title: GM19249_VDR_ChIP-exo_VD_stimulated

city: Hinxton

first: Giuseppe

last: Gallone

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: Wellcome Trust Sanger Institute

data_processing:
Data Processing and Peak Calling: Briefly, we mapped the ChIP-exo sequence reads (Peconics Inc., USA; single-end 40bp) against the hg19 build of the human reference genome [Kuhn et al., 2013] using BWA (v. 0.7.4, [Li and Durbin, 2009]) followed by Stampy (v 1.0.21 [Lunter and Goodson, 2011]). We filtered the reads to retain only uniquely mapping reads with MAPQ > 20 and removed reads mapping to empirical blacklist regions identified by the ENCODE consortium [Dunham et al., 2012]. For peak calling, we first computed strand cross-correlation profiles [Kharchenko et al., 2008] of read start densities to obtain consensus estimates of the ChIP-exo digested fragment sizes, which we corrected for the presence of phantom peaks [Kundaje et al., 2013] using a mappability-corrected approach to cross-correlation inference (MaSC, [Ramachandran et al., 2013]). We used the crosscorrelation based estimates for the digested fragment size as a MACS2 (version 2.0.10, [Feng et al.,2012]) input parameter to obtain peak calls. Separately, to increase sensitivity, we called peaks using GPS/GEM (v. 2.4.1, [Guo et al., 2012]) with recommended ChIP-exo options --smooth 3 --mrc 20. We then pooled, for each sample, the two sets of peak calls (Supplementary Material). Finally, we used DiffBind [Stark and Brown, 2011] to manipulate the per-sample merged peaksets and to obtain consensus peakset (CPo3 , CPo10 , CPo20 ) based on an overlap threshold. To do this, we normalised the read numbers using DiffBind's embedded EdgeR routines, based on the Trimmed Means of M's (TMM) algorithm [Robinson and Oshlack, 2010].
Interval Overlap Enrichment Analysis: We used the Genomic Association Tester [Heger et al., 2013] to perform the randomization-based interval enrichment analyses. All analyses were based on 10,000 randomisations over the chosen background, and backgrounds differed depending on the specific analysis performed. All analyses accounted for genome-wide patterns of GC content variability and, where relevant, for uniquely mappable regions (40bp reads). For the enrichment analysis of VDR-BVs in GWAS intervals and QTLs, we used an in-house bootstrapping pipeline to perform LD-filtering (to retain only LD-independent foreground and background variants) and DAF matching. Further details on annotations, background and analytical design are provided in the publication.
Motif Discovery: Briefly, we carried out de novo motif analysis using multiple parallel approaches: MEME-ChIP [Ma et al., 2014] from the MEME suite [Bailey et al., 2009], XXmotif [Hartmann et al., 2013] and PScanChIP [Zambelli et al., 2013] from the Weeder/MoDtools suite [Pavesi et al., 2006]. For the MEME-ChIP and XXmotif analyses, we used the peak intervals in CPo10 and extracted the sequence underlying each interval 150bp from a repeat-masked version of the hg19 reference [Kuhn et al., 2013]. For the PScanChIP analysis we used as the input the full set of CPo3 binding regions with Jaspar PWM descriptors, to which we added the best heterodimeric RXR:VDR PWM found by XXmotif and the best monomeric VDR PWM found by DREME (MEME-ChIP package). The global background chosen for the analysis consisted of built-in PScanChIP DNase I digital genomic footprinting data for the LCL CEPH individual NA12865.
Differential Binding Analyses: We performed both allele-specific (VDR-ASB) and regression on genotype (VDR-QTL) differential binding analyses. For the VDR-ASB tests, we utilised the sequence composition of ChIP-exo sequence reads overlapping heterozygous SNPs to determine the sequences originating from each allele separately [McDaniell et al., 2010; Pickrell et al., 2010; Rozowsky et al., 2011] and to identify allele-specific binding events showing significant difference in the number of mapped reads between parental alleles. We employed a modified version of the AlleleSeq pipeline [Rozowsky et al., 2011] to carry out the VDR-ASB analysis. Briefly, we tested for significant allelic imbalance among all read pile-ups intersecting a variant showing heterozygous genotype, given a null hypothesis of 50% paternal versus 50% maternal reads. We followed Rozowsky et al. in controlling for two major sources of bias typically encountered when running an allele-specific analysis of short read data: a bias due to mapping to the reference hg19 genome [Degner et al., 2009] and a bias due to unannotated copy number variants skewing the read counts for some of the SNPs being tested [Pickrell et al., 2011]. In addition, we corrected for a third source of potential erroneous ASB SNP calls by removing any significant allelic imbalance hypothesis falling under repeat regions contained in the ENCODE blacklist data [Dunham et al., 2012]. For the VDR-QTL tests, we analysed all 27 LCL samples simultaneously. We grouped the samples based on the genotypes of the underlying variant, and carried out QTL association testing between the variant's genotype (under the assumption of an additive genetic model [Stephens and Balding, 2009]) and the phenotype at that location (the VDR binding affinity based on the quantile-normalised ChIP-exo peak size at that location). We used an in-house pipeline based on SNPs and indels imputed with IMPUTE2 [Howie et al., 2009] and Bayesian regression modelling based on SNPTEST [Marchini et al., 2007] and BIMBAM [Servin and Stephens, 2007]. Bayesian methods for analysing SNP associations are now an established tool in GWAS analysis [Scott et al., 2007; Burton et al., 2007; Wakefield, 2009] and show advantages over the use of p-values in power and interpretation [Stephens and Balding, 2009] though they require tighter initial modelling assumptions when compared to frequentist methods.
Variant Annotation: We annotated all variants associated with differences in VDR binding and obtained by pooling the VDR-QTL and the VDR-ASB variants (VDR-Binding Variants, VDR-BVs) according to the guidelines in Khurana et al. [2013] and using a customised version of the Funseq2 suite of algorithms [Fu et al., 2014]. We added additional VDR-centric information to Funseq2: VDR CPo3 binding regions, motif intervals from the PScanChIP analysis for the VDR:RXR Jaspar DR3 motif and for the DREME VDR monomer, and VDR dimer/monomer PWM information. Gene annotation used Funseq2's default (Gencode, v. 16) and the HOT annotation in Funseq was filtered to only retain LCL HOT information. We ran Funseq using the -m 2 -nc options so that all annotation referred to the ancestral allele of the variant.
Genome_build: hg19
Supplementary_files_format_and_content: fastq and bed files are provided

