Capsella grandiflora dividing flower buds 2

tag: developmental stage


title: Heart, ACC2 iKO, HFD, RT15


title: Heart, WT, HFD, RT14


title: Capsella grandiflora dividing flower buds 1


title: Capsella grandiflora expanding/maturing flower buds 3

source_name: expanding/maturing flower buds

value: expanding/maturing flower buds


title: ZBTB1 KO Untreated ATAC


title: Heart, WT, HFD, RT16


title: Wild Type Untreated ATAC

value: Wild type


title: Heart, ACC2 iKO, HFD, RT13


title: Capsella grandiflora expanding/maturing flower buds 2


title: Heart, WT, HFD, RT12


title: Capsella grandiflora expanding/maturing flower buds 1


title: Heart, ACC2 iKO, control, RT9

value: chow


title: Sox6_ChIP-Seq

first: Shinsuke

last: Ohba

address: 7-3-1 Hongo, Bunkyo-ku

department: Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine

institute: The University of Tokyo

data_processing:
DNA-sequence information was aligned to the unmasked mouse genome reference sequence mm9 by bowtie aligner
Peak calling was performed by two-sample analysis on CisGenome software with FDR<0.01 with the input control without antibody immunoprecipitation.
CisGenome software does not give quantitative data.
Genome_build: mm9
Supplementary_files_format_and_content: .bed file reports peaks

source_name: Primary rib chondrocytes

growth_protocol: Neonatal ICR wild-type mice postnatal day 1 rib

extract_protocol:
Rib chondrocytes were manually dissected from ribs of P1 neonatal wild-type ICR mice to include proliferative and prehypertrophic regions and to exclude mature hypertrophic regions.Superficial soft tissue was removed, and ribs were washed in DMEM. Segmented ribs were initially digested in 0.05% Trypsin/EDTA (T4174; Sigma-Aldrich) for 30 minutes at 37 °C, and then in 0.3% Collagenase D (1088858; Roche) for 45 minutes at 37 °C.Rib chondrocytes isolated from newborn wild-type ICR mice were immediately cross-linked with 1% formaldehyde for 10 minutes at room temperature. The crosslinking was quenched by addition of 2.5 M Glycine at the final concentration of 130 mM. Twenty million cells were used for a ChIP reaction. After washing with phosphate buffered saline (PBS) twice, cells were lysed in Lysis buffer (50 mM HEPES-KOH pH 7.5,140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% IGEPAL CA-630, 0.25% Triton-X 100) at 4 ℃ with agitation for 10 minutes, and then washed with Buffer 2 (10 mM Tris-HCl pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 minutes at room temperature. Chromatin was sonicated in Buffer 3 (10 mM Tris-HCl pH8.0, 1 mM EDTA, 0.5 mM EGTA) by 10 sessions of 30 pulses (1 sec on and 1 sec off) at 50% amplitude using the Branson Advanced-Digital sonifier 250 (Branson Ultrasonics Corporation, Danbury, CT) in order to obtain 100 – 600 bp of DNA fragments. Lysate was cleared by centrifugation and addition of 20% N-Lauroylsarcosine Sodium Salt (L9150; Sigma-Aldrich, St. Louis, MO) at the final concentration of 0.5%. One hundred microlitters of Dynabeads M-280 Sheep anti-Rabbit IgG (112-03D; Life Technologies, Carlsbad, CA) was combined with 10 μg of anti-Sox6 antibodies (ab30455; Abcam, Cambridge, UK). The beads/antibody complex was incubated with the lysate overnight at 4 ℃. Beads were washed 5 times with RIPA buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 0.7% Sodium Deoxycolate, 1% IGEPAL CA-630) and once with TE buffer containing 50 mM NaCl. DNA was eluted with Elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) at 65 ℃ for 15 minutes, and the eluate was incubated overnight at 65 ℃ for reverse crosslinking. After the eluate was treated with RNase (R4642; Sigma-Aldrich) and proteinase K (25530015; Invitrogen), DNA was purified by MinElute PCR Purification kit (28004; Qiagen).
Libraries were constructed with ThruPLEX DNA-seq Kit (R400429; Rubicon Genomics, Ann Arbor, MI) according to manufacturer’s instructions.

