title: med23 ref4-3 rep3

city: West Lafayette

first: Clint

last: Chapple

address: 175 S. University St.

department: Department of Biochemistry

institute: Purdue University

data_processing:
Casava1.8.2 software was used for basecalling.
Trimmomatic and/or fastx_clipper were used to remove adapters. Poor quality bases (less than Phred-20) were removed (clipped) from both the 5' and 3' ends of the unaligned reads. After adapter removal and quality clipping any reads below a minimum (30 bases) length were discarded. Reads were then mapped to TAIR10 assembly of the Arabidopsis genome using Tophat v2.1.0 with default parameters.
The raw count matrix was generated for each sample using HTSeq-count v0.6.1 (Anders et al., 2015) with the following parameters: -s reverse -r pos -m intersection-nonempty -t exon -i gene_id.
Differential expression analysis was performed using the edgeR package as follows: edgeR analysis began with a count table comprising 33,602 genes. Genes expressed at low levels were then filtered out by removing any genes for which there was not at least 1 count per million in at least four of the samples. This resulted in a list of 18,842 expressed genes. Counts were then normalized using TMM normalization. Next, the “ANOVA-like” procedure in EdgeR was used to identify genes that were differentially expressed between any of the genotypes (FDR < 0.05). This resulted in a list of 14,688 differentially expressed genes. To determine which of these genes were differentially expressed in each of the mutants compared to wild type, the exact test for the negative binomial distribution (Robinson and Smyth, 2008) was used followed by a Bonferroni correction to maintain a gene-wise error rate of 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-separated values file of the raw count matrix for all samples.

source_name: Whole rosettes

growth_protocol: Seeds were sown nine per 4" x 4" pot and positions of the pots were randomized. Seeds were held at 4C for two days before transferring to 23C under a 16 hr light, 8 hr dark photoperiod. Material was harvested 6.5 hours after subjective dawn on the 18th day after transferring to the growth chamber.

extract_protocol:
For each sample, five whole rosettes were pooled from different pots and ground under liquid nitrogen. Approximately 100 mg of the ground tissue was used to extract total RNA using the Qiagen RNEasy Plant Mini kit (Cat#74904) with on-column DNAse treatment (Cat#79254).
Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat#RS-122-2103) was used with 2 ug of total RNA for the construction of dual barcoded sequencing libraries.

value: 18 days

value: Whole rosettes


title: im-nc_hen2-4_rep2

status: Public on Feb 16 2018

type: SRA

city: College Station

first: Akihito

last: Fukudome

state: Texas

address: Dept. Horticultural Sciences MS2133 Texas A&M Univ.

country: USA

institute: Texas A&M University

description:
im-ncRNA-seq_hen2-4(2)
im-nc_samtools_bedcov.txt

library_source: transcriptomic

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings. Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
Raw sequenced reads (.fastq files) were uploaded to Galaxy (https://usegalaxy.org/). The following data processing was done using Galaxy.
Sequenced reads were trimmed for adapter and low-quality sequences by using Trim Galore! (v0.4.0), then mapped with Tophat (v2.0.14) against reference assembly Ensembl TAIR10 from Illumina iGenome, using default parameters except -i/--min-intron-length 60 -I/--max-intron-length 6000.
Coverage depth of regions of interest was calculated by SAMtools_BedCov (v1.2).
Genome_build: Arabidopsis TAIR10 (Ensembl)
Supplementary_files_format_and_content: im-nc_samtools_bedcov.txt file includes raw coverage counts (a sum of coverage depth per base in each region of interest) for each sample, computed by SAMtools_BedCov.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: im-nc_hen2-4, 7-day-old seedling

growth_protocol: 7-day-old seedlings horizontally grown on ¼ MS media containing 0.5% sucrose.

extract_protocol:
Seedling roots were flash frozen immediately after harvesting and subjected to total RNA extraction using miRNeasy Plant Mini kit (QIAGEN).
The total RNA was submitted to Texas A&M AgriLife Genomics & Bioinformatics Service for RNA-seq analysis (paired-end, 125-bp). After validating the integrity and purity of total RNA using Nanodrop, sequencing libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Plant kit.  To enrich intermediate non-coding RNA (im-ncRNA), fragmentation step was omitted, and library cDNA with 100-500nt were purified using Pippin (Sage Science) prior to sequencing by Illumina HiSeq (125 nt, paired-end).

tag: ecotype

value: Colombia

tag: genotype

tag: age

tag: tissue

value: root


title: LM1-Z1

city: Los Angeles

first: Meng

last: Li

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

data_processing:
Basecalls generated on Nextseq 500 by RTA v2
Raw data files in FASTQ format was analyzed with Partek Flow v4
FASTQ files were trimmed with Quality Score method
Trimmed reads were mapped with Star 2.4.1d to human hg38 genome build with Gencode v23 as guidance
Mapped reads were quantificed to Gencode v23 uisng Partek E/M method
Quantified reads were normalized by Upper Quartile method
Normalized reads were analzyed for differentially expression using Partek's Gene Specific Analysis method
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file includes normalized read counts (upper quartile normalization with offset 1) for genes in all samples

organism: Homo sapiens

source_name: Unfixed Fresh Frozen Human Liver

growth_protocol: Not applicable

extract_protocol:
Unfixed fresh frozen liver tissue embedded in OCT compound were cryo-cut followed by tissue collection via Laser Captured Microdissection methods. The RNA was extracted with RNeasy Micro Kit (QIAGEN).
1ng of RNA per sample was subjected to first-stranded cDNA synthesis followed by PCR amplification (11 cycles) using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Then, the amplified cDNA was used for the establishement of libraries using standard Illumina protocols.

treatment_protocol: Not applicable

tag: patient

tag: zone

tag: gender

value: Male


title: med23 ref4-3 rep2

state: IN


title: im-nc_Col_rep3

description:
im-ncRNA-seq_Col(3)
im-nc_samtools_bedcov.txt

source_name: im-nc_Col, 7-day-old seedling

value: wild-type


title: No Treatment total, rep2

city: Indianapolis

first: Ann

last: Collier

address: 635 N Barnhill Dr MS4067

institute: Indiana University School of Medicine

description:
mRNA-Seq
NT2
Processed data file: Total_RNA_cuffdiff.xlsx

data_processing:
FASTQ format converted using FASTQgroomer (Galaxy version 1.0.4).
Reads mapped to genome using Tophat (Galaxy version 2.1.0).
FPKM calculated using Cufflinks (Galaxy version 2.2.1.0).
Transcript assemblies merged using Cuffmerge (Galaxy version 2.2.1.0).
Differential expression for total RNA performed on total samples using Cuffdiff an Cuffmerge assembly (Galaxy version 2.2.1.3).
Percent shifts for polysome fractions calculated by difference in percent total of polysome fractions between each treatment group. i.e. polysome FPKM for NT divided by the sum of the polysome and monosome FPKMs for that sample. Then subtract NT by UVB for each replicate to get a shift.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *total_cufflinks.xls: Excel files include FPKMs for the 'total' samples.
Supplementary_files_format_and_content: Percent_shift_calculations.xlsx: Excel file includes FPKMs for the fractionated samples
Supplementary_files_format_and_content: Total_RNA_cuffdiff.xlsx: Excel file includes differential expression for total RNA.

source_name: Human skin

growth_protocol: N-TERT keratinocytes (Dickson et al., 2000) were cultured in EpiLife media (Invitrogen, Carlsbad, CA) supplemented with human keratinocyte growth supplement (HKGS, Invitrogen) and 1000U Penicillin-Streptomycin (Roche, Indianapolis, IN).

extract_protocol:
RNA was isolated using Trizol followed by phenol/chloroform extraction. The concentration and quality of total RNA samples were first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control.
The samples are first spiked-in with ERCC Mix 1 to no treatment and Mix 2 to all treated. Then five hundred nanograms of RNA per sample were used to prepared dual-indexed strand-specific cDNA library using TruSeq Stranded mRNA Library PrepKit (Illumina). The resulting libraries were assessed for its quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. One and a half pico molar pooled libraries were sequenced with 2x75bp paired-end configuration on NextSeq500 (Illumina) using NextSeq 500/550 High Output Kit. A Phred quality score (Qscore) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: UVB irradiation of N-TERT keratinocytes was carried out using Philips FS20T12 UVB broadband light sources as described previously (Lewis et al., 2010). A IL1700 radiometer and a SED240 UVB detector (International Light, Newburyport, MA) were used to measure UVB intensity prior to each experiment using a distance of 8cm from the light source to the culture dish. Cells were always irradiated in EpiLife media, which eliminates any UVC wavelengths, followed by normal incubation settings (37°C and 5% CO2).

tag: cell line

value: N-TERT

tag: cell type

value: keratinocytes

tag: treatment

value: 0 J/m2 UVB + 8hr incubation

tag: fraction

value: Whole Cell Lysate


title: med16 ref4-3 rep2


title: med16 ref4-3 rep4


title: med23 ref4-3 rep1


title: med5b-3 ref4-3 rep4

value: med5b-3 ref4-3


title: med16 ref4-3 rep1


title: med5b-3 ref4-3 rep2


title: med2 ref4-3 rep4


title: med5b-3 ref4-3 rep3


title: med16 ref4-3 rep3


title: med2 ref4-3 rep2


title: med23 rep4


title: med5b-3 ref4-3 rep1


title: med2 ref4-3 rep3


title: med2 ref4-3 rep1


title: med23 rep3


title: im-nc_Col_rep1

description:
im-ncRNA-seq_Col(1)
im-nc_samtools_bedcov.txt


title: med23 ref4-3 rep4


title: med23 rep1


title: med23 rep2


title: med16 rep4


title: med16 rep2


title: med16 rep3


title: med16 rep1


title: med5ab rep3

value: med5a-1 med5b-1


title: med5ab rep2


title: med5ab rep1


title: med2 rep4


title: med2 rep3


title: med2 rep2


title: med2 rep1


title: ref4-3 rep4


title: ref4-3 rep3


title: ref4-3 rep2


title: ref4-3 rep1


title: WT rep2

value: wild type


title: WT rep4


title: WT rep1


title: NahG-Désirée_PVY2

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: small RNAs

data_processing:
Sequenced reads were trimmed for adaptor sequence. Low complexity reads containing at most two distinct nucleotides were removed.
For identification of known and novel miRNAs reads shorter than 18 nt and longer than 25 nt long, reads without adaptor, reads matching tRNA/rRNA sequences in RFAM version 10, the Genomic tRNA Database and EMBL, release 95, and reads not mapped to Solanum tuberosum genome (PGSC_DM_v4.3) using the filter tool from UEA sRNA Toolkit. The remaining reads were compared to all known miRNAs registered in miRBase database release 21, allowing no mismatches. The sequences that perfectly matched with mature miRNAs from other plants than potato, were mapped to the potato genome in order to identify MIR loci. For all identified MIR loci the pre-miRNA sequence was extracted. Some of these miRNA sequences were considered  as miRNA variants/isomiRs and numbered by decreasing read number. To identify novel unannotated miRNAs, filtered reads were submitted to miRCat tool of the UEA sRNA Toolkit using suggested parameters for plants with minimum size of 18 and maximum size of 24 nt. Reads were first mapped to the genome, then the 100 and 200 nt long windows around the aligned reads were extracted and folded using RNAfold. The novelty of potato specific miRNAs was verified with miRPlant version 5 using default parameters.
Identification of phasiRNAs and PHAS loci was done with ta-siRNA prediction tool developed by Chen, Li, and Wu (2007) and both, the genome (PGSC_DM_v4.3) and the transcriptome sequences of potato with annotations from Ramšak et al. (2014). Minimum and maximum lengths of sRNAs were set at 18 and 25 nt, and the p-value threshold at 0.0001.
To identify vsiRNAs, first, the quality filtered reads from one of PVYNTN-infected samples were mapped to the sequenced genome of PVYNTN (isolate NIB-NTN, accession no. AJ585342) to obtain the consensus PVYNTN genome sequence infecting the plants. This was done to account for possible emerged mutations between our and the sequenced isolate of PVYNTN as described by Kutnjak et al. (2015). Second, the quality filtered reads of lengths 20-24 nt from all PVYNTN-infected samples were mapped to the reconstructed consensus PVYNTN genome using CLC Genomics Workbench (http://www.clcbio.com/) allowing only 100 % identity.
Genome_build: Solanum tuberosum DM genome (PGSC_DM_v4.3) available at http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml
Genome_build: StNIB potato transcriptome available at http://www.gomapman.org/export/input/stNIB-v1_data
Genome_build: PVYNTN (isolate NIB-NTN, accession no. AJ585342) available at http://www.ncbi.nlm.nih.gov/nuccore/54021378
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and RPM values of all identified small RNAs.
Supplementary_files_format_and_content: Consensus PVYNTN genome sequence in FASTA format.