source_name: Lymphoblastoid cell line, EBV transformed

growth_protocol: Calcitriol stimulated lymphoblastoid cells were grown and prepared for ChIP as described previously with some modifications [Ramagopalan et al., 2009] and adapted for ChIP-exo [Rhee and Pugh, 2011, 2012]. Briefly, cells were incubated in phenol red free RPMI-1640, 10% charcoal stripped FBS, 2mM glutamine-L, penicillin with streptomycin solution (100 U/mL + 100 microG/mL) medium at 37C and 5% CO2. Cells were harvested after stimulation for 36 hours with 0.1 uM calcitriol (Sigma) and crosslinked using a 1% formaldehyde buffer for 15 minutes at room temperature and quenched with 0.125 M glycine.

extract_protocol:
Cells were lysed and chromatin sheared by sonication into fragments of 200-1000 bp. VDR-bound genomic DNA regions were isolated using a rabbit polyclonal antibody against VDR (Santa Cruz Biotechnology, sc-1008). Immunoprecipitated chromatin was then processed enzymatically on magnetic beads. Samples were polished, A-tailed, ligated to sequencing library adaptors and then digested with lambda exonuclease to remove nucleotides from 5' ends of double stranded DNA. Singlestranded DNA was eluted and converted to double-stranded DNA by primer annealing and extension. A second sequencing adaptor was ligated to exonuclease treated ends, PCR amplified, gel purified and sequenced.
Libraries were prepared for Illumina as described in Rhee and Pugh [2012].

tag: cell line

tag: population

value: YRI

tag: family

tag: gender

value: M


title: GM19248_VDR_ChIP-exo_VD_stimulated

status: Public on Mar 17 2017

type: SRA

country: United Kingdom

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: GM19247_VDR_ChIP-exo_VD_stimulated

value: F


title: RNA130128RH_8

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

country: USA

institute: Oregon Health and Science University

description: Low Drinker: not BD, not HD, and not VHD

library_source: transcriptomic

data_processing:
Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection
Alignment: Reads were aligned to MacaM assembly (Zimin et al., 2014) using STAR v.2.3.0e (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax=3,outFilterScoreMinOverLread=0.33,outFilterMismatchNoverLmax=0.03, outFilterMultimapNmax=1.
After removing one sample outlier from the set, upper-Quartile normalization was performed using the edgeR Bioconductor package. Genes with at least 100 average reads per sample and exons with more than 10 average reads were retained for further analysis.
Genome_build: MacaM
Supplementary_files_format_and_content: RNASeq017_exon_reads_UQNormalized_for_GEO.csv: first column has the exon ID (a combination of chromosome number, start, and end location of exon, and gene symbol). subsequent 30 columns provide the normalized reads for each sample for each exon
Supplementary_files_format_and_content: RNASeq017_gene_reads_UQNormalized_for_GEO.csv: first column has the Gene Symbol, and subsequent 30 columns provide the normalized reads for each sample for each gene

molecule: total RNA

organism: Macaca mulatta

source_name: Dissected Tissue (Brain) - Cortical Area 32 (A32)

extract_protocol:
Monkeys were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session. Preparation of brain tissue was described previously (Davenport et al., 2014) and the tissues were collected as part of the MATRR. Necropsy occurred at the time when they would normally begin their drinking session; monkeys were anesthetized with ketamine (10 mg/kg) and maintained on isoflurane. The brains were perfused with ice-cold oxygenated artificial cerebral spinal fluid, removed (< 5 min post-mortem) and sectioned according to each monkey’s individual MRI (Daunais et al., 2010). The prefrontal cortex was isolated, and Area 32 was dissected and frozen in liquid nitrogen.
Library formation (TruSeq Stranded RNA-Seq with RiboZero Gold rRNA depletion) and sequencing on a HiSeq 2000 were all performed according to Illumina’s specifications at the OHSU Massively Parallel Sequencing Shared Resource. Libraries were multiplexed 4 per lane, yielding approximately 50 million total reads per sample.

treatment_protocol: Male rhesus monkeys that were experimentally naïve at the onset of alcohol induction (Macaca mulatta, n = 31, 4-11 years-old, 6-8 kg) were used. They were first induced to drink 4% (w/v) ethanol and then allowed to self-administer ethanol for over 12 months under open access conditions (22h/d, 7d/wk) with concurrent meals and continuous access to water. They were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session.The monkeys were from four cohorts, referred to as cohorts 4, 5, 7a and 7b in the Monkey Alcohol Tissue Research Resource (www.MATRR.com). These cohorts where selected because they all had approximately 90 days of induction followed by approximately two 6-month periods of alcohol open access. All monkeys were individually housed (quadrant cages, 0.8 m x 0.8 m x 0.9 m) in a room with controlled light cycle (11 hours lights on, 13 hours lights off), temperature (20-22oC) and humidity (65%). The monkeys had visual, auditory and olfactory contact with other monkeys. They were weighed weekly.

tag: matrr (monkey alcohol tissue research resource) id

tag: cohort

value: COHORT 7b

tag: avg age at beginning of 1.5 g/kg etoh induction

tag: avg age after second 6 months of open access

tag: Sex

value: Male

tag: drinking category

value: LD


title: Immature sample 3

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

data_processing:
Contigs assembled with Trinity v.2.2
Reads aligned to contigs using NCBI blastn
Supplementary_files_format_and_content: SuppFile1.xls; normalized counts in Excel spreadsheet

organism: Thlaspi arvense

source_name: Nectary tissue

extract_protocol:
Two types of RNA samples were prepared from pennycress nectaries: mature nectaries (equivalent to Stage 14–15 flowers from Arabidopsis thaliana), and immature nectaries (equivalent to Stage 11–12 flowers from Arabidopsis thaliana). Mature nectaries secrete nectar, whereas immature nectaries are pre-secretory. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 40 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4–8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Up to four nectaries were collected per flower, with approximately 100 nectaries being processed as a single RNA sample. Each biological replicate was represented by nectaries pooled from different sets of plants. RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX).
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