treatment_protocol: Wild type, not treated

value: ICR

tag: age

value: rib

value: Primary rib chondrocytes

value: anti-Sox6 (ab30455; Abcam, Cambridge, UK)


title: Heart, WT, control, RT10


title: Wild Type No Asparagine ATAC


title: Heart, WT, control, RT8


title: Heart, ACC2 iKO, HFD, RT11


title: ch12_Med14Nsmash_chipseq_SP1_APR60h_input

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

description:
input
SP1_merged_peaks.bed

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)

source_name: CH12 B cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of -mercaptoethanol (Thermo Fisher Scientific). A 3xFlag and small molecule–assisted shutoff (SMASh) tag was introduced to the N-terminus of Med14 using CRISPR-Cas9 based knock-in via homologous recombination. Single cell clones were established and degradation of Med14 was assessed by western blotting for Med14 (Abcam) after treatment of cells with 3 M Asunaprevir (MCE).

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 3000 or Novaseq 6000 (Illumina).

value: lymphoma cell line


title: ch12_Med14Nsmash_chipseq_SP1_DMSO_input

description:
input
SP1_merged_peaks.bed

value: DMSO


title: HUVEC_ETV2_Flag3_2

first: Ying

last: Liu

address: 1300 York Ave

department: Medicine

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using BWA (version 0.5.9) with default parameters
Duplicates were removed using Picard (version 1.69).
The software MACS2 was applied to the ChIP-seq data with sequencing data from input DNA as control to identify genomic enrichment (peak) of ETV2 (FDR<0.05). The software SICER1.1 was applied to the ChIP-seq data with sequencing data from input DNA as control to identify genomic enrichment (peak) of histone modifications, and compare the enrichment change between different cell types.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files include all unique reads that mapped to a single best-matching location.

source_name: Human Umbilical Vein Endothelial Cells (HUVEC)

growth_protocol: complete EC media

extract_protocol:
To identify genome-wide localization of ETV2 in R-VEC, ChIP assays were performed with approximately 1x10e7 cells per experiment. Cells introduced with triple flagged ETV2 lentivirus were used for the ETV2 ChIP. Briefly, cells were crosslinked in 1% paraformaldehyde (PFA) for 10 min at 37°C, then quenched by 0.125M glycine. Chromatin was sheared using a Bioruptor (Diagenode) to create fragments of 200-400 bp, immunoprecipitated by 2–5 ug of antibody bound to 75 ml Dynabeads M-280 (Invitrogen) and incubated overnight at 4°C. Magnetic beads were washed and chromatin was eluted. The ChIP DNA was reverse-crosslinked and column-purified.   To identify genome-wide localization of K4me3, K27me3, and K27ac modification, small-scale ChIP assays were performed with approximately 1x104 cells per experiment. Briefly, cells were washed once with nuclei extraction buffer (10 mM Tris-HCl pH 8.5, 2 mM EDTA, 140 mM NaCl, 5 mM MgCl2, 0.6% NP40, 1x EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride). The chromatin was fragmented for 5 min using MNase at 25 °C, diluted in ChIP buffer (10 mM Tris-HCl pH 8.0, 2 mM EDTA, 90 mM NaCl, 0.1% Triton X-100, 0.1% NaDOC, 1x EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride), and then immunoprecipitated with 1 ug of antibody bound to 10 ml Pierce Protein A/G Magnetic Beads (Invitrogen) and incubated overnight at 4°C. Magnetic beads were washed and chromatin was eluted. The ChIP DNA was reverse-crosslinked, purified by phenol chloroform, and precipitated by ethanol.
ChIP samples were prepared for sequencing using KAPA Hyper Prep Kit.

treatment_protocol: HUVEC lenti ETV2

value: HUVEC

value: Flag (Sigma F1804)

value: lenti ETV2

tag: growth

value: induction (flat 2d)


title: Heart, ACC2 iKO, control, RT6


title: HUVEC_ETV2_Flag3_1

tag: treatment


title: Input_8h_rep2

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
The raw reads (single-end, 50 bp) were aligned to mouse reference genome hg19 using bowtie (v1.1.0) allowing up to one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: Peak calling was performed using MACS (v1.4.2) with the default cutoff of P ≤ 1 × 10-8. Clonal reads were automatically removed by MACS.

source_name: UMRC6, Glucose media for 8h

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle's Medium  with 10% foetal bovine serum (FBS), 2 mM glutamine and100 U penicillin / 0.1 mg/ml streptomycin. When the cells were approximately 80% confluent,  1:3 split was carried out to keep sub-culturing.

