title: prim-273-CD44-

city: Fukuoka

first: Michitaka

last: Nakano

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Sciences

institute: Kyushu University

description: Gene expression of primary CRCs' CD44- non-CSCs

hyb_protocol: cRNA (800 ng) was hybridized to the microarray chip (SurePrint G3 Human Gene Expression 8x60K v2, Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT sensitivity is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw expression data was imported and normalized by using GeneSpring GX software (Agilent Technologies)

label_protocol: Cyanine3-labeled cRNA from each sample was prepared to mRNA amplification by using Low Input Quick Amp Labeling Kit (one-color) (Agilent Technologies) according to the manufacture's instruction.

extract_protocol: Target populations ranging in number from 5000 cells were double-sorted directly to Trizol reagent (Life Technologies). Total RNA extracted in accordance with the manufacture's instruction.

tag: disease state

value: colorectal cancer

tag: tissue (system)

value: primary

tag: fraction (sorted cells)

value: CD44- non-CSCs


title: prim-272-CD44+

status: Public on Nov 09 2018

type: RNA

country: Japan

description: Gene expression of primary CRCs' CD44+ CSCs

molecule: total RNA

organism: Homo sapiens

value: CD44+ CSCs


title: prim-273-CD44+


title: Adiponectin treated vs non-treated 4

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

country: Poland

institute: University of Warmia and Mazury

description: US45103052_252644010751_S01_GE2_107_Sep09_1_4.txt:cy3ByCy5Signal

hyb_protocol: Two differentially labelled samples (from adiponectin treated and non-treated, control samples) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 60°C. After the hybridization process, the microarrays were washed.

scan_protocol: Microarrays were scanned at 5 μm resolution with an Agilent’s High-Resolution C Microarray Scanner according to the manufacturers's protocol.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pigs that were and were not treated with adiponectin.

organism: Sus scrofa domesticus

source_name: pituitary non-treated

label_protocol: The RNA isolated from the control and adiponectin treated cells were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader . 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

growth_protocol: The study was performed on mature gilts (Large White × Polish Landrace) aged 7 to 8 months, with body weights of 120–130 kg, raised on a private farm, as described in our previous study. Pituitaries (n=4) were harvested in the mid-luteal phase (day 10-12) of the porcine oestrous cycle. Gilts were observed daily for oestrus behaviour in the presence of an intact boar. The onset of the second oestrus was marked as day 0 of the oestrous cycle. The mid-luteal phase of the oestrous cycle was also confirmed based on ovarian morphology. Pigs were slaughtered by qualified abattoir worker.

extract_protocol: Total RNA from each AP cell culture was isolated with the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer's instructions. Additionally, RNA was purified by on-column digestion of DNA with DNase I (Qiagen, USA). The concentration and purity of the isolated RNA were determined by spectrophotometry (Infinite 200 PRO, Tecan Group, Switzerland). The RNA integrity number (RIN) was evaluated in the Agilent Bioanalyser 2100 (Agilent Technology, USA). RNAs were stored at −80 °C until the microarray analysis.

treatment_protocol: Anterior pituitary lobes were washed with fresh DMEM, minced into 1- to 2-mm pieces and trypsinised with 0.25% trypsin (7–8 times, 10 min., 37°C). Dispersed pituitary cells were transferred to plastic tubes, repeatedly centrifuged at 1,200 g for 10 min, and washed with DMEM three times. After the final centrifugation, pituitary cells were filtered through a nylon filter (60 μm mesh) and counted in a hemocytometer. Cell viability (90–97%) was determined by trypan blue dye exclusion. Pituitary cells were then resuspended in McCoy’s 5A medium with 10% horse serum, 2.5% foetal calf serum (FCS), 240 U/ml nystatin and 100 μg/ml gentamycin, supplemented with 0.1% vitamins and 0.01% nonessential amino acids. One millilitre of dispersed cell suspension (1 x 10^6/ml) was transferred to each 24-well culture plate. The cells were allowed to attach for 48 h (37°C, 95% O2 and 5% CO2). After preculture, the cells were incubated for 24 h (37°C, 95% O2 and 5% CO2) in 1ml of McCoy’s 5A medium (without serum) containing bacitracin (2 x 10-5 M) with or without (control culture) recombinant human adiponectin (BioVendor, USA) at a concentration of 10 μg/ml.

tag: race

value: Large White x Polish Landrace

tag: gilts age

value: mature; 7-8 months

tag: gilts weight

tag: period of pregnancy

value: days 10 to 12

tag: tissue

value: Anterior pituitary lobes

tag: cell type

value: pituitary cells

tag: treatment

value: none (untreated control)

source_name: pituitary adiponectin-treated

value: recombinant human adiponectin (10 μg/ml)


title: prim-272-CD44-


title: Adiponectin treated vs non-treated 2

description: US45103052_252644010751_S01_GE2_107_Sep09_1_2.txt:cy3ByCy5Signal


title: prim-275-CD44+


title: prim-275-CD44-


title: Adiponectin treated vs non-treated 3

description: US45103052_252644010751_S01_GE2_107_Sep09_1_3.txt:cy5ByCy3Signal


title: org-247 CD44-

description: Gene expression of organoids' CD44- non-CSCs

value: organoid


title: prim-271-CD44-


title: org-247 CD44+

description: Gene expression of organoids' CD44+ CSCs


title: prim-271-CD44+


title: Adiponectin treated vs non-treated 1

description: US45103052_252644010751_S01_GE2_107_Sep09_1_1.txt:cy5ByCy3Signal


title: org-253 CD44-


title: org-253 CD44+


title: CBX2KO_rep2

type: SRA

first: Tetsuya

last: Sato

address: 3-1-1, Maidashi Higashi-ku

library_source: transcriptomic

data_processing:
Read quality was checked for each sample using FASTQC (version 0.11.5).
Reads were mapped to the reference mouse genome UCSC version mm10 using option ‘-library-type fr-secondstrand’ in TopHat version 2.1.0.
Transcripts were then assembled in Cufflinks version 2.2.1 using option ‘-u -library-type fr-secondstrand’, and expression was calculated as fragments per kilobase of exon per million mapped fragments (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample

organism: Mus musculus

source_name: tibial and femoral bone marrow

extract_protocol:
Total RNA was prepared using RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen) from tibial and femoral bone marrow obtained from 3-week-old Cbx2-/- (n=3, average body weight 4.0 g) and wild type mice (n=3, average body weight 12.3 g). Libraries were constructed using TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol, and sequenced by 50 bp single-end sequencing on Illumina HiSeq 1000.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: age

tag: genotype


title: WILD_rep1

value: wile type


title: CBX2KO_rep1


title: CBX2KO_rep3


title: WILD_rep3


title: OXA treated vs non-treated myometrium 3

description: US45103052_252644011042_S01_GE2_107_Sep09_1_3.txt:cy5ByCy3Signal

hyb_protocol: Two differentially labelled samples (from OXA treated and non-treated, control samples) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 60°C. After the hybridization process, the microarrays were washed.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pigs that were and were not treated with OXA.

source_name: myometrium non-treated

label_protocol: The RNA isolated from the control and OXA treated tissues were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader . 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

growth_protocol: Four mature gilts descended from the private breeding farm (Large White x Polish Landrace) were used in the study (n = 4). All animals were at the age of 7-8 months and the weight of 120 to 130 kg. The gilts used in the study were on days 15 to 16 of gestation. As the first day of gestation we considered the first day after coition. Gilts were inseminated on days 1 to 2 of the oestrous cycle. The presence and morphology of conceptuses confirmed the stage of pregnancy. 15 to 16 days after coition, gilts were slaughtered by qualified abattoir worker.

extract_protocol: Total RNA was extracted from tissues using peqGOLD TriFast isolation system according to the manufacturer’s instructions. RNA purity and quantity were measured spectrophotometrically . RNA quality was checked using RNA 6000 Nano Assay Kit on an Agilent 2100 Bioanalyzer. RNA integrity number (RIN) score between 8 and 10 were used for microarray analysis and quantitative real-time PCR (qPCR) experiments. RNAs were stored at −80 °C until the microarray analysis.

treatment_protocol: Small, irregular explants (3 mm of thickness, 100 mg ± 10%) of the myometrial tissue were obtained from the middle of uterine horns. Tissue explants were washed three times in medium M199 and placed in the separate sterile culture vials with 2 mL medium 199 containing 0.1% BSA , 5% dextran/charcoal-stripped new-born calf serum. Explants were preincubated for 2 h (37°C, 95% O2, 5% CO2). To examine the influence of OXA on the  myometrial transcriptome, slices were treated with OXA (10 nM) and incubated for another 24 h at the same conditions. Control tissues were incubated in the absence of OXA, under the same conditions. All cultures were prepared in duplicates in four separate experiments for each group (n = 4). After the incubation, myometrial explants were frozen and stored at -80°C for further analyses.