tag: developmental stage

value: immature


title: RNA130128RH_14

description: Binge Drinker:  ethanol consumption of >= 2 g/kg for >= 55% of days AND a recorded BEC >= 80 mg/dl at least once per year

value: BD


title: Immature sample 2


title: RNA130128RH_7

description: Heavy Drinker: ethanol consumption of >= 3 g/kg for >= 20% of days

value: COHORT 7a

value: HD


title: Immature sample 1


title: RNA130128RH_6


title: GM19236_VDR_ChIP-exo_VD_stimulated


title: GM19235_VDR_ChIP-exo_VD_stimulated


title: RNA130128RH_5

description: Very Heavy Drinker: average daily ethanol intake exceeding 3 g/kg AND have >= 10% of open access days with an ethanol intake exceeding 4 g/kg

value: VHD


title: GM19215_VDR_ChIP-exo_VD_stimulated


title: RNA130128RH_18


title: RNA130128RH_4


title: RNA130128RH_3

value: COHORT 5


title: GM19214_VDR_ChIP-exo_VD_stimulated


title: GM19190_VDR_ChIP-exo_VD_stimulated


title: GM12872_VDR_ChIP-exo_VD_stimulated

value: CEU


title: GM19189_VDR_ChIP-exo_VD_stimulated


title: GM19191_VDR_ChIP-exo_VD_stimulated


title: GM19213_VDR_ChIP-exo_VD_stimulated


title: GM12752_VDR_ChIP-exo_VD_stimulated


title: GM12716_VDR_ChIP-exo_VD_stimulated_FailedQC

description: failed analytical QC


title: GM19237_VDR_ChIP-exo_VD_stimulated


title: GM12489_VDR_ChIP-exo_VD_stimulated


title: GM12264_VDR_ChIP-exo_VD_stimulated


title: GM12383_VDR_ChIP-exo_VD_stimulated


title: GM11919_VDR_ChIP-exo_VD_stimulated


title: GM11832_VDR_ChIP-exo_VD_stimulated


title: GM11918_VDR_ChIP-exo_VD_stimulated


title: GM11829_VDR_ChIP-exo_VD_stimulated


title: GM10847_VDR_ChIP-exo_VD_stimulated


title: GM10846_VDR_ChIP-exo_VD_stimulated_FailedQC

description: failed analytical QC


title: GM07045_VDR_ChIP-exo_VD_stimulated


title: GM06997_VDR_ChIP-exo_VD_stimulated_FailedQC

description: failed analytical QC


title: GM07029_VDR_ChIP-exo_VD_stimulated


title: GM06989_VDR_ChIP-exo_VD_stimulated


title: GM06986_VDR_ChIP-exo_VD_stimulated


title: RNA130128RH_2


title: input

status: Public on Mar 16 2017

city: Madrid

first: Carlos

last: Martinez

state: Madrid

address: C/Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

data_processing:
Sequencing of IP DNA fragments performed in genome analyzer II. Generation of FASTQ files.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v-2.0.6.
Samtools used to transform SAM to BAM formats (samtools view, sort and index)
BAM files passed to MACS v1.4 for calling peaks with default options.
Genome_build: mm9
Supplementary_files_format_and_content: BED file with significant peaks was generated using MACS v1.4; Default options : band width = 300, model fold = 10,30 and pvalue cutoff = 1.00e-05.

organism: Mus musculus

source_name: Mouse Stem Cells

growth_protocol: Mouse embryonic stem cells (Dido3deltaCT reconstituted with HADido3) were grown in self-renewal conditions in stem cell media supplemented with leukemia inhibitory factor (LIF)

extract_protocol:
ES cells were fixed with 1% formaldehyde, lysed in cell lysis buffer with proteinase inhibitor cocktail  and PMSF.  Chromatin was sonicated in a  Bioruptor and fragments of ~200-500 base pairs  were diluted with RIPA buffer and immunoprecipitated with anti-HA polyclonal antibody (ChIP-grade ab 9110; Abcam) coupled to magnetic beads coated with anti-rabbit immunoglobulin (overnight, 4ºC).  Beads were washed extensively and precipitates eluted, reverse crosslinked, and DNA was purified on Qiagen columns.
DNA libraries were prepared for sequencing using Trueseq DNA Sample Preparation kit (Illumina) protocols

tag: strain

tag: genotype

tag: antibody


title: Dido_ChIPSeq

value: anti-HA polyclonal antibody (ChIP-grade ab 9110; Abcam)


title: RNA130128RH_1


title: MCF7 Dnase-seq

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street

country: Canada

institute: University of Toronto

description: Dnase-seq

data_processing:
Library strategy: DNAse-seq
GRO-seq reads were mapped to the human genome (hg19) using Bowtie with default parameters.
 RNA-seq reads were aligned to human genome (hg19) with tophat (v2.1.1). ChIP-seq and Dnase-seq reads were aligned to human genome (hg19) with Bowtie.
MACS2 was used for ChIP-seq and Dnase-seq peak calling with the parameter "–SPMR" on to produce bedGraph files, which were then converted to bigwiggle files
Htseq (v0.5.4p3) was used to get gene level read counts for GRO-seq data and DESeq2 (v1.8.2) was used for differential gene analysis; GFOLD (v1.1.3) was used to generate gene level read count and carry out differential expression analysis.
bedGraph files for GRO-seq were generated using genomeCoverageBed function
in the BEDTools(v2.20.1) suite with total signal of 10 million, replicates were then combined before converted to bigwiggle files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle files were converted from bedGraph with bedGraphToBigWig function in BLAT suite. For GRO-seq and RNA-seq data, score equals to reads per 20 million; for ChIP-seq and Dnase-seq data, score equals to reads per million.

source_name: MCF7 breast cancer cell line

growth_protocol: The MCF-7 cells were obtained from ATCC and cultured in DMEM media supplemented with 10% FBS, 1% Pen-Strep and 1% Glutamine in a 5% CO2 humidified incubator.