extract_protocol:
Chromatin immunoprecipitation was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003) following the instructions of the manufacturer. 20 μg of chromatin was incubated overnight with 5 μl H2Aub antibody (Cell Signaling Technology, 8240). 100 ng fly chromatin and 0.5 μg H2Av antibody (ActiveMotif, 61686) was added in each tube as spike-in control. Purified ChIP-DNA was verified by agarose gel to make sure properly fragmented and sent to Sequencing and Microarray Facility at MD Anderson Cancer Center for ChIP-seq.
ChIP–seq samples were sequenced using the Illumina HiSeq 2000 .

treatment_protocol: UMRC6 cultured in 15cm-dish at 95% confluency were treated fresh media with or without glucose for 8 hours. Then cells were fixed in media containing 1% formaldehyde and subjected to ChIP according to manufacture's instructions (Cell Signaling Technology, #9003).

tag: cell type

value: Glucose media for 8h


title: wild type aged rep3 [treatment 4]

city: Bydgoszcz

first: Katarzyna

last: Bilińska

address: M.Skłodowskiej-Curie 9

country: Poland

institute: Nicolaus Copernicus University

description: Sample 30

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Then the RNA-Seq reads are aligned to the reference genome (mm10) using Bowtie vs 2.3.3.1 generating genome alignments.
Operating on the RNA-Seq alignments and Cuffinks processing, Cuffidfff tracks the mapped reads and determines the fragment per kilobase per million mapped reads (FPKM) for each transcript in all the samples.
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, the genes are listed with the expression values (FPKM) in a tab separated text  file.
Supplementary_files_format_and_content: For each pair of samples (control vs. case), the differential expression values such as fold change and p-value are computed at gene level and are listed in a tab separated text file.

source_name: wild type aged_olfactory mucosa

extract_protocol:
Olfactory mucosa were dissected from nasal cavity under binocular microscope and immediately frozen on dry ice. RNA was extracted using QIAGEN RNeasy Plus Mini kit with gDNA Eliminator columns, the concentration of which was measured using NanoDrop DS-11 FX Spectrophotometer.
The library preparation protocol was self-established and validated on the basis of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: wild type aged

value: post natal day 750

tag: Sex

value: male

value: olfactory epithelium


title: Heart, WT, control, RT5

value: WT

value: Heart


title: Input_8h_rep1

tag: chip antibody


title: NGSD_34692

city: Bethesda

first: Heidi

middle: G

last: Parker

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

description: genomic DNA extracted from blood was genotyped using the CanineHD Whole-Genome Genotyping BeadChip (Illumina)

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio 2.0 with GT module (Illumina).

organism: Canis lupus

source_name: blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols. DNA was extracted from skin using the DNeasy Blood And Tissue kit (Qiagen) following recommended protocol.

tag: sub-type

value: New Guinea Singing Dog


title: wild type aged rep2 [treatment 4]

description: Sample 15


title: HUVEC_ETV2_K27ac_1

value: H3K27ac (Active Motif 39133)


title: Heart, ACC2 iKO, control, RT4

value: ACC2 iKO

value: chow


title: NGSD_33254


title: HUVEC_ETV2_K27me3

value: H3K27me3 (millipore 07-449)


title: PS2-KO rep3 [treatment 3]

description: Sample 5

source_name: PS2-KO_olfactory mucosa

value: post natal day 60


title: Input_0h_rep2

source_name: UMRC6, Glucose free media for 8h

value: Glucose free media for 8h


title: NGSD_35131


title: NGSD_31969


title: NGSD_34696


title: Heart, WT, control, RT3


title: NGSD_34695


title: NGHW_34326

value: Highland Wild Dog


title: NGSD_35130


title: NGSD_34697


title: PS2-KO rep2 [treatment 3]

description: Sample 4


title: Input_0h_rep1


title: DING_03521

value: Dingo


title: HUVEC_ETV2_K4me3_1

value: HUVEC

value: H3K4me3 (Cell Signaling 9727)

value: lenti ETV2

value: induction (flat 2d)


title: Heart, WT, control, RT1


title: H2Aub_8h_rep2

value: Glucose media for 8h

value: H2Aub (Cell Signaling Technology, #8240)


title: PS2-KO rep1 [treatment 3]

description: Sample 31

value: male

value: olfactory epithelium


title: NGSD_35133

value: New Guinea Singing Dog


title: NGSD_34698


title: APLP2-KO rep3 [treatment 2]

description: Sample 8

source_name: APLP2-KO_olfactory mucosa


title: HUVEC_ETV2_input_3


title: HUVEC_ETV2_input_2


title: NGHW_34327


title: APLP2-KO rep2 [treatment 2]

