title: Jeu_3_c4h

status: Public on Aug 27 2017

first: Fei

last: Lan

address: No131 Dongan Road, Xuhui District.

institute: Institute of Biochemical Science

data_processing:
base_calling: CASAVA package (Illumina v1.6)
The extracted reads from Illumina HiSeq platform were processed to quality control and then trimmed of library adapters using customized scripts. The resulting reads were then mapped to human genome assembly hg19 using TopHat
CuffDiff was applied from the package CuffLinks20 to identify differentially expressed genes. The sequencing data was mapped to the merged transcript and each transcript expression levels were estimated using FPKM (Fragments Per Kilobase of transcript per Million reads mapped) values by Cufflinks the result of the differential expression test are reported as log ratios of the FPKM values.
Quantile-based normalization was used to identify differentially expressed genes21. Genes with a p-value of < 0.05 were considered to be differentially expressed. On the basis of the p values, the false discovery rate (FDR) was calculated by the method of Benjamini-Hochberg, and gene with p-values greater than FDR were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values for each Sample

source_name: Jeu_3 cell line

growth_protocol: The human placental choriocarcinoma cell line BeWo and JEG-3 (CCTCC, Wuhan, China) were incubated in DMEM/F-12 (Invitrogen, Germany) supplemented with 10% FBS (Invitrogen) and 1% Pen/Strep (Invitrogen). For hypoxia experiments, cells were incubated in a hypoxic chamber (Tri-Gas incubator, Heal Force, HF100) and exposed to a 1% oxygen atmosphere, whereas normoxic control cells were kept at regular atmosphere (20.9% oxygen).

extract_protocol:
The placenta tissue were extracted and immediately immersed in an RNA stabilization reagent (RNase later sample and assay technology; Qiagen, Valencia, CA).The placentas were then homogenized in Qiazol (Qiagen) with a pestle homogenizer, and total RNA was extracted from the homogenized mixture with a RNeasy mini kit (Qiagen). The total RNA of cells were prepared using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendations. To eliminate potential contamination with genomic DNA, the samples were subjected to additional treatment with recombinant DNaseⅠ(Qiagen) for 30min at 370C. The resulting 8 individual samples (4 from the severely preeclampsia group and 4 from the control group) and cells were then assessed with a spectrophotometer to determine their quality and total RNA concentration (NanoDrop 2000c, Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

tag: condition

value: normal


title: Jeu_3_c2h

type: SRA

city: Shanghai

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: mES HiChIP H3K27ac 25m biological replicate 2 technical replicate 1

status: Public on Aug 28 2017

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_25m.hic
mES_HiChIP_H3K27ac_25m_B2.hic

library_source: genomic

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm9
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.

molecule: genomic DNA

organism: Mus

source_name: v6.5 embryonic stem cell line

growth_protocol: Grown on gelatin-coated plates with KO DMEM supplemented with LIF

extract_protocol:
Protein enrichment of 3C library
Nextera

treatment_protocol: Crosslinked with 1% formaldehyde

tag: cell type

value: ES cell

tag: Sex

value: male


title: BY4741_Stressed_1784042160_C50_BY15

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

data_processing:
Sequenced reads were mapped to S288c reference R64-2-1 using BWA mem
FeatureCounts was used to sum read counts per gene
Identical fragments were collapsed to a single count using XXXXX
Data were normalized by SCNorm method (Bacher et al. 2017)
Picard-tools MarkDuplicates.jar  REMOVE_DUPLICATES=true
Genome_build: S288C R64-2-1

organism: Saccharomyces cerevisiae BY4741

source_name: S. cerevisiae BY4741, salt stressed

growth_protocol: Cells were grown in rich YPD medium in shake flasks to early log phase in batch cultures in shaker flasks at 30C.

extract_protocol:
Cells were sorted on the C1 fluidim and lysed in the system according to manufaturer protocol.
Libraries were generated by SMART-seq method.

treatment_protocol: Sodium chloride was added to 0.7M final concentration and cells were collected at 30 min after treatment.

tag: tissue

value: individual cell


title: Jeu_3_c8h


title: Jeu_3_c24h


title: Jeu_3_4h

value: hypoxic


title: Jeu_3_24h


title: Bewo_c8h

source_name: BeWo cell line

value: BeWo


title: YJ160_2

city: Boston

first: L.

middle: Stirling

last: Churchman

state: Massachusetts

address: 77 Avenue Lois Pasteur, NRB 356

institute: Harvard Medical School

description: Nascent RNA attached to RNAPII

data_processing:
Library strategy: NET-Seq
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
Only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python .
Negative values in the bedgraph file indicates the Crick strand mappings.
Genome_build: sacCer3 (Saccharomyces Cerevisiae)
Supplementary_files_format_and_content: bedgraph

organism: Kluyveromyces lactis

source_name: Whole cell lysate

growth_protocol: K. lactis and D. hansenii were grown in custom medium containing: SC Amino Acid mix (Sunrise Science) (0.2%), Yeast extract (1.5%), Peptone (1%), Dextrose (2%), Adenine (0.01%), Uracil (0.01%), and Tryptophan (0.01%), as previously described (Tsankov et al., 2010). All YAC containing culture was grown in slightly modified medium containing: SC –Tryptophan –Uracil mix (Sunrise Sciences) (0.2%), Yeast extract (1.5%), Peptone (1%), Dextrose (2%), and Adenine (0.01%) (Hughes et al., 2012). All yeast culture was grown at 30°C, except that D. hansenii was cultured at 28°C.

extract_protocol:
Frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.
NET-Seq libraries were constructed and sequenced as previously described with minor modifications (Churchman and Weissman 2012). An improved version of NET-seq DNA linker featured 6 random nucleotides at 5’ terminus was used to further increase ligation efficiency, as well as minimizing ligation bias and library amplification artifacts.

treatment_protocol: Rpb3 was epitope-tagged at C-terminus with 3X-Flag tag and expressed from its endogenous locus. In order to accommodate alternative codon usage in D. hansenii (i.e., CUG translated as serine, instead of leucine) (Moura et al., 2007), codons of the epitope tag and selection marker were modified accordingly. To promote higher efficiency of gene targeting through homologous recombination in K. lactis and D. hansenii, extra long homologous regions adjacent to the target site (up to 1000 bp) were used to flank the epitope tag and selection marker. Electroporation based transformation method were also optimized to achieve high-efficiency transformation in K. lactis and D. hansenii. Further details of strain construction are available upon request.

tag: strain

value: CLIB 210

value: Whole cell lysate


title: Bewo_c2h


title: Jeu_3_16h


title: P65KO-rep1

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description:
MM10.AB3_l1
Processed data file: Supp_Raw_Counts.txt

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and had an expression change of two folds or greater. The called differentially expressed genes must also have at least 2 FPKMs (fragments per kilobase of exon length per million mapped fragments) in one or both of the two cell types being compared. A minimum fold change of 1.5 was also required to call the DE genes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include normalized log2-RPKM values for each library.
Supplementary_files_format_and_content: The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.

organism: Mus musculus

source_name: Spleen+peripheral LNs, Treg cells, P65KO

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: strain/background

tag: genotype/variation

value: Spleen + peripheral lymph nodes

value: CD4+Foxp3+ Treg


title: Bewo_c24h


title: Bewo_c4h


title: BY4741_Stressed_1784042160_C50_BY10


title: Bewo_2h


title: Bewo_c16h


title: Bewo_4h


title: Bewo_24h


title: Bewo_16h


title: Vegetalpole_RNAseq [SMV3]

status: Public on Aug 26 2017

city: Jinan

first: Ming

last: Shao

state: Shandong

address: 27# Shan Da Nan Lu Road

department: School of Lifesciences

institute: Shandong University

description: poly A enriched mRNA

data_processing:
Clean data were filtered by NGSQCToolkit（v2.3）with a parameter of cutOffQualScore 30
Alignment of clean data to reference cDNA, Danio_rerio.Zv9.73.cdna.all.fa.gz
Analysis of differentially expressed genes by EdgeR
Genome_build: Zv9
Supplementary_files_format_and_content: xls files were generated by EdgeR; They provide the RPKM value,FDR etc. for each zebrafish gene.

organism: Danio rerio

source_name: Vegetal pole explant

extract_protocol:
Dechorionate the embryos and then total RNA was prepared via Trizol extraction followed by isopropanol extraction.
The mRNA libraries were constructed using the TruSeq RNA Library Preparation Kit

value: AB

tag: developmental stage

value: 0-20 mins post fertilization

value: fertilized eggs

tag: tissue subtype

value: Vegetal pole explant


title: Jeu_3_c16h


title: H1_ChIP-Seq (paired)

city: Jerusalem

first: Raghu

last: Edupuganti

address: 2-543, Silberman Building

department: Dept. of Genetics

country: Israel

institute: The Hebrew University

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie  0.12.7 , taking only uniquely aligned reads with no more than 2 mismatches.
Peaks were extracted using MACS 1.4 (zhang 2008, genome biol), using a minimal P-value cutoff 10E-4 and a fold change range for a model building between 8-30
For the H1, reads were aligned to the mm9 genome assembly using LifeScope 2.5 with default parameters. Aligned reads were then filtered for MAPQ values < 10 and duplicates reads were removed. Reads density track was generated using only the first read of a pair.
Genome_build: mm9

source_name: Mouse ESCs

growth_protocol: R1 ESC was  grown on gelatinized culture dishes with mMEFs in regualr ESC medium.

extract_protocol:
DNA was fragmented by 10 minutes sonication on Covaris S2 according to protocol, and then the library was constructed using SOLiD library construction reagents (life technologies #4443713)
Cells were harvested with trypsin and ChIP was performed as previously described (Gokhman et al., Nature structural & molecular biology  2013).

value: mESC

tag: chip antibody

value: Anti linker histone H1 (provided by Bustin M)


title: Animalpole_RNAseq [SMA3]

description: poly A enriched mRNA

source_name: Animal pole explant

value: Animal pole explant


title: H1_ChIP-Seq (single)


title: SETbeta_HA_ChIP-Seq

source_name: KH2 cells over-expressing SETbeta

growth_protocol: R1 and KH2  ESCs were  grown on gelatinized culture dishes in regualr ESC medium.

extract_protocol:
Library was constructed using NEBNext CHiPSeq library preparation kit (New England Biolabs E6260)
Cells were harvested with trypsin and ChIP was performed as previously described (Gokhman et al., Nature structural & molecular biology  2013).