value: days 15 to 16

value: myometrial tissue obtained from the middle of uterine horns

source_name: myometrium OXA-treated

value: OXA (10 nM)


title: OXA treated vs non-treated myometrium 4

description: US45103052_252644011042_S01_GE2_107_Sep09_1_4.txt:cy3ByCy5Signal


title: OXA treated vs non-treated myometrium 1

description: US45103052_252644011042_S01_GE2_107_Sep09_1_1.txt:cy5ByCy3Signal


title: org-240-2 CD44+


title: OXA treated vs non-treated myometrium 2

description: US45103052_252644011042_S01_GE2_107_Sep09_1_2.txt:cy3ByCy5Signal


title: WILD_rep2


title: SalmonellaMucispirillum_lumen rep3

city: Munich

first: Bärbel

last: Stecher

address: Pettenkoferstr. 9a

department: Max von Pettenkofer Institute

country: Germany

institute: Ludwig Maximilian University of Munich

description:
Treatment Salmonella and Mucispirillum
SalMucCBDW0ANXX_2_58097_CAGATC

data_processing:
Base calling with Illumina Casava 1.8
Converting bam to fastq format using bedtools
Filtering and removing adapters using Trimmomatic V0.30
Mapping to reference genomes with BWA
M. schaedleri ASF457 - WGS NZ_AYGZ.1'  corresponds to the assembly 'Muci_scha_ASF457_V1', however identifiers correspond to the genome  'M. schaedleri ASF457 - WGS NZ_AYGZ.1' on http://www.genoscope.cns.fr/agc/microscope/mage/index.php?
Processing of aligned reads with htseq-count from the HTSeq Python package (flags ‘-m union -s no -t gene -a 10’)
Genome_build: MicroScope (http://www.genoscope.cns.fr/agc/microscope/home/) Salmonella enterica subsp. enterica serovar Typhimurium SL1344 SALTS, Mucispirillum schaedleri ASF457 - WGS NZ_AYGZ.1
Supplementary_files_format_and_content: count files were generated with htseq-count; first column contains locs tags (corresponding to the identifiers for the respective genomes of both organisms publically available at http://www.genoscope.cns.fr/agc/microscope/mage/index.php?); second column contains raw read counts

organism: Microbiota

source_name: Cecum content of ASF3 C57BL/6J mice

extract_protocol:
Nucleic acids were extracted using a phenol:chloroform extraction method and treated with DNase I (Thermo Scientific) until DNA free. RNA was cleaned up and concentrated using the GeneJET RNA cleanup kit and Concentration Micro Kit (Thermo Scientific). rRNA was removed using the Ribo-Zero bacterial kit (Illumina, San Diego, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: host mouse strain

value: gnotobiotic C57BL/6J

tag: harboring strains

value: ASF356, ASF519, ASF361, ASF457, Salmonella Typhimuriumavir pM1419

value: Cecum


title: Barnesiella viscericola, replicate 1

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Chicago

description:
processed data file : BV_tRNA_Counts.xlsx
Barnesiella viscericola, biological replicate 1,  which had tRNA subsequently isolated

data_processing:
We removed low-quality reads from the raw sequencing results using illumina-utils 17 (available from https://github.com/merenlab/illumina-utils). For the analysis of 16S rRNA gene amplicons data we used the program ‘iu-merge-pairs’ with default parameters, which merged partially overlapping paired-end Illumina reads while simultaneously removing any pair with more than 3 mismatches at the overlapped region. For pairs with three or less mismatches, we picked the base to be used in the final merged sequence from the read with the higher Q-score.
We used Minimum Entropy Decomposition 11 with default parameters to cluster high-quality 16S rRNA gene amplicons at 1-nt resolution, and GAST 18 to assign taxonomy to each read individually.
To recover tRNA sequences in this dataset we also used the program ‘iu-merge-pairs’, but with two additional flags and an additional parameter: --retain-only-overlap (to keep only the overlapping region while trimming tailing ends from both reads in a pair), --marker-gene-stringent (to align the reverse-complement of the second read even if the alignment occurs between the end of the second read and the beginning of the first read --which is a unique case for short inserts), and --max-num-mismatches 0 (to remove any pair if there was a disagreement between the aligned portions to increase the quality dramatically as described in 17).
We developed a new software tool to identify tRNA sequences in the raw sequencing results: tRNA-seq-tools (available from https://github.com/merenlab/tRNA-seq-tools). We used the tRNA-seq-tools program ‘trna-profile’ with default parameters to identify all sequences that matched our criteria for standard tRNA.
Supplementary_files_format_and_content: Bacterial tRNA counts in Excel file format

organism: Barnesiella viscericola

source_name: bacterial culture

growth_protocol: We grew E. coli, B. subtilis, and S. aureus cultures at 37°C in Erlenmeyer flasks with a 10:1 flask medium ratio at 225rpm. We grew E. coli and B. subtilis in LB Lennox and S. aureus in tryptic soy broth. We grew B. viscericola in serum vials under strict anaerobic conditions at 37°C in chopped meat medium as previously described1. We harvested all cultures at midlog by centrifugation.

extract_protocol:
We lysed pelleted bacteria in 400μL of 0.3M NaOAc/HOAc, 10mM EDTA pH 4.8 with an equal volume acetate saturated phenol chloroform pH 4.8. We placed samples in a reciprocating bead beater for 45 seconds on  maximum intensity using FastPrep lysing matrix B. We centrifuged samples at 21,000rcf for 15  minutes at 4°C before re-extraction and ethanol precipitation of total RNA.Total tRNA was subsequently isolated using a denaturing 10% polyacrylamide gel followed by passive gel elution and ethanol precipitation.
Homemade protocol based on Illumina protocols. Deacylated RNAs with or without the demethylation were first treated with T4 Polynucleotide Kinase (Epicentre) at 37C° for 30 min to further warrant a free 3' hydroxyl group for template switching. Template-switching reactions were performed as described7. Briefly, we used an initial template-primer substrate consisting of a 41-nt RNA oligonucleotide (5’-AGA UCG GAA GAG CAC ACG UCU AGU UCU ACA GUC CGA CGA UC/3SpC3/-3’) that contains Illumina Read1 and Read2 primer-binding sites and a 3’ blocking group (three carbon spacer; IDT) annealed to a complementary 32P-labeled DNA primer with a single-nucleotide 3’ overhang, T, which facilitates the template switch to full-length tRNA that mostly contain a 3’ CCA end. For g2RT template-switching reactions, average 100 ng of demethylated tRNAs or 1 μg of demethylated total RNA were mixed with the initial template-primer substrate (100 nM) and g2RT (1 μM of TeI4cΔEn or 500 nM of GsI-IIC RT) in reaction medium containing 450 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl, pH 7.5, and DTT (1 mM for TeI4cΔEn or 5 mM for GsI-IIC RT). For template-switching with TeI4cΔEn RT, the reactions were pre-incubated at room temperature for 30 min, initiated by adding 25 mM dNTPs to a final concentration of 1 mM and incubating at 60°C for 30 min. For template-switching with GsI-IIC RT, the pre-incubation step is not required. The reactions were terminated by adding 5 M NaOH to a final concentration of 0.25 M, incubating at 95°C for 3 min, and neutralizing with 5M HCl. The cDNAs resulting from template switching were analyzed in a denaturing 6% polyacrylamide gel, electroeluted using a D-tube Dialyzer Maxi with MWCO of 6-8 kDa (EMD Millipore), and ethanol precipitated with 0.3 M sodium acetate in the presence of 25 µg of linear acrylamide (Life Technologies). The purified cDNAs were then circularized with CircLigase II (Epicentre) using manufacture’s protocol with extended incubation time of 5 hours at 60°C, phenol-CIA extracted, ethanol precipitated and amplified with Phusion-HF (Thermo Scientific) using Illumina multiplex (5’- AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GAC GAT C -3’) and barcode (5’- CAA GCA GAA GAC GGC ATA CGA GAT BARCODE GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T -3’) primers for 12 cycles of 98°C for 5 sec, 60°C for 10 sec and 72°C for 10 sec. The PCR products were sequenced on Illumina HiSeq 2000 system.

treatment_protocol: Sequenced tRNA was derived from bacterial pellets. DM refers to demethylase treatment. This is a cocktail of AlkB and AlkB engineered mutants that remove modifications from the tRNAs. This treatment was performed after isolation of tRNA from mouse cecum.

value: no demethylase

value: bacterial culture

tag: molecule subtype

value: tRNA


title: SalmonellaMucispirillum_lumen rep2

description:
Treatment Salmonella and Mucispirillum
SalMucCBDW0ANXX_2_58096_GCCAAT


title: Barnesiella viscericola, replicate 2

description:
processed data file : BV_tRNA_Counts.xlsx
Barnesiella viscericola, biological replicate 2, which had tRNA subsequently isolated


title: org-240 CD44-

value: colorectal cancer

value: CD44- non-CSCs


title: Dam+ salmonella 6mACEseq Ab151230

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

library_source: genomic

data_processing:
Library strategy: 6mACEseq
Basecalls performed using FASTQ Generation v1.0.0
Sequenced reads were trimmed of adapter sequence using Cutadapt v1.8.1 then mapped to the corresponding genome using Bowtie2 v2.2.6 with parameters -q -p 30 -N 1 --no-mixed --no-discordant
The coordinates for the first nucleotide and the total number of associated mapped reads were consolidated (bedgraph file) and used for 6mA site/peak-calling: A potential site was under consideration only if it possessed at least 1 read in all replicates. For each potential site, the probability of reads beginning at that site was calculated using the maximum-likelihood estimates of the parameters of a negative binomial distribution using the counts of read-starts in a 1,000nt window centered around the site. Probabilities at each candidate site across replicates were then combined via Fisher’s method for combining p-values. Multiple-testing correction using the Benjamini-Hochberg procedure was implemented and sites where the false discovery rate <0.01 were deemed significant (bed file).
Genome_build: 14028S
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of mapped reads. Bed files of significantly called 6mA sites.