organism: Solanum tuberosum

source_name: PVYNTN-infected potato plants

growth_protocol: Plants were grown in a growth chamber and kept at 21 C in the light and 18 C in the dark, at a relative humidity of 75%, with 70–90 mmol/m2/s2 radiation and a 16-h photoperiod.

extract_protocol:
Total RNA was extracted from homogenised leaf tissue using TRIzol reagent (Invitrogen).
small RNA libraries were prepared for sequencing using standard Illumina protocols at Seqmatic.

treatment_protocol: After 4 weeks of growth in soil, the potato plants were inoculated with the sap of PVYNTN-infected plants (isolate NIB-NTN, accession no. AJ585342). For the mock inoculated plants, the same procedures were performed with the sap of healthy potato plants. Three plants for each treatment were used. PVYNTN- and mock-inoculated leaves of each genotype (Désirée, NahG-Désirée) were collected three days post inoculation (3 dpi) and immediately frozen in liquid nitrogen.

tag: cultivar

value: NahG-Desiree

value: leaf

value: PVYNTN infection


title: NahG-Désirée_mock3

description: small RNAs

source_name: control-mock inoculated potato plants

value: control


title: NahG-Désirée_PVY1

description: small RNAs


title: NahG-Désirée_mock2

description: small RNAs


title: med5ab rep4

value: 18 days


title: Désirée_PVY3

description: small RNAs

value: Desiree


title: NahG-Désirée_mock1

description: small RNAs


title: Désirée_PVY1

description: small RNAs


title: Désirée_PVY2

description: small RNAs


title: Désirée_mock1

description: small RNAs


title: Désirée_mock3

description: small RNAs


title: Désirée_mock2

description: small RNAs


title: mESC_Rsf1_ChIP-seq

city: Birmingham

first: Hengbin

last: Wang

state: AL

address: 720 20th St S Kaul Bldg 430

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

library_source: genomic

data_processing:
For RNA-seq data, reads were mapped to hg19 or mm10 using STAR version 2.5.1b. Differentially expressed genes (q-value≤0.05) were identified with Cuffdiff. The log2 fold change is a direct output from Cuffdiff. For visualization, the mapped reads were converted into BedGraph format using BEDTools.   For ChIP-seq data, reads were mapped to hg19 or mm10 using bowtie version 1.1.2. Bam files are sorted by Samtools and PCR duplicates were removed using Picard (http://picard.sourceforge.net). Peak calling was perform using MACS-1.4.2. For MNase-seq, Reads were analyzed and profiled using Danpos.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample or wig file

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cell

growth_protocol: DMEM medium (High glucose, Gibco MT-10-013) supplemented with 50unit/ml penicillin and streptomycin (Life technologies, 15070-063), 18% murine ESC defined FBS (Thermo Scientific, SH30070.03E), 2mM L-glutamine (Cellgro, 25-005-CI), 1mM sodium pyruvate (Gibco, 11360-070), 1X nonessential amino acids (Cellgro, 25-025-CI, 100X stock), 1X nucleoside (Millipore, ES-008-D, 100X stock), 0.007% β-mercaptoethanol (Fisher, O3446I), and 1000unit/ml mLIF (Millipore, ESGRO) on irradiated mouse embryonic fibroblasts (Millipore, PMEF-NL) or 0.1% gelatin coated plates

extract_protocol:
Cells were cross-linked with 1% formaldehyde. Chromatin was disrupted into 100-250 bp fragments by sonication and precipitated using antibody and protein A beads as indicated in the text and protein A beads. After elution from the beads and reversing the cross-linking, the DNA fragments in immunoprecipitates were extracted with phenol/chloroform and recovered by ethanol precipitation.
Immunoprecipitated DNA was ligated with 3’- and 5’-adapters for amplification and sequencing by using Illumina II.

value: Rsf1Flag Knockin

tag: strain

tag: passages

tag: chip antibody

value: Flag Beads (Sigma, A2220)


title: SJAML010733_R2-subj6-2014-01-17

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the human hg19 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
raw counts were converted to FPKM
Genome_build: hg19
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map to transcripts for each defined gene.
Supplementary_files_format_and_content: FPKM

source_name: AML tumor sample

growth_protocol: Bone marrow samples were obtained at initial relapse of AML before cessation of sorafenib treatment and at the development of TKI resistance for genomic analysis. Samples were enriched for leukemic blasts by ficoll purification.

extract_protocol:
RNA was extracted with Trizol
RNA sequencing libraries for each tumor sample were prepared using approximately 1μg total RNA using the Illumina TruSeq RNA Sample Prep v2 Kit per manufacturer’s instructions.

tag: relapse or diagnosis

value: relapse


title: mESC_Rsf1_ubH2Adel_ChIP-seq_rep1

value: Rsf1Flag Knockin with RNF2 KO


title: mESC_Rsf1_ubH2Adel_ChIP-seq_rep2


title: mESC_Flag_ChIP-seq

data_processing:
For RNA-seq data, reads were mapped to hg19 or mm10 using STAR version 2.5.1b. Differentially expressed genes (q-value≤0.05) were identified with Cuffdiff. The log2 fold change is a direct output from Cuffdiff. For visualization, the mapped reads were converted into BedGraph format using BEDTools.   For ChIP-seq data, reads were mapped to hg19 or mm10 using bowtie version 1.1.2. Bam files are sorted by Samtools and PCR duplicates were removed using Picard (http://picard.sourceforge.net). Peak calling was perform using MACS-1.4.2. For MNase-seq, Reads were analyzed and profiled using Danpos.
Genome_build: hg19,mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

tag: strain background

tag: genotype/variation

value: WT

value: mouse embryonic stem cell


title: SJAML010733_R1-MG-13-08


title: SJAML010730_D1-TB-09-0886

value: diagnosis


title: SJAML010729_R2-TB-10-6152


title: SJAML010730_R2-TB-11-1372


title: SJAML010728_R2-TB-10-2162


title: NahG-Désirée_PVY3

description: small RNAs

tag: genotype


title: WT rep3

tag: ecotype

tag: age

value: Whole rosettes


title: HepG2 cells treated with MI503, Replicate1

city: Gaithersburg

first: Jingya

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

data_processing:
Sequencing quality was confirmed using FastQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Sequenced reads were aligned to human reference genome using Bowtie and Tophat (version 2.0.3) (https://ccb.jhu.edu/software/tophat/index.shtml)
Reads Per Kilobase of transcript per Million mapped reads (RPKM) was generated and Differential gene expression analysis was done using program Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/)
Genes with FDR < 0.05 and a fold change greater that 2-fold were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM data that contains the Reads Per Kilobase of transcript per Million mapped reads (RPKM) values for each gene in each sample

source_name: HepG2 cells

growth_protocol: HepG2 cells were plated in the 12-well plates at the initial concentration of 0.4x106 cells/ml

extract_protocol:
Total RNA was isolated from cells using RNeasy kit (Qiagen), amplified, and quality was assessed using the TapeStation (Agilent) following manufacturer’s instructions
Library was prepped using the Illumina TruSeq mRNA kit (Illumina) following manufacturer’s instructions

treatment_protocol: Cells were treated with 3 μM MI-503 or DMSO (0.25%) in triplicates. After 3 days of treatment viable cell number was adjusted to the original concentration in the DMSO treated samples and the same dilution factor was used to adjust cell number in the MI-503 treated cells. Media was changed and compound or DMSO was re-supplied at that time. Cells were harvested after 3 more days of incubation.

tag: dosage

value: 2 uM

tag: treatment time

value: 6 days


title: SJAML010729_R1-MG-10-62


title: HepG2 cells treated with MI503, Replicate3


title: Dusp6 mutant 20 dpa

status: Public on Feb 18 2018

city: Pittsburgh

first: Michael

last: Tsang

state: PA

address: 3501 Fifth Ave

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
fastq files were analyzed using CLC genomics workbench 9.0
sequence reads were mapped onto Danio rerio GRC.z10
EDGE test was performed usng CLC genomics workbench. Uninjured WT and Dusp6 mutant hearts were merged to represent uninjured baseline heart transcriptome. For differential gene analysis, this merged group was compared to WT at 20 days post amputation and to Dusp6 mutant at 20 dpa.
Genome_build: GRC.z10
Supplementary_files_format_and_content: Excel file with EDGE output.

organism: Danio rerio

source_name: Adult heart_Dusp6_20dpa

growth_protocol: Zebrafish adult at 6months-1year of age.

extract_protocol:
Ventricles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit (Cat# 74004).
TS RNA

treatment_protocol: Adults hearts were injured through ventricular resection and allowed to recover until 20 days post amputation.

value: dusp6 pt30a/pt30a

tag: tissue

value: heart ventricle

value: 6 months to 1 year


title: HepG2 cells treated with MI503, Replicate2


title: HepG2 cells treated with DMSO, Replicate1

value: DMSO


title: HepG2 cells treated with DMSO, Replicate2


title: R1-D567 Input DNA

city: Minneapolis

first: Scott

middle: M

last: Dehm

state: MN

address: 8806 420 Delaware

department: Masonic Cancer center

institute: University of Minnesota

data_processing:
ChIP-seq reads  were trimmed for adaptor sequence,aligned to the hg19 genome assembly using BWA 0.7.4
Reads with mapping quality less than 1 were discarded.
peaks were called using MACS v2 with pair end mode
Genome_build: hg19
Supplementary_files_format_and_content: BED format, detected peaks by MACS2

source_name: R1-D567 prostate cancer cell line

extract_protocol:
R1-AD1 and R1-D567 cells were seeded at 5 x 106 cells/10 cm plate in RPMI 1640, settled for 48 hrs, then treated with vehicle (0.1% DMSO) or VPC14449 (50 µM) in RPMI 1640 for 24 hrs. Cells were re-fed with RPMI 1640 + 10% CSS supplemented with 50 µM VPC-14449 (or DMSO control) and 1 nM DHT (or ethanol control) for an additional 4 hrs prior to cross-linking. Nuclear pellets were sonicated on ice for 8 cycles at 40% amplitude using a 450 Sonifer (Branson). Each cycle consisted of 10 sec pulse/10 sec rests for 1 min, with 2 min rests between cycles. Lysates were immunoprecipitated with Protein A/G Plus agarose beads (Santa Cruz Biotechnology) pre-blocked with tRNA (Sigma). DNA was purified using a PCR purification kit (Qiagen). For ChIP-seq, 2-10ng of DNA (ChIP-enriched or input) was used for library creation with a TruSeq ChIP Sample Preparation Kit (Illumina cat #IP-202-1012) and sequenced at the Univeristy of Minnesota Genomics Center using an Illumina HiSeq2000 at 1X50bp.
2 ng of DNA (ChIP-enriched and input) was used for library creation with a Truplex ChIP sample Preprarion Kit (Rubicon Genomics).