extract_protocol:
GRO-seq: Nuclear run-on RNA was further purified with TURBO DNA-freeTM kit (Life Technologies,  AM1907) to remove residue DNA contamination. RNA-seq: Total RNA was extracted from synchronized MCF-7 cells with TRIZOL REAGENT (Life Technologies, 15596026) and fragmentized with sonication. ChIP-seq: Chromatin from synchronized MCF-7 cells was digested with Nuclease micrococcal from Staphylococcus aureus (Sigma Aldrich, N3755-50UN) and dialyzed with Slide-A-Lyzer Dialysis Cassettes (Thermo Fisher Scientific, PI66380). Dynabeads Protein A (Life Technologies, 10002D) and G (Life Technologies, 10004D) were used for immunoprecipitation with antibodies against H3K4me2 (EMD Millipore, 07-030) and H3K27ac (Abcam, ab4729).
GRO-seq and RNA-seq libraries were constructed with Encore Complete RNA-Seq DR Multiplex System 1-8 (Nugen Technologies lnc, 0333-32). ChIP-seq libraries were constructed with ThruPLEX DNA-seq kit (Rubicon) and sequenced to 50bp with Illumina HiSeq machine.

treatment_protocol: Cells are synchronized to three different cell cycle stages: G0/G1, S and M phase with hormone starvation, double thymidine and thymidine/Noco treatment respectively.

tag: cell type

value: breast cancer


title: MCF7 H3K27ac M phase

description:
Two replicates are merged:
H3K27ac M phase rep1
H3K27ac M phase rep2

data_processing:
GRO-seq reads were mapped to the human genome (hg19) using Bowtie with default parameters.
 RNA-seq reads were aligned to human genome (hg19) with tophat (v2.1.1). ChIP-seq and Dnase-seq reads were aligned to human genome (hg19) with Bowtie.
MACS2 was used for ChIP-seq and Dnase-seq peak calling with the parameter "–SPMR" on to produce bedGraph files, which were then converted to bigwiggle files
Htseq (v0.5.4p3) was used to get gene level read counts for GRO-seq data and DESeq2 (v1.8.2) was used for differential gene analysis; GFOLD (v1.1.3) was used to generate gene level read count and carry out differential expression analysis.
bedGraph files for GRO-seq were generated using genomeCoverageBed function
in the BEDTools(v2.20.1) suite with total signal of 10 million, replicates were then combined before converted to bigwiggle files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle files were converted from bedGraph with bedGraphToBigWig function in BLAT suite. For GRO-seq and RNA-seq data, score equals to reads per 20 million; for ChIP-seq and Dnase-seq data, score equals to reads per million.


title: MCF7 H3K27ac S phase

description:
Two replicates are merged:
H3K27ac S phase rep1
H3K27ac S phase rep2


title: MCF7 H3K27ac G0/G1

description:
Two replicates are merged:
H3K27ac G0/G1 rep1
H3K27ac G0/G1 rep2


title: MCF7 RNA-seq G0/G1

description: RNA-seq G0/G1


title: MCF7 GRO-seq S phase

description:
nascent RNA; Two replicates are merged:
GRO-seq S phase rep1
GRO-seq S phase rep2

data_processing:
Library strategy: GRO-seq
GRO-seq reads were mapped to the human genome (hg19) using Bowtie with default parameters.
 RNA-seq reads were aligned to human genome (hg19) with tophat (v2.1.1). ChIP-seq and Dnase-seq reads were aligned to human genome (hg19) with Bowtie.
MACS2 was used for ChIP-seq and Dnase-seq peak calling with the parameter "–SPMR" on to produce bedGraph files, which were then converted to bigwiggle files
Htseq (v0.5.4p3) was used to get gene level read counts for GRO-seq data and DESeq2 (v1.8.2) was used for differential gene analysis; GFOLD (v1.1.3) was used to generate gene level read count and carry out differential expression analysis.
bedGraph files for GRO-seq were generated using genomeCoverageBed function
in the BEDTools(v2.20.1) suite with total signal of 10 million, replicates were then combined before converted to bigwiggle files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle files were converted from bedGraph with bedGraphToBigWig function in BLAT suite. For GRO-seq and RNA-seq data, score equals to reads per 20 million; for ChIP-seq and Dnase-seq data, score equals to reads per million.


title: MDA-MB-231_scrambledsi_replicate_3

city: Vancouver

first: Gregg

last: Morin

state: BC

address: 675 W 10th Ave

institute: University of British Columbia

data_processing:
STAR v2.5 software used for alignment
htseq-count v0.6.1 software used to cound reads overlapping genes
DESeq v1.6.3 used for differential expression analysis
MISO v0.4.9 used to detect differential splicing events between treated and control samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file reporting counts

molecule: polyA RNA

source_name: Breast

extract_protocol:
MDA-MB-231 cells treated with CDK12 siRNA or scrambled siRNA were harvested in Trizol (Invitrogen) and total RNA was isolated using the Rneasy kit (Qiagen).
Library construction was performed on total RNA at the Michael Smith Genome Sciences Centre using the ssRNA-seq pipeline for mRNA libraries

tag: treatment

value: scrambled siRNA


title: GM10831_VDR_ChIP-exo_VD_stimulated


title: MDA-MB-231_CDK12si_replicate_2

value: CDK12 siRNA-1


title: MCF7 GRO-seq M phase

description:
nascent RNA; Two replicates are merged:
GRO-seq M phase rep1
GRO-seq M phase rep2


title: MDA-MB-231_scrambledsi_replicate_2


title: MDA-MB-231_scrambledsi_replicate_1


title: MCF7 RNA-seq S phase

description: RNA-seq S phase


title: MDA-MB-231_CDK12si_replicate_1


title: MCF7 GRO-seq G0/G1

description:
nascent RNA; Two replicates are merged:
GRO-seq G0/G1 rep1
GRO-seq G0/G1 rep2


title: 184-hTert_CDK12si_replicate_3

data_processing:
gsnap v2012-07-20 software used for alignment
htseq-count v0.6.1 software used to cound reads overlapping genes
DESeq v1.6.3 used for differential expression analysis
MISO v0.4.9 used to detect differential splicing events between treated and control samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file reporting counts