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Bacteria

growth_protocol: Bacteria were cultivated overnight at 37oC in L-Broth.

extract_protocol:
Bacteria were lysed overnight in SNET lysis buffer (400mM NaCl, 1% SDS, 20mM Tris pH 8, 5mM EDTA, 200µg/ml Proteinase K) at 56oC with shaking at 1,000rpm. Genomic DNA was purified from cell lysate using Phenol-chloroform-Isoamyalcohol (25:24:1), precipitated with 50% isopropanol. The DNA pellet was washed once with 100% ethanol and once with 70% ethanol before being reconstituted in IDTE (10mM Tris pH 8, 0.1mM EDTA).
Genomic DNA was first sonicated to ~150bp and treated with RNAseA/T1 (Ambion AM2286) for 1hr at 37oC then purified using 1.8X volume Agencourt AMpure XP beads (Beckman A63880). 5µg of sonicated and RNA-free genomic DNA was then incubated with 4µg anti-6mA antibody (Synaptic Systems 202003) in 1X IP buffer (150mM NaCl, 10mM Tris pH 7.4, 0.1% IGEPAL) overnight at 4oC. This antibody-genomic DNA mixture was then crosslinked with 0.15J 254nm UV radiation six times before being mixed with 40µl BSA-blocked Protein-A-dynabeads (Life Technologies 10002). Beads bound with crosslinked genomic DNA were then washed with 500µl of the following buffers in this order: Wash buffer 1 (1M NaCl, 50mM HEPES-KOH pH 7.4, 1% Triton X-100, 0.1% Sodium Deoxycholate, 2mM EDTA), Wash buffer 2 (0.5M NaCl, 50mM HEPES-KOH pH 7.4, 1% IGEPAL, 0.1% Sodium Deoxycholate, 2mM EDTA), Wash buffer 3 (1% Sodium Deoxycholate, 25mM LiCl, 10mM Tris pH 8, 1% Triton X-100, 2mM EDTA), TE (10mM Tris pH 8, 1mM EDTA) and finally 10mM Tris pH 8. Genomic DNA was then subjected to progressive on-bead reactions as follows: End-repair with 6U T4 DNA polymerase (NEB M0203) at 12oC for 30min, end-phosphorylation with 30U T4 PNK (NEB M0201) and T4 DNA ligase buffer (NEB B0202) at 37oC for 30min, first adapter ligation with 1500U T4 DNA ligase (NEB M0202) and 202.5pmol first adapter at 25oC for 2hr, fill-in DNA synthesis with 20U Phi29 DNA polymerase (NEB M0269), a second round of end-phosphorylation using the same conditions, Lamda exonuclease digestion with 20U Lambda exonuclease (NEB M0262) at 37oC for 30min and finally RecJf exonuclease digestion with 90U RecJf (NEB M0264) at 37oC for 30min. The same bead-wash steps were carried out between each reaction. DNA was then eluted off beads with elution buffer (0.5% SDS, 0.2M NaCl, 25mM Tris pH 8, 2mM EDTA) and treated with 8,000U of proteinase K  (Thermo Scientific EO0491) overnight at 65oC with shaking at 1,000rpm. The eluted ssDNA was ethanol-precipitated before undergoing the following reactions as follows: Annealing of PG162 primer to the reverse adapter and primer extension with 20U Phi29 polymerase, second adapter ligation with 1000U T4 DNA ligase and 30.15pmol forward adapter, dsDNA purification with 1.7x volume Ampure XP beads, 18 cycles amplification with Phusion High-fidelity PCR mastermix (NEB M0530) and finally, primer-dimer removal with 0.8X volume AMpure XP beads before undergoing sequencing on the Illumina Miseq or Nextseq single-end platforms.

tag: 6ma antibody

tag: passage number

value: Dam+


title: org-240-2 CD44-

tag: disease state

tag: tissue (system)


title: org-240 CD44+

tag: fraction (sorted cells)

value: CD44+ CSCs


title: SalmonellaMucispirillum_lumen rep4

description:
Treatment Salmonella and Mucispirillum
SalMucCBDW0ANXX_2_58098_ACTTGA


title: Salmonella_lumen rep4

description:
Treatment Salmonella
SalMucCBDW0ANXX_2_58094_TGACCA

value: ASF356, ASF519, ASF361, Salmonella Typhimuriumavir pM1419


title: SalmonellaMucispirillum_lumen rep1

description:
Treatment Salmonella and Mucispirillum
SalMucCBDW0ANXX_2_58095_ACAGTG


title: Salmonella_lumen rep2

description:
Treatment Salmonella
SalMucCBDW0ANXX_2_58092_CGATGT


title: Dam+ salmonella 6mACEseq

data_processing:
Library strategy: 6mACE-seq
Basecalls performed using FASTQ Generation v1.0.0
Sequenced reads were trimmed of adapter sequence using Cutadapt v1.8.1 then mapped to the corresponding genome using Bowtie2 v2.2.6 with parameters -q -p 30 -N 1 --no-mixed --no-discordant
The coordinates for the first nucleotide and the total number of associated mapped reads were consolidated (bedgraph file) and used for 6mA site/peak-calling: A potential site was under consideration only if it possessed at least 1 read in all replicates. For each potential site, the probability of reads beginning at that site was calculated using the maximum-likelihood estimates of the parameters of a negative binomial distribution using the counts of read-starts in a 1,000nt window centered around the site. Probabilities at each candidate site across replicates were then combined via Fisher’s method for combining p-values. Multiple-testing correction using the Benjamini-Hochberg procedure was implemented and sites where the false discovery rate <0.01 were deemed significant (bed file).
Genome_build: UTI89 (Escherichia), 14028S (Salmonella), hg38 (human)
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of mapped reads. Bed files of significantly called 6mA sites.

value: Synaptic systems 202003


title: Salmonella_lumen rep3

description:
Treatment Salmonella
SalMucCBDW0ANXX_2_58093_TTAGGC


title: Mimics-1

city: 北京

first: shuai

last: chen

state: State...

address: 北京市海淀区中关村南大街22号

institute: THE PEKING UNIVERSITY

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hours at 45℃ on GeneChip Human Gene 1.0.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

label: biotin

source_name: SCC-15 cells transfected with miR-585-5p mimics

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetix protocol from 2 ug total RNA.

growth_protocol: 3*10^5 of SCC-15 cells were seeded in 6-well plate and transfected with mimics (30nM) 24 hours later.

extract_protocol: RNA was extracted by Qiangen RNA Isolation Kit according to the manufacturer' instructions

treatment_protocol: 36 hours after transfection,cells were collected for further total RNA extracion.

value: Tongue squamous cell carcinoma cell line

tag: cell line

tag: transfection

value: miR-585-5p mimics


title: PTL2_OTH

city: Fort Collins

first: Anne

middle: C

last: Avery

state: CO

address: 1619 Campus Delivery Colorado State University

department: Microbiology, Immunology, Pathology

institute: Colorado State University

data_processing:
Sequences were aligned to the CanFam3.1 genome using TopHat2
HTSeq and DESeq2 software were used to quantify reads and normalize gene expression
Genome_build: CanFam3.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Canis lupus familiaris

source_name: T-cell lymphoma cells

extract_protocol:
RNA extraction was performed using the Purelink RNA mini Kit (Thermo Fisher Scientific, Waltham, MA) and quality was measured with an Agilent 2100 Bioanalyzer System. All samples had a RIN value greater than 8.80.
RNA was shipped to Novogene Corporation Inc (Sacramento CA) where the libraries were constructed and sequenced. Briefly, mRNA was enriched using oligo(dT) beads and randomly fragmented. Random hexamer primer and reverse transcriptase were used for first strand cDNA synthesis followed by second strand synthesis via custom synthesis buffer (Illumina, San Diego, CA), dNTPs, RNAse H, and Escherichia coli polymerase I. Double-stranded cDNA fragments were purified and end-repaired by A-tailing and ligation of sequencing adapters. cDNA inserts were selected and enriched via PCR.