description: Sample 7


title: H2Aub_0h_rep2


title: DAOY cells, siSMO2

city: Zhoukou

first: Li

last: Guoyin

address: Wenchang street

department: College of Life Science and Agronomy

country: China

institute: Zhoukou Normal University

description:
fpkm.txt
total.table.txt
single.table.txt
GO.BP.report.txt
GO.BP.enrichment.txt
GO.CC.report.txt
GO.MF.report.txt
GO.MF.enrichment.txt
KEGG.txt
ppi.edge.txt
ppi.node.txt

source_name: daoy medulloblastoma cells

extract_protocol:
Three cases of paired siNC and siSMO cells were prepared for the extraction of total RNA. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Daoy cells were plated in 6-well plates at 80% confluence, transfected with SMO siRNA (siSMO,50 nM), or a negative control siRNA (siNC,50 nM) with Lipofectamine®2000 in Opti-MEM medium (Invitrogen), according to the manufacturer’s protocol. The transfected cells were incubated at 37°C for an additional 48h and total RNA was extracted using the TRIzol reagent (Invitrogen).

tag: cell line

value: DAOY

value: human medulloblastoma cells

tag: subtype

value: Sonic Hedgehog

value: SMO knockdown


title: Heart, ACC2 iKO, control, RT7

value: ACC2 iKO

value: chow

value: Heart


title: H2Aub_0h_rep1

value: Glucose free media for 8h


title: HUVEC_ETV2_input_1

value: HUVEC


title: DAOY cells, siSMO1


title: DAOY cells, siSMO3


title: NGHW_34328

description: genomic DNA extracted from skin was genotyped using the CanineHD Whole-Genome Genotyping BeadChip (Illumina)

source_name: skin

value: Highland Wild Dog


title: APP-KO rep3 [treatment 1]

description: Sample 28

source_name: APP-KO_olfactory mucosa

tag: strain background

value: APP-/-

value: post natal day 60


title: DAOY cells, siNC3

value: control


title: HUVEC_ETV2_IgG

value: lenti ETV2

value: induction (flat 2d)


title: Heart, ACC2 iKO, control, RT2


title: APP-KO rep2 [treatment 1]

description: Sample 19

value: male

value: olfactory epithelium


title: H2Aub_8h_rep1

value: Glucose media for 8h

value: H2Aub (Cell Signaling Technology, #8240)


title: HUVEC_ETV2_K4me3_2

value: H3K4me3 (Cell Signaling 9727)


title: APLP2-KO rep1 [treatment 2]

description: Sample 25


title: WT rep3 [normal]

description: Sample 3

source_name: WT_olfactory mucosa

value: wild type


title: DAOY cells, siNC1

value: DAOY

value: human medulloblastoma cells

value: Sonic Hedgehog


title: APP-KO rep1 [treatment 1]

description: Sample 18


title: HUVEC_K27ac_1

treatment_protocol: HUVEC CTRL

value: H3K27ac (Active Motif 39133)

value: CTRL

value: flat (2D)


title: HUVEC_K27me3_2

value: HUVEC

value: H3K27me3 (millipore 07-449)


title: WT rep2 [normal]

description: Sample 2

value: post natal day 60


title: WT rep1 [normal]

description: Sample 1


title: HUVEC_K27me3_1


title: HUVEC_K4me3_1


title: HUVEC_K27ac_2


title: Traf3KO-p100KO-RED-Rep1

city: Nashville

first: Maria

last: Fomicheva

state: TN

address: 465 21st Avenue S., U 3200 MRBIII, Dept. of Cell and Developmental Biology Vanderbilt University

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Sequenced reads were demultiplexed, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Illumina software
CLC Workbench was used for sequence mapping, data shown as reads per million mapped reads (RPM)
CLC Workbench was used to compare NT vs Traf3 KO and Traf3 KO vs Traf3/p100 double KO

source_name: EpH4 mammary gland cell line

growth_protocol: EpH4-FUCCI cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (Atlanta Biologicals), and 1x penicillin/streptomycin (Life Technologies).