treatment_protocol: Doxycyclin was added to a final concentration of 1 μg/ mL to samples 4,5,6, and 7. SET isoforms were overexpressed fro 8 hours.

value: anti-HA (sc-805, Santa Cruz)


title: Jeu_3_2h


title: R1_input


title: Healthy Donor 6 CD34+ non-targeting shRNA control

city: Bethesda

first: Jeffery

middle: L.

last: Miller

state: MD

address: 10 Center Drive Room 9N311

department: NIDDK

institute: NIH

data_processing:
The data were processed using RTA version 1.13.48 and CASAVA 1.8.2, The sequence reads were aligned to hg19 reference build using  Illumina’s Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) mapping algorithm.
Bam files were converted to Fastq using SamtoFastq.
FASTQ file was processed with FASTQ-Masker module of Fastxtoolkit (version  0.0.14) to mask any sequence base with a quality score lower than 30 with an N prior to aligning against the Human Genome hg19 build with Spliced Transcripts Alignment to a Reference (STAR) software (PMID: 23104886). Gene transcript quantitation was performed using HTseq (version 0.6.1p1: http://www-huber.embl.de/HTSeq/doc/overview.html).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample generated using HTseq.

source_name: CD34+ Cells

growth_protocol: Human adult CD34+ cells were cultured in 21 days three phase serum free media as described in previous publication PMID: 23798711.

extract_protocol:
Qiagen miRNAeasy Kit
GLOBINclear Kit (Life Technologies), RiboZero GOLD (Illumina, San Diego, CA) then paired-end sequenced.

treatment_protocol: Briefly, cells were transduced with Sigma shRNA Clone TRCN0000005418 targeting RIOK3 gene Lentiviral particles on culture day 3.  After 24 hours, puromycin was added for 3 more days than transferred into phase 2 medium without puromycin for 7 more days as described in previouls publication PMID: 23798711.

tag: time-point

value: Day 14 Culture

value: CD34+ Cells

tag: transduced with

value: non-targeting shRNA negative control


title: SETalpha_HA_ChIP-Seq

source_name: KH2 cells over-expressing SETalpha


title: SET_ChIP-Seq

value: anti-SET (ab85389, Abcam)


title: Healthy Donor 3 CD34+ non-targeting shRNA control


title: Healthy Donor 1 CD34+ non-targeting shRNA control


title: Donor 2_ CD34+ Cells_RIOK3_knockdown

value: shRNA Clone TRCN0000005418 to knockdown RIOK3 gene expression


title: Healthy Donor 5 CD34+ non-targeting shRNA control


title: Donor 1_ CD34+ Cells_RIOK3_knockdown


title: Bewo_8h

value: BeWo

value: hypoxic


title: Donor 3_ CD34+ Cells_RIOK3_knockdown


title: KH2_input

source_name: KH2 cells


title: G9a_Mutant_rep1

status: Public on Aug 25 2017

city: Nijmegen

first: Tom

last: Koemans

address: Geert Grooteplein 10

department: Human genetics

country: Netherlands

institute: Radboudumc

data_processing:
Quality control: fastqc and Htseq_qa.py
RNA-seq: Reads were mapped to the Drosophila genome (BDGP R5/dm3 using the Burrows Wheeler Aligner (BWA, version 0.6.1) with standard settings allowing 1 mismatch. Only the uniquely mapped reads were used for further analysis and total alignment efficiency was between 63% and 79% for G9a samples and between 79% and 81% for trr samples. Total read count data was generated by the python script HTSeq-count (http://www-huber.embl.de/HTSeq/doc/overview.html) with gene annotations extracted from the file Drosophila_melanogaster.BDGP5.75.gtf, available at http://www ensembl.org. In all samples, over 96% of aligned reads, mapped unambiguously to exons. The unambiguously mapped reads, ranging from 18 to 25 million reads for G9a samples and from 26 to 28 million reads for trr samples, were used for further analysis of differential gene expression by DeSeq2. Hierarchical clustering based on euclidean distances with pearson correlation using the normalized expression values and variance stabilizing tranformation, revealing a high degree of similarity between biological replicates.
genome build: BDGP R5/dm3
processed data files format and content: text file with raw counts.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Drosophila heads

growth_protocol: Flies were cultured according to standard methods at 25 degrees with a 12 hour light dark cycle

extract_protocol: cDNA 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 ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel.

treatment_protocol: Wild type, UAS/Gal4 mediated knock down of Trr and G9a mutant Drosophila melanogaster heads

value: head

value: adult (0-5 days old)

tag: genotype

value: G9aDD1 (Kramer et al., 2011)

tag: extraction protocol

value: Total RNA was extracted from 50 µl aliquots of frozen fly heads using the RNAeasy lipid tissue mini kit (Qiagen). For trr knockdown, two biological replicates were used, for G9a mutants, three biological replicates were used for each condition. mRNA was purified using the Oligotex kit (Qiagen) and cDNA was synthesized using the SuperScript III First Strand synthesis kit (Thermo Fisher) using random hexamers as primers. Second strand cDNA was synthesized using E. Coli polymerase and T4 ligase (New England Biolabs Inc. (NEB)). Remaining RNA was removed using 2 units RNaseH (NEB) before the cDNA was purified using the MinElute PCR purification kit (Qiagen). DNA end repair was performed followed by ligation of Illumina sequencing adaptors and size selection for 300 bp by 2% E-gel (Invitrogen). Fragments were linearly amplified (15 PCR cycles), as validated by quantitative real-time PCR (qPCR), and sample quality was assessed using the Agilent Bioanalyser 2100.


title: G9a_Mutant_rep3


title: trr_WT_rep2

value: Elav-Gal4 / + ; dicer2 / + ; P{y[+t7.7]=CaryP}attP2 / +


title: trr_Mutant_rep2

value: Elav-Gal4 / + ; dicer2 / + ; P{TRiP.HMS01019}attP2 / +


title: trr_Mutant_rep1


title: trr_WT_rep1


title: G9a_Mutant_rep2


title: HOXB13.sample2.unbound

city: Palo Alto

first: Zheng

last: Zuo

address: Stanford

institute: Stanford university

description: In vitro protein-DNA binding reactions

data_processing:
Methylation property identification: For any particular DNA variant inside library, it carries particular barcode to indicate its methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated. Thus acording to the unique methylation barcode information, each read was identified and sorted to its methylation type.
Variant reads counting and sorting: For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Energy logo visualization: Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions. Futhermore, besides conventional G-T-A-C bases, we used two extra “M" and ”W" to represent methylated cytosine on upper and lower strand of DNA respectively, in which the height of M or W indicate the extra binding energy contribution between methylated and unmethylated base.
Supplementary_files_format_and_content: All processed data were saved in .excel files, including the methylation property, bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.

organism: synthetic construct

source_name: mouse HOXB13

growth_protocol: No

extract_protocol:
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1 and PE2 PCR primers were used to PCR amplify extracted DNA by at least 8 cycles (95C 15s, 52C 15s, 72C 30s). For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.

treatment_protocol: All EMSA reactions were done in 12% Tris-glycine gel, 200V, 30mins

tag: dna library composition

value: Including unmethylated dsDNA library HOXB13-UN, top hemimethylated HOXB13-tH, bottom hemimethylated HOXB13-bH, and duplexmethylated HOXB14-dM

tag: recombinant protein used

value: mouse HOXB13 DNA binding domain (In vitro expreesed by NEB Purexpress system)


title: HOXB13.sample2.bound

description: In vitro protein-DNA binding reactions

value: Including unmethylated dsDNA library HOXB13-UN, top hemimethylated HOXB13-tH, bottom hemimethylated HOXB13-bH, and duplexmethylated HOXB13-dM


title: G9a_WT_rep3

value: G9a+/+ (Kramer et al., 2011)


title: G9a_WT_rep2


title: G9a_WT_rep1


title: SCOV3-Vector

first: Archis

last: Bagati

state: MASSACHUSETTS

address: 450 brookline ave.

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were  mapped to GRCh38 whole genome and GENECODE gene annotation database v25  using Tophat 2.0.9 with  parameters -g 1 -p 10
Raw count data are generated by HTSeq using intersection-strict mode
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count  values for each sample

source_name: Melanoma

growth_protocol: SK-Mel-147 and SCOV3 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS, 1% Pen-Strep

extract_protocol:
Cells were collected using cell scrapers, flash frozen on dry ice, and RNA was harvested using RNA isolation kit (Life Technologies). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentiviral pLV-Puro vector encoding either vector or FOXQ1 cDNA were infected into SK-Mel-147 and SCOV3 cells at the same time followed by selection usingpuromycin.

value: Ovarian Carcinoma


title: SK-Mel-147-FOXQ1 rep2

value: Melanoma


title: SCOV3-FOXQ1


title: Healthy Donor 4 CD34+ non-targeting shRNA control

value: Day 14 Culture

value: CD34+ Cells

value: non-targeting shRNA negative control


title: Donor 4_ CD34+ Cells_RIOK3_knockdown

value: shRNA Clone TRCN0000005418 to knockdown RIOK3 gene expression


title: SK-Mel-147-Vector rep2


title: Healthy Donor 2 CD34+ non-targeting shRNA control


title: SK-Mel-147-Vector rep1


title: Jeu_3_8h

tag: Stage

tag: condition

value: hypoxic


title: 4-sip73_2

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

data_processing:
Sequenced reads were trimmed for adaptor sequence.  Followed by 14 bases from the 5' and 1 base from the 3' were trimmed, then mapped to hg38 whole genome using STAR 2.4.1d with default parameters performed in PartekFlow
Normalized data was generated using Total count(Reads per million) plus 0.0001 (TXsf = (106 x Xsf)/TMRs where Xsf here is the raw read of sample S on feature F, andTMRs is the total mapped reads of sample S)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized values for eachsSample

source_name: DAOY siRNA targeting p73

extract_protocol:
Qiagen RNeasy Mini Kit according to the manufacturer’s instructions
Ribosome depleted, pair-end RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: DAOY

tag: cell type

value: medulloblastoma cell line

tag: transfected with

value: siRNA targeting p73 (ID:2671-AMBION)

tag: timepoint

value: transient - 48 hours


title: 3-sip73_1

value: siRNA targeting p73  (ID:2671-AMBION)


title: 2-control_2

source_name: DAOY siRNA control

value: non-targeting control siRNA


title: 1-control_1


title: OGT control RNA-seq-1

city: Athens

first: Huabei

last: Guo

state: GA

address: 315 Riverbend Rd.