value: PTCL

tag: breed

value: Rhodesian Ridgeback

value: 4 years

tag: Sex

value: female

tag: neutering

value: spayed

value: T-cell lymphoma cells


title: Control-1

address: 北京市海淀区中关村南大街22号

source_name: SCC-15 cells transfected with miR-NC

tag: cell type

value: miR-NC


title: PTL1_OTH

value: Cavalier King Charles Spaniel

value: 3 years


title: Dam+ salmonella 6mACEseq SySy202111

value: Synaptic Ssystems 202111


title: PTL3_OTH

value: Collie

value: 11 years

value: male

value: castrated


title: Mimics-2

address: 北京市海淀区中关村南大街22号


title: Variant 14_2 vs WT_2

city: Wageningen

first: Jeroen

middle: Steven

last: Koomen

address: Bornse Weilanden 9

country: Netherlands

institute: Wageningen University

description: WT vs variant 14, biological duplo, 2 of 2 dyeswap

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 150ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: 8 x 15K Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2505C, using the extended dynamic range scan mode and 10 micron scan resolution according to the Agilent protocol.

data_processing: Lowess normalization, as implemented in MicroPrep. Inter-slide differences were corrected based on total intensity per slide using Postprep, with median intensity of the different probes per gene as gene expression intensity. CyberT was used to compare the different transcriptomes resulting in gene expression ratios and false discovery rates (FDR) for each gene.

organism: Listeria monocytogenes LO28

source_name: Variant 14_2

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2004

tag: genotype/variation

value: variant 14

value: WT


title: PTL3_BOX

value: Boxer

tag: age

value: 6 years


title: Variant 15_3 vs WT_3

description: WT vs variant 15, biological triplo, 3 of 3 dyeswap

source_name: Variant 15_3

value: variant 15


title: Salmonella_lumen rep1

description:
Treatment Salmonella
SalMucCBDW0ANXX_2_58057_ATCACG

value: gnotobiotic C57BL/6J

value: ASF356, ASF519, ASF361, Salmonella Typhimuriumavir pM1419

tag: tissue

value: Cecum


title: PTL2_BOX

value: PTCL

value: 8 years

value: female

value: spayed

value: T-cell lymphoma cells


title: Variant 15_2 vs WT_2

description: WT vs variant 15, biological triplo, 2 of 3 dyeswap

source_name: Variant 15_2


title: Control-2

address: 北京市海淀区中关村南大街22号

value: Tongue squamous cell carcinoma cell line

value: miR-NC


title: Dam- salmonella 6mACEseq

value: Synaptic systems 202003

tag: genotype

value: Dam-


title: WT_2 vs variant 14_2

description: WT vs variant 14, biological duplo, 2 of 2

value: variant 14


title: PTL1_BOX

value: male

value: castrated


title: Variant 15_1 vs WT_1

description: WT vs variant 15, biological triplo, 1 of 3 dyeswap

source_name: Variant 15_1

value: WT


title: CNTRL2

source_name: sorted CD4+ T-cells

value: healthy control

value: hound

value: 1 year

value: normal CD4+ control lymphocytes


title: CNTRL3


title: CNTRL1


title: WT_3 vs variant 15_3

description: WT vs variant 15, biological triplo, 3 of 3

value: variant 15


title: KO_H3K36me3_Rep1

status: Public on Nov 08 2018

city: ShangHai

first: Lijun

last: Wang

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
KO_IP1vsInput.bed
KO_IP1vsIGG.bed

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using bowtie2
peaks were called using macs14
Genome_build: GRCm38
Supplementary_files_format_and_content: bed files were generated using macs14

source_name: Setd2 fl/fl BMSCs infected with lentivirus expressing Cre recombinase as Setd2 knockout

growth_protocol: Bone marrow stromal cells from Setd2 fl/fl mice were collected and passaged twicecultured in a-MEM containing 10% FBS and 1% penicillin/streptomycin

extract_protocol:
After 4-day puromycin treatment, GFP- and Cre-BMSCs were fixed by 1% formaldehyde for 10 min and terminated by glycine for 5 min (final concentration = 0.125 M). After 2 times washing by pre-cooling PBST (protease inhibitor containing), cells were scraped and resuspended in SDS-lysis buffer respectively (50 mM Tris-HCl Ph 7.5, 10 mM EDTA, 1% SDS and protease inhibitor), and sonicated. Cells were centrifuged to obtain cell extracts, which then were added to pre-cleaning protein G agarose and rotated for 1 hr at 4 ℃. Extracts were centrifuged and supernatants were harvested to new tube. ChIP assay was performed using H3K36me3 antibody(abcam,ab9050). Normal IgG(Millipore,12-371) was used as negative control.
Libraries were prepared according to Illumina's instructions

treatment_protocol: Setd2 fl/fl BMSCs were infected with lentivirus expressing GFP and Cre, respectively, with 2μg/ml puromycin treatment for 4 days.

value: Setd2 fl/fl BMSCs

tag: lentivirus

value: Cre recombinase

tag: passages

tag: strain


title: KO_Igg

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
KO_IP1vsIGG.bed
KO_IP2vsIGG.bed


title: KO_H3K36me3_Rep2

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
KO_IP2vsInput.bed
KO_IP2vsIGG.bed


title: bioinhivid treated_(PrimeView)

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: Array hybridization were performed per recommended specifications (Asuragen, Austin, TX).

scan_protocol: Scanning were performed per recommended specifications (Asuragen, Austin, TX).

data_processing: Genechip PrimeView Human Arrays were utilized (Affymetrix, Santa Clara, CA). CEL files were analyzed utilizing R/Bioconductor package, oneChannelGUI. Briefly, normalization of expression values was performed utilizing the “Expresso” option, selecting “RMA” as the background correction, “quantiles” as normalization, “pmonly” as the PM correction, and “MAS” as the expression. Probes were filtered with IQR settings of 0.25. P values were calculated using a two-tailed Student’s t-test.

source_name: HeLa

label_protocol: Per Affymetrix Protocol

growth_protocol: DMEM+ 10%FBS+1% antibiotic at 37oC at 5%CO2

extract_protocol: RNA was isolated from Hela si control and Hela si ZMYND8 cells utilizing the RNeasy Mini Prep Kit per manufacturer’s instructions (Qiagen, Valencia, CA).

treatment_protocol: Transient transfection using interferrin transfection reagent

value: HeLa

value: ZMYND8 knockdown


title: WT_H3K36me3_Rep1

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
WT_IP1vsInput.bed
WT_IP1vsIGG.bed

source_name: Setd2 fl/fl BMSCs infected with lentivirus expressing GFP as WT control

value: GFP


title: KO_Input

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
KO_IP1vsInput.bed
KO_IP2vsInput.bed


title: Variant 14_1 vs WT_1

description: WT vs variant 14, biological duplo, 1 of 2 dyeswap

source_name: Variant 14_1


title: WT_1 vs variant 15_1

description: WT vs variant 15, biological triplo, 1 of 3


title: 4-3-14 Bioinivid T2_(PrimeView)


title: WT_1 vs variant 14_1

description: WT vs variant 14, biological duplo, 1 of 2


title: RNA Seq_KO_Rep2

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using Hisat2
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx file contain counts for each sample

extract_protocol:
Cells were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions

treatment_protocol: Setd2 fl/fl BMSCs were infected with lentivirus expressing GFP and Cre respectively.  6 × 10^5 cells were seeded into a well of 6-well-plate and with 2μg/ml puromycin treatment for 4 days.


title: WT_Igg

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
WT_IP1vsIGG.bed
WT_IP2vsIGG.bed


title: 4-3-14 Bioinivid T3_(PrimeView)


title: RNA Seq_KO_Rep1


title: RNA Seq_WT_Rep1


title: WT_2 vs variant 15_2

description: WT vs variant 15, biological triplo, 2 of 3


title: WT_Input

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
WT_IP1vsInput.bed
WT_IP2vsInput.bed


title: Control set 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Control set 2

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen Inc).


title: MCF-7 set 1

source_name: MCF-7 set 1


title: 28-Feb-15 Bioinivid Control 2_(PrimeView)


title: RNA Seq_WT_Rep2


title: 28-Feb-15 Bioinivid Control 3_(PrimeView)


title: bioinhivid control_(PrimeView)


title: MCF-7 set 2

source_name: MCF-7 set 2


title: Control set 1

source_name: Control set 1


title: WT_H3K36me3_Rep2

description:
WT_MergeVSKO_Merge.PeakAnno.xlsx
WT_IP2vsInput.bed
WT_IP2vsIGG.bed


title: NSAP14091501_Mouse_Merkel_cells_1

city: New York

first: Benjamin

middle: U

last: Hoffman

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

data_processing:
Alignment software use in 2014 alignment was bwa version 0.5.9. Sorted files were made by samtools, version 0.1.9
Differential analysis was performed with DEseq2 (version 1.18.1) in R (version 3.4.3)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated manually with raw reads and gene lengths obtained from the UCSC mm10 library with the TxDb.Mmusculus.UCSC.mm10.knownGene package in R (version3.4.0)
Genome_build: mm10
Supplementary_files_format_and_content: excel  files include differential analysis and RPKM values for each sample

source_name: Epidermal cell

extract_protocol:
To isolate Merkel cells and keratinocytes for RNA-seq, dorsal skin from 7-8-week old female mice was removed and placed in a plastic dish, epidermis-side down.  Skin was scraped with a scalpel to remove fat and muscle.  Skin was then floated epidermis-side up in 0.25% trypsin for 2 hours at 37°C.  Epidermis was separated from the dermis, broken into smaller pieces, and recovered in culture media (CnT02, Chemicon) for 30 min with a stir bar.  A 70-µm cell strainer was used to collect single cells.  Cells were incubated with the Cd49f-PE antibody (BD Pharmingen) for 30 minutes on ice.  GFP+/PE- Merkel cells and GFP-/PE+ keratinocytes were purified from the epidermal-cell suspension with FACS, directly into Trizol (ThermoFisher).
Total RNA was isolated using commercially available reagents (Qiagen RNeasy kit) and DNAse-treated according to manufacturer's instructions to remove contaminating genomic DNA.  First and second strand cDNA synthesis, and cDNA amplification was performed with the Ovation RNA-Seq System V2 (NuGEN).  The cDNA library was prepared with the Ovation Ultralow System V2 (NuGEN).