value: prostate cancer cell line

tag: cell line


title: R1-D567 ChIP-Seq_AR_VPC

source_name: R1-D567 prostate cancer cell line treated with VPC14449

tag: cell type

value: AR-Antibody [Santa Cruz sc-816 (N-20)]


title: R1-D567 ChIP-Seq_AR_DMSO

source_name: R1-D567 prostate cancer cell line treated with DMSO


title: R1-AD1 ChIP-Seq_AR_DMSODHT

source_name: R1-AD1 prostate cancer cell line treated with  VPC14449 and DHT


title: R1-AD1 ChIP-Seq_AR_DMSOETH

source_name: R1-AD1 prostate cancer cell line treated with DMSO and DHT


title: R1-AD1 Input DNA

source_name: R1-AD1 prostate cancer cell line


title: R1-AD1 ChIP-Seq_AR_VPCDHT


title: M7NC4

city: Bethesda

first: Prachi

last: Mishra

state: MD

address: 37 convent drive

institute: National Cancer Institute

description: RNA sequencing data

data_processing:
read alignment: TopHat
Software used to count reads: HT-seq
Genome_build: Hg19
Supplementary_files_format_and_content: text file with raw read counts

source_name: Breast cancer cells

extract_protocol:
Cells were trypsinised, and RNA was harvested using Trizol reagent. Illumina HiSeq 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

value: Breast cancer cells

tag: treatment

value: 1mM Control compound


title: M7UNT3

description: RNA sequencing data

value: Untreated


title: M7VC4

description: RNA sequencing data

value: Control- Empty Vector expression


title: M7UNT2

description: RNA sequencing data


title: M7UNT4

description: RNA sequencing data


title: M7UNT1

description: RNA sequencing data


title: SJAML010728_R1-MG-9-212

value: relapse


title: M7NC3

description: RNA sequencing data


title: M7NC2

description: RNA sequencing data


title: M7ADH2

description: RNA sequencing data


title: M7ADH1

description: RNA sequencing data


title: M7ADH4

description: RNA sequencing data


title: M72HG3

description: RNA sequencing data

value: 1mM octyl-2HG


title: HepG2 cells treated with DMSO, Replicate3


title: M72HG4

description: RNA sequencing data


title: M72HG2

description: RNA sequencing data


title: M72HG1

description: RNA sequencing data


title: M12UNT4

description: RNA sequencing data

source_name: Mammary epithelial cells

value: Mammary epithelial cells


title: M12VC1

description: RNA sequencing data


title: M12VC4

description: RNA sequencing data


title: M12UNT3

description: RNA sequencing data


title: M12VC2

description: RNA sequencing data


title: M12UNT2

description: RNA sequencing data


title: M12NC4

description: RNA sequencing data


title: M7VC2

description: RNA sequencing data


title: M12NC2

description: RNA sequencing data


title: M12NC3

description: RNA sequencing data


title: M7VC1

description: RNA sequencing data


title: M12ADH4

description: RNA sequencing data


title: M12ADH3

description: RNA sequencing data


title: M122HG4

description: RNA sequencing data


title: M122HG2

description: RNA sequencing data


title: M12ADH2

description: RNA sequencing data


title: CPL4RNAi_rep3

description:
CPL4RNAi(3)
Gene_differential_exp.txt
TSS_groups_differential_exp.txt
samtools_bedcov_dcpm.txt

data_processing:
The HiSeq Control Software 2.0.5 in combination with RTA 1.17.20.0 (real time analysis) performed the initial image analysis and base calling. In addition, CASAVA-1.8.2 generated and reported run statistics and the final FASTQ files comprising the sequence information which was used for all subsequent bioinformatics analyses. Sequences were de-multiplexed according to the 6bp index code with 1 mismatch allowed.
Raw sequenced reads (.fastq files) were uploaded to Galaxy (https://usegalaxy.org/). The following data processing was done using Galaxy.
Sequenced reads were trimmed for adapter and low-quality sequences by using Trim Galore! (v0.4.0), then mapped with Tophat (v2.0.14) against reference assembly Ensembl TAIR10 from Illumina iGenome, using default parameters except -i/--min-intron-length 60 -I/--max-intron-length 6000.
Differential expression levels of genes and TSS groups were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) by running Cuffdiff (v2.2.1.3) with default parameters.
Coverage depth of regions of interest was calculated by SAMtools_BedCov (v1.2).
Genome_build: Arabidopsis TAIR10 (Ensembl)
Supplementary_files_format_and_content: tab-deliminated text files include output values from Cuffdiff, includling FPKM (value 1 = Col, value 2 = CPL4RNAi), fold-changes and statistics (significant if q-value < 0.05) from biological triplicates. samtools_bedcov.txt file includes raw coverage counts (a sum of coverage depth per base in each region of interest) for each sample, computed by SAMtools_BedCov.

source_name: CPL4RNAi, 10-day-old seedling

growth_protocol: 10-day-old seedlings horizontally grown on ¼ MS media containing 0.5% sucrose.

extract_protocol:
Seedlings were flash frozen immediately after harvesting and subjected to total RNA extraction using RNeasy Plant Mini kit (QIAGEN).
The total RNA was submitted to Otogenetics Corporation (Norcross, GA) for RNA-seq analysis (paired-end, 100-bp). After validating the integrity and purity of total RNA using Agilent Bioanalyzer and OD260/280, 2 µg of total RNA was used for rRNA depletion using Ribo-Zero™ Plant Leaf RZPL1224 and Ribo-Zero™ Magnetic Plant Leaf MRZPL1224/MRZPL116t (EpiCentre). Recovered total RNA from rRNA depletion was subjected for cDNA synthesis using SMARTer PCR cDNA Synthesis kit (Clontech Laboratories, Inc., Mountain View, CA USA, catalog# 634925).

value: Colombia

value: CPL4 knockdown

value: whole seedling


title: CPL4RNAi_rep1

description:
CPL4RNAi(1)
Gene_differential_exp.txt
TSS_groups_differential_exp.txt
samtools_bedcov_dcpm.txt


title: Col_rep1

description:
Col(1)
Gene_differential_exp.txt
TSS_groups_differential_exp.txt
samtools_bedcov_dcpm.txt

source_name: Col, 10-day-old seedling

value: wild-type


title: CPL4RNAi_rep2

description:
CPL4RNAi(2)
Gene_differential_exp.txt
TSS_groups_differential_exp.txt
samtools_bedcov_dcpm.txt


title: Col_rep2

description:
Col(2)
Gene_differential_exp.txt
TSS_groups_differential_exp.txt
samtools_bedcov_dcpm.txt


title: Tomato_OX

city: Wuhan City

first: JIE

last: YE

state: Hubei Province

address: No. 1, Shizishan Road

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina HiSeq 2500 used for RNA-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. lycopersicum whole genome by Tophat
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Heizn1706
Supplementary_files_format_and_content: tab-delimited text files include the number of  RPKM values of each gene for each Sample.
Identifiers in our processed data (e.g. Solyc04g024500.2 etc.) are searchable in SGN (Sol Genomics Network) (ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.4_release/)

organism: Solanum lycopersicum

source_name: fruit

growth_protocol: Plant growth and cultivation was carried out according to commercial practices with a day/night temperature of 28/20°C. Plants were pruned so that fruits were on one vine per plant.

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
The fruits from CK and OX1 harvested at ripening stage were frozen in liquid nitrogen and kept at -80°C until use.. Total RNA was extracted using a ZP411-2 GREENspin RNA quick extraction kit (ZOMANBIO, Beijing), excluding polyphenols and polysaccharides from the sample according to the manufacturer’s instructions

treatment_protocol: To collect fruit samples from red ripening stages, flowers were tagged when fully opened (anthesis) and fruits were harvested from 3 individual plants of each genotype at 49 days after flowering (DAF)

tag: developmental stage

value: red ripening

value: fruit

value: ALMT9 over-expression line


title: dC-T_K4me3 ChIP

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

source_name: IPSC

growth_protocol: FX52 iPSCs were cultured either with mTeSRª1 medium (STEMCELL, #85850) or on irradiated mouse embryonic fibroblasts (MEFs) with standard hESCs medium:  [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (Gibco HI FBS, 10082-147), 5% KnockOut Serum Replacement (Invitrogen), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza), 0.1 mM _-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)].

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

treatment_protocol: FX52 iPSCs were transfected with dCas9-inactive Tet1 + CGG sgRNA, dCas9-Tet1 + CGG sgRNA or mock transfected

tag: transfection

value: transfected with dCas9-Tet1 + CGG sgRNA

tag: antibody manu.

value: Millipore

tag: antibody catalog


title: dC-T_RNAPII ChIP

tag: chip antibody

value: RNA Pol II (8WG16)

value: Abcam


title: Col_rep3

description:
Col(3)
Gene_differential_exp.txt
TSS_groups_differential_exp.txt
samtools_bedcov_dcpm.txt


title: dC-T_K9me3 ChIP


title: Tomato_CK

data_processing:
Illumina HiSeq 2500 used for RNA-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. lycopersicum whole genome by Tophat
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Identifiers in our processed data (e.g. Solyc04g024500.2 etc.) are searchable in SGN (Sol Genomics Network) (ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.4_release/)
Genome_build: Heizn1706
Supplementary_files_format_and_content: tab-delimited text files include the number of  RPKM values of each gene for each Sample.

value: wild type


title: dC-dT_RNAPII ChIP

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA    fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

value: transfected with dCas9-inactive Tet1 + CGG sgRNA


title: M122HG3

description: RNA sequencing data


title: dC-T_input


title: dC-dT_K27me3 ChIP


title: dC-T_K27Ac ChIP


title: dC-dT_K4me3 ChIP


title: dC-dT_input


title: dC-dT_K27Ac ChIP


title: dC-dT_K9me3 ChIP


title: mock_input

value: mock transfected


title: mock_RNAPII ChIP


title: mock_K9me3 ChIP


title: mock_K4me3 ChIP


title: mock_K27me3 ChIP


title: mock_K27Ac ChIP


title: Cas9 ChIP from a mock FXS iPSC line

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

data_processing:
Reads are de-multiplexed and mapped to human genome (hg19) using STAR (Dobin et al., 2013), requiring unique mapping and perfect mismatch.
mapped reads were collapsed using the program samtools rmdup
collapsed reads were sampled from each sample to match sequencing depth
a bam file containing sampled reads were converted to a bigwig file containing normalized read density (rpm, read per million)
Peaks are called using MACS (Zhang et al., 2008) with equal number of collapsed reads sampled to match sequencing depth. For off-target comparison shown in Figure 2, all IP samples were compared to the same input sample with a peak p value cut off of 10-15. For peaks shown in Figure 2C, a p value cut off of 10-3 is used but requires the peak to be called over both a matched input sample and an IP sample from mock iPSCs.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for normalized read density

source_name: FX52 iPSCs

growth_protocol: FXS iPSCs were cultured either with mTeSR™1 medium (STEMCELL, #85850) or on irradiated mouse embryonic fibroblasts (MEFs) with standard hESCs medium:  [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (Gibco HI FBS, 10082-147), 5% KnockOut Serum Replacement (Invitrogen), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)].