department: CCRC

institute: University of Georgia

data_processing:
ChIP-seq basecalls performed using CASAVA version 1.4
ChIP-seq  reads were aligned to the human Hg19 reference genome by Bowtie2.0 with one unique read allowed.
The ChIP-seq enrichment peaks were called by MACVS1.4 and then further annotated with genome distribution and Ontology enrichment by Great 2.0.2
The RNA-seq was performed using Illumina HiSEQ2K platform using PhiX as a reference control (Illumina, San Diego, USA).
The resultant FASTQ files from RNA-seq were imported into CLC Genomics Workbench and aligned to the human hg19/B37 reference sequence.
For RNA-seq, total exon reads or transcript reads per kilobasepair per million (RPKM) were used as gene expression values. The R/Bioconductor package DESeq was used to test differential expression for sequence count data.
Genome_build: hg19 for both ChIP and RNA-seq
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample  for RNA-seq

source_name: colon tumor cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal adenocarcinoma

tag: derivation

value: Isolated from primary tumor

tag: chip antibodies


title: O-GlcNAc ChIP-1

value: O-GlcNAc:RL2, ab2739,Abcam


title: Input-2


title: OGT knockdown RNA-seq-1


title: O-GlcNAc ChIP-2


title: H3K27m3 ChIP-2

value: H3K27m3:cat 39155, Active Motif


title: OGT control RNA-seq-2


title: Input-1


title: SK-Mel-147-FOXQ1 rep1


title: OGT knockdown RNA-seq-2


title: Antonis_P7_2

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

data_processing:
CASAVA 1.8.4 - configureBclToFastq.pl --input-dir runs/150924_D00198_0427_BC7WFRACXX/Data/Intensities/BaseCalls/ --output-dir process/150924_D00198_0427_BC7WFRACXX/ --sample-sheet process/150924_D00198_0427_BC7WFRACXX/ --ignore-missing-bcl --ignore-missing-stats --use-bases-mask y51,i6n,y51
configureBclToFastq.pl --input-dir  runs/150115_SN725_0455_BC65VDACXX/Data/Intensities/BaseCalls/ --output-dir process/150115_SN725_0455_BC65VDACXX/ --sample-sheet process/150115_SN725_0455_BC65VDACXX/ --ignore-missing-stats --ignore-missing-bcl --use-bases-mask Y51,I6nn,Y51
TopHat 2.0.12 -tophat/2.0.12/tophat --keep-fasta-order --keep-tmp -z0 --no-coverage-search --bowtie1 --library-type fr-unstranded --max-multihits 20 --rg-id Antonis_IgG_1 --rg-sample Antonis_IgG_1 --rg-platform illumina --rg-center MAYO --rg-library hg19 -o /data2/bsi/secondary//Thompson_Aubrey_eat05/mrnaseq/150115_SN725_0455_BC65VDACXX_rerun/alignment/tophat_Antonis_IgG_1 -G /data2/bsi/RandD/MAPRSeq/2.0/refs/Ensemble_GeneExon_hg19.mod.gtf --segment-length 25 --transcriptome-index /data2/bsi/RandD/MAPRSeq/2.0/refs/tophat/transcriptome/hg19/index --fusion-search --fusion-ignore-chromosomes chrM,M --fusion-min-dist 50000 -p 4 --mate-inner-dist 63 --mate-std-dev 65 ncbi/hg19/indexed/allchr Antonis_IgG_1.FCC65VDACXX_L4_ITTAGGC.bam.R1.fastq.gz Antonis_IgG_1.FCC65VDACXX_L4_ITTAGGC.bam.R2.fastq.gz
Picard 1.140 -jre1.6.0_20/bin/java -Xmx6g -Xms512m -jar picard/1.140/picard.jar MergeSamFiles accepted_hits.bam unmapped.bam OUTPUT=sorted.bam SO=coordinate CREATE_INDEX=true MAX_RECORDS_IN_RAM=1000000 VALIDATION_STRINGENCY=SILENT
Genome_build: HG19
Supplementary_files_format_and_content: Tophat produced bam files

source_name: Caco2 cells

growth_protocol: Caco2 cells grown as recommended (MEM supplemented with 10% FBS, non-essential amino-acids, and sodium pyruvate). Cells were grown to confluency.

extract_protocol:
after immunopreipitation (or for total cell lysate), RNA was extracted using Trizol and purfied using the PureLink kit (Ambion) whole-transcriptome isolation protocol.
RNA libraries were prepared using 200-500 ng of total RNA according to the manufacturer’s instructions for the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).Libraries were sequenced at 4 or 8 samples per lane to generate 15-33 million read pairs per sample following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3. The flow cells were sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12data collection software. Base-calling is performed using Illumina’s RTA version 1.17.21.3

treatment_protocol: no additional treatments

value: colon

tag: sample type

value: PLEKHA7 IP

tag: experiment


title: Total_4

value: Total RNA control


title: Antonis_P7_3


title: Antonis_IgG_4

value: negative control IP


title: Antonis_P7_4


title: Total_1


title: Total_2


title: TREX_WT_3

city: Stockholm

first: Marek

last: Bartosovic

address: Solnavagen 9

country: Sweden

institute: Karolinska Institute

description:
ribo-zero depleted total RNA
processed data file: DESeq2_FTO_KO.csv, DEXSeq_FTO_KO.csv

data_processing:
Collapsing: CLIP reads were collapsed and only unique reads were used for downstream analyses
Trimming: Reads were quality and adapter trimmed using trimGalore! v. 0.3.3
Alignment:  Reads were aligned to the human reference genome version hg19 by tophat v.2.0.14
Alignment: For CLIP experiments, reads were aligned both with tophat's --GTF option and without and only position with the least number of mismatches were used in downstream analyses
CLIP clustering: CLIP reads were counted in 50bp window along the genome and regions with >10 reads in region and log2 enrichment >1 over input RNA-Seq in at least two replicates were considered as binding sites
Differential expression (DE): Read counting in genes was performed using Htseq-count with parameters -f bam -r name -s yes -i gene_id and DE analyzed with DESeq2 according to manual
Differential exon usage (DEX): Read counting in exons was perfomed using DEXSeq script dexseq_count.py with parameters -s yes -p yes -f bam-r name. DEX analysis was performed using DEXSeq according to manual
Genome_build: hg19
Supplementary_files_format_and_content: CLIP: tsv with genomic coordinates (fields 1-4); Number of reads overlapping with interval (field 5); and enrichments of CLIP replicates over RNAseq (Fields 6-9)
Supplementary_files_format_and_content: RNAseq: csv with output from DESeq/DEXSeq supplemented with raw counts in each replicate

source_name: Flp-in T-REx 293

growth_protocol: Control cell line

extract_protocol:
total RNA was isolated using TriPure reagent
ScriptSeq v2, according to manufacturers instructions

treatment_protocol: Untreated

value: Flp-in T-REx 293


title: Antonis_P7_1


title: Total_3


title: Antonis_IgG_1


title: Antonis_IgG_2


title: FTO_KO_3

source_name: Flp-in T-REx 293-FTO_KO

growth_protocol: HEK293-Flp-In T-Rex cells were transfected with pX461 plasmid contatining Cas9 nuclease and sgRNAs targeting intron 2 of FTO. Protein KO was detected by western blot

value: Flp-in T-REx 293-FTO_KO


title: TREX_WT_2


title: Antonis_IgG_3


title: TREX_WT_1


title: FTO_KO_2


title: FTO_KO_1


title: FTO_Input3

description:
ribo-zero depleted total RNA
processed data file: FTO_clusters.tsv

source_name: Flp-in T-REx 293-3xFLAG-FTO

growth_protocol: HEK293-Flp-In T-Rex cells were stably transfected with pcDNA5/FRT/TO plasmid and clonaly selected for expression of 3xFLAG-FTO. Cells were induced with 100ng/ml of Doxycycline 24 prior to the RNAseq library preparation.

treatment_protocol: 100 ng/ml Doxycycline for 24h

value: Flp-in T-REx 293-3xFLAG-FTO


title: FTO_CLIP2

description:
3xFLAG-FTO bound RNA
processed data file: FTO_clusters.tsv

growth_protocol: HEK293-Flp-In T-Rex cells were stably transfected with pcDNA5/FRT/TO plasmid and clonaly selected for expression of 3xFLAG-FTO. Cells were induced with 100ng/ml of Doxycycline 24 prior to CLIP experiment.

extract_protocol:
FTO - RNA complexes were stabilized with UV crosslinking and purified by immunoprecipitation with FLAG M2 antibodies.
3` ppA DNA linker was ligated on beads. 5` RNA linker was ligated to the purified  RNA. RT was performed using superscript III reverse transcriptase and cDNA library was amplified by 24 cycles of PCR with goTaq DNA polymerase


title: FTO_Input2


title: H3K27m3 ChIP-1


title: FTO_CLIP3


title: 104_G2

city: Vienna

first: Johanna

last: Gassler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute for Molecular Biotechnology

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bowtie2 with increased stringency parameters: --score-min -L 0.6,0.2--very-sensitive
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

source_name: zygote pronucleus

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample preparation protocol.