source_name: Breast cancer_184-hTert_CDK12si

extract_protocol:
SK-BR-3 and 184-hTERT cells treated with CDK12 siRNA or scrambled siRNA were harvested in Trizol (Invitrogen) and total RNA was isolated using the Rneasy kit (Qiagen).
Library construction was performed on total RNA at the Michael Smith Genome Sciences Centre using the ssRNA-seq pipeline for mRNA libraries


title: 184-hTert_CDK12si_replicate_1


title: 184-hTert_scrambledsi_replicate_1


title: 184-hTert_scrambledsi_replicate_3


title: 184-hTert_CDK12si_replicate_2


title: SK-BR-3_scrambledsi_replicate_3


title: SK-BR-3_scrambledsi_replicate_2


title: SK-BR-3_scrambledsi_replicate_1


title: SK-BR-3_CDK12si_replicate_3

source_name: Breast cancer_SK-BR-3_CDK12si


title: SK-BR-3_CDK12si_replicate_1


title: SK-BR-3_CDK12si_replicate_2


title: MCF7 H3K4me2 G0/G1

description:
Two replicates are merged:
H3K4me2 G0/G1 rep1
H3K4me2 G0/G1 rep2


title: MCF7 H3K4me2 S phase

description:
Two replicates are merged:
H3K4me2 S phase rep1
H3K4me2 S phase rep2


title: MCF7 H3K4me2 M phase

description:
Two replicates are merged:
H3K4me2 M phase rep1
H3K4me2 M phase rep2


title: MDA-MB-231_CDK12si_replicate_3


title: 184-hTert_scrambledsi_replicate_2


title: MCF7 RNA-seq M phase

description: RNA-seq M phase


title: hMeDIP-seq Undifferentiated HL-60 Replicate-3

city: West Lafayette

first: Joseph

last: Irudayaraj

state: IN

address: 225 S. University Street

department: Bindley Bioscience Center

institute: Purdue University

description:
001601_U3-B
undifferHm_C
Hydroxymethylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5hmeDip-seq.txt

data_processing:
The Illumina sequencing reads were mapped to the human reference genome (GRCh37/hg19, 2009 Assembly) using the BWA-MEM alignment algorithm of Burrows-Wheeler Aligner (BWA) v0.7.2 with default parameters.The output Sequence Alignment/Map (SAM) files were transferred into a binary format (BAM) using SAMtools v0.1.18 and filtered using the bamUtils module of NGSUtils v0.5.0 to remove low-quality reads.
To identify the regions enriched for 5mC/5hmC in the MeDIP-seq/hMeDIP-seq data, filtered BAM files of all samples were pooled together and then transformed into BED format using BAMToBED utility of BEDTools v2.17.0. SICER v1.1 with the recommended parameters (window size 200 bp, fragment size 100 bp, gap size 200 bp, effective genome fraction 0.74, and E-value threshold 100).
The differentially methylated or hydroxymethylated regions (DMRs or DHMRs, respectively), defined as the regions of the genome in which the levels of 5mC or 5hmC changed (either increased or decreased) upon differentiation of HL-60 cells, were further analyzed based on the number of sequencing reads detected in each sample. These differential methylation or hydroxymethylation analyses were processed with the exactTest function of EdgeR suite v2.11, a statistical model based on a Negative-Binomial distribution. For each region enriched for 5mC or 5hmC, the logarithmic ratio of fold change (base 2), P-value, and False Discovery Rate (FDR) were derived. DMRs and DHMRs with FDR<0.01 were included in analyses reported here, and were mapped to sites corresponding to the human reference genome GRCh37/hg19, 2009 Assembly.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and counts per million reads used for differential methylation or hydroxymethylation analyses.
Supplementary_files_format_and_content: Columns: ID: genomic locations of methylated or hydroxymethylated regions; logFC: log2 fold change from edgeR analysis; logCPM: log2 counts per millions reads from edgeR analysis; PValue: pvalue from edgeR analysis; FDR: FDR from edgeR analysis; column F to column K: raw reads counts for each sample; Gene: gene in/closest to the region; Gene_Dist: distance to the gene; Promoter: promoter in/near the region; Promoter_Dist: distance to the promoter; CpG: CpG island in/near the region; CpG_Dist: distance to the CpG island.

source_name: HL-60, undifferentiated, hMeDIP

growth_protocol: HL-60 cells were grown in RPMI medium (Life Technologies, Inc.) and supplemented with 10% Fetal Bovine Serum (FBS) (Atlanta Biologicals, Inc.) and 1% Penicillin- Streptomycin (Life Technologies, Inc.).

extract_protocol:
Genomic DNA was isolated from three biological replicates of 3x10^6 differentiated (SYTOX Blue-, CD11b+) or undifferentiated (SYTOX Blue-, CD11b-) HL-60 cells using the DNeasy Blood & Tissue Kit (Qiagen, Inc.) following manufacturer’s instructions. 2.5 μg of the isolated genomic DNA from each biological replicate was resuspended in 130 μl Tris EDTA, pH 8.0, and sheared using a Covaris S2 instrument with the following settings: Duty Cycle: 10%, Intensity: 5, Cycles per Burst: 200 and Time: 240 seconds. The sheared DNA was purified by binding to an equal volume (~130 μl) of AMPure beads (Beckman Coulter, Inc.). This and all other AMPure purifications were performed as directed by the manufacturer.
Libraries were constructed using the Illumina TruSeq DNA Sample Preparation Kit (Illumina, Inc. Cat# PE-940-2001), largely as directed by the "Low-Throughput" section of the kit manual but with the following changes; sheared DNA was blunted and extended by a single 3’ "A" using double the normal volumes of kit reagents. Each sample was divided in two parts (one half for MeDIP and the other half for hMeDIP) and subsequently 12 libraries were constructed. Each library was ligated to a different index-tag adapter (Index Adaptor). Instead of using the methylated adapters provided in the TruSeq kit, the sequences of TruSeq unique and Universal Adaptors were obtained from Illumina, Inc. and unmethylated versions of each adaptor were synthesized (IDT, Inc.) for use (sequences are available upon request from Illumina). The titers of the libraries, which ranged between 2.9 and 7.33 nM, were determined in duplicate by qPCR on a StepOne (Applied Biosystems, Inc.) instrument and a SYBR-Green Library Quantification Kit - Illumina (Kapa Biosystems, Inc.). 40 µl of library adapter ligated DNAs was subjected to methylated and hydroxymethylated DNA immunoprecipitation using kits from Diagenode, Inc. (meDIP: mc-magme-048; hmeDIP: AF-110-0016), following the manufacturer’s instructions.