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We transduced EpH4-FUCCI mammary epithelial cell line with non-targeted (NT), Traf3, or Traf3 plus p100 sgRNA lentiviruses. The cells were seeded at 100,000 cells/cm2 and cultured for 4 days, then trypsinized with 0.25% Trypsin (Gibco) and sorted on a FACSAria lll for mCherry+ (G1/G0) cells

value: EpH4 mammary gland cell line stably expressing ES-FUCCI construct

value: Traf3/p100 double KO

tag: day postconfluency

tag: experimental repeat


title: Traf3KO-p100KO-RED-Rep2


title: HUVEC_input


title: DAOY cells, siNC2

value: control


title: Traf3KO-RED-Rep1

value: Traf3 KO


title: NT-RED-Rep1

value: NT


title: HUVEC_K4me3_2


title: ch12_Med14Nsmash_chipseq_Brd4_DMSO_input

description:
input
Brd4_merged_peaks.bed

value: lymphoma cell line

value: DMSO


title: Traf3KO-RED-Rep2


title: ch12_Med14Nsmash_chipseq_Brd4_APR48h_input

description:
input
Brd4_merged_peaks.bed


title: D0_MSC: MSC pre-injury at Day 0

city: Ann Arbor

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
QC: We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample. We use TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) to trim low-quality bases (quality score lower than 20), adapter sequences (nextera adapter, required overlap of 6bp), and end-repair bases from the 3’ end of reads. Reads shorter than 20bp after trimming are discarded.
Aligment: We align trimmed reads to mm10 with Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4.1) with the ATAC specific parameters -X 2000 --no-mixed --no-discordant, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads are marked with Picard (Picard) (v2.20.2). Alignments to autosomes are kept (i.e. sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard are removed, and alignments below a MAPQ threshold are removed (< 10). These filtering steps are performed with samtools (Li et al., 2009) (v1.2). Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) are removed with bedtools (Quinlan and Hall, 2010) (v2.28.0).
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: Sample-wise peaks are called with macs2 (Zhang et al., 2008) (v2.1.2) with the ATAC specific flags -f BAM --nomodel --shift -100 --extsize 200. Peaks over all samples are then merged with bedops (Neph et al., 2012) (v2.4.36).
Differential Methylation: For each model and contrast, we use the edgeR R Bioconductor package (McCarthy et al., 2012) (v3.26.5) to identify differential open chromatin regions (DOCRs). For each sample, the read count falling in the merged peaks is determined, and a library size normalization factor is determined. With no replicates, we manually tune the BCV (biological coefficient of variance) parameter. We then fit each model using the glmFit function, and test each contrast with a likelihood ratio test. With replicates, the common, trended, and tagwise negative binomial dispersions are calculated. We then fit each model using the glmQLFit function, and test each contrast with an empirical Bayes quasi-likelihood F-test. The DOCRs are then annotated to CpG island and genic annotations using the annotatr R Bioconductor package (v1.10.0)
Genome_build: mm10
Supplementary_files_format_and_content: Tab dellimited .txt file of basic alignment statistics and methylation statistics for each sample
Supplementary_files_format_and_content: BED files (*summits.bed)

source_name: MSC pre-injury at Day 0

extract_protocol: ATAC-Seq libraries were prepared at the UM Epigenomics Core by using the Omni-ATAC protocol for cells as described in Corces et al., 2017 without modifications.

value: Mesenchymal Stem Cells (MSC)


title: D7_MSC_IMMOB: MSC immobilized at Day 7 post-injury

source_name: MSC immobilized at Day 7 post-injury


title: Capsella rubella 10 day old seedlings 3

organism: Capsella rubella

source_name: 10 day old seedlings

value: 10 day old seedlings


title: Capsella rubella 10 day old seedlings 2


title: NT-RED-Rep2


title: Capsella rubella dividing flower buds 3

source_name: dividing flower buds

value: dividing flower buds


title: Liver of Balb/cBy mice at 20week-old, biological rep2

city: ChengDu

first: Yulong

last: Chen

address: No.1,Keyuan Fourth Road

institute: Molecular medicine researh center

description: Gene expression data from liver of Balb/cBy male mice after High fatty Diet-fed

hyb_protocol: Following Fragment and Label Single-Stranded cDNA, 27ul of biotin-labeled ss-cDNA sample were hybridized for 16 hr at 45℃ on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with robust multi-array average (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotinylated ss-cDNA

source_name: liver of Balb/cBy mice, 12week High-fatty diet fed

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChipTM WT PLUS Reagent Kit, 2014, Affymetrix)

growth_protocol: Balb/c and Balb/cBy were housed in conventional animal facility in individual cages under controlled temperature (23 degree) and illumination (12-h light/12-h dark cycle)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Eight week-old male mice were given High fatty diet (58% of energy as fat) for a period of 12 weeks.