tag: strain background

tag: genotype/variation

value: wildtype

tag: sex/reassigned-sex

value: maternal


title: FTO_Input1

tag: genotype


title: 102_G2

value: bad


title: 101_G2


title: 103_G2


title: FTO_CLIP1


title: 100_G2

value: paternal


title: 99_G2


title: 90_G2


title: 94_G2


title: 87_G2


title: 86_G2


title: 92_G2


title: 89_G2


title: 91_G2


title: 82_G2


title: 96_G2


title: 93_G2


title: 85_G2


title: 97_G2


title: 88_G2


title: 84_G2


title: 80_G2


title: 79_G2


title: 77_G2


title: 75_G2


title: 78_G2


title: 73_G2


title: 76_G2


title: 72_Scc1_flox

value: mixed (B6, 129, Sv)


title: 98_G2


title: 95_G2


title: 71_Scc1_flox


title: 70_Scc1_flox


title: 69_Scc1_flox


title: 68_Scc1_flox


title: 65_Scc1_flox


title: 62_Scc1_flox


title: 74_G2


title: 67_Scc1_flox


title: 64_Scc1_flox


title: 55_Scc1_KO


title: 60_Scc1_flox


title: 57_Scc1_KO


title: 51_Scc1_KO


title: 49_Scc1_KO


title: 50_Scc1_KO


title: 58_Scc1_flox


title: 56_Scc1_KO


title: 48_Scc1_KO


title: 53_Scc1_KO


title: 61_Scc1_flox


title: 66_Scc1_flox


title: 45_Scc1_KO


title: 43_Scc1_KO


title: 46_Scc1_KO


title: 44_Scc1_KO


title: 42_Scc1_KO


title: 41_Scc1_KO


title: 40_Scc1_KO


title: 52_Scc1_KO


title: 83_G2


title: 39_Scc1_KO


title: 37_Scc1_KO


title: 81_G2


title: 28_Wapl_KO

value: mixed (mainly C57BL/6J)

value: Wapldelta(m)/+(p)


title: 31_Wapl_KO


title: 26_Wapl_KO


title: 25_Wapl_KO


title: 29_Wapl_flox

value: Waplfl(m)/+(p)


title: 33_Wapl_flox


title: 32_Wapl_KO


title: 35_Scc1_KO


title: 24_Wapl_KO


title: 34_Wapl_KO


title: 27_Wapl_KO


title: 22_Wapl_flox


title: 38_Scc1_KO


title: 21_Wapl_flox


title: 20_Wapl_flox


title: 19_Wapl_flox


title: 18_Scc1_flox


title: 17_Scc1_flox


title: 15_Scc1_flox


title: 14_Scc1_flox


title: 12_Scc1_flox


title: 9_Scc1_KO


title: 10_Scc1_KO


title: 11_Scc1_flox


title: 4_Scc1_KO


title: 8_Scc1_KO


title: 5_Scc1_KO


title: 2_Scc1_KO


title: 63_Scc1_flox


title: 6_Scc1_KO


title: 7_Scc1_KO


title: 3_Scc1_KO


title: FPKM_FFE

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

institute: Fudan University

data_processing:
Raw sequencing reads was aligned to mouse genome mm9 and analyzed through a Streamlined Analysis and Annotation Pipeline (SAAP-RRBS)
Raw reads were mapped to mouse genome mm9. Transcripts were assembled using TopHat and quantified through Cufflinks. Fragments per kilobase of transcript per million mapped reads (FPKM) representing transcription level was generated using this package for subsequent comparison.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include methyl/unmethl reads and FPKM values for each Sample
Supplementary_files_format_and_content: peak

source_name: liver

extract_protocol:
Genomic DNA was isolated and purified from homogenized liver tissue using a serial phenol: chloroform extraction. Trizol reagent was used for extracting total RNA following the manufacturer’s protocol.
Total RNA samples are converted to Illumina sequencing libraries using Illumina’s Truseq RNA Sample Preparation Kit; The final libraries from RRBS were prepared for sequencing as per the manufacturer’s instructions in the Illumina cBot and HiSeq Paired end cluster kit version 3.

treatment_protocol: 8-month old male mice were randomized to control or fast-food diets with sedentary lifestyles or voluntary running wheels in their cages, rendering 4 experimental groups: normal chow diet with sedentary lifestyle (NCC), normal chow diet with exercise (NCE), fast food diet with sedentary lifestyle (FFC), and fast food diet with exercise (FFE). Mice were maintained on the interventions for 4 months.

tag: species

value: 129 X C57BL/6 X FVB

tag: age

value: 12 month

tag: genome type

value: wild type


title: FPKM_Aging 25 months

value: 25 month


title: FPKM_Aging 4 months

value: 4 month


title: 1_Scc1_KO


title: 47_Scc1_KO


title: FPKM_Aging 9 months

value: 9 month


title: FPKM_FFC


title: FPKM_NCE


title: FPKM_NCC


title: FPKM_Aging 12 months


title: FPKM_Aging 18 months

value: 18 month


title: 13_Scc1_flox


title: sibling at 36hpf

city: Pittsburgh

first: Jeffrey

middle: M

last: Gross

state: Pennsylvania

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

description: processed data file: Tet23_36hpf_GE_all.xlsx

data_processing:
base-calling, demultiplexing done at University of Pittsburgh Genomic Research Core
fastq files quality checked using FastQC
mapped using CLC Genomics Grid Worker 7.5.1
gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1
Genome_build: GRCz10
Supplementary_files_format_and_content: Tet23_36hpf_GE_all.xlsx

source_name: whole eye tissue

growth_protocol: zebrafish embryos raised under standard condition

extract_protocol:
whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol
RNA samples were processed for RNAseq using Ambion poly-A capture kit and NEB Next kit for cDNA synthesis and library prep.

tag: strain

value: TL

value: sibling control

tag: tissue

value: dissected eyes

value: 36 hour-postfertilization


title: tet2-/-;tet3-/- mutants at 36hpf

value: tet2-/-;tet3-/- mutants


title: 59_Scc1_flox

value: maternal


title: InputDNA_for_trr_ChIPseq_wildtype

data_processing:
Quality control: fastqc and Htseq_qa.py
ChIP-seq: Reads were mapped to the Drosophila genome (BDGP R5/dm3 using BWA 0.6.1 with standard settings allowing 1 mismatch. Total alignment efficiency was more than 95%. Duplicate reads and reads with a mapping quality score (MAPQ) below 15 were excluded from downstream analysis. For each biological replicate, trr binding sites were identified using MACS2 with input DNA as control (MACS2 for trr_ChIP_seq_wildtype_rep1: band width=300, mfold: 5,50, p-value: 1*10^-3, regional labda: 1000-10000. For trr_ChIPseq_wildtype_rep2: band width: 300, mfold: 3,100, q-value: 1*10^-5, lambda: 500-5000). Bindings sites on chromosome U, Uextra and mitochondrial genome were not used for further analysis. Remaining putative trr binding regions were visualized in a heatmap that was sorted based on k-means clustering of read intensity around the centre of the peak using the python script fluff_heatmap.py (https://github.com/simonvh/fluff). Individual clusters were examined visually in the genome browser to assess the quality of the peaks within the clusters. Two clusters (8 and 15) of replicate 1 were identified that contained many false positive peaks with a relatively small binding region and cluster 15 had very few reads around the centre. Peaks within these clusters were removed from downstream analysis. For trr_rep2 all clusters appeared to represent high quality trr binding sites. Trr binding regions from both biological replicates were merged and concatenated and the number of reads present in these regions were counted in each sample individually using HTSeq. and normalized to library size. The ratio and mean of reads in each binding region was calculated between the two biological duplicates to identify trr binding sites that are consistent between the two biological replicates. We included all binding sites with a mean number of reads > 100 and < 2 fold difference in normalized read count between the two biological replicates.
genome build: BDGP R5/dm3
processed data files format and content: wig file

extract_protocol: Input libraries were prepared for sequencing using standard Illumina protocols (Trueseq)

value: head

tag: developmental stage

value: adult (0-5 days old)

value: Wild type

tag: chip antibody

value: none (input)

tag: extraction protocol

value: Chromatin was extracted from 50 µl aliquots of frozen wildtype fly heads, aged between 0 and 5 days old, in biological duplicates. Fly heads were crushed in PBS (Sigma) and crosslinked with formaldehyde (Sigma) at a final concentration of 1% for 30 minutes. Crosslinking was terminated using glycine (Invitrogen) at a final concentration of 125mM and crosslinked material was immediately washed twice in PBS and centrifuged at 13000rpm, for 15 minutes at 4 degrees. The pellet was resuspended in buffer 1 (15 mM Tris-Hcl (pH 7.5), 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.1 mM sucrose) and the solution was homogenized using a QiaShredder column (Qiagen). Cells were lysed using buffer 1 supplemented by 2% triton-X-100 (Sigma) and a crude nuclear extract was collected by centrifugation (6000 rpm, 10 minutes at 4 degrees). Nuclei were re-suspended in incubation buffer (0.15% SDS, 1% triton x-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris) supplemented with 0.1% BSA (Sigma) and 1x protease inhibitor (Roche) and subjected to sonication (Diagenode Bioruptor) for 30 minutes (30 seconds on/off cycle using the “high intensity” mode), yielding average DNA fragments of 150-300 base pairs. Immunoprecipitation reactions were performed overnight in incubation buffer with 3 ng of anti-trr antibody (gift from Dr. A. Mazo), protease inhibitor cocktail (Roche), BSA, and pre-blocked protein A/G agarose beads (Santa Cruz). Chromatin-antibody-bead complexes were recovered by centrifugation (4000rpm, 2 minutes at four degrees) and washed twice with low salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris pH 8, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris pH 8, 500 mM NaCl), once with LiCl wash buffer (10 mM Tris pH 8.0, 1% Na-deoxycholate, 1% NP-40, 250 mM LiCl, 1 mM EDTA) and twice with TE buffer. Chromatin was eluted in 1% SDS, 0.1M NaHCO3, 200 mM NaCl and decroslinked at 65° Celcius (C) for four hours. DNA was purified by phenol/chloroform extraction and ethanol precipitated using linear acrylamide (Ambion) and sodium acetate at -20 degrees. Library preparation for Illumina sequencing was performed using the Truseq DNA sample prep kit V2 (Illumina) with approximately 3 ng of starting DNA 15 PCR cycles for amplification. Library fragment size was assessed using the 2100 Agilent Bioanalyser and was shown to be between 200 and 400 bp.


title: pol IV iTto estradiol-induced sRNA seq

city: Columbus

first: R. Keith

last: Slotkin

state: OH

address: 500 Aronoff Laboratory, 318 W. 12th Ave.

department: Molecular Genetics

institute: The Ohio State University

data_processing:
Illumina software was used for basecalling. Sequenced reads were de-multiplexed and trimmed for adaptor sequence. Sequences were masked for low-quality sequence and filtered for reads 18-28 nt in size (UEA small RNA tool v 2.5.0 used).
Wig files represent bowtie alignments of siRNA to the transgene T-DNA sequence, normalized to reads per milllion, at each base.  Tracks were created for combined 21 and 22 nt size class as well as 24 nt size class for both sense and antisense strand.
Genome_build: TAIR10 + iTto transgene sequence
Supplementary_files_format_and_content: First column: small RNA sequence. Second column: normalized abundance (Reads per million) of the small RNA.