treatment_protocol: Cellular differentiation was induced by treatment with 211 mM DMSO (Sigma-Aldrich, Inc.) corresponding to 1.5% (v/v final concentration) for seven days, with medium replaced daily. Cellular differentiation was assessed by flow cytometric analysis of CD11b expression.

value: myeloid leukemia cell line

tag: differentiation state

value: undifferentiated

value: anti-5-hydroxymethylcytosine (Diagenode, cat # EF-131-0050, lot# 002)


title: MeDIP-seq Differentiated HL-60 Replicate-2

description:
001604_D2-A
differMe_B
Methylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5meDip-seq.txt

source_name: HL-60, differentiated, MeDIP

tag: cell line

value: differentiated

value: anti-5-methylcytosine (Diagenode, cat # mcg-906-025, lot # D003)


title: hMeDIP-seq Differentiated HL-60 Replicate-3

description:
001607_D3-B
differHm_C
Hydroxymethylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5hmeDip-seq.txt

source_name: HL-60, differentiated, hMeDIP


title: MeDIP-seq Differentiated HL-60 Replicate-1

description:
001602_D1-A
differMe_A
Methylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5meDip-seq.txt


title: MeDIP-seq Undifferentiated HL-60 Replicate-1

description:
001596_U1-A
undifferMe_A
Methylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5meDip-seq.txt

source_name: HL-60, undifferentiated, MeDIP


title: MeDIP-seq Differentiated HL-60 Replicate-3

description:
001606_D3-A
differMe_C
Methylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5meDip-seq.txt


title: hMeDIP-seq Undifferentiated HL-60 Replicate-2

description:
001599_U2-B
undifferHm_B
Hydroxymethylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5hmeDip-seq.txt


title: MeDIP-seq Undifferentiated HL-60 Replicate-3

description:
001600_U3-A
undifferMe_C
Methylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5meDip-seq.txt


title: hMeDIP-seq Differentiated HL-60 Replicate-2

description:
001605_D2-B
differHm_B
Hydroxymethylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5hmeDip-seq.txt


title: MeDIP-seq Undifferentiated HL-60 Replicate-2

description:
001598_U2-A
undifferMe_B
Methylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5meDip-seq.txt


title: hMeDIP-seq Undifferentiated HL-60 Replicate-1

description:
001597_U1-B
undifferHm_A
Hydroxymethylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5hmeDip-seq.txt


title: Control_ovary_rep3_7804_S20

city: Minneapolis

first: Micah

last: Gearhart

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
Minkina_etal_normalized_FPKM.csv
Minkina_etal_raw_counts.csv
Supplementary_Table_1.csv

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters:ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the GRCm38 build of the mouse genome with STAR (version STAR_2.4.2a_modified)
Mapped reads were indexed and sorted with samtools 1.0
Gene quantification and deferential expression was performed using the GenomicAlignments (1.8.4) and DESeq2 (1.12.3) packages in Bioconductor.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: bigWig, normalized FPKMs, raw counts, log2FoldChange

source_name: 6 week Ovary

growth_protocol: Animals were raised in conventional housing.

extract_protocol:
Whole gonads were dissected and homogenized in Trizol.  RNA was purified using RNAeasy Micro Kit ( Qiagen 74004).
polyA+ mRNA using KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads (Kapa Biosystems KK8420/1)

treatment_protocol: None.

tag: age

value: 6 weeks old

tag: genotype/variation

value: Dmrt1 +/+; Rara f/f; Rarb f/f; Rarg f/f; Sf1-Cre-

value: C57BL/6; 129 Mixed

value: ovary


title: Control_ovary_rep5_7807_S25


title: Rar_mutant_ovary_rep2_7801_S23

value: Dmrt1 +/+; Rara f/f; Rarb f/f; Rarg f/f; Sf1-Cre+


title: Control_ovary_rep4_7805_S21


title: Rar_mutant_ovary_rep3_7803_S24


title: Control_ovary_rep2_7802_S26


title: EE_rep1_H3K9me3_ChIP-seq

city: Beijing

first: Jisong

last: Guan

address: Tsinghua University, Haidian district, Beijing

department: School of life science

country: China

institute: Tsinghua University

data_processing:
For ChIP-seq analysis, basecalls were performed using CASAVA version 1.7. ChIP-seq reads were aligned to the mm10 genome assembly using BWA 0.7.12. Peaks were called using MACS2 with the following setting: q-value<0.05, enrichment Fold>2.5.
For RNA-seq analysis, 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 using Tophat2 (version v2.0.12) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP-seq analysis, bedgraph files were generated using macs2 pileup, and then were transferred to bigwig files using bedGraphToBigWig. UCSC genome browser was used for visualization of raw intensities. Scores represent degree of coverage of the indicated gene regions.
Supplementary_files_format_and_content: For alternative splicing analysis from RNA-seq results, we used the splice junction counts plus the exon body counts as the input for rMATS (version v3.2.5) according to standard operating procedures (-length 150 -c 0.05 -ec 20 -analysis P). Excel files for RNA-seq including inclusion count and exclusion count for each alternative splicing event.

source_name: hippocampus

growth_protocol: Mice were housed in a vivarium, with the light/dark cycle of 12h-12h.

extract_protocol:
Mouse was perfused with 4% PFA solution, and hippocampus was homogenized and fixed in 1% PFA for 10 minutes. Chromatin was fragmented by sonication to obtain fragments 100–1000 bp in length. For each ChIP assay, 2 ug of antibodies were coupled to 200 ul magnetic beads. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer and quality-controlled using Agilent’s Bioanalyzer.
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 100-300bp DNA fragments.

treatment_protocol: Mice were placed in enriched cages equipped with various toys for 24 hours. The enriched cages are more than 4 folds larger in space than the home cage and have 2 floors. The toys include a running wheel, a climbing ladder, a running ball, mazes and colorful blocks. After 1 day EE treatment, mice were kept in home cage for another 1 week.