value: Epidermis

value: 7-8 weeks

value: female

value: Merkel cells


title: NSAP14091503_Mouse_Merkel_cells_2


title: NSAP14091504_Mouse_keratinocytes_2

value: Basal keratinocytes


title: NSAP14091502_Mouse_keratinocytes_1


title: n5_d2

city: Toronto

first: Diana

last: Resetca

state: ON

department: Medical Biophysics

country: Canada

institute: University of Toronto

data_processing:
RNA-seq reads were mapped and quantified using the STAR aligner (v2.5.2a) against GRCh37 with Gencode Annotations v24 lifted to GRCh37.
Library normalization was performed using TMM (Trimmed Mean of M-values) from the BioConductor package edgeR (v3.16.5) in the R statistical environment (v3.3.1).
Differential expression analyses were conducted on RNAseq data subset for MYC-bound target genes (n=9,368), as defined as being proximal to MYC binding regions as confirmed using WT-MYC ChIPseq data. Read counts were provided to EBSeq (v1.12.0) for differential expression analyses (Leng et al., 2013). Read counts of each mutant were compared to the read counts of WT-MYC. Given the Bayesian nature of EBSeq, one model was used to test all genes simultaneously, therefore no additional multiple testing adjustment was made. Genes were deemed significantly differentially expression if PPDE (Posterior Probability of the genes being Differentially Expressed) ≥ 0.95 which is equivalent to 1-PPDE < 0.05 and the measure is comparable to FDR < 0.05 in other test settings (eg, DESeq method).
Genome_build: GRCh37
Supplementary_files_format_and_content: fold-change

source_name: Human SH-EP/TET21/N (TET21) neuroblastoma cell line

growth_protocol: WT-MYC expressing TET21 cells were treated with 1µg/mL doxycycline for 7 days prior to harvest. 6 x 106 cells harvested.

extract_protocol: RNA libraries were prepared using standard Illumina protocol

value: neuroblastoma cell line

tag: myc deletion status

value: MYC 2


title: n4_d2


title: n7_d3a

value: MYC 3a


title: n6_d3a


title: n6_d2


title: n5_d3a


title: n5_d3b

value: MYC 3b


title: n7_d2


title: n6_d1

value: MYC 1


title: n4_d3b


title: n5_d1


title: n6_d4

value: MYC 4


title: n7_d4


title: n7_d1


title: n6_d3b


title: n7_d3b


title: n4_d3a


title: n5_d4


title: n4_d1


title: n4_d4


title: HSR065: Mst1/Mst2-KO_rep3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: CD4+YFP+Treg cells from Foxp3YFP-CreStk4f/fStk3f/f mouse

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: CD45.2+CD45.1⎽CD4+YFP+ cells were sorted from bone marrow chimeras of RAG1-/- recipient mice transplanted 2 month prior with bone marrow from either Foxp3YFP-Cre or Foxp3YFP-CreStk4f/fStk3f/f mice togther with WT CD45.1 mice (CD45.2+:CD45.1+=1:1)

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: CD4+YFP+Treg cells


title: n7_d0x

value: MYC 0x


title: HSR066: Mst1/Mst2-KO_rep4


title: HSR061: Treg_WT_rep5

source_name: CD4+YFP+Treg cells from Foxp3YFP-Cre mouse

value: wild type


title: HSR062: Mst1/Mst2-KO_rep1


title: HSR064: Mst1/Mst2-KO_rep2


title: n4_d0x


title: n7_WT

value: WT MYC


title: n6_d0x


title: n6_WT


title: HSR060: Treg_WT_rep4


title: HSR059: Treg_WT_rep3


title: HSR058: Treg_WT_rep2


title: n5_d0x


title: n5_WT


title: HeLa Non Sync ATAC-seq R1T1

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Reads were mapped to hg19 using bowtie2. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
PCR duplicates, ChrM etc were removed to obtain bam files of valid reads. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Bam files of valid reads were converted to bed files for use for V-plots. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Bam files were converted to BigWigs binned at 20bp. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Peaks were called using HOMER. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing valid reads for V-plots, bigwig files containing ATAC-seq signal of read ends, bed files containing peaks called by HOMER on ATAC-seq data

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 and HFF cells were cultured glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin. U2OS cells were cultured in low glucose medium with 10% heat-inactivated FBS and pen-strep

extract_protocol:
For each ATAC-seq library, 50,000 cells or the equivalent in mitotic chromatin clusters were used
ATAC-seq was performed according to published protocol (Buenrostro et al, Curr. Protoc. Mol. Bio, 2015)

treatment_protocol: Cells were harvested as non-synchrous without treatment or arrested in mitosis using Thymidine treatment and Nocodazole (mitotic cells). Mitotic chromatin was purified from mitotic cells using percoll gradients.  See supplemental methods for more information

tag: protocol

value: ATAC-seq

tag: enzyme

value: Human adenocarcinoma cells

value: HeLa-S3 (CCL-2.2)


title: HeLa Non Sync ATAC-seq R1T2


title: n7_EV

value: EV


title: HeLa Mitotic Cell ATAC-seq R2T1


title: HeLa Mitotic Cell ATAC-seq R2T2


title: U87_Input

city: CHICAGO

first: Peiwen

last: Chen

state: IL

address: 303 East Superior Street, Suite 6-512

institute: Northwestern University

data_processing:
Raw reads were aligned using bowtie (version 1.1.2) (Langmead B et.al., 2009) to build version hg19 of the human genome retaining only uniquely mapped reads.
MACS1.4 (Zhang et al., 2008) was used to call peaks in using Input ChIP-seq as control sample using default p value cut-off of 1e-5.
bamCoverage from deeptools (Ramírez Fet.al., 2016) was used to make RPKM normalized bigwig track extending the reads to 200bp fragment length.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using deeptools bamCoverage 2.3.3

source_name: glioma cells

growth_protocol: SF763 PTEN-KO and U87 cells were cultured in Gibco DMEM with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Chromatin from formaldehyde-fixed cells (SF763 PTEN-KO cell and U87 cells, 10 x106 cells for CHD1 antibody and 1x106 cells for H3K4me3 antibody) were cross-linked using 1% paraformaldehyde for 10 minutes and reactions were quenched by 0.125 M glycine for 5 minutes at room temperature. Cells were lysed with ChIP lysis buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 140 mM NaCl, 1% Triton X-100, 0.2% SDS, 0.1% deoxycholic acid) for 30 minutes on ice. Chromatin fragmentation was performed using a Diagenode Bioruptor®Pico sonicator (30 secs on and 30 secs off for 45 cycles) to achieve a DNA shear length of 200 to 500 basepairs. Solubilized chromatin was then incubated overnight with their respective antibody-Dynabead (Life Technologies) mixture (H3K27ac antibody: Abcam #ab4729). Immune complexes were then washed 3 times with RIPA buffer, once with RIPA-500 (RIPA with 500 mM NaCl), and once with LiCl wash buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). Elution and reverse crosslinking were performed in direct elution buffer (10 mM Tris-Cl [pH 8.0], 5 mM EDTA, 300 mM NaCl, 0.5% SDS) with proteinase K (20 mg/ml) at 65°C overnight. Libraries were prepared using NEBNext Ultra DNA Library kit (E7370) from NEB.

value: Glioma

value: WT

tag: chip antibody


title: U87_H3K27Ac

tag: cell line

value: H3K27Ac (Abcam, lot ab4729)