organism: Arabidopsis thaliana

source_name: stage 1-12 inflorescence

growth_protocol: Plants were grown on soil in 18 hour long days at 23ºC.

extract_protocol: For the total RNA libraries, total RNA was extracted using Trizol reagent and enriched using the MirVana microRNA isolation kit. Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Induction was achieved using the 20 uM beta-estradiol spray or mock induction using the same spray without the inclusion of estradiol. T1 plants were sprayed as they transitioned to flowering, and were sprayed once every day for 7 or more days before inflorescence tissue collection.

tag: ecotype

value: Col

tag: induced

value: 20 uM beta-estradiol spray


title: trr_ChIPseq_wildtype_rep1

extract_protocol: ChIP-seq libraries were prepared for sequencing using standard Illumina protocols (Trueseq)

value: anti_Trr (Johnston et al., 2011)


title: pol V iTto estradiol-induced sRNA seq


title: wt Col iTto mock-induced sRNA seq

value: mock


title: wt Col iTto estradiol-induced sRNA seq


title: Ptpn11E76K+MSPC

city: Atlanta

first: LEI

last: Dong

address: 1760 Haygood Drive NE, HSRB E3642

institute: Emory University

data_processing:
Raw image data file from high-throughput sequencing(like Illumina HiSeqTM2500/MiseqTM) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling, version 1.4).
Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat Version V2.0.9
For each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor.
Genome_build: mm9
Supplementary_files_format_and_content: read count

source_name: Mesenchymal stem/progenitor cells

extract_protocol:
MSPCs (CD45-Ter-119-CD31-CD140+Sca-1+)  were freshly isolated from the BM of Ptpn11E76K/+/Nestin-Cre+ and Ptpn11+/+/Nestin-Cre+ mice
RNA was extracted using the Rneasy Midi kit (Qiagen). Total RNA samples were enriched for polyadenylated transcripts using the Oligotex mRNA Mini kit (Qiagen)

value: BM derived Mesenchymal stem/progenitor cells


title: WT air

city: Guangzhou

first: Lujun

last: Yu

state: Guandong

address: xingangxilu 135

institute: Sun Yat-sen University

data_processing:
Illumina library construction, sequencing, and sequence analysis were conducted as previously described (Yu et al., 2012; van Veen et al., 2016)
The software used was Tophat and Cufflinks.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: leaf

treatment_protocol: Four-week-old wild-type (WT) and 671 myc2-2 mutant plants were submergence-treated in the dark for 24 h and rosettes were harvested at 0 and 24 h after reoxygenation. For each genotype, the leaf sample collected from six independent plants was used for RNA sequencing,

value: leaf

value: wild type

tag: treatment

value: before submergence


title: WT R3

value: 3h after submergence


title: myc2 R3


title: myc2 air


title: sibling at 72hpf

data_processing:
base-calling, demultiplexing done at the Genome Sequenicng and Analysis Facility, UT Austin
fastq files quality checked using FastQC
mapped using TopHat with annotated spliced junction
gene counting and differentially expressed genes identified using Tuxedo Suite (Trapnell et al., 2012)
Genome_build: GRCz10

value: TL

value: sibling control

value: dissected eyes

value: 72 hour-postfertilization


title: 36_Scc1_KO

value: mixed (B6, 129, Sv)

value: paternal


title: tet2-/-;tet3-/- mutants at 72hpf

value: tet2-/-;tet3-/- mutants


title: Wildtype 4

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
RNA-seq reads were mapped to the mm9 mouse genome assembly using STAR version 2.4.2a with the following parameters : --sjdbOverhang 99 --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --outFilterMultimapNmax 40 --twopassMode Basic

Genome_build: mm9
Supplementary_files_format_and_content: BigWig files of genome read density were generated using bamCoverage from the deepTools package

source_name: Blastocyst

growth_protocol: Embryos were isolated from naturally mated females at E3.5 and immediately subjected to RNA isolation.

extract_protocol:
RNA was isolated using the pico pure isolation kit (Arkturus) according to manufacturers instructions.
cDNA was generated using the SMART-Seq® Ultra® Low Input RNA Kit (Clontech), followed by sequencing library preparation using the Nextera XT DNA Library Preparation Kit (Illumina) according to manufacturers instructions.

treatment_protocol: mutant and wildtype females and not treated further.

value: wildtype


title: Maternal Trim28 mutant 2


title: Maternal Trim28 mutant 1


title: Maternal Trim28 mutant 4


title: Maternal Trim28 mutant 3


title: Wildtype 3


title: Ptpn11++MSPC


title: 16_Scc1_flox


title: 23_Wapl_KO

value: mixed (mainly C57BL/6J)

value: Wapldelta(m)/+(p)

value: maternal


title: wt Col leaf sRNA seq

source_name: juvenile leaf

treatment_protocol: No estradiol spraying protocol was used for this control

value: Col


title: Wildtype 1


title: RRBS_beta-cat_TG+DEN

city: Shanghai

value: unknown

value: beta-catenin transgenic


title: RRBS_25MO_2

value: 25 month

value: wild type


title: RRBS_18MO_2

value: 18 month


title: RRBS_18MO_1


title: RRBS_12MO_1

value: 12 month


title: RRBS_beta-cat_TG


title: RRBS_25MO_1


title: RRBS_9MO_2

value: 9 month


title: RRBS_12MO_3


title: RRBS_12MO_2


title: RRBS_9MO_3


title: RRBS_18MO_3


title: RRBS_4MO_3

value: 4 month


title: RRBS_9MO_1


title: trr_ChIPseq_wildtype_rep2

source_name: Drosophila heads

value: head

value: adult (0-5 days old)

value: Wild type

value: anti_Trr (Johnston et al., 2011)

value: Chromatin was extracted from 50 µl aliquots of frozen wildtype fly heads, aged between 0 and 5 days old, in biological duplicates. Fly heads were crushed in PBS (Sigma) and crosslinked with formaldehyde (Sigma) at a final concentration of 1% for 30 minutes. Crosslinking was terminated using glycine (Invitrogen) at a final concentration of 125mM and crosslinked material was immediately washed twice in PBS and centrifuged at 13000rpm, for 15 minutes at 4 degrees. The pellet was resuspended in buffer 1 (15 mM Tris-Hcl (pH 7.5), 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.1 mM sucrose) and the solution was homogenized using a QiaShredder column (Qiagen). Cells were lysed using buffer 1 supplemented by 2% triton-X-100 (Sigma) and a crude nuclear extract was collected by centrifugation (6000 rpm, 10 minutes at 4 degrees). Nuclei were re-suspended in incubation buffer (0.15% SDS, 1% triton x-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris) supplemented with 0.1% BSA (Sigma) and 1x protease inhibitor (Roche) and subjected to sonication (Diagenode Bioruptor) for 30 minutes (30 seconds on/off cycle using the “high intensity” mode), yielding average DNA fragments of 150-300 base pairs. Immunoprecipitation reactions were performed overnight in incubation buffer with 3 ng of anti-trr antibody (gift from Dr. A. Mazo), protease inhibitor cocktail (Roche), BSA, and pre-blocked protein A/G agarose beads (Santa Cruz). Chromatin-antibody-bead complexes were recovered by centrifugation (4000rpm, 2 minutes at four degrees) and washed twice with low salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris pH 8, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris pH 8, 500 mM NaCl), once with LiCl wash buffer (10 mM Tris pH 8.0, 1% Na-deoxycholate, 1% NP-40, 250 mM LiCl, 1 mM EDTA) and twice with TE buffer. Chromatin was eluted in 1% SDS, 0.1M NaHCO3, 200 mM NaCl and decroslinked at 65° Celcius (C) for four hours. DNA was purified by phenol/chloroform extraction and ethanol precipitated using linear acrylamide (Ambion) and sodium acetate at -20 degrees. Library preparation for Illumina sequencing was performed using the Truseq DNA sample prep kit V2 (Illumina) with approximately 3 ng of starting DNA 15 PCR cycles for amplification. Library fragment size was assessed using the 2100 Agilent Bioanalyser and was shown to be between 200 and 400 bp.


title: RRBS_FFE_2

value: 129 X C57BL/6 X FVB


title: RRBS_FFE_3


title: RRBS_4MO_2


title: Wildtype 2

value: wildtype


title: RRBS_FFC_3


title: RRBS_FFE_1


title: RRBS_FFC_2


title: Oocyst sporozoite, alba4-null Replicate 2

city: University Park

first: Scott

middle: E.

last: Lindner

address: W224 Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Penn State University

description:
489_614_oo-spz_CuffDiff.xlsx
614

data_processing:
The resulting data was mapped to the P. yoelii 17XNL strain reference genome (plasmodb.org, v27) using Tophat2 in a local Galaxy instance.
Gene and transcript expression profiles for both WT and alba4-null assemblies were generated using Cufflinks (Galaxy version 2.2.1.0), merged into a separate large transcript assemblies with Cuffmerge (Galaxy version 2.2.1.0).
Resulting assemblies were compared using Cuffdiff (Galaxy version 2.2.1.3). Differential transcript abundances were measured in fragments per kilobase of transcript per million mapped fragments (FPKM). All default parameters were used for this analysis, except that a masked file containing known non-coding RNAs was applied and the number of maximum fragments per locus allowed was increased from 50,000 to 1,000,000. For the purified schizont and gametocyte samples, three biological replicates were merged for WT and pyalba4- profiles. Oocyst sporozoite samples used two biological replicates for this analysis.
Genome_build: PlasmoDB-28_Pyoeliiyoelii17X_Genome.fasta
Supplementary_files_format_and_content: Excel files are the resulting CuffDiff output with FPKM values and statistics, taking into account the replicate datasets per life cycle stage.

organism: Plasmodium yoelii

source_name: Oocyst sporozoites

growth_protocol: Naïve female mice were infected with either WT-GFP or alba4-null parasites, and parasitemia was allowed to reach 1%. Schizonts and gametocytes were harvested from these mice. Naïve female mosquitoes were allowed to take a blood meal from mice infected with either WT-GFP or alba4-null parasites, and sporozoites were collected from the midguts ten days post-blood meal. Two million sporozoites were used per replicate per parasite line.