value: 3 months old

tag: tissue

value: hippocampus

tag: chip-antibody

value: H3K9me3 (diagenode, Cat. C15410193)

value: WT


title: Control_ovary_rep1_7707_S27


title: Rar_mutant_ovary_rep1_7715_S30


title: Dmrt1_het_Rar_mutant_ovary_rep2_7713_S29

description:
Minkina_etal_normalized_FPKM.csv
Minkina_etal_raw_counts.csv

value: Dmrt1 fl/+; Rara f/f; Rarb f/f; Rarg f/f; Sf1-Cre+


title: Dmrt1_het_Rar_mutant_ovary_rep1_7558_S28


title: EE_rep2_H3K9me3_ChIP-seq


title: hMeDIP-seq Differentiated HL-60 Replicate-1

description:
001603_D1-B
differHm_A
Hydroxymethylated DNA immunoprecipitation
Processed data file: Hl60_Differentiation_5hmeDip-seq.txt


title: Control_rep2_RNA-seq

source_name: primary cortical neuron

growth_protocol: Cortical cultures were maintained in Neurobasal medium (Invitrogen) containing 2% B27 supplement, 2 mM Glutamax and Penicillin/Streptomycin (Invitrogen) for 12-14 days.

extract_protocol:
Cells were lysed using TRIzol reagent, RNA was extracted by isopropanol precipitation and diluted in RNase-free water.
10ug RNA was DNase I (Fermentas, Cat. EN0521) treated at 37°C for 30 min. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After

treatment_protocol: DIV11 cortical neuron cultures were treated with final solution by mixing 30% depolarization buffer(170 mM NaCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES) , 30% old neuronal medium (in the culture dish) and 40% fresh neuronal medium for 10 minutes and washed out and then replaced with old medium. The culture dish was maintained in incubator for 24 hours and harvested.

value: ICR

value: cultured corticol neurons derived from E16 ICR mice at DIV11

value: primary cortical neuron


title: KCl_rep2_RNA-seq

treatment_protocol: DIV11 cortical neuron cultures were treated with final solution by mixing 30% depolarization buffer(170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES) , 30% old neuronal medium (in the culture dish) and 40% fresh neuronal medium for 10 minutes and washed out and then replaced with old medium. The culture dish was maintained in incubator for 24 hours and harvested.


title: Control_H3K9me3_ChIP-seq

treatment_protocol: Mice were kept in home cage.


title: KCl_rep1_RNA-seq


title: RpS3puc_3_RNAseq

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
Low quality or too short reads were discarded, the sequences were trimmed to remove adapter sequences
Sequences were mapped to the Drosophila transcriptome (Flybase v5.57) using bwa 0.6.2, number of mapped reads was counted per transcript and summed per gene. RPKM values were calculated as read per kilobase of each transcript per milion reads.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files contains RPKM values for each sample

organism: Drosophila melanogaster

growth_protocol: Flies and larvae were raised on a a standard wheat flour-based food supplemented with yeast at 25°C. Wing discs were collected from L3 wandering larvae.

extract_protocol:
50 wing discs of indicated genotype were collected and frozen in RNAlater solution (per sample). Following that the RNA was isolated using RNeasy mini kit (Qiagen).
Illumina TruSeq protocol using 1 μg total RNA.

value: esg-Gal4, UAS-GFP/UAS-Puc; FRT82, RpS3[Plac92], ubi-GFP/+

value: Wing discs


title: Control_rep1_RNA-seq


title: RpS3puc_2_RNAseq


title: Cbx1/3 conditional KO (day 4)

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned on mouse genome (mm9) using tophat2 (version 2.1.0) with option "--no-coverage search".
Gene expression (raw counts of mapped reads and FPKM) was analyzed using our in-house program.
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.

source_name: ES cells

extract_protocol:
Genomic DNA was isolated using QIAGEN All-prep kit
Library was prepared according to Illumina TruSeq protocol.

value: Embryonic stem cell

tag: time


title: mahj1_RNAseq_run2

description:
mahj1_RNAseq_run1 and mahj1_RNAseq_run2 are technical replicates, data from both sequencing runs were pooled
processed data file: mahj1_RNAseq_run1and2.txt

source_name: mahj

value: hs-FLP, stauGFP/+; FRT42D, mahj/FRT42D, mahj


title: Cbx1/3 conditional KO (day 8)


title: mahj2_RNAseq_run2

description:
mahj2_RNAseq_run1 and mahj2_RNAseq_run2 are technical replicates, data from both sequencing runs were pooled
processed data file: mahj2_RNAseq_run1and2.txt


title: RpS3puc_1_RNAseq


title: RpS3_2_RNAseq

value: FRT82B, RpS3[Plac92], ubi-GFP/+


title: RpS3_1_RNAseq


title: WT8_RNAseq

source_name: WT

value: yw


title: H3K9me2 ChIP-seq of Pcgf6 conditional KO ES cells (OHT-)

description: Immunoprecipitated genomic sequence

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using bowtie2 (version 2.1.0) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files having normalized read count covering whole genome.

growth_protocol: ES cells were cultured in standard condition

extract_protocol:
Genomic DNA was isolated using QIAGEN All-prep kit.
Library was prepared according to Illumina TruSeq protocol.

treatment_protocol: Cells were cultured with complete, cysteine deficient, or valine deficient media with SCF and TPO for 24 hours.

value: background strain:C57BL/6

tag: chip antibody


title: H3K9me2 ChIP-seq of Pcgf6 conditional KO ES cells (OHT+)

description: Immunoprecipitated genomic sequence


title: Cbx1/3 WT


title: WT6_RNAseq

value: FRT82, ubi-GFP


title: RpS3star_1_RNAseq

value: FRT82B, RpS3*/+


title: WT5_RNAseq


title: WT7_RNAseq


title: Pcgf6 fl/fl PGCLC (OHT+)_S03484

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using tophat2 (version 2.8.0) with default parameters.
Aligned seqeunces were converted to relative expression using cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] plain text containig FPKM (fragments per kilobase exon per million reads) values.