tag: strain

value: Balb/cBy

tag: gender

value: male

value: liver


title: Liver of Balb/c mice at 20week-old, biological rep3

description: Gene expression data from liver of Balb/c male mice after High fatty Diet-fed

source_name: liver of Balb/c mice, 12week High-fatty diet fed

value: Balb/c


title: Capsella rubella dividing flower buds 2


title: HUVEC_ETV2_K27ac_2

source_name: Human Umbilical Vein Endothelial Cells (HUVEC)

value: HUVEC

value: H3K27ac (Active Motif 39133)

value: lenti ETV2

value: induction (flat 2d)


title: Liver of Balb/cBy mice at 20week-old, biological rep1


title: Liver of Balb/c mice at 20week-old, biological rep1


title: Liver of Balc/c(WT) mice at 20week-old, biological rep2

source_name: liver of Balb/c  mice, 12week High-fatty diet fed

value: Liver of High-fatty diet fed Balb/c male mice


title: Liver of Balb/cBy mice at 20week-old, biological rep3


title: Liver of Balc/cBy(KD) mice at 20week-old, biological rep1

source_name: liver of Balb/cBy  mice, 12week High-fatty diet fed

value: Liver of High-fatty diet fed Balb/cBy male mice


title: Liver of Balc/cBy(KD) mice at 20week-old, biological rep3


title: Liver of Balc/c(WT) mice at 20week-old, biological rep1


title: Liver of Balc/c(WT) mice at 20week-old, biological rep3


title: Liver of Balc/cBy(KD) mice at 20week-old, biological rep2


title: CCE2_#114_LSD1i_24hr

city: Otsu

first: Goichi

last: Tatsumi

address: Seta Tsukinowa-cho

institute: Shiga University of Medical Science

description: Gene expression data from human erythroid leukemia (HEL) cell lines.

hyb_protocol: Following fragmentation, 5.5 ug of single stranded DNA was hybridized for 17 hr at 45C on GeneChip Human Gene 2.0 ST Arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Hybridized microarrays were scanned using an Affymetrix GeneChip Scanner.

data_processing: Images from scanned chips were processed by using the default settings of Affymetrix GeneChip Command Console (AGCC) software. The CEL files created by AGCC were imported into Affymetrix Expression Console software. Expression signals of all genes (probe sets) were calculated using the RMA algorithm (default settings), and obtained the CHP files.

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Human erythroid leukemia (HEL) cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin in 37C at 5% CO2.

extract_protocol: Total RNA was extracted by using an RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: HEL cells were cultured in the RPMI 1640 medium supplemented with a LSD1 inhibitor (NCD38) (2 microM) or vehicle (DMSO) for 24 hours.

value: HEL

value: Erythroleukemia cell line

tag: genotype/variation

value: Bi-allelic deletion of GFI1-SE

value: LSD1i 24hr


title: CCE2_#216_LSD1i_24hr


title: CCE2_#141_LSD1i_24hr


title: wild type aged rep1 [treatment 4]

description: Sample 14

source_name: wild type aged_olfactory mucosa

tag: genotype

value: wild type aged

value: post natal day 750

tag: tissue

value: olfactory epithelium


title: Capsella rubella dividing flower buds 1

tag: developmental stage

value: dividing flower buds


title: Capsella rubella expanding/maturing flower buds 2

source_name: expanding/maturing flower buds

value: expanding/maturing flower buds


title: Liver of Balb/c mice at 20week-old, biological rep2

value: male

value: liver


title: Capsella rubella expanding/maturing flower buds 1


title: Capsella rubella 10 day old seedlings 1

value: 10 day old seedlings


title: CCE2_#216_DMSO_24hr

value: DMSO 24hr


title: CCE2_#114_DMSO_24hr


title: PDX160812

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Alignment was performed using STAR with default settings
The reference genome was hg19.
The gene counts were aligned by STAR 2.4.2.8 using HTSeq-counter
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: PDX primary culture

growth_protocol: Primary cultures for human GBM primary or PDX  tissues were established in SFM with EGF, FGF, PDGF-AA and NRG1 (10 ng/ml each).

extract_protocol:
Qiagen Rneasy Extraction kit
Manufactory Protocol

value: Glioblastoma PDX cell culture


title: Capsella rubella expanding/maturing flower buds 3


title: PDX160927


title: CCE2_#141_DMSO_24hr


title: PDX160721


title: PDX160412