extract_protocol:
Following purification of the parasite samples, RNA from all sample types was isolated by the QIAgen RNeasy Kit using the manufacturer’s protocol with the additional on-column DNaseI digestion. RNA yields were quantified spectrophotometrically, and the quality of all samples was confirmed by measuring RNA Integrity Number (RIN) using the Agilent Bioanalzyer.
A barcoded library was made from each sample by using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's protocol. qPCR was performed to determine the concentration of each library and an equimolar pool was made of all libraries.


title: Oocyst sporozoite, alba4-null Replicate 1

description:
489_614_oo-spz_CuffDiff.xlsx
614


title: RRBS_DEN

value: C57BL/6 X FVB


title: Oocyst sporozoite, WT-GFP Replicate 2

description:
489_614_oo-spz_CuffDiff.xlsx
489

value: wt


title: Oocyst sporozoite, WT-GFP Replicate 1

description:
489_614_oo-spz_CuffDiff.xlsx
489


title: Gametocyte, alba4-null Replicate 2

description:
489_614_Gametocyte_Cuffdiff.xlsx
614

source_name: Gametocytes


title: 30_Wapl_flox

value: mixed (mainly C57BL/6J)

value: Waplfl(m)/+(p)

value: maternal


title: RRBS_FFC_1

value: wild type


title: Gametocyte, alba4-null Replicate 1

description:
489_614_Gametocyte_Cuffdiff.xlsx
614


title: RRBS_NCE_2


title: RRBS_NCE_1


title: RRBS_NCE_3


title: Gametocyte, WT-GFP Replicate 3

description:
489_614_Gametocyte_Cuffdiff.xlsx
489


title: RRBS_NCC_2


title: RRBS_NCC_1


title: Gametocyte, WT-GFP Replicate 2

description:
489_614_Gametocyte_Cuffdiff.xlsx
489


title: Schizont, alba4-null Replicate 2

description:
489_614_Schizont_ Cuffdiff.xlsx
614

source_name: Schizonts


title: Gametocyte, WT-GFP Replicate 1

description:
489_614_Gametocyte_Cuffdiff.xlsx
489


title: Schizont, alba4-null Replicate 3

description:
489_614_Schizont_ Cuffdiff.xlsx
614


title: RRBS_4MO_1


title: Input DNA in latent cells

city: sacramento

first: Yoshihiro

last: Izumiya

address: 4645 Second Avenue

institute: UC Davis Medical Center

data_processing:
Basecalls performed using CASAVA version 1.7
Data were trimmed by Trimmomatic trimming tool
The ChIP-Seq data (FASTQ sequence reads) was aligned to human hg19 reference genome and reference KSHV genome sequence (Human herpesvirus 8 strain JSC-1 clone BAC16, GenBank: GQ994935.1) with Bowtie 2
Peak finding was performed with the MACS2 program following the developer’s manual. The default settings with a minimum FDR (q-value) cut-off of 0.05 were used.
Genome_build: hg19 + KSHV genome (GQ994935.1)
Supplementary_files_format_and_content: MACS2 generated bed file

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: TREx-F3H3-K-Rta BCBL-1 cells

growth_protocol: TREx-F3H3-K-Rta BCBL-1 cells were grown in RPMI 1640 medium supplemented with 15% fetal calf serum (FBS). Cells were treated with or without 1 µg/mL doxycycline for 24 h

extract_protocol:
DNA was sonicated to an average size of ~300 bp using a Diagenode Bioruptor. Chromatin DNA from 1 X 108 cells was used per immunoprecipitation assay with 10 µg of ZIC2 antibody
ChIP-enriched and input DNA samples were used to generate Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KR0453) according to manufacturer’s recommendations.

tag: pathogen

value: KSHV

value: peritoneal effusion

tag: cell type

value: KSHV positive B cell lymphoma

tag: passages


title: Schizont, WT-GFP Replicate 3

description:
489_614_Schizont_ Cuffdiff.xlsx
489


title: ZIC2 ChIP-Seq in latent cells

value: ZIC2 (Abcam, ab150404)


title: Schizont, WT-GFP Replicate 2

description:
489_614_Schizont_ Cuffdiff.xlsx
489


title: Schizont, WT-GFP Replicate 1

description:
489_614_Schizont_ Cuffdiff.xlsx
489


title: ZIC2 ChIP-Seq in lytic cells


title: ChIP-seq_EB-KH2_H3K27ac

status: Public on Aug 24 2017

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: ChIP DNA

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) or mouse genome assembly (mm9) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: mm9
Supplementary_files_format_and_content: wig file and peak bed file

source_name: Mouse KH2 cells

growth_protocol: Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin. KH2 cells were cultured on primary embryonic fibroblasts in standard ES medium and differentiated to EBs by LIF withdrawal for 8 days.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

tag: cell line

value: H3K27ac antibody, Abcam, ab4729, GR132150-4


title: Input DNA in lytic cells


title: ChIP-seq_ESC-KH2_H3K27ac_rep2

description: ChIP DNA


title: ChIP-seq_ESC-KH2_H3K27ac_rep1

description: ChIP DNA


title: Gametocyte, alba4-null Replicate 3

description:
489_614_Gametocyte_Cuffdiff.xlsx
614


title: RRBS_NCC_3

value: 12 month


title: ATAC-seq_EB-KH2_rep3

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) or mouse genome assembly (mm9) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: wig file and peak bed file

growth_protocol: Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin. KH2 cells were cultured on primary embryonic fibroblasts in standard ES medium and differentiated to EBs by LIF withdrawal for 8 days

extract_protocol: For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

value: differentiated EBs


title: ATAC-seq_EB-KH2_rep2


title: ATAC-seq_ESC-KH2_rep4

value: ESCs


title: ATAC-seq_ESC-KH2_rep2


title: ATAC-seq_ESC-KH2_rep1


title: CAPTURE-ChIP-seq_EB-KH2_sgEsrrb-SE

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v1.0.0 with the following parameters: --best --strata -k 2 -m 2 for HBG samples and --best --strata -k 1 -m 1 for the rest samples.  Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file, peak bed file

source_name: mouse KH2 cells

tag: streptavidin dynabeads

value: ThermoFisher 65602


title: Schizont, alba4-null Replicate 1

description:
489_614_Schizont_ Cuffdiff.xlsx
614

tag: genotype


title: CAPTURE-ChIP-seq_EB-KH2_sgSox2-SE


title: CAPTURE-ChIP-seq_ESC-KH2_sgUtf1-SE


title: CAPTURE-ChIP-seq_ESC-KH2_sgSox2-SE


title: CAPTURE-ChIP-seq_ESC-KH2_sgOct4-SE


title: CAPTURE-3C-seq_EB-KH2_sgSox2-SE

description: Processed data file: CAPTURE-3C-seq_EB-KH2_sgSox2-SE_interaction.txt

data_processing:
Library strategy: 3C-seq
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie2 v2.2.8 with default parameters. The reads with low mapping qualit and duplicate reads were removed after the aligment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (http://wiki.wubrowse.org/Long-range).
Genome_build: hg19
Supplementary_files_format_and_content: Pairwise Interaction Format

extract_protocol: For 3C-seq analysis using the Illumina NextSeq500, 10-20 ng of 3C DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.


title: CAPTURE-ChIP-seq_ESC-KH2_sgEsrrb-SE


title: CAPTURE-ChIP-seq_EB-KH2_sgUtf1-SE


title: CAPTURE-3C-seq_EB-KH2_sgUtf-1-SE

description: Processed data file: CAPTURE-3C-seq_EB-KH2_sgUtf-1-SE_interaction.txt


title: CAPTURE-3C-seq_EB-KH2_sgOct4-SE

description: Processed data file: CAPTURE-3C-seq_EB-KH2_sgOct4-SE_interaction.txt


title: CAPTURE-3C-seq_EB-KH2_sgEsrrb-SE

description: Processed data file: CAPTURE-3C-seq_EB-KH2_sgEsrrb-SE_interaction.txt


title: CAPTURE-3C-seq_ESC-KH2_sgOct4-SE

description: Processed data file: CAPTURE-3C-seq_ESC-KH2_sgOct4-SE_interaction.txt


title: CAPTURE-3C-seq_ESC-KH2_sgSox2-SE

description: Processed data file: CAPTURE-3C-seq_ESC-KH2_sgSox2-SE_interaction.txt


title: ATAC-seq_EB-KH2_rep4


title: ATAC-seq_EB-KH2_rep1


title: MKO+CCl4_3

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Illumina Bcl2fastq2 2.17 software used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the genome using STAR (version 2.4.0k)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools
To compute gene expression, GRCm38.p4 GFF3 genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3
The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3
Genome_build: GRCm38.p4 Ensembl version 81
Supplementary_files_format_and_content: DESeq 1.8.3 normalized counts

source_name: hepatic F4/80+ cells

growth_protocol: 3 month old male mice were used for the experiment and maintained on normal chow

extract_protocol:
liver of treated mice were digested and F4/80+ cells were immunoselected by magnetism-assisted cell sorting, mRNA was isolated by silica membrane spin columns
Messenger (polyA+) RNAs were purified from 30 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: mice were administered intraperitonneal carbon tetrachloride to induce experimental fibrosis

tag: background strain

value: KO

value: liver

value: macrophage

tag: gender

value: male

value: 3 months


title: MKO+CCl4_2

tag: age


title: CAPTURE-3C-seq_ESC-KH2_sgUtf-1-SE

description: Processed data file: CAPTURE-3C-seq_ESC-KH2_sgUtf-1-SE_interaction.txt


title: MKO+CCl4_1


title: MWT+CCl4_2

value: WT


title: MWT+CCl4_1


title: MWT+CCl4_3


title: CAPTURE-ChIP-seq_EB-KH2_sgOct4-SE


title: Knockdown-732

city: Nanjing

first: Mantang

last: Qiu

state: Jiangsu

address: 42 Baiziting

department: Thoracic Surgery

institute: Cancer Institute of Jiangsu Province

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: lung cancer cell_SBF2-AS1 siRNA

growth_protocol: A549 cells are cultured with RPMI 1640 medium supplemented with 10% fetal bovine serum, 100U/ml penicillin, and 100mg/ml streptomycin in humidified air with 37 °C with 5% CO2. Before transfection, A549 cells were plated into 6-well plate.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Ion  Proton Sequencing Protocol

treatment_protocol: siRNA are transfected with Lipofectamine iMAX reagent according to the manufacturer’s protocol

value: lung cancer cell

value: siRNA targeting SBF2-AS1


title: ATAC-seq_ESC-KH2_rep3


title: Knockdown-670


title: ATAC-seq_K562_HBD-1kb_KO-rep2

source_name: Human K562 cells

tag: genotype/variation

value: HBD-1kb intergenic region knockout


title: ATAC-seq_K562_HBD-1kb_KO-rep3


title: ATAC-seq_K562_Control-rep2

value: control


title: ATAC-seq_K562_Control-rep3


title: ATAC-seq_K562_Control-rep1


title: CAPTURE-3C-seq_ESC-KH2_sgEsrrb-SE

description: Processed data file: CAPTURE-3C-seq_ESC-KH2_sgEsrrb-SE_interaction.txt


title: RNA-seq_K562_WT-rep1

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads) using Cufflinks.
Differential gene expression analyses were performed using DEseq.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene RPKM values

growth_protocol: Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For RNA-seq analysis using the illumina NextSeq500, 0.1-2 ug of total RNA was processed for library generation using the TruSeq RNA Sample Preparation v2 Kit (Illumina) following the manufacturer’s protocol.