extract_protocol:
Collected cells were washed with PBS twice, and then re-suspended in 3.5 ml of sonication buffer. Sonication was performed for 10 cycles with 0.5 min pulse on and 1 min rest, and 24 watts in ice-water mixture. Then cell lysate was spun down with 14,000 x rpm for 10 min at 4 °C. 50 ul of supernatant was saved as input for gDNA. 10 ul of anti-CTCF antibody (EMD Millipore: 07729) was added and incubate overnight at 4 °C. 50 ul protein G dynabeads was added into antibody-cell lysate mixture and incubate overnight at 4 °C. Then beads were washed with sonication buffer, sonication buffer with high salt (500 mM NaCl), LiCl wash buffer, and TE buffer. Bound protein-DNA complex was eluted from beads by incubation in a 65 °C oven for 15 min, and then reverse cross-linked under 65 °C over-night. The bound DNA was purified with Qiagen QIAquick PCR Purification Kit
Illumina TruSeq DNA sample Preparation v2

treatment_protocol: Cells were cross-linked by 1% formaldehyde in the medium for 10 min in room temperature, and then quenched by adding 0.125 M Glycine for 5 min.

tag: sample type


title: Cas9 ChIP from line 2

value: lentiviral integration of a dCas9-Tet1 transgene and a CGG repeat guide RNA


title: dC-T_K27me3 ChIP


title: Input of Cas9 ChIP from line 3


title: Cas9 ChIP from line1


title: Cas9 ChIP from line 3


title: 2mm_Pt15

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

data_processing:
Fastq data files were aligned to the human Hg38 RefSeq genome with Novoalign read aligner version 2.08.02
Novoaligned SAM files were parsed into binary BAM files using SamTransriptomeParser application from USeq software version 8.8.5
Raw and normalized read counts (RPKM) and differentially expressed genes were identified using DESeq2 and the DefinedRegionDifferentialSeq application from USeq software version 8.8.5
SAMtoUSeq application was used to make normalized read data tracks for visualization in the Integrated Genome Browser from USeq software version 8.8.5
Genome_build: Hg38
Supplementary_files_format_and_content: Excel file with RefSeq ID and sample RPKM values for all genes with ≥ 10 raw reads

source_name: Duodenum

extract_protocol:
Qiagen RNAeasy Mini kit
Illumina TruSeq Stranded Total RNA treated with Ribozero Gold, 50 cycle single end reads

treatment_protocol: Erlotinib 75 mg/day and sulindac 150 mg twice daily for six months (Phase II clinical trial NCT 01187901)

tag: patient cohort

value: Familial adenomatous polyposis

value: Polyp

tag: timepoint

value: Endpoint

value: Placebo

tag: patient number


title: 3mm_Pt18


title: HN-R1

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

institute: Henan Agricultural University

data_processing:
Raw reads were pre-processed to remove low quality regions and adapter sequences.
Clean reads from each sample were aligned to the maize reference genome (B73 RefGen_v3, http://www.maizegdb.org/assembly/) using TopHat2
Aligned reads from TopHat2 mapping were subjected to String Tie for DeNovo transcript assembly
The R package edgeR was used to identify the differentially expressed genes.The expression of each gene was normalized to fragments per kilobase of transcript per million reads (FPKM) to compare among different samples.
Genome_build: B73 RefGen_v3 (http://www.maizegdb.org/assembly/)
Supplementary_files_format_and_content: tab-delimited text file containing FPKM values

organism: Zea mays

source_name: High Nitrogen supply_the sixth Leaf

growth_protocol: maize inbred B73 grown in hydroculture.

extract_protocol:
The maize leaf 6 was harvested, flash frozen and stored at -80℃.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: maize inbred B73

value: the sixth Leaf

tag: nitrogen supply

value: 4mM nitrogen (HN)


title: 4mmB_Pt16


title: 4mmB_Pt17


title: HN-R2


title: 8mm_Pt20


title: 6mm_Pt20


title: 4mmA_Pt17


title: 4mm_Pt19


title: 4mm_Pt20


title: 4mmB_Pt13


title: LN-R2

source_name: Low Nitrogen supply_the sixth Leaf

value: 0.04mM nitrogen (LN)


title: 3mm_Pt14


title: 6mm_Pt11


title: 8mm_Pt11


title: End_Pt19

value: Uninvolved


title: Input of Cas9 ChIP from line 1


title: 4mmA_Pt13


title: 2mm_Pt12


title: End_Pt18


title: End_Pt17


title: End_Pt15


title: LN-R1


title: End_Pt16


title: Pre AM_rep2

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

country: Japan

institute: University of Fukui

data_processing:
library stategy: RNA-Seq (SAGE)
CLC Genomics Workbench 8
Sequenced reads were trimmed 21 bp below NlaII and then mapped to mm9.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files

source_name: Pre AM

extract_protocol:
Total RNAs were extracted by using RNeasy Mini Kit (Qiagen).
Purified cDNA was digested with anchoring enzymes (NlaIII), resulting fragments were bound to streptavidin-coated beads (Dynabeads streptavidin M-280), and non-biotinylated cDNA fragments were removed by washing. Adapter-1 (5'– ACACTCTTTCCCTACACGACGCTCTTCCGATCTCAGCAGCATG –3’, 5'– /Phos/CTGCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAG TGT/AmMO/ –3’) was ligated to cDNA fragments on the beads and after washing digested with EcoP15I. EcoP15I-digested and released fragments (adapter-1- tags) were ligated to adapters-2 (5'– /Phos/AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/AmMO/ –3’, 5'– GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT –3’). Tags sandwiched between two adapters were amplified by PCR using PhusionHigh polymerase and GEX primers (5′- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTT CCGATCT -3′ and 5′- CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTC -3′, X; barcodes). The PCR regime consisted of 98°C for 30sec, 10–15 cycles at 98°C for 10sec, 60°C for 30sec and 72°C for 30sec. PCR products were run on an 8% non-denaturing polyacrylamide gel. After staining with SYBR green (Takara Bio), the band at 155–160bp was cut out from the gel, and DNA purified after its elution from the gel pieces.

treatment_protocol: WT mice which were untreated or were injected intravenously with BNL cells 21 days ago

tag: strain

value: BALB/c

tag: injected with

value: none (untreated)

tag: lung metastasis

value: without lung metastasis

value: alveolar macrophage (AM)


title: End_Pt20

tag: tissue


title: Pre AM_rep1

tag: cell type


title: 4mmA_Pt16

tag: treatment


title: End_Pt13


title: Day 21_AM_rep2

source_name: Day 21_AM

value: mouse hepatocellular carcinoma (HCC) cell line, BNL

value: with lung metastasis


title: Day 21_AM_rep1


title: 2mm_Pt9

value: Drug


title: 6mmC_Pt10


title: 3mm_Pt7


title: 3mm_Pt8


title: 6mmD_Pt10


title: 2mm_Pt5


title: 6mmB_Pt10


title: 3mm_Pt6


title: End_Pt12


title: 6mmA_Pt10


title: 4mm_Pt1


title: 6mmB_Pt2


title: 2mm_Pt3


title: End_Pt7


title: End_Pt8


title: End_Pt14


title: End_Pt6


title: End_Pt2


title: 4mm_Pt2


title: End_Pt3


title: 5mm_Pt2


title: 6mmA_Pt2


title: End_Pt9


title: Base_Pt16

value: Baseline


title: 3mm_Pt4

value: Familial adenomatous polyposis


title: Base_Pt15


title: Base_Pt10


title: End_Pt10


title: End_Pt5


title: Base_Pt19


title: Base_Pt20


title: Base_Pt13


title: Base_Pt11


title: Base_Pt14


title: Base_Pt9


title: Base_Pt12


title: End_Pt11


title: Base_Pt8


title: End_Pt4


title: End_Pt1


title: Base_Pt6


title: Base_Pt3


title: Base_Pt2


title: Base_Pt4


title: Input-ChiPSeq TGF-beta

city: London

first: Caroline

middle: S

last: Hill

address: 1 Midland Road

department: Developmental Signalling

country: United Kingdom

institute: Francis Crick Institute

description: ChiP-Seq

data_processing:
Reads were aligned to the human GRCh37/hg19 genome assembly using BWA version 0.6 with a maximum mismatch of 2 bases
Picard tools version 1.81  was used to sort, mark duplicates and index the resulting alignment bam files.
Normalised tdf files for visualisation purposes were created using IGVtools software; (http://software.broadinstitute.org/software/igv/) by extending reads by 50 bp and normalising to 10 million mapped reads per sample
Peaks were called by comparing stimulated samples to the respective untreated samples using MACS version 1.4.2, using mfold change parameters of between 5 and 30.
Peaks called by MACS were annotated using the annotatepeaks command in the Homer software (http://homer.salk.edu/homer/).
Genome_build: hg19
Supplementary_files_format_and_content: Normalised wig files were created from alignment bam files using IGVTools count function and normalised to 10 million reads.

growth_protocol: DMEM, 10% FCS, overnight starvation in OptiMEM prior to ligand stimulation.

extract_protocol:
Cross-linking with 4% formaldehyde for 5 min at room temperature followed by isolation of nuclei, sonication and immunoprecipitation.
Following end repair, poly-A-tailing and adapter ligation, Illumina TruSeq ChIP sample preparation kits were used to generate the libraries. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems, Cape Town, South Africa).  The PCR was run before gel isolation using the Invitrogen SizeSelect E-gel system (SizeSelect gel protocol, Thermo Fisher Scientific).  Post PCR we used AMPure XP beads (AMPure bead protocol, Beckman Coulter, Inc.) at a 1:1 ratio to maintain size integrity. Samples were multiplexed and 101-bp single end reads were generated on an Illumina HiSeq 2500.

treatment_protocol: Either untreated or treated with 2ng/mL TGF-beta for 1 h.

value: Breast cancer derived cell line

tag: cell line

value: TGF beta, 1 h

tag: antibody


title: SMAD3-ChiPSeq TGF-beta

description: ChiP-Seq

value: SMAD3, Abcam 28379


title: Base_Pt1


title: Beads-ChiPSeq TGF-beta

description: ChiP-Seq


title: pSMAD1/5-ChiPSeq Untreated

description: ChiP-Seq

value: Untreated

value: pSMAD1/5, Cell Signaling Technologies 11971


title: Input-ChiPSeq Untreated

description: ChiP-Seq


title: mESC_Rsf1_KO_MNase-seq_rep2

source_name: mouse embryonic stem cell

extract_protocol:
Cell pellets were resuspended in Buffer A (0.25 M sucrose, 60 mM KCl, 10 mM NaCl, 15 mM MES pH 6.5, 5 mM MgCl2, 1 mM CaCl2, 0.5% Triton X-100, 1 mM DTT, 0.2 mM PMSF, 0.5 g/ml leupeptin, 0.7 g/ml pepstatin, and 1 g/ml aprotinin) and incubated on ice for 15 min. Nuclei were collected by centrifugation at 3600 rpm for 10 min and washed once with TNM Buffer (10 mM Tris–HCl pH 8.0, 10 mM NaCl, 2 mM MgCl2, 0.3 M Sucrose, 1 mM DTT, 0.2 mM PMSF, 0.5 g/ml leupeptin, 0.7 g/ml pepstatin, 1 g/ml aprotinin) containing 5 mM CaCl2 (final). 5 l micrococcal nuclease (200 U/l) was added to nuclei suspension and incubated at 37oC for 20 min to give a complete digestion. After incubation, digested nuclei were collected by centrifuging at 3600 rpm for 10 min and resuspended in nucleosome extraction buffer (20 mM Tris HCl pH 7.9, 10 mM EDTA, 0.5 M NaCl). After incubation on ice for 10 min, nuclei were centrifuged at 13,200 rpm for 10 min. The supernatant contains mononucleosomes. Mononucleosomes were treated with 50 μg/ml protease K (Cat. # EO0491, Fisher) at 45°C for 1 hr and then resolved on 1.2% agarose. Gels containing mononucleosomes at the size of 150 bp were excised and purified with Qiagen gel purification kit (Cat# 28704, Qiagen, Waltham, MA, USA). The recovered chromatin DNAs were sequenced using HiSeq v4 PE50 250 M reads 25GB max output in the Hudsonalpha Institute.
The recovered chromatin DNAs were ligated with 3’- and 5’-adapters for amplification and sequencing by using Illumina II.