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R2T1

description:
MOAM-HeLa-MFCl-R2T1
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: SF763 PTEN-KO_Input

value: PTEN-KO


title: n4_EV

value: neuroblastoma cell line


title: SF763 PTEN-KO_H3K27Ac


title: n5_EV


title: ChIP_n1_WT_MYC

data_processing:
WT-MYC ChIPseq reads were aligned using STAR aligner (v2.5.2a) mapped against GRCh37 with Gencode Annotations v24 lifted to GRCh37.
Reads with low mapping quality (MAPQ < 20) were filtered out after alignment.
All filtered BAM files were sorted using SAMtools (v1.3). Duplicated reads were removed using picard tool (v2.7.1, MarkDuplicates). Quality control and fragment size estimation were conducted using ENCODE phantompeakqualtools
Peaks were identified using MACS2 (v2.1.0) with default settings (Zhang et al., 2008). Peaks were filtered out if part of the ENCODE false positive sites (Consortium, 2012) using bedtools (v1.3).
Genome_build: GRCh37
Supplementary_files_format_and_content: bed file contains genomic coordinates of MYC peaks

growth_protocol: WT-MYC expressing TET21 cells were treated with 1µg/mL doxycycline for 7 days prior to harvest. 6 x 106 cells were fixed with 1% formaldehyde in PBS for 10 minutes prior to harvest.

extract_protocol:
Lysates were sonicated using a Bioruptor® Pico (Diagenode). ChIP was performed with 2µg of a rabbit polyclonal anti-MYC antibody (prepared in-house) incubated with samples overnight at 4ºC.
Samples were subsequently washed and de-crosslinked prior to purification using a Qiaquick PCR purification kit (Qiagen) and library preparation.

value: rabbit polyclonal anti-MYC antibody (produced in-house)N-262


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R2T2

description:
MOAM-HeLa-MFCl-R2T2
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: n6_EV


title: HSR057: Treg_WT_rep1


title: HFF Mitotic Cell ATAC-seq R1T3

description:
MOAM-HFFnc-MC-R1T3
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw

source_name: HFF

value: foreskin (hTERT transformed foreskin fibroblasts Benanti)


title: HFF Mitotic Cell ATAC-seq R1T1

description:
MOAM-HFFnc-MC-R1T1
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: n4_WT


title: HFF Mitotic Cell ATAC-seq R1T5

description:
MOAM-HFFnc-MC-R1T5
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Cell ATAC-seq R1T4

description:
MOAM-HFFnc-MC-R1T4
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Cell ATAC-seq R1T6

description:
MOAM-HFFnc-MC-R1T6
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Cell ATAC-seq R1T7

description:
MOAM-HFFnc-MC-R1T7
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: Input_n1_WT_MYC


title: HFF Mitotic Cell ATAC-seq R1T8

description:
MOAM-HFFnc-MC-R1T8
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Cell ATAC-seq R1T2

description:
MOAM-HFFnc-MC-R1T2
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: PS19/C3aR KO1

city: Houston

first: Hui

last: Zheng

state: Texas

address: One Baylor Plaza

department: Huffington Ceter on Aging

institute: Baylor College of Medicine

data_processing:
Raw reads were mapped to mm10 using TopHat v2.0.9 with default parameters (-r 100 –p 8).
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under the exons of the gene (union of all the exons of the gene). This read counts obtained are analogous to the expression level of the gene.
Using the obtained read counts, differential gene analyses were carried out using the DESeq2 package in the R environment.
Genome_build: mm10
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
Total RNA from hippocampi of 9 month old WT, C3aR KO, PS19 and PS19/C3aR KO male mice was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer`s instructions.
The RNAseq analysis was performed using 76-nucleotide paired-end sequencing on an Illumina HiSeq 4000 platform. Raw reads were aligned to the Mus musculusgenome (UCSC mm10) using TopHat v2.0.9 with default parameters (-r 100 –p 8). Htseq-count function of HTSeq was used to accumulate the number of aligned reads that fall under the exons of the gene (union of all the exons of the gene) to present the expression of each gene.

value: 9 month old

value: PS19/C3aR KO


title: PS19/C3aR KO4


title: PS19/C3aR KO2


title: PS195


title: PS19/C3aR KO5


title: PS19/C3aR KO3


title: PS192


title: PS193


title: PS194


title: C3aR KO4

value: C3aR KO


title: C3aR KO3


title: A2780 5 uM cisplatin-30m

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

description: Gene expression data from cisplatin treated cell line

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GenChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: A2780 5 uM cisplatin-30m

label_protocol: Biotinylated cRNA were prepared using MessageAmp Premier RNA Amplication Kit (ThermoFisher) according to the manufacturer's protocol with 100ng total RNA as starting material.

growth_protocol: A2780 ovarian cancer cells were grown in RPMI media containing 10% fetal bovine serum, 100 U/ml penicillin, and 100µg/ml streptomycin (Sigma-Aldrich, St. Louis, MO) in a humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Ambion, Austin, TX).

treatment_protocol: When cells reached 70% confluency, cisplatin was added to a final concentration of 5μM or 10μM for different time points - 30 minutes, 1 hour, 2 hours, and 16 hours.

value: ovarian cancer cell line


title: A2780 10 uM cisplatin-2hr

source_name: A2780 10 uM cisplatin-2hr


title: C3aR KO5


title: A2780 5 uM cisplatin-2hr

source_name: A2780 5 uM cisplatin-2hr


title: A2780 5 uM cisplatin-16hr

source_name: A2780 5 uM cisplatin-16hr


title: A2780 0hr

description: Gene expression data from untreated cell line


title: placenta_IVF-ET_B3

city: Beijing

first: Liang

last: Zhao

state: Beijing

address: No. 31, Xinjiekou East Street, Xicheng District, Beijing

department: Department of Obstetrics and Gynecology

institute: Beijing Jishuitan Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

source_name: human placenta villous in first trimester from in vitro fertilization and embryo transfer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of placental villous tissues from patient were extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: placental villous tissues

tag: condition

value: first trimester from IVF-ET


title: placenta_IVF-ET_B8


title: A2780 5 uM cisplatin-1hr

source_name: A2780 5 uM cisplatin-1hr


title: PS191


title: C3aR KO2


title: A2780 10 uM cisplatin-30m

source_name: A2780 10 uM cisplatin-30m


title: placenta_control_N18

source_name: human placenta villous in first trimester from natural pregnancy

value: first trimester from natural pregnancy


title: WT4


title: HFF Non Sync ATAC-seq R2T2

description:
MOAM-HFFnc-NS-R2T2
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw

value: ATAC-seq


title: HFF Non Sync ATAC-seq R2T1

description:
MOAM-HFFnc-NS-R2T1
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: A2780 10 uM cisplatin-16hr

source_name: A2780 10 uM cisplatin-16hr


title: placenta_control_N17


title: placenta_IVF-ET_B4


title: placenta_IVF-ET_B5


title: placenta_control_N19


title: HFF Non Sync ATAC-seq R2T3

description:
MOAM-HFFnc-NS-R2T3
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: WT2


title: WT1


title: HFF Non Sync ATAC-seq R2T4

description:
MOAM-HFFnc-NS-R2T4
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: placenta_control_N16


title: A2780 10 uM cisplatin-1hr

source_name: A2780 10 uM cisplatin-1hr


title: C3aR KO1


title: WT3


title: HFF Mitotic Cell ATAC-seq R2T1

description:
MOAM-HFFnc-MC-R2T1
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: WT5


title: HFF Mitotic Cell ATAC-seq R2T2

description:
MOAM-HFFnc-MC-R2T2
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Cell ATAC-seq R2T4

description:
MOAM-HFFnc-MC-R2T4
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Cell ATAC-seq R2T3

description:
MOAM-HFFnc-MC-R2T3
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R1T1

value: Bone

value: U2OS with H2B-GFP and Halo tagged CTCF received from Anders Hansen in Xavier Darzacq lab in Berkeley


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R1T2


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R1T3


title: SUDHL-1 CEBP beta ChIP-Seq DMSO

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

data_processing:
Standard open-source software tools were used to collect and analyze the ChIP-seq data.  The bcl2fastq script, FASTQC, Bowtie2, BEDTools, UCSC tools, IGV, and MACS2 were used to demultiplex the data, assess the read quality, align the data to the genome, convert the data into tracks, visualize the data, and call peaks.
The FASTQC software was used to assess read quality.  The quality of the data was also assessed with Bowtie2's alignment statistics, the number of peaks called by MACS2, and by the tracks in IGV.
Narrow peaks were called with the MACS2 v2.1.1 software using input as controls and a q-value cutoff of 0.001.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

growth_protocol: JB6 and SU-DHL1 cells are cultured in RPMI containing 10% FBS, P/S, and glutamine (typically 2–3 × 106 cells into a T75 flask).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: JB6 and SU-DHL1 cells were cultured in fresh media for 4 hours and then treated with DMSO or 300 nM crizotinib for 3 hours.