title: RNA-seq_K562_WT-rep2


title: RNA-seq_K562_FB-dCas9-BirA_sgHS1-5-rep2


title: RNA-seq_K562_FB-dCas9-BirA_sgHS1-5-rep3


title: RNA-seq_K562_FB-dCas9-BirA_sgHS1-5-rep1


title: RNA-seq_K562_FB-dCas9-BirA_sgHS2-rep1


title: 54_Scc1_KO

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bowtie2 with increased stringency parameters: --score-min -L 0.6,0.2--very-sensitive
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

source_name: zygote pronucleus

tag: strain background

value: mixed (B6, 129, Sv)

tag: sex/reassigned-sex

value: maternal


title: RNA-seq_K562_FB-dCas9-BirA_sgHS2-rep2


title: RNA-seq_K562_FB-dCas9-BirA_sgHBG-rep3


title: RNA-seq_K562_FB-dCas9-BirA_sgGal4-rep3


title: RNA-seq_K562_FB-dCas9-BirA_sgHBG-rep1


title: RNA-seq_K562_FB-dCas9-BirA_sgHBG-rep2


title: ChIP-seq_K562_NUP98

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file and peak bed file

tag: chip antibody

value: Cell Signaling, C39a3, 2598


title: RNA-seq_K562_FB-dCas9-BirA_sgGal4-rep2


title: ChIP-seq_K562_NUP153


title: ChIP-seq_K562_JQ1-6h_RNAPII

source_name: Human K562 cells - JQ1 6 hrs treatment


title: RNA-seq_K562_FB-dCas9-BirA_sgGal4-rep1


title: ChIP-seq_K562_JQ1-6h_BRD4


title: NC-1

source_name: lung cancer cell_negative_control (NC)

value: negative control siRNA


title: ChIP-seq_K562_JQ1-2h_RNAPII

source_name: Human K562 cells - JQ1 2 hrs treatment


title: ATAC-seq_K562_HBD-1kb_KO-rep1


title: NC-2


title: ChIP-seq_K562_DMSO_BRD4

source_name: Human K562 cells - control treatment


title: CAPTURE-ChIP-seq_K562_sgHBG-Flag


title: CAPTURE-ChIP-seq_K562_sgHBG-Streptavidin


title: CAPTURE-ChIP-seq_K562_sgHBG-Cas9


title: CAPTURE-ChIP-seq_K562_sgHS2-Flag


title: RNA-seq_K562_FB-dCas9-BirA_sgHS2-rep3


title: CAPTURE-ChIP-seq_K562_sgHBG-sg2-rep2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHBG_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHBB-sg2-rep2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHBB-sg2_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHBG-sg2-rep1


title: CAPTURE-ChIP-seq_K562_sgHS2-Streptavidin


title: CAPTURE-ChIP-seq_K562_sgHBB-sg2-rep1


title: CAPTURE-ChIP-seq_K562_sgHS5-sg2-rep2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS5-sg2_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS5-sg2-rep1


title: CAPTURE-ChIP-seq_K562_sgHS4-sg2-rep2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS4-sg2_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS2-sg2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS2-sg2_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS3-sg2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS3-sg2_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS1-sg2-rep1

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS1-sg2_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS1-sg2-rep2


title: CAPTURE-ChIP-seq_K562_sgHS4-sg2-rep1


title: CAPTURE-ChIP-seq_K562_sgGal4-rep2


title: ChIP-seq_K562_DMSO_RNAPII


title: CAPTURE-ChIP-seq_K562_no_sgRNA-rep1


title: ChIP-seq_K562_JQ1-2h_BRD4


title: CAPTURE-ChIP-seq_K562_sgGal4-rep3


title: CAPTURE-ChIP-seq_K562_sgGal4-rep1


title: CAPTURE-ChIP-seq_K562_sgGal4-rep4


title: CAPTURE-ChIP-seq_K562_sgHS1-5-rep6

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS1-5_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS1-5-rep3


title: CAPTURE-ChIP-seq_K562_sgHS1-5-rep2


title: CAPTURE-ChIP-seq_K562_sgHS1-5-rep5


title: CAPTURE-ChIP-seq_K562_sgHS2-Cas9


title: CAPTURE-ChIP-seq_K562_sgHS1-5-rep1


title: CAPTURE-ChIP-seq_K562_sg3'HS1-rep1

description: Processed data file: CAPTURE-ChIP-seq_K562_sg3'HS1_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sg3'HS1-rep2


title: CAPTURE-ChIP-seq_K562_sgHBG-rep1


title: CAPTURE-ChIP-seq_K562_sgHBG-rep3


title: CAPTURE-ChIP-seq_K562_sgHBG-rep2


title: CAPTURE-ChIP-seq_K562_sgHBG-rep4


title: CAPTURE-ChIP-seq_K562_sgHBD-1kb-rep2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHBD-1kb_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS5-rep3

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS5_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS5-rep2


title: CAPTURE-ChIP-seq_K562_sgHBB-rep1

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHBB_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS5-rep1


title: CAPTURE-ChIP-seq_K562_sgHS4-rep1

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS4_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS3-rep3

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS3_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS4-rep2


title: CAPTURE-ChIP-seq_K562_sgHS2-rep2

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS2_vs_sgGal4_merged.txt


title: CAPTURE-ChIP-seq_K562_sgHS3-rep2


title: CAPTURE-ChIP-seq_K562_sgHS1-5-rep4


title: CAPTURE-ChIP-seq_K562_sgHS3-rep1


title: CAPTURE-ChIP-seq_K562_sgHS2-rep4


title: CAPTURE-ChIP-seq_K562_sgHS2-rep5


title: CAPTURE-ChIP-seq_K562_sgHS2-rep3


title: CAPTURE-ChIP-seq_K562_sgHS2-rep1


title: CAPTURE-ChIP-seq_K562_sgHS1-rep1

description: Processed data file: CAPTURE-ChIP-seq_K562_sgHS1_vs_sgGal4_merged.txt


description: Processed data file: CAPTURE-3C-seq_K562-HBD-1k-del_sg3'HS1-combined_interaction.txt


title: CAPTURE-ChIP-seq_K562_sgHS1-rep2


title: CAPTURE-3C-seq_K562-HBD-1k-del_sg3'HS1-rep1


title: CAPTURE-ChIP-seq_K562_sgHBD-1kb-rep1


description: Processed data file: CAPTURE-3C-seq_K562-HBD-1k-del_sgHS3-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS3--sg4-rep1

description: Processed data file: CAPTURE-3C-seq_K562_sgHS3-sg4-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS3--sg4-rep3


title: CAPTURE-3C-seq_K562_sgHS3--sg4-rep2


title: CAPTURE-3C-seq_K562-HBD-1k-del_sgHS3-rep2


title: CAPTURE-3C-seq_K562_sgHS3-sg4-combined


title: CAPTURE-3C-seq_K562_sgHS3--sg3-rep2

description: Processed data file: CAPTURE-3C-seq_K562_sgHS3-sg3-combined_interaction.txt


title: CAPTURE-3C-seq_K562-HBD-1k-del_sgHS3-rep1


title: CAPTURE-3C-seq_K562_sgHS3--sg2-rep3

description: Processed data file: CAPTURE-3C-seq_K562_sgHS3-sg2-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS3--sg3-rep1


title: CAPTURE-3C-seq_K562_sgHS3-sg2-combined


title: CAPTURE-3C-seq_K562_sgHS3--sg2-rep1


title: CAPTURE-3C-seq_K562_sgHS2-sg5-combined

description: Processed data file: CAPTURE-3C-seq_K562_sgHS2-sg5-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS2--sg5-rep3


title: CAPTURE-3C-seq_K562_sgHS3--sg2-rep2


title: CAPTURE-3C-seq_K562_sgHS2--sg5-rep2


title: CAPTURE-3C-seq_K562-HBD-1k-del_sg3'HS1-rep2


title: CAPTURE-3C-seq_K562_sgHS2--sg4-rep2

description: Processed data file: CAPTURE-3C-seq_K562_sgHS2-sg4-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS2--sg5-rep1


title: CAPTURE-3C-seq_K562_sgHS2--sg4-rep1


title: CAPTURE-3C-seq_K562_sgHS2-sg3-combined

description: Processed data file: CAPTURE-3C-seq_K562_sgHS2-sg3-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS2-sg4-combined


title: CAPTURE-3C-seq_K562_sgHS2--sg3-rep2


title: CAPTURE-3C-seq_K562_sgHS2--sg3-rep3


title: CAPTURE-3C-seq_K562_gDNA_control

description: Processed data file: CAPTURE-3C-seq_K562_gDNA_control_interaction.txt


title: CAPTURE-3C-seq_K562_sgGal4_no_capture_control

description: Processed data file: CAPTURE-3C-seq_K562_sgGal4_no_Processed data file: CAPTure_control_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS3-sg3-combined


title: CAPTURE-3C-seq_K562_sgHS2--sg3-rep1


title: CAPTURE-3C-seq_K562_sg3'HS1-combined

description: Processed data file: CAPTURE-3C-seq_K562_sg3'HS1-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sg3'HS1-rep3


title: CAPTURE-3C-seq_K562_sg3'HS1-rep2


title: CAPTURE-3C-seq_K562_sgHBD-2kb-rep2

description: Processed data file: CAPTURE-3C-seq_K562_sgHBD-2kb-combined_interaction.txt