tag: genotype

value: Rsf1 KO

tag: passages


title: mESC_Rsf1_KO_RNA-seq_rep2

description: processed data file: mESC_RNA-seq_FPKM.txt

extract_protocol:
Samples for mRNA were prepared following the Illumina mRNA sequencing sample preparation guide. Briefly, total RNA was extracted with Trizol (Cat # 15596026, Invitrogen, Carlsbad, CA, USA).
mRNA was specifically enriched from total RNA using oligo(dT) beads and hydrolyzed into small pieces. The fragments were then reverse-transcribed into first-strand cDNA using random hexamer primers, followed by second strand synthesis using DNA polymerase I. The short cDNA strands were ligated with 3’- and 5’-adapters for amplification and sequencing (Illumina HiSeq v4 (pair end,50 bp, 50 M reads) in the HudsonAlpha Institute for Technology (Huntsville, AL, USA). Primer sequences are available upon request.


title: mESC_control_Mnase-seq

value: WT


title: SMAD3-ChiPSeq Untreated

description: ChiP-Seq


title: mESC_control_RNA-seq


title: ChIP-Seq-WRKY46-Myc

city: wuhan

first: Liang

last: Hu

address: bayi street

institute: wuhan university

description: After transfected with WRKY46-Myc for 16-22 h, rice protoplasts were washed with PBS and incubated in lysis buffer,used as a starting material and proteins were immunoprecipitated using antibodies against Myc (MBL, M192-3).

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
bwa version: 0.7.8 mapping to reference genome
peak Calling
Genome_build: oryza sativa japonica genome (Tigr7)
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Oryza sativa

growth_protocol: Plants were grown in a controlled growth chamber. Rice protoplasts were prepared using a 7-day-old normal green rice seedlings.

extract_protocol:
The chromatin immunoprecipitation experiment was performed, following a previously reported protocol (Gendrel et al., 2005) with several modifications.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols(NEBNext Ultra DNA Library Prep Kit for Illumina). Brifely, for ChIPSeq library construction, 10ng-20ng ChIP eluted DNA was used as initiation and after adaptor ligation, PCR with 15-18 cycles was used to amplify library. Size selection of ChIPSeq library by electrophoresis gel.

treatment_protocol: Rice protoplasts transfected with WRKY46-Myc or WRKY72-Myc by polyethyleneglycol (PEG) method (Chen et al., 2006).

value: Rice protoplasts

tag: vector

tag: chip antibody


title: ChIP-Seq-WRKY72-Myc

description: After transfected with WRKY72-Myc for 16-22 h, rice protoplasts were washed with PBS and incubated in lysis buffer,used as a starting material and proteins were immunoprecipitated using antibodies against Myc (MBL, M192-3).

source_name: Rice protoplasts transfected with WRKY72-Myc


title: HeLa_control_RNA-seq

description: processed data file: HeLa_RNA-seq_FPKM.txt

source_name: human HeLa cell

growth_protocol: DMEM, 10%FBS

treatment_protocol: 10 nM siRNA was transfetced into cells. 48 hrs later, total RNAs were extracted.

value: HeLa


title: HeLa_RNF2_KD_RNA-seq

value: RNF2 KD


title: mESC_Rsf1_KO_MNase-seq_rep1

extract_protocol:
Cell pellets were resuspended in Buffer A (0.25 M sucrose, 60 mM KCl, 10 mM NaCl, 15 mM MES pH 6.5, 5 mM MgCl2, 1 mM CaCl2, 0.5% Triton X-100, 1 mM DTT, 0.2 mM PMSF, 0.5 g/ml leupeptin, 0.7 g/ml pepstatin, and 1 g/ml aprotinin) and incubated on ice for 15 min. Nuclei were collected by centrifugation at 3600 rpm for 10 min and washed once with TNM Buffer (10 mM Tris–HCl pH 8.0, 10 mM NaCl, 2 mM MgCl2, 0.3 M Sucrose, 1 mM DTT, 0.2 mM PMSF, 0.5 g/ml leupeptin, 0.7 g/ml pepstatin, 1 g/ml aprotinin) containing 5 mM CaCl2 (final). 5 l micrococcal nuclease (200 U/l) was added to nuclei suspension and incubated at 37oC for 20 min to give a complete digestion. After incubation, digested nuclei were collected by centrifuging at 3600 rpm for 10 min and resuspended in nucleosome extraction buffer (20 mM Tris HCl pH 7.9, 10 mM EDTA, 0.5 M NaCl). After incubation on ice for 10 min, nuclei were centrifuged at 13,200 rpm for 10 min. The supernatant contains mononucleosomes. Mononucleosomes were treated with 50 μg/ml protease K (Cat. # EO0491, Fisher) at 45°C for 1 hr and then resolved on 1.2% agarose. Gels containing mononucleosomes at the size of 150 bp were excised and purified with Qiagen gel purification kit (Cat# 28704, Qiagen, Waltham, MA, USA).
The recovered chromatin DNAs were ligated with 3’- and 5’-adapters for amplification and sequencing by using Illumina II.


title: pSMAD1/5-ChiPSeq TGF-beta

description: ChiP-Seq


title: HeLa_RSF1_KD_RNA-seq

value: RSF1 KD


title: Base_Pt5

tag: patient cohort

value: Uninvolved


title: WT_sRNA-seq

city: Daejeon

first: Hogyu David

last: Seo

address: 291 Daehak-ro

country: South Korea

institute: KAIST

data_processing:
Prepared libraries were sequenced on a HiSeq2500 with single-end method (50-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (Novocraft technologies, Malaysia).
Significantly enriched peaks were identified using Homer and mapped reads were quantified using DeepTools and bwtool.
For sRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using Novoalign.
The number of mapped reads was further analyzed using RSeQC
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: bigWig files of the processed raw files

organism: Schizosaccharomyces pombe

source_name: WT

growth_protocol: Grow cells in  YES medium at 30°C

extract_protocol: ChIP-seq libraries for genome-wide sequencing were prepared using 10 ng of input DNA or 1 to 10 ng of eluted ChIP DNA using NEXTflex ChIP-Seq kit, Bioo Scientific (cat.5143).  RNA-seq libraries were made using NEXTflex™ Small RNA-Seq Kit v3 (BIOO) from the isolated sRNA.


title: rpt4-1ago1_sRNA-seq


title: Rpn1-Flag ChIP-seq


title: rpt4-1_sRNA-seq


title: Pre1-Flag ChIP-seq_2


title: No-tag_control_Flag ChIP-seq


title: clr4_H3K9me2 ChIP-seq 2


title: mESC_Rsf1_KO_RNA-seq_rep1

data_processing:
For RNA-seq data, reads were mapped to hg19 or mm10 using STAR version 2.5.1b. Differentially expressed genes (q-value≤0.05) were identified with Cuffdiff. The log2 fold change is a direct output from Cuffdiff. For visualization, the mapped reads were converted into BedGraph format using BEDTools.   For ChIP-seq data, reads were mapped to hg19 or mm10 using bowtie version 1.1.2. Bam files are sorted by Samtools and PCR duplicates were removed using Picard (http://picard.sourceforge.net). Peak calling was perform using MACS-1.4.2. For MNase-seq, Reads were analyzed and profiled using Danpos.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample or wig file


title: mRNA X^XYcongo CNS Replica 2

city: Boston

first: Bernardo

last: Lemos

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

description: Replica 2

data_processing:
Reads were trimmed using Trimgalore under default quality parameters (-q 30 --phred33)
Trimmed reads were mapped against the reference genome (annotation 6.07) using bowtie2 under --sensitive option
Samtools was used to convert between SAM and BAM files and to sort BAM files.
We used GFold function count to extract read counts for annotated genes from sorted BAM files according to the GTF file (annotation 6.07).
Read counts were used to calculate differential expression using DESeq2 (version 1.8.1), R software (version 3.2.3), and RStudio (version 0.99.467).
Genome_build: dmel_r6.08_FB2015_05 (ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.08_FB2015_05/)
Supplementary_files_format_and_content: Text files (*.txt) contain read counts. Supplementary files (*.csv) are expression data calculated by DESeq2, and combined files by the Fisher's method.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Larval Central Nervous System

growth_protocol: Molasses medium was prepared in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. The food was stirred until boiling on a heat block. After 10 minutes of boiling, the heat source was turned off and the food left at room temperature with constant stir until reaching 65oC. At this point 5 mL of phosphoric acid and 8 mL of 10% tegosep (w/v) diluted in ethanol were added to the mix. All strains were reared at 23oC and 14-hour light cycle.

extract_protocol:
Total RNA was isolated with Trizol. In order to check the quality of the RNA extracts, samples were run in an 1% TAE-Agarose gel and integrity of the mRNA was estimated based on the sharpness of the ribosomal RNA bands. Samples that did not meet this quality control were re-extracted. Concentration of all samples was accessed with Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For mRNA-Seq, total RNA was subjected to mRNA isolation with magnetic beads linked to poly-T tails (Dynabeads® mRNA DIRECT™ Purification Kit) for two cycles. The quality of mRNA preparations was accessed with Agilent 2100 Bioanalyzer system (Agilent Technologies).
Samples with intact mRNA and less than 15% of rRNA contamination were subjected to library synthesis using the automated Apollo 324™ NGS Library Prep system with PrepX RNA-Seq kit (Wafergen). Final product of each library was subjected to 15 cycles of PCR enrichment in reactions containing one barcode for each sample. Final libraries were purified with magnetic beads to an average size of 350 bp and checked with Agilent 2200 TapeStation (Agilent Technologies). Samples were normalized with Qubit 3.0 Fluorometer, and twelve libraries were combined in a single mix. Multiplexed mix was submitted to 150 cycles of paired-end sequencing (2x150bp) using HiSeq 2500 (Illumina). Two biological replicates were sequenced for each sample.

treatment_protocol: Genetic manipulation for generation of Y-chromosome aneuploidy strains

value: Central nervous system

tag: age

value: Third-instar larvae

value: X^X/Ycongo

tag: gender

value: female


title: WT_H3K9me2 ChIP-seq 2


title: WT_H3K9me2 ChIP-seq 1


title: mRNA X^XYcongo CNS Replica 1

description: Replica 1


title: mRNA X^XYohio CNS Replica 2

description: Replica 2

value: X^X/Yohio


title: mRNA X^XYohio CNS Replica 1

description: Replica 1


title: clr4_H3K9me2 ChIP-seq 1


title: mRNA X^YYohio testis Replica 2

description: Replica 2

source_name: Testis

value: Testis

value: X^Y/Yohio

value: male


title: ago1_sRNA-seq


title: mRNA X^YYcongo testis Replica 2

description: Replica 2

value: X^Y/Ycongo


title: mRNA X^YYcongo testis Replica 1

description: Replica 1


title: mRNA X^X CNS Replica 2

description: Replica 2

value: X^X


title: mRNA X^YYohio testis Replica 1

description: Replica 1


title: A2Y-3

city: chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

description: domestic pig

data_processing:
Illumina Casava1.82 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to itself assembly genome using Tophat.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Transcripts were assembled by Stringtie version 1.3.3.
Assembled transcripts from each sample were merged into a consensus transcriptome using previously published custom Python scripts.
Cuffcompare version 2.2.1 was used to remove the transcripts that were annotated as “c” and “=”.
Remaining transcripts that contained a known protein-coding domain were removed by Hmmscan and BLASTX.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
Genome_build: Sus_scrofa.Sscrofa10.2
Supplementary_files_format_and_content: Tab-delimited text files include log2(FPKM+1) values for each Sample.