tag: disease state

value: Anaplastic large cell lymphoma

value: Lymphoma

tag: treatment

value: DMSO

value: CEBP beta


title: SUDHL-1 STAT3 ChIP-Seq Crizotinib

value: 300 nM Crizotinib


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R1T4


title: SUDHL-1 STAT3 ChIP-Seq DMSO


title: JB6 STAT3 ChIP-Seq DMSO


title: JB6 STAT3 ChIP-Seq Crizotinib


title: SUDHL-1 CEBP beta ChIP-Seq Crizotinib


title: JB6 CEBP beta ChIP-Seq Crizotinib


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R2T2


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R2T3


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R2T4


title: U2OS H2B-GFP Halo-CTCF Non Sync ATAC-seq R2T1


title: JB6 input DNA


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R1T1


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R1T2


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R1T3


title: HFF Non Sync ATAC-seq R1T1

description:
MOAM-HFFnc-NS-R1T1
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: JB6 CEBP beta ChIP-Seq DMSO


title: SUDHL-1 input DNA


title: HFF Non Sync ATAC-seq R1T3

description:
MOAM-HFFnc-NS-R1T3
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Non Sync ATAC-seq R1T2

description:
MOAM-HFFnc-NS-R1T2
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R1T4


title: WASP -/-, biological rep5

hyb_protocol: as suggested by Affymetrix

scan_protocol: GeneChip Scanner 3000 by Affymetrix

data_processing: Probe summarization and normalization using Robust Multi-array Average (RMA) method was performed using R package 'Affy'

source_name: T cell lymphoma

label_protocol: as suggested by Affymetrix

growth_protocol: NPM-ALK transgenic mice were crossed with WAS-deficient mice (all on c57BL/6 background). Mice were bred and received standard rodent chow and drinking water ad libitum. Total RNA was extracted from primary lymphoma that spontaneously developed in NPM-ALK or NPM-ALK/WASP-/- mice.

extract_protocol: Trizol extraction of total RNA from primary T cell lymphoma was performed according to the manufacturer's instructions.

value: Primary mediastinal lymphoma

value: WASP -/-


title: HFF Non Sync ATAC-seq R1T4

description:
MOAM-HFFnc-NS-R1T4
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw

value: foreskin (hTERT transformed foreskin fibroblasts Benanti)


title: WASP -/-, biological rep2


title: WASP -/-, biological rep3


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R2T3


title: WT, biological rep4

value: WT


title: WT, biological rep3


title: WASP -/-, biological rep4


title: WASP -/-, biological rep1


title: WT, biological rep5


title: WT, biological rep2


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R2T2


title: HFF Mitotic Chromatin ATAC-seq R1T1

description:
MOAM-HFFnc-MClu-R1T1
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Chromatin ATAC-seq R1T2

description:
MOAM-HFFnc-MClu-R1T2
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R2T1


title: HFF Mitotic Chromatin ATAC-seq R1T3

description:
MOAM-HFFnc-MClu-R1T3
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: U2OS H2B-GFP Halo-CTCF Mitotic Cell ATAC-seq R2T4


title: pr.str.v3

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than 10-6 were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

source_name: Prostate

growth_protocol: The treated gestating female rats were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from the F1 generation of control or vinclozolin lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring. F3 generation males were euthanized at 18-22 days for testis collection. The F1- F3 generation offspring were not themselves treated directly with vinclozolin. The control and vinclozolin lineages were housed in the same room and racks with lighting, food and water.

extract_protocol:
Ventral prostate epithelial and stromal cells were isolated. Ventral prostates were removed from 19-21 day old rats and cleaned of fat, then digested in 50 ml Hank’s Buffered Salt Solution (HBSS) with 0.5 mg/ml collagenase type II (Sigma C1764) and 66μg/ml DNAse (Sigma DN25) with agitation at 37° for 4 hours. After gravity settling for 10 min. the supernatant containing the stromal cells was removed. The supernatant was centrifuged at 30xg for 4 min. to pellet contaminating epithelial cells, and then the supernatant centrifuged again at 190xg for 6 min to pellet the stromal cells. This wash is repeated 1-2 more times. To clean the epithelial cells from the original gravity settled pellet, the pellet is resuspended in HBSS, centrifuged at 30xg for 4 min., and the supernatant discarded. This wash is repeated 1-2 more times. The cell pellet was resuspended in 820 μL DNA extraction buffer (0.05M Tris HCl, pH 8; 0.01M EDTA; 0.5% SDS) and 80 μl proteinase K (20 mg/ml) added. The sample was incubated at 55°C for 2-3 hours under constant rotation. Then 300 μl of protein precipitation solution (Promega A795A) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 17,000xg for 30 minutes at 4°C. One ml of the supernatant was transferred to a 2 ml tube and 2 μl of Glycoblue cryoprecipitant (Thermo Fisher Scientific AM9516) and 1 ml of cold 100% isopropanol were added. The sample was mixed well by inverting the tube several times then incubated at -20°C for at least one hour. After precipitation, the sample was centrifuged at 17,000xg for 20 min at 4°C. The supernatant was discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol and incubated at -20°C for 20 minutes. Samples were centrifuged for 10 min at 4°C at 17,000xg and the supernatant discarded. Pellet was air-dried at RT (about 5 minutes), then resuspended in 100 μl of nuclease free water. The genomic DNA was fragmented using the Covaris M220. Genomic DNA was diluted to 130 μl with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The remaining DNA was diluted with TE buffer to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 10 min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the DNA-antibody mixture was incubated overnight with rotation at 4˚C.   The following day 50μl of pre-washed anti-mouse IgG magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were added to the DNA-antibody mixture, then incubated for 2h on a rotator at 4˚C. Then the DNA-antibody-bead mixture was placed into a magnetic rack for 1-2 minutes and the supernatant discarded, then the pellet washed with 1xIP buffer 3 times. The washed sample is then resuspended in 250μl digestion buffer (5mM Tris PH8, 10.mM EDT4, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml)) and incubated for 2-3 hours on a rotator at 55˚. 250μl of buffered Phenol-Chloroform-Isoamylalcohol solution were added to the sample and the tube vortexed for 30 sec then centrifuged at 17,000xg for 5min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. Then 250μl chloroform were added to the supernatant from the previous step, vortexed for 30sec and centrifuged at 17,000xg for 5min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of Glycoblue (20mg/ml) (Invitrogen AM9516), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated at -20˚C for >1 hour.  The DNA precipitate was centrifuged at 17,000xg for 20min at 4˚C and the supernatant removed. The pellet was washed with 500μl cold 70% ethanol and incubated at -20˚C for 15 min. then centrifuged again at 17,000xg for 5min at 4˚C and the supernatant discarded. The pellet was air-dried at RT (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured using a Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer.

treatment_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD®™ (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and received ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. On days 8 through 14 of gestation, the females received daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day) or dimethyl sulfoxide (DMSO). These rats were the F0 generation. The vinclozolin was obtained from Chem Service Inc. (West Chester, PA) and was injected in a 20 microliter DMSO vehicle.

value: Prostate

value: Stromal

value: Vinclozolin


title: pr.str.v2


title: HFF Mitotic Chromatin ATAC-seq R2T2

description:
MOAM-HFFnc-MClu-R2T2
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Chromatin ATAC-seq R2T1

description:
MOAM-HFFnc-MClu-R2T1
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HFF Mitotic Chromatin ATAC-seq R2T3

description:
MOAM-HFFnc-MClu-R2T3
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: LEWzizi4

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Gene expression data from lumbar spinal cord of 4-months-old LEWzizi rat

hyb_protocol: 3.5 µg of each fragmented and labelled sample were hybridized to a GeneChip Rat Gene 2.0 ST Array.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G (with AGCC v3.1.1 software)

data_processing: The data were analyzed with Affymetrix Expression Console software (v4.0.1.36) using RMA algorithm for data normalization.

label: Biotin

source_name: Lumbar spinal cord

label_protocol: Biotinylated cRNA samples were prepared using the Affymetrix GeneChipTM WT Plus Kit from 60 ng total RNA.

extract_protocol: RNA was isolated from 40 mg tissue using the peqGOLD Total RNA Kit and peqGOLD DNase I Digest Kit according to the manufacturer's instructions.

value: LEWzizi

value: attractin-mutant

value: Lumbar spinal cord

value: 4 months


title: pr.epi.v1

value: Epithelial


title: LEWzizi1


title: pr.epi.v2


title: pr.epi.v3


title: Lewis2

description: Gene expression data from lumbar spinal cord of 4-months-old Lewis rat

value: Lewis

value: wildtype


title: pr.str.c3

value: Control


title: LEWzizi3


title: Lewis4


title: pr.epi.c2


title: Lewis5


title: LEWzizi2


title: LEWzizi5


title: pr.str.c2


title: Lewis1


title: Lewis3


title: WT, biological rep1


title: HFF Mitotic Chromatin ATAC-seq R2T4

description:
MOAM-HFFnc-MClu-R2T4
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw

value: ATAC-seq


title: pr.epi.c1


title: pr.str.v1


title: HFF Mitotic Chromatin ATAC-seq R1T4

description:
MOAM-HFFnc-MClu-R1T4
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed
MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: pr.str.c1


title: gran.v3

description: vin.granulosa.csv.gz

source_name: Granulosa cells

growth_protocol: The treated gestating female rats were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from the F1 generation of control, DDT or vinclozolin lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring. F3 generation males were euthanized at 18-22 days for testis collection. The F1- F3 generation offspring were not themselves treated directly with vinclozolin or DDT. The control, DDT and vinclozolin lineages were housed in the same room and racks with lighting, food and water.