description: Processed data file: CAPTURE-3C-seq_K562_sgHBD-1.5kb-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHBD-2kb-rep1


title: CAPTURE-3C-seq_K562_sg3'HS1-rep1


title: CAPTURE-3C-seq_K562_sgHBD-2kb-combined


title: CAPTURE-3C-seq_K562_sgHBD-1.5kb-rep2


title: CAPTURE-3C-seq_K562_sgHBD-1.5kb-rep1


title: CAPTURE-3C-seq_K562_sgHBD-1kb-combined

description: Processed data file: CAPTURE-3C-seq_K562_sgHBD-1kb-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS2--sg4-rep3


title: CAPTURE-3C-seq_K562_sgHBD-1kb-rep2


title: CAPTURE-3C-seq_K562_sgHBD-1kb-rep1


title: CAPTURE-3C-seq_K562_sgHBG-rep3

description: Processed data file: CAPTURE-3C-seq_K562_sgHBG-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHBD-1kb-rep3


title: CAPTURE-3C-seq_K562_sgHBG-combined


title: CAPTURE-3C-seq_K562_sgHS4-rep2

description: Processed data file: CAPTURE-3C-seq_K562_sgHS4-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS4-combined


title: CAPTURE-3C-seq_K562_sgHBG-rep1


title: CAPTURE-3C-seq_K562_sgHBB-rep3

description: Processed data file: CAPTURE-3C-seq_K562_sgHBB-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHBB-combined


title: CAPTURE-3C-seq_K562_sgHBB-rep2


title: CAPTURE-3C-seq_K562_sgHBB-rep1


title: CAPTURE-3C-seq_K562_sgHS4-rep1


title: CAPTURE-3C-seq_K562_sgHS3-rep3

description: Processed data file: CAPTURE-3C-seq_K562_sgHS3-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS3-combined


title: CAPTURE-3C-seq_K562_sgHS3-rep2


title: CAPTURE-3C-seq_K562_sgHS3-rep1


title: CAPTURE-3C-seq_K562_sgHS2-rep3

description: Processed data file: CAPTURE-3C-seq_K562_sgHS2-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHS2-combined


title: CAPTURE-3C-seq_K562_sgHS2-rep2


title: CAPTURE-3C-seq_K562_sgHS2-rep1


title: CAPTURE-3C-seq_K562_sgHS1-combined

description: Processed data file: CAPTURE-3C-seq_K562_sgHS1-combined_interaction.txt


title: CAPTURE-3C-seq_K562_sgHBG-rep2


title: RNA-seq in SKNMC cell line infected with shGFP

city: Boston

first: Sowmya

last: Iyer

state: MA

institute: Massachusetts General Hospital

description: SKNMC.shGFP.RNAseq

data_processing:
Reads were aligned to hg19 using STAR. Mapped reads were filtered to exclude PCR duplicates and reads mapping to known ribosomal RNA coordinates, obtained from rmsk table in the UCSC database
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression was calculated using featureCounts. Only primary alignments with mapping quality of 10 or more were counted.

source_name: SKNMC

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (Clontech).  1 μg of total RNA was treated with Ribogold zero to remove ribosomal RNA. Remaining RNA was used to construct Illumina sequencing libraries with random primers according to manufacturer instructions using the Truseq Stranded RNA LT Kit.
RNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: source type

value: cell line


title: CAPTURE-3C-seq_K562_sgHS1-rep1


title: RNA-seq in SKNMC cell line infected with shEWSFLI1


title: Med1cKO rep4

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
Raw files were uploaded into Illumina's BaseSpace hub (basespace.illumina.com) and aligned to mus musculus mm10 genome using the TopHat Alignment Version 1.0.0 App and selecting "Trim TruSeq Adapters" option.
Transcripts were assembled and differential expression was determined using the BaseSpace Cufflinks Assembly and DE Version 1.1.0 App selecting mm10 reference genome and "Stranded" polyA enriched sequences.
FPKM tables and CuffDiff results of differential gene expression of were downloaded and significantly expressed genes (FDR<0.05) were used for analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files contain FPKM values for each sample and summary differential gene expression data.

source_name: Med1cKO_Ventricle Tissue

extract_protocol:
Ventricles were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
polyA RNA was enriched and TruSeq RNA stranded libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: post natal day 21

tag: tissue

value: cardiac; ventricles


title: Med1cKO rep2


title: WT rep4

source_name: WT_Ventricle Tissue


title: WT rep2


title: Med1cKO rep3


title: Med1cKO rep1


title: WT rep1


title: RNA-seq in A673 cell line infected with shEWSFLI1


title: RNA-seq in A673 cell line infected with shGFP


title: BAF155 ChIP-seq in SKNMC cell line

data_processing:
Reads were aligned to hg19 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Genome_build: hg19
Supplementary_files_format_and_content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

value: BAF155 (generated in-house epitope=aa924-1004; C-terminus)


title: BAF155 ChIP-seq in SKNMC cell line infected with shEWSFLI1


title: Mouse Whole Blood MeDIP-seq

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

institute: Washington University in St. Louis

data_processing:
Sequencing reads were aligned to rat rn4 or mouse mm9 with BWA
For MeDIP-seq, redandunt reads were discard
For MRE-seq, reads were filtered by MRE recognization site in genome.
Aligned results were further processed by methylQA (http://methylqa.sourceforge.net/) to get bigWig files
Genome_build: rn4, mm9
Supplementary_files_format_and_content: bigWig

source_name: Mouse Whole Blood

extract_protocol:
For MeDIP, 5–15 μg DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA), than DNA was sonicated to ~100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2–5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg ml−1, Eurogentec. Catalog No. BI-MECY-0100). For this, DNA was heat-denatured at 95 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4 °C with rocking agitation in 500 μl immunoprecipitation buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 4 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg ml−1, Jackson Immunoresearch. Catalog No. 315-005-008) and 100 μl Protein A/G beads (Pierce Biotechnology. Catalog No. PI20421) were added and incubated for an additional 2 h at 4 °C with agitation. After immunoprecipitation a total of six immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg ml−1proteinase K for 2 h at 55 °C and then allowed to cool to room temperature. MeDIP DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen).
Fifteen cycles of PCR were performed on 5 μl of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.
For MRE:  DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100–300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 µl used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 μl used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.

tag: strain

value: Whole blood


title: SMARCA2 ChIP-seq in SKNMC cell line infected with shEWSFLI1

value: SMARCA2 (Active Motif #39805)


title: Mouse Whole Blood MRE-seq


title: SMARCA2 ChIP-seq in SKNMC cell line infected with shGFP


title: CAPTURE-3C-seq_K562_sgHS1-rep2

value: ThermoFisher 65602


title: WT rep3


title: ARPE-19 TB40epi rep2 120hpi

city: Chicago

first: Adam

last: Oberstein

state: IL

address: 835 South Wolcott Ave.

department: Microbiology and Immunology

institute: University of Illinois

description: processed data column header: AO.24

data_processing:
Illumina Casava1.7 software used for basecalling.
Concatenated human/HCMV fasta and annotation (.gtf) files were created for mapping and feature counting by combining sequences and annotations from gencode human genome Release 24 (GRCh38.p5) and TB40E-BAC4 (EF999921.1).
Align sequencing fragments were mapped to the concatenated genome using HISAT2 version 2.0.3 (Kim et al., 2015)
Strand-specific fragment counts were generated at the gene level using featureCounts (Liao et al., 2014), requiring a minimum mapping quality score of 10 and concordantly mapped fragment ends on the same chromosome.
In order to eliminate compositional bias, HCMV counts were removed prior to normalization and ratio determination.
Ratio determination and significance calling was performed using DESeq2 (Love et al., 2014) with dispersion estimates fit with local regression.
Genome_build: gencode human genome Release 24 (GRCh38.p5) and TB40E-BAC4 (EF999921.1).
Supplementary_files_format_and_content: rawdata_table.tab: Tab-delimited count matrix (gene.id vs. Sample) containing gene-level summarized raw counts from featureCounts. This file contains human and HCMV counts.

source_name: adult retina

growth_protocol: DMEM supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, 2 mM glutamax (Gibco), 10 mM Hepes pH 7.4, 0.1 mM MEM Non-Essential Amino Acids (Gibco), 100 units/ml Penicillin G, and 100 μg/ml Streptomycin Sulfate.

extract_protocol:
Trizol fractionation followed by Rneasy column and Dnase treatment.
According to manufacturer's instructions using a KAPA Stranded RNA-Seq Kit with RiboErase (Kappa Biosytems).

treatment_protocol: 2h infection at 3 MOI based on IE1-titering (fluorescent focus assay) on each cell type.

value: epithelial

tag: treatment

value: HCMV-infected

tag: replication

value: biological replicate 2


title: ARPE-19 mock rep1 120hpi

description: processed data column header: AO.21

tag: cell type

value: mock

value: biological replicate 1


title: ARPE-19 TB40epi rep1 120hpi

description: processed data column header: AO.23


title: ARPE-19 mock rep2 120hpi

description: processed data column header: AO.22


title: MRC-5 TB40epi rep2 120hpi

description: processed data column header: AO.20

source_name: embryonic lung

value: fibroblast


title: HA ChIP-seq in A673 cell line infected with HA-EWSR1


title: HA ChIP-seq in A673 cell line infected with GFP


title: MRC-5 TB40epi rep1 120hpi

description: processed data column header: AO.19


title: MRC-5 mock rep2 120hpi

description: processed data column header: AO.18


title: ARPE-19 TB40epi rep1 72hpi

description: processed data column header: AO.15


title: MRC-5 mock rep1 120hpi

description: processed data column header: AO.17


title: ARPE-19 TB40epi rep2 72hpi

description: processed data column header: AO.16


title: BAF155 ChIP-seq in SKNMC cell line infected with shGFP


title: ARPE-19 mock rep2 72hpi

description: processed data column header: AO.14


title: MRC-5 TB40epi rep2 72hpi

description: processed data column header: AO.12


title: MRC-5 mock rep2 72hpi

description: processed data column header: AO.10


title: ARPE-19 mock rep1 72hpi

description: processed data column header: AO.9


title: MRC-5 mock rep1 72hpi

description: processed data column header: AO.13


title: MRC-5 TB40epi rep1 72hpi

description: processed data column header: AO.11


title: ARPE-19 TB40epi rep1 24hpi

description: processed data column header: AO.7