organism: Sus scrofa domesticus

source_name: spleen

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Strand-specific cDNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

tag: development stage

value: 2 years old


title: mRNA X^X CNS Replica 1

description: Replica 1


title: mRNA X^XYcongo ovary Replica 1

description: Replica 1

source_name: Ovary

value: Ovary


title: mRNA X^XYohio ovary Replica 2

description: Replica 2


title: A2Y-2

description: domestic pig


title: mRNA X^XYohio ovary Replica 1

description: Replica 1


title: mRNA X^XYcongo ovary Replica 2

description: Replica 2


title: A2Y-1

description: domestic pig


title: mRNA X^Y (control) testis Replica 1

description: Replica 1

value: X^Y


title: mRNA X^X (control) ovary Replica 1

description: Replica 1


title: Pre1-Flag ChIP-seq_1


title: A180d-3

description: domestic pig

value: 180 days old


title: mRNA X^YYcongo whole body Replica 2

description: Replica 2

source_name: Whole Body

value: Whole Body


title: A180d-2

description: domestic pig


title: mRNA X^YYcongo whole body Replica 1

description: Replica 1


title: mRNA X^Y (control) testis Replica 2

description: Replica 2


title: W30d-2

description: domestic pig

value: weaned for 30 days


title: B0d-2

description: domestic pig

value: just after birth


title: A180d-1

description: domestic pig


title: W30d-3

description: domestic pig


title: mRNA X^Y (control) whole body Replica 2

description: Replica 2


title: B0d-3

description: domestic pig


title: B0d-1

description: domestic pig


title: mRNA X^Y (control) whole body Replica 1

description: Replica 1


title: mRNA X^X (control) ovary Replica 2

description: Replica 2


title: mRNA X^XYcongo whole body Replica 2

description: Replica 2


title: E55d-2

description: domestic pig

value: 55 days before birth


title: E55d-3

description: domestic pig


title: mRNA X^X (control) whole body Replica 1

description: Replica 1


title: E55d-1

description: domestic pig


title: KK43 replicate 2

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.35 as default parameter, then mapped to Salmonella enterica serivar Typhimurium 14028s whole genome using bowtie v. 2.2.4 with parameters -t --very-sensitive
The mapped reads were counted by featureCounts (http://bioinf.wehi.edu.au/featureCounts/) and normalized by using DESeq2.
Genome_build: NCBI accession - PRJNA33067, assembly ID - GCA_000022165.1
Supplementary_files_format_and_content: Tab-delimited text file including counts and locus_tags for genes of Salmonella enterica serovar Typhimurium 14028s

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: RNA from Salmonella Typhimurium 14028s harboring pBAD113 which contains mgtC leader

growth_protocol: The strains were grown in N-minimal media to exponential phase, and harvested after arabinose treatment.

extract_protocol:
After cell harvest, RNA samples were prepared using RNeasy kit. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Bacteria) (MRZMB126, Illumina, USA) was used. Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 10 mM L-arabinose was added to the media for 15 min.

value: pBAD113 which contains mgtC leader

tag: growth medium

value: N-minimal media

tag: growth phase

value: exponential phase

tag: induction

value: 15 min induction by 10 mM L-arabinose


title: mRNA X^XYohio whole body Replica 1

description: Replica 1

value: X^X/Yohio

value: female


title: NahG-Désirée_PVY_degradome

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

institute: National Institute of Biology

data_processing:
Library strategy: degradome-seq
Sequenced reads were trimmed for adaptor sequence and reads shorter than 10 nt after trimming were discarded.
The data were analyzed using CleaveLand4 (http://sites.psu.edu/axtell/software/cleaveland4/) using all our experimentally identified sRNAs and the transcriptome sequences of cv. Désirée with annotations from Ramšak et al. (2014) allowing for maximum three mismatches. The CleaveLand4 script first uses Bowtie to map reads to transcriptome/mRNAs and quantify the density of observed 5' ends at each nt of the transcriptome/mRNAs. The script then uses GSTAr (https://github.com/MikeAxtell/GSTAr) to align miRNAs to transcriptome/mRNAs for target prediction of miRNAs. After loading degradome density (generated by Bowtie) and alignment of miRNAs (generated by GSTAr), the script searches the degradome density file to see if there are any degradome reads at the predicted slicing site.
All identified degradation targets were classified into five categories based on the abundance of the PARE tag reads mapped to the corresponding cleavage site relative to the total number of PARE tag reads that matched the target mRNA. Categories 0-3 with high cleavage signal were kept for further analyses.
Genome_build: StNIB potato transcriptome available at http://www.gomapman.org/export/input/stNIB-v1_data
Supplementary_files_format_and_content: Excel spreadshet includes identified sRNA targets, mapped read counts (DegradomeReadNumber) as well as traget cleavage site information and statistics.

source_name: PVYNTN-infected potato plants

extract_protocol:
Total RNA was extracted from homogenised leaf tissue using TRIzol reagent (Invitrogen). For each treatment the three samples were pooled.
degradome (PARE) RNA libraries were prepared for sequencing using standard Illumina protocols at LC Sciences, USA.

tag: cultivar

value: Desiree

value: leaf

value: PVYNTN infection

value: NahG-Desiree


title: DN345 replicate 2

source_name: RNA from Salmonella Typhimurium 14028s harboring pBAD18, the empty vector

value: pBAD18, the empty vector


title: mRNA X^XYcongo whole body Replica 1

description: Replica 1

tag: tissue

value: X^X/Ycongo


title: mRNA X^X (control) whole body Replica 2

description: Replica 2

value: X^X


title: DN345 replicate 1


title: mRNA X^YYohio whole body Replica 1

description: Replica 1

value: Whole Body

value: X^Y/Yohio

value: male


title: mRNA X^YYohio whole body Replica 2

description: Replica 2


title: WB-3

description: Wild Boar

organism: Sus scrofa

value: spleen

value: 2 years old


title: Désirée_PVY1_degradome


title: W30d-1

description: domestic pig

value: weaned for 30 days


title: WB-2

description: Wild Boar


title: mRNA X^XYohio whole body Replica 2

description: Replica 2


title: Désirée_MOCK_degradome

source_name: control-mock inoculated potato plants

value: control


title: Control-2_RRBS

status: Public on Feb 15 2018

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Sequencing reads were trimmed by trim galore 0.3.7 with --RRBS option for RRBS and default option for RNA-seq.
RRBS reads were aligned using bismark v0.14.0 and bowtie 1.1.1. RNA-seq reads were aligned by TopHat v2.1.1.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: bedgraph files of CpG methylation were generated using bismark_methylation_extractor. fpkm_tracking files were generated by Cufflinks.

source_name: No cell control

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium (11875-093, Gibco) plus 15% fetal bovine serum (26140-079, Gibco) and 100 U/ml penicillin-streptomycin (15140-122, Gibco) at 37 ℃ in a humidified incubator with 5% CO2. Cells were sub-cultured every 2-3 days to maintain them in exponential growth phase.

extract_protocol:
The mouse lines C57Bl/6 and 126S6/SvEv weres bred and maintained in groups of 3-4 per cage with food ad libitum. 8-10 week old mice were anesthetized with isoflurane and decapitated. The tissue was rapidly dissected and frozen on dry ice and stored at -80 ℃ until used for nuclei isolation.  The tissue was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100) with freshly added 50 μl protease inhibitor cocktail (P8340, Sigma-Aldrich), 5 μl 100 mM PMSF and 5 μl 1 M DTT. In addition, 7.5 μl 40 U/μl RNase inhibitor (N2611, Promega) was also added when RNA-seq was conducted. Once thawed, the tissue was homogenized by slowly doucing for 15 times with a loose pestle (D9063, Sigma-Aldrich) and 25 times with a tight pestle (D9063, Sigma-Aldrich). The homogenate was filtered with 40 µm nylon mesh cell strainer (22363547, Fisher Scientific) and then transferred into a 15 ml centrifugation tube. The sample was centrifuged at 1000 g for 10 min. The supernatant was removed and the cell pellet was gently resuspended in 1 ml cold nuclei extraction buffer with freshly added 10 μl protease inhibitor cocktail, 1 μl of 100 mM PMSF and 1 μl of 1 M DTT. 1.5 μl of 40 U/μl RNase inhibitor was mixed with the nuclei extraction buffer when RNA-seq was conducted. The 1 ml sample suspension was split into two 1.5-ml micro-centrifuge tubes (500 μl in each tube). Each sample (500 μl) was gently mixed with 0.75 ml of 50% iodixanol to yield 30% iodixanol solution. 50% iodixanol was prepared by adding 0.4 ml diluent (150 mM KCl, 30 mM MgCl2, and 120 mM Tris-HCl, pH 7.8) to 2 ml of 60% iodixanol (D1556, Sigma). The samples were then centrifuged at 10,000 g for 20 min before the supernatant was removed. The nuclei in each tube were incubated on ice for 10 min in 0.5 ml Dulbecco's phosphate-buffered saline (14190144, Life Technologies) containing 2.0% normal goat serum (50062Z, Life Technologies). The nuclei were resuspended and then pooled together (generating ~1 ml in total). For RNA-seq, 3 μl of 40 U/μl RNase inhibitor was added into the nuclei suspension. The integrity and the number of nuclei were checked under the microscope. 32 μl of 2 ng/μl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was incubated with the nuclei suspension (~1 ml) for 1 h at 4 ℃ on an end-to-end rotator. The stained samples were sorted using a FACS (BD FACSAria, BD Biosciences) with 50,000 to 100,000 unlabeled nuclei used as non-staining control. Human genomic DNA was purified from GM 12878 cells using QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s protocol and suspended in 50 µl EB buffer. Mouse genomic DNA was purified using QIAamp DNA Blood Midi Kit (Qiagen) from nuclei and suspended in 200 µl AE buffer (10 mM Tris-Cl, 0.5 mM EDTA, pH 9.0). The eluate was reloaded on the column membrane and spun to maximize DNA yield. Mouse DNA was concentrated by ethanol precipitation to 20 µl EB buffer. RNA was extracted from ~10,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment step was included following kit instructions to remove gDNA contamination.
RRBS library construction. 5 µl genomic DNA (0.2-6 ng/µl) was digested by adding 1 µl of 20 U/µl MspI enzyme (R0106S, NEB), 2 µl NEB buffer2 and 12 µl H2O at 37 ℃ for 1 h and inactivated at 80 ℃ for 20 min. The fragment size was examined using 2.5% agarose gel (16550100, Thermo Fisher) in 0.5× TBE buffer (15581044, Thermo Fisher). The 3’ terminal of digested DNA was end-repaired and an extra A which was required by adapter ligation was added on both strands in a single reaction. 1 µl of 5 U/µl Klenow exo- enzyme (M0212M, NEB) and 1.1 µl dNTP mixture (10 mM dATP, 1 mM dGTP and 1 mM dCTP, N0446S, NEB) were added into 20 µl digested sample. Ten-fold excess of dATP was added to increase A-tailing efficiency. The sample was incubated at 30 ℃ for 20 min (end-repair), 37 ℃ for 20 min (A-tailing) and 75 ℃ for 20 min (enzyme inactivation). The DNA (22.1 µl) was then purified by phenol–chloroform extraction and ethanol precipitation. DNA pellet was then resuspended in 17 μl EB buffer. 16.4 µl sample was transferred to a new 200 µl PCR tube. 1 µl of 2000 U/µl T4 ligase (M0202T, NEB), 2 µl of supplied 10× T4 ligase buffer, 0.6 µl NEXTflex bisulfite-seq barcode (1.6-6 µM) were mixed with the sample for ligation. The ligation reaction was carried out at 16 ℃ for 16 h and followed by 65 ℃ for 10 min for heat inactivation. The heating of the thermal cycler lid was turned off to protect the T4 ligase. Gel-free procedure 17, 28 instead of gel cutting was used for RRBS library construction. Ligated DNA (20 µl) was purified using AMPure XP beads with bead suspension to sample volumetric ratio of 1.5: 1. The DNA was eluted from Ampure beads by 20 µl EB buffer. The elute was concentrated by ethanol precipitation and then suspended in 0.7 µl to facilitate loading into the microfluidic device. The converted DNA was amplifed by PCR (13 cycles for 10 ng, and 16-18 cycles for 1-0.3 ng). After PCR amplification, a double size selection using AMPure XP beads was performed. Large DNA fragments were removed by adding 30 μl AMPure bead suspension and incubating for 5 min. The beads that had large DNA bound were discarded and the supernatant was preserved. 30 μl AMPure bead suspension were then added into the supernatant and incubated for 5 min. The supernatant was discarded and DNA bound to beads was eluted into 7 μl EB buffer.mRNA-seq library construction. RNA was extracted from ~100,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment was included following manufacturer instructions to remove gDNA contamination. The RNA quality was detected by High Sensitivity RNA ScreenTape System (Agilent) to yield RNA integrity number (RIN) > 6. mRNA-seq libraries were prepared using SMART-seq v4 Ultra Low Input RNA kit (Clontech) and Nextera XT DNA library prep kit (Illumina) following instructions.