extract_protocol:
F3 generation rats from vinclozolin, DDT and control lineages were treated with Pregnant Mare Serum Gonadotropin (Sigma cat, St. Louis, MO) (10 IU PMSG injected IP) at 20-22 days of age. Two days later animals were sacrificed and ovaries removed. The ovarian bursa and its adherent fat were removed from each ovary and the ovaries processed for granulosa cell collection. The ovaries were suspended in the Ham’s F-12 base medium used for all procedures (Thermo Scientific). Following sequential 30 minute incubations at 37 °C in 6 mM EGTA in F-12 (to decrease Ca2+ - mediated cell adhesion) and then 0.5 M sucrose in F-12 (to increase osmotic pressure within follicles), ovaries were returned to F-12. Granulosa cells were released into the medium from antral follicles using 30-gauge needles and gentle pressure. Oocytes were removed by aspiration under a dissecting microscope. Granulosa cells from 4-9 rats from the same treatment group were pooled and collected into 1.5 ml tubes, allowed to settle for 10 minutes and supernatant discarded. Three pools of granulosa cells were prepared from different animals and ovaries for each treatment group.  Samples were stored at −70° until the time of DNA isolation. A DNA sample was mixed with 820 μl DNA extraction buffer and 80 μl 0.1M DTT (dichlorodiphenyltrichloroethane) added. The sample was incubated at 65°C for 15 minutes. Following this incubation 80 μl proteinase K (20 mg/ml) was added and the sample was incubated at 55°C for 2 hours under constant rotation. Then 300 μl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) were added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 17,000xg for 20 minutes at 4°C. One ml of the supernatant was transferred to a 2 ml tube and 2 μl of Glycoblue (Thermo-Fisher AM9515) and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20°C freezer for at least one hour. After precipitation, the sample was centrifuged at 17,000xg for 20 min at 4°C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol and incubated at -20°C for 20 minutes. Samples were centrifuged for 10 min at 4°C at 17,000xg and the supernatant discarded. The pellet was air-dried at room temperature (about 5 minutes). The pellet was then resuspended in 100 μl of nuclease free water. Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed. The genomic DNA was sonicated using the Covaris M220 the following way: up to 6μg of pooled granulosa cell genomic DNA was diluted to 130 μl with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) into a Covaris tube. The Covaris was set to the 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The remaining DNA was diluted with TE buffer to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 10 min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the DNA-antibody mixture was incubated overnight with rotation at 4˚C.   The following day 50μl of pre-washed anti-mouse magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were added to the DNA-antibody mixture, then incubated for 2h on a rotator at 4˚C.  Then the DNA-antibody-bead mixture was placed into a magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed bead mixture is then resuspended in 250μl digestion buffer (5mM Tris PH8, 10.mM EDT4, 0.5% SDS with 3.5μl Proteinase K (20mg/ml)). The sample was then incubated for 2-3 hours on a rotator at 55˚. 250μl of buffered Phenol-Chloroform-Isoamylalcohol solution were added to the sample and the tube vortexed for 30 sec then centrifuged at 17,000xg for 5min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250μl chloroform were added to the supernatant from the previous step, vortexed for 30sec and centrifuged at 17,000xg for 5min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of Glycoblue (20mg/ml) (Invitrogen AM9516), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated at -20˚C for >1 hour.  The DNA precipitate was centrifuged at 17,000xg for 20min at 4˚C and the supernatant removed. The pellet was washed with 500μl cold 70% ethanol and incubated at -20˚C for 15 min. then centrifuged again at 17,000xg for 5min at 4˚C and the supernatant discarded. The pellet was air-dried at RT (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured using a Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer.

treatment_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD®™ (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and received ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. On days 8 through 14 of gestation, the females received daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), DDT (25 mg/kg BW/day), or dimethyl sulfoxide (DMSO). These rats were the F0 generation. The vinclozolin and DDT were obtained from Chem Service Inc. (West Chester, PA) and were injected in a 20 microliter DMSO vehicle.


title: HeLa Non Sync ATAC-seq R1T3

source_name: HeLa-S3 cells

value: Human adenocarcinoma cells

value: HeLa-S3 (CCL-2.2)


title: pr.epi.c3


title: gran.v1

description: vin.granulosa.csv.gz


title: gran.d2

description: ddt.granulosa.csv.gz

value: DDT


title: HeLa Mitotic Cell ATAC-seq R1T3


title: gran.d1

description: ddt.granulosa.csv.gz


title: HeLa Mitotic Cell ATAC-seq R1T2


title: HeLa Mitotic Cell ATAC-seq R1T4


title: sc.v2: Sertoli Cells Vinclozolin

source_name: Sertoli Cells

extract_protocol:
The 20-day-old rats were sacrificed and the testes dissected. Testes were washed two times with HBSS. The tunica albuginia was removed from each testis and discarded. The tissue was then chopped with a razor blade until it appeared homogeneous and then underwent sequential enzymatic digestion and wash steps to isolate the purified Sertoli cells. The first step uses trypsin (0.25%) and DNase (0.3 mg/ml) followed by a trypsin inhibitor (0.3 mg/ml) incubation and washes. The next digestion step involves collagenase (0.5 mg/ml) and DNase followed by the final digestion with hyaluronidase (1 mg/ml) and DNase. The final pellet will contain the purified Sertoli cells. DNase I (Sigma DN-25), Collagenase (Sigma C1639), Hyaluronidase (Sigma #H3757), Trypsin Inhibitor Type I-S (Sigma T-6522). Sertoli cell pellets were resuspended in 100 μL 1xPBS, then combined with 820 μL DNA extraction buffer (50 mM, Tris HCl, 10 mM EDTA, pH 8.0, 0.5% SDS) and 80 μl proteinase K (20 mg/ml). The sample was incubated at 55ºC for at least 2 hours under constant rotation. Then 300 μl of protein precipitation solution (Promega, A7953) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 14,000 rpm for 30 minutes at 4ºC. One ml of the supernatant was transferred to a 2 ml tube and 2 μl of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20ºC freezer for at least one hour. After precipitation the sample was centrifuged at 14,000 rpm for 20 min at 4ºC. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol and centrifuged for 10 min at 4ºC at 14,000 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 μl of nuclease free water. Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: DNA isolated from Sertoli cell pools (3 pools each of control, DDT and vinclozolin lineage animals) was sonicated using the Covaris M220 the following way: the genomic DNA was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95˚C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the beads washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution is then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚ C and then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20˚C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer.

value: Sertoli cells


title: gran.c3

description: ddt.granulosa.csv.gz, vin.granulosa.csv.gz


title: gran.c2


title: gran.c1


title: sc.v1: Sertoli Cells Vinclozolin


title: sc.d3: Sertoli Cells DDT


title: sc.v3: Sertoli Cells Vinclozolin


title: HeLa Mitotic Chromatin (fresh) ATAC-seq R1T2

description:
MOAM-HeLa-MCl-R1T2
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: sc.d1: Sertoli Cells DDT


title: HeLa Mitotic Chromatin (fresh) ATAC-seq R1T1

description:
MOAM-HeLa-MCl-R1T1
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: sc.d2: Sertoli Cells DDT


title: sc.c3: Sertoli Cells Control


title: sc.c2: Sertoli Cells Control


title: HeLa Mitotic Chromatin (fresh) ATAC-seq R1T3

description:
MOAM-HeLa-MCl-R1T3
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: SF763_PTEN KO_Rep3

description: Gene expression data from SF763 PTEN-KO cells

hyb_protocol: Standard hyb protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

scan_protocol: Standard scan protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

source_name: Glioma cell line

label_protocol: Standard label protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

growth_protocol: SF763 cells were cultured in Gibco DMEM with 10% FBS.

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

treatment_protocol: PTEN CRISPR KO was performed in SF763 cells using CRISPR/Cas9 system.

value: Glioma

value: PTEN-KO


title: sc.c1: Sertoli Cells Control


title: gran.v2

description: vin.granulosa.csv.gz


title: HeLa Non Sync ATAC-seq R1T4


title: gran.d3

description: ddt.granulosa.csv.gz


title: SF763_PTEN KO_Rep2


title: HeLa Mitotic Chromatin (fresh) ATAC-seq R1T4

description:
MOAM-HeLa-MCl-R1T4
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HeLa Mitotic Cell ATAC-seq R1T1


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R1T1

description:
MOAM-HeLa-MFCl-R1T1
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: SF763_PTEN KO_Rep1


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R1T2

description:
MOAM-HeLa-MFCl-R1T2
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: SF763_WT_Rep3

description: Gene expression data from SF763 PTEN-WT cells

value: WT


title: SF763_WT_Rep2


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R1T3

description:
MOAM-HeLa-MFCl-R1T3
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: SF763_WT_Rep1


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R1T4

description:
MOAM-HeLa-MFCl-R1T4
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: HeLa Non Sync ATAC-seq R2T2


title: HeLa Non Sync ATAC-seq R2T1


title: HeLa Mitotic Cell ATAC-seq R2T3