value: No cell control


title: KK43 replicate 1

value: pBAD113 which contains mgtC leader

value: N-minimal media

value: exponential phase

value: 15 min induction by 10 mM L-arabinose


title: WB-1

description: Wild Boar


title: Control-1_RRBS


title: GM-sc21_RRBS

source_name: GM12878 cell line

value: GM12878 cell line


title: GM-sc20_RRBS


title: GM-sc22_RRBS


title: GM-sc18_RRBS


title: NahG-Désirée_MOCK_degradome

growth_protocol: Plants were grown in a growth chamber and kept at 21 C in the light and 18 C in the dark, at a relative humidity of 75%, with 70–90 mmol/m2/s2 radiation and a 16-h photoperiod.

value: Desiree

value: leaf

value: NahG-Desiree


title: GM-sc13_RRBS


title: GM-sc15_RRBS


title: GM-sc14_RRBS


title: GM-sc11_RRBS


title: GM-sc16_RRBS


title: GM-sc12_RRBS


title: GM-sc10_RRBS


title: GM-sc09_RRBS


title: GM-sc08_RRBS


title: GM-sc06_RRBS


title: GM-sc05_RRBS


title: GM-sc04_RRBS


title: GM-sc19_RRBS


title: GM-sc01_RRBS


title: GM-sc17_RRBS


title: GM-Zymo-1ng-R2_RRBS


title: GM-sc02_RRBS


title: GM-Zymo-1ug-R2_RRBS


title: GM-parallel-1ng-U3_RRBS


title: GM-parallel-1ng-U2_RRBS


title: GM-Zymo-1ug-R1_RRBS


title: GM-parallel-1ng-U4_RRBS


title: GM-sc03_RRBS


title: GM-parallel-1ng-U1_RRBS


title: GM-sc07_RRBS


title: GM-Zymo-1ng-R1_RRBS


title: GM_10ng_RRBS_rep1

extract_protocol:
The mouse line C57Bl/6 was bred and maintained in groups of 3-4 per cage with food ad libitum. 8-10 week old mice were anesthetized with isoflurane and decapitated. The cerebellum was rapidly dissected and frozen on dry ice and stored at -80 ℃ until used for nuclei isolation.  Cerebellum was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100) with freshly added 50 μl protease inhibitor cocktail (P8340, Sigma-Aldrich), 5 μl 100 mM PMSF and 5 μl 1 M DTT. In addition, 7.5 μl 40 U/μl RNase inhibitor (N2611, Promega) was also added when RNA-seq was conducted. Once thawed, the tissue was homogenized by slowly doucing for 15 times with a loose pestle (D9063, Sigma-Aldrich) and 25 times with a tight pestle (D9063, Sigma-Aldrich). The homogenate was transferred into an ultracentrifugation tube (355631, Beckman Coulter) and underlayered with 9.5 ml sucrose cushion (1.8 M sucrose, 3 mM Mg(Ac)2 and 10 mM Tris-HCl). The homogenate was centrifuged at 32,300 rpm (107,164g) for 2.5 h at 4 ℃ with 70 Ti rotor (Optima L-90K Ultracentrifuge, Beckman Counter). The spinning was slowly braked to avoid disturbing the nuclei pellet. All the supernatant was removed and the nuclei was gently resuspended in 0.4 ml 10% normal goat serum (50062Z, Life Technologies) and 1.6 ml Dulbecco's phosphate-buffered saline (14190144, Life Technologies). For RNA-seq, 3 μl 40 U/μl RNase inhibitor was added into nuclei suspension. The integrity and the number of nuclei were checked under the microscope. 32 μl 2 ng/μl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was incubated with the nuclei suspension (2 ml) for 1 h at 4 ℃ on an end-to-end rotator. The stained samples were sorted using a FACS (BD FACSAria, BD Biosciences) with 50,000 to 100,000 unlabeled nuclei used as non-staining control. Human genomic DNA was purified from GM 12878 cells using QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s protocol and suspended in 50 µl EB buffer. Mouse genomic DNA was purified using QIAamp DNA Blood Midi Kit (Qiagen) from nuclei and suspended in 200 µl AE buffer (10 mM Tris-Cl, 0.5 mM EDTA, pH 9.0). The eluate was reloaded on the column membrane and spun to maximize DNA yield. Mouse DNA was concentrated by ethanol precipitation to 20 µl EB buffer. RNA was extracted from ~10,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment step was included following kit instructions to remove gDNA contamination.
RRBS library construction. 5 µl genomic DNA (0.2-6 ng/µl) was digested by adding 1 µl of 20 U/µl MspI enzyme (R0106S, NEB), 2 µl NEB buffer2 and 12 µl H2O at 37 ℃ for 1 h and inactivated at 80 ℃ for 20 min. The fragment size was examined using 2.5% agarose gel (16550100, Thermo Fisher) in 0.5× TBE buffer (15581044, Thermo Fisher). The 3’ terminal of digested DNA was end-repaired and an extra A which was required by adapter ligation was added on both strands in a single reaction. 1 µl of 5 U/µl Klenow exo- enzyme (M0212M, NEB) and 1.1 µl dNTP mixture (10 mM dATP, 1 mM dGTP and 1 mM dCTP, N0446S, NEB) were added into 20 µl digested sample. Ten-fold excess of dATP was added to increase A-tailing efficiency. The sample was incubated at 30 ℃ for 20 min (end-repair), 37 ℃ for 20 min (A-tailing) and 75 ℃ for 20 min (enzyme inactivation). The DNA (22.1 µl) was then purified by phenol–chloroform extraction and ethanol precipitation. DNA pellet was then resuspended in 17 μl EB buffer. 16.4 µl sample was transferred to a new 200 µl PCR tube. 1 µl of 2000 U/µl T4 ligase (M0202T, NEB), 2 µl of supplied 10× T4 ligase buffer, 0.6 µl NEXTflex bisulfite-seq barcode (1.6-6 µM) were mixed with the sample for ligation. The ligation reaction was carried out at 16 ℃ for 16 h and followed by 65 ℃ for 10 min for heat inactivation. The heating of the thermal cycler lid was turned off to protect the T4 ligase. Gel-free procedure 17, 28 instead of gel cutting was used for RRBS library construction. Ligated DNA (20 µl) was purified using AMPure XP beads with bead suspension to sample volumetric ratio of 1.5: 1. The DNA was eluted from Ampure beads by 20 µl EB buffer. The elute was concentrated by ethanol precipitation and then suspended in 0.7 µl to facilitate loading into the microfluidic device. The converted DNA was amplifed by PCR (13 cycles for 10 ng, and 16-18 cycles for 1-0.3 ng). After PCR amplification, a double size selection using AMPure XP beads was performed. Large DNA fragments were removed by adding 30 μl AMPure bead suspension and incubating for 5 min. The beads that had large DNA bound were discarded and the supernatant was preserved. 30 μl AMPure bead suspension were then added into the supernatant and incubated for 5 min. The supernatant was discarded and DNA bound to beads was eluted into 7 μl EB buffer.mRNA-seq library construction. RNA was extracted from ~100,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment was included following manufacturer instructions to remove gDNA contamination. The RNA quality was detected by High Sensitivity RNA ScreenTape System (Agilent) to yield RNA integrity number (RIN) > 6. mRNA-seq libraries were prepared using SMART-seq v4 Ultra Low Input RNA kit (Clontech) and Nextera XT DNA library prep kit (Illumina) following instructions.


title: Vehicle3-mRNA-R2

source_name: Vehicle treated frontal cortex

value: Vehicle treated frontal cortex

value: 8-10 weeks

tag: strain


title: GM_10ng_RRBS_rep2


title: Vehicle3-mRNA-R1


title: GM_0.3ng_RRBS_rep1


title: GM_3ng_RRBS_rep2


title: GM_1ng_RRBS_rep2


title: GM_1ng_RRBS_rep1


title: Vehicle2-mRNA-R1


title: GM_3ng_RRBS_rep1


title: Vehicle2-mRNA-R2


title: Vehicle1-mRNA-R2


title: Clozapine3-mRNA-R2

source_name: Clazapine treated frontal cortex

value: Clazapine treated frontal cortex


title: Clozapine2-mRNA-R2


title: Clozapine1-mRNA-R2


title: Vehicle1-mRNA-R1


title: Clozapine2-mRNA-R1


title: Clozapine3-mRNA-R1


title: Clozapine1-mRNA-R1


title: Vehicle6_R2_RRBS


title: Vehicle4_R1_RRBS


title: Vehicle5_R2_RRBS


title: Clozapine6_R2_RRBS


title: Vehicle6_R1_RRBS


title: Vehicle4_R2_RRBS


title: GM_0.3ng_RRBS_rep2


title: Clozapine6_R1_RRBS


title: Clozapine5_R1_RRBS


title: Clozapine4_R2_RRBS


title: Clozapine5_R2_RRBS


title: Clozapine4_R1_RRBS


title: Vehicle3 R1 RRBS

data_processing:
Sequencing reads were trimmed by trim galore 0.3.7 with --RRBS option for RRBS and default option for RNA-seq.
RRBS reads were aligned using bismark v0.14.0 and bowtie 1.1.1. RNA-seq reads were aligned by TopHat v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files of CpG methylation were generated using bismark_methylation_extractor. fpkm_tracking files were generated by Cufflinks.


title: Vehicle5_R1_RRBS


title: Vehicle3 R2 RRBS


title: exp_H3K27me3_rep_2

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

description: processed data file: H3K27me3_peaks.bed

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3
Peaks were called with MACS
Genome_build: mm10
Supplementary_files_format_and_content: bed files with peaks summarized across replicates and treatments and bedgraph files for each sample.

source_name: immortalized mouse embryonic fibroblast cell line

growth_protocol: Cells grown in DMEM (low glucose) containing 10% FBS at 37 degrees Celsius in 5% CO2.

extract_protocol:
Cells harvested by trypsinization and fixed with formaldehyde prior to lysis.  Chromatin prepared via MNase digestion and sonication.  Either ChIP-enriched chromatin or non-enriched input chromatin used for library construction.
ThruPLEX DNA-seq 48D Kit (Rubicon Genomics cat# R400406)

treatment_protocol: Gene rearrangement induced by adding doxycycline to media at 1 microgram/mL final concentration.

tag: day

value: anti-H3K27me3 (Abcam cat# ab6002)


title: exp_H3K27me3_rep_1

description: processed data file: H3K27me3_peaks.bed

tag: cell line


title: ctl_succinyllysine_rep_1

description: processed data file: succinyllysine_peaks.bed

tag: antibody

value: anti-succinyllysine (PTM Biolabs cat# PTM-401)


title: exp_H3K4me3_rep_2

description: processed data file: H3K4me3_peaks.bed

value: anti-H3K4me3 (Abcam cat# ab8580, lot# GR273043-4)


title: ctl_H3K27me3_rep_1

description: processed data file: H3K27me3_peaks.bed


title: exp_succinyllysine_rep_2


title: ctl_H3K4me3_rep_2

description: processed data file: H3K4me3_peaks.bed


title: exp_input_rep_1

value: none (input control)


title: ctl_input_rep_2


title: ctl_succinyllysine_rep_2


title: exp_H3K4me3_rep_1

description: processed data file: H3K4me3_peaks.bed


title: exp_input_rep_2


title: ctl_H3K4me3_rep_1

description: processed data file: H3K4me3_peaks.bed


title: exp_succinyllysine_rep_1


title: Clozapine3 R1 RRBS


title: Vehicle2 R2 RRBS


title: Vehicle1 R2 RRBS


title: Clozapine3 R2 RRBS


title: Vehicle1 R1 RRBS


title: Clozapine2 R2 RRBS


title: Vehicle2 R1 RRBS


title: Clozapine2 R1 RRBS


title: ctl_H3K27me3_rep_2

description: processed data file: H3K27me3_peaks.bed


title: Clozapine1 R1 RRBS


title: ctl_input_rep_1


title: NeuN-_mRNA_rep2

source_name: Glial cell from cerebellum


title: NeuN+_mRNA_rep1

source_name: Neuron from cerebellum


title: NeuN+_mRNA_rep2


title: NeuN-_0.5ng_RRBS_rep2


title: Homogenate_10ng_RRBS_rep1

source_name: Cerebellum


title: NeuN-_0.5ng_RRBS_rep1


title: NeuN+_10ng_RRBS_rep2


title: NeuN-_10ng_RRBS_rep2


title: NeuN+_0.5ng_RRBS_rep1


title: Homogenate_10ng_RRBS_rep2


title: NeuN+_0.5ng_RRBS_rep2


title: Homogenate_0.5ng_RRBS_rep1


title: siER_exp2_RNA-Seq_PolyA-

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description:
double-stranded RNA complementary to ESR1 mRNA (siRNA) (48h)
PolyA-depleted RNA

data_processing:
RNA-Seq read alignment was performed using BWA v. 0.6.1 (Li et al., 2009) with option bwasw and -T = 15. Gencode v19 was used as reference transcriptome dataset. while hg19 as human reference genome assembly.
Read alignment files were used as input for CIRI v. 1.2 (Gao et al., 2014)  applied in default settings with -P and -low options.
The circRNAs predicted in at least two out of the three biological replicates in each culture condition and associated with an average number of BS supporting read > 2 were selected.
The number of back-splicing supporting reads was normalized using DESeq2 v.1.14.1 R package (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

growth_protocol: MCF-7 were growth separately in four culture conditions: i) hormone-deprived (HD) media ii) HD+ 17b-estradiol (6h) iii) medium added of FSC 5% iv) double-stranded RNA complementary to ESR1 mRNA (siRNA) (48h)

extract_protocol: The starting RNA-seq datasets were obtained from libraries generated with the TruSeq stranded library preparation kit (Illumina) using as input material RNA depleted of both poly(A+) and ribosomal RNAs fractions.

tag: cell type

value: breast cancer cell line


title: siCTRL_strip_E_exp3_RNA-Seq_PolyA-

description:
HD+ 17b-estradiol (6h)
PolyA-depleted RNA


title: Homogenate_0.5ng_RRBS_rep2


title: siER_exp3_RNA-Seq_PolyA-


title: NeuN+_10ng_RRBS_rep1


title: siCTRL_strip_exp2_RNA-Seq_PolyA-

description:
medium added of FSC 5%
PolyA-depleted RNA


title: Clozapine1 R2 RRBS


title: siCTRL_strip_exp3_RNA-Seq_PolyA-


title: siER_exp1_RNA-Seq_PolyA-


title: NeuN-_10ng_RRBS_rep1


title: siCTRL_strip_E_exp2_RNA-Seq_PolyA-


title: siCTRL_DMEM_exp2_RNA-Seq_PolyA-

description:
hormone-deprived (HD) media
PolyA-depleted RNA


title: siCTRL_strip_E_exp1_RNA-Seq_PolyA-


title: siCTRL_strip_exp1_RNA-Seq_PolyA-


title: siCTRL_DMEM_exp3_RNA-Seq_PolyA-


title: siCTRL_DMEM_exp1_RNA-Seq_PolyA-


title: Homogenate_mRNA_rep1


title: Spd1

city: Bariloche

first: Nicolas

last: Bellora

state: Rio Negro

address: Quintral 1250

department: IPATEC

country: Argentina

institute: CONICET

data_processing:
adapter contamination removed from the original reads with the cutadapt v0.9.4 software (http://code.google.com/p/cutadapt/).  Reads shorter than 25bp after adapter trimming and quality filtering were discarded
aligned to Ensembl (v66) annotated human transcripts using Bowtie v0.12.5, allowing two mismatches (--best -v 2 -a)
reads over the 500nts at the 3' end of transcripts were used to generate read-count tables for all samples. Only genes that had at least an average of 10 read counts were analyzed for evidence of differential abundance
full-quantile normalization with the EDA package
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts

source_name: spindles extraction

growth_protocol: HeLa S3 cells  were grown in DMEM 10% FBS

extract_protocol:
After a release (35-45min), mitotic cells were collected by mitotic shake-off and treated without adding RNases to the lysis buffer
Library generation was done with the kit NEBNext Ultra RNA Library Prep Kit (New England Biolabs), following manufacturer´s instructions and 14-15 cycles of library amplification. Previous Poly A purification was only performance on Input samples in only one step of purification. Size selection of the libraries and purification were done by magnetic beads (Agencourt AMPure XP, Beckman Coulter). Finally, library quantification was performance with Qubit DNA HS (Life Technologies) and fragment size distribution with Bioanalyzer DNA HS (Agilent)

treatment_protocol: Hela S3 cells cells were first synchronized with thymidine for 16h and then synchronized at the G2/M border with 9 μM RO3306 for 21h

value: Hela S3


title: Sync2

source_name: synchronous cell culture


title: Spd2


title: Sync1


title: Control

description: control

source_name: asynchronous cell culture


title: Adjacent supposedly normal tissue (Par2N)

city: Montreal

first: Timothy

middle: L

last: Reudelhuber

state: Quebec

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

data_processing:
Base calls were made using the Illumina CASAVA 1.8 pipeline.
Low-quality bases (any leading or trailing base with a quality below 3, and any window of 4 bases with an average quality below 15) were removed with Trimmomatic (v0.22).
The sequences were aligned to the human reference genome hg19 using Tophat (v2.0.6).
Assembly and abundance were determined using Cufflinks (v2.0.2).
The gene expression levels are represented as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file with FPKM values of protein-coding genes for each sample. Outputted by Cuffdiff.

source_name: Kidney tissue adjacent to reninoma tumor, supposedly normal

extract_protocol:
Biopsies of reninomas were obtained at surgery from 4 anonymous patients (Paris1, Paris2, Montreal, Rotterdam) and snap frozen in liquid nitrogen. Total RNA was isolated using Trizol (Invitrogen) from 10 mg pieces of each tumor or biopsy and was further purified using RNeasy MinElute Cleanup spin (#74204, QIAGEN) according to manufacturer's instructions and eluted in a final volume of 10 μL.
RNA libraries were prepared for sequencing using standard Illumina protocols. Eight microliters of RNA was used as input and library preparation was conducted according to manufacturer's instructions ("Low-Throughput (LT) Protocol" TruSeq RNA Sample Preparation Guide, Illumina). Resulting library preps were assessed for quality and concentration using the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: supposedly normal kidney tissue adjacent to reninoma tumor

tag: patient


title: Reninoma from Paris (Par2)

source_name: Reninoma tumor

value: reninoma tumor


title: Reninoma from Rotterdam (RotB2)

value: Rotterdam


title: Reninoma from Paris (Par1B2


title: Reninoma from Paris (Par1B3)


title: MCF_Y537S_Wm_DOX__THZ1_24hrs_Rep2

first: Rinath

last: Jeselsohn

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

data_processing:
ChIP-seq reads were aligned using bowtie
Peaks were called using MACS2 with default parameters, including a q value < 0.001
bedgraph to wig file conversion was done using the UCSC tool bedGraphToBigWig
A binding intensity matrix was generated using bamliquidator
Differential Binding analysis was peformed using custom R code, and further analysis was done using DeepTools v2.2.3
Genome_build: hg19
Supplementary_files_format_and_content: bigwig  files for ER ChIP
RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.6
All analysis was performed by inputting fastq files into VIPER: https://bitbucket.org/cfce/viper/overview
Association of ChIP-seq data with RNAseq data was done using BETA v1.0.7
Genome_build: hg19
Supplementary_files_format_and_content: Count Matrix Files

growth_protocol: MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.

extract_protocol: Cell lines were cultured in white DMEM with CDT and Doxycycline. They were treated for  24 hrs with DMSO as vehicel or THZ1 10nm. Cells were extracted using the Rneasy (Qiagen # 74104) kit with the substitution of Trizol instead of Buffer RLT. Preparation for sequaencing is done using the Illumina Truseq RNAseq v2 kit (15025063)

tag: genotype/variation

tag: condition

value: White_ Medium + Doxycycline+THZ1_24hrs


title: MCF_Y537S_WM_DOX_veh_24hrs_Rep2

value: White_ Medium+Doxycycline + veh ( DMSO)


title: MCF_Y537S_Wm_DOX__THZ1_24hrs_Rep3


title: MCF_Y537S_WM_DOX_veh_24hrs_Rep1


title: MCF_Y537S_WM_DOX_veh_24hrs_Rep3


title: MCF7_E2_H3K27Ac_Rep1

extract_protocol: Cell lines before ChIP were grown in   White Medium DMEM with CDT. Cells expressing the Y537S mutation were grown in Doxycyclin.The cells with WT-ER were stimulated with E2 x45 minutes prior to cross linking for the ChIP experiment. Cells were sonicated, then cell lysate was incubated with antibody to extract protein-DNA complex of interest, Library Preparation is performed using the Rubicon 48S kit

value: WT ER

value: White Medium + E2


title: MCF7_Y537S_H3K27Ac_Rep2

value: White Medium+Doxycycline


title: MCF7_E2_H3K27Ac_Rep3


title: MCF7_E2_H3K27Ac_Rep2


title: Evx1as+/- S9

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
Basecalls performed using CASAVA version
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: bigwig; reads signal

source_name: laser capture microdissected Evx1as+/- E7.0 Primtive streak layer 9

growth_protocol: Wild-type ESCs or 4x polyA KI ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction. For embryo sections, embryo was freshly embedded in OCT and subjected to cryosection and followed by Geo-seq for spatial transcritpome analysis.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: Embryonic day 7 embryo

value: Evx1as+/- Primtive streak layer


title: MCF_Y537S_Wm_DOX__THZ1_24hrs_Rep1