source_name: Pcgf6 fl/fl PGCLC (OHT+)

value: PGCLC

value: OHT+

value: Pcgf6 -/-


title: Pcgf6 fl/fl PGCLC (OHT-)_S03481

source_name: Pcgf6 fl/fl PGCLC (OHT-)

value: OHT-

value: control


title: Pcgf6 fl/fl EpiLC (OHT+)_S03483

source_name: Pcgf6 fl/fl EpiLC (OHT+)

value: EpiLC


title: Pcgf6 fl/fl ESC (OHT+)_S03482

source_name: Pcgf6 fl/fl ESC (OHT+)

value: ESC


title: Ring1A/B-dKO ESC (Negative cont for RING1B-ChIP)

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using bowtie2 (version 2.1.0) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle format having RPKM values with 100bp window

source_name: Embryonic stem cell

value: Ring1b antibody (Clone#3)


title: Pcgf6 fl/fl ESC_OHT+ day8

value: Flag antibody


title: Pcgf6 fl/fl ESC (OHT-)_S03479

source_name: Pcgf6 fl/fl ESC (OHT-)


title: Pcgf6 fl/fl ESC_OHT- (wild-type control)


title: Bmi1/Mel18-dKO ESC (Constitutive KO)


title: Mga siRNA_S02117

source_name: Mga siRNA

value: Mga siRNA

value: Mga -/-


title: Pcgf6 fl/fl EpiLC (OHT-)_S03480

source_name: Pcgf6 fl/fl EpiLC (OHT-)


title: Pcgf6 fl/fl ESC_OHT+ day4

value: Embryonic stem cell


title: mahj2_RNAseq_run1

value: hs-FLP, stauGFP/+; FRT42D, mahj/FRT42D, mahj

value: Wing discs


title: Max siRNA_S02116

source_name: Max siRNA

value: Max siRNA

value: Max -/-


title: AllStars Negative Control siRNA_S02115

source_name: AllStars Negative Control siRNA

value: AllStars Negative Control siRNA


title: Mga siRNA_S02113


title: RpS3star_2_RNAseq

value: FRT82B, RpS3*/+


title: Max siRNA_S02112


title: mahj1_RNAseq_run1


title: AllStars Negative Control siRNA_S02111


title: Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT+ day4; Ring1A/B-dKO)_S01672

value: OHT+


title: RpS15_2_RNAseq_run2

description:
RpS15_2_RNAseq_run1 and RpS15_2_RNAseq_run2 are technical replicates, data from both sequencing runs were pooled
processed data file: RpS15_2_RNAseq_run1and2.txt


title: WT3_RNAseq

value: yw


title: Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT+ day4; Ring1A/B-dKO)_S01669


title: Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT+ day2; Ring1A/B-dKO)_S01671


title: Pcgf6 fl/fl ESC (OHT+ day8)_S01456

source_name: Pcgf6 fl/fl ESC (OHT+ day8)

value: Pcgf6 -/-


title: Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT-; Ring1A-/-)_S01667

value: OHT-


title: Pcgf6 fl/fl ESC (OHT+ day4)_S01455

source_name: Pcgf6 fl/fl ESC (OHT+ day4)


title: Pcgf6 fl/fl ESC (OHT+ day4)_S01449


title: WT1_RNAseq_run2

description:
WT1_RNAseq_run1 and WT1_RNAseq_run2 are technical replicates, data from both sequencing runs were pooled
processed data file: WT1_RNAseq_run1and2.txt


title: RpS15_1_RNAseq_run2

description:
RpS15_1_RNAseq_run1 and RpS15_1_RNAseq_run2 are technical replicates, data from both sequencing runs were pooled
processed data file: RpS15_1_RNAseq_run1and2.txt


title: Atro 2 ChIP-seq

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

data_processing:
Uniquely mapping reads where mapped to the Drosophila melanogaster genome (release 5)
Log2 ratio between IP and input read density was calculated
Data was median smoothed using 100 bp windows
Smoothed ratio values every 10 bp was extracted
Genome_build: Drosophila melanogaster genome release 5
Supplementary_files_format_and_content: sgr files containing smoothed log2 ratio of IP over input (10 bp resolution)

source_name: S2 cells

growth_protocol: Drosophila S2 cells (catalog #006 from the Drosophila Genomics Resource Center) were grown to a density of 0.2 – 1 x 107 cells/ml and fixed in 1 % formaldehyde for 15 min at ambient temperature. The reaction was quenched by 0.16 M glycine pH 7.0 for 5 min and washed in PBS.

extract_protocol:
After fixation, the cells were washed and sonicated using a Bioruptor (Diagenode) to generate chromatin extract. Chromatin extract was cleared by centrifugation and used in ChIP with anti-Drosophila Atro 4H6 antibody, pre-bound to a mix of Protein A and G Dynabeads. Atro bound DNA was purified, and sent to Uppsala Genome Center for SOLiD (TM) ChIP-Seq Library preparation (Rev date 18 March 2010), size selection (100-150 bp + adapters 90bp ≈250 bp), and SOLiD sequencing.
Libraries were prepared for sequencing using standard SOLiD protocols

value: Antibody 4H6 raised against the peptide SRQSPLHPVP in Drosophila Atro


title: Atro 1 ChIP-seq


title: Pcgf6 fl/fl ESC (OHT-)_S01448

value: ESC

value: control


title: RpS15_1_RNAseq_run1


title: WT2_RNAseq_run2

description:
WT2_RNAseq_run1 and WT2_RNAseq_run2 are technical replicates, data from both sequencing runs were pooled
processed data file: WT2_RNAseq_run1and2.txt


title: RpS15_2_RNAseq_run1


title: Pcgf6 fl/fl ESC (OHT+ day8)_S01450


title: Pcgf6 fl/fl ESC (OHT-)_S01454


title: WT4_RNAseq


title: Dexamethasone and Belinostat co-treated rep3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the hg38 reference genome with tophat2; version 2.1.0; parameters: --library-type fr-firststrand -p 3 -G hg38g.gtf –b2-sensitive
Multi-mapping reads were removed with samtools by filtering on the mapq field. command: samtools view -b -q 5
non-normalized read abundances were obtained with htseq-count using default setting, but with the stranded option set to reverse (-s reverse)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: hg38
Supplementary_files_format_and_content: processed files contain the output from htseq-count for each sample (raw abundance data).

source_name: A549 cells

growth_protocol: A549 cells (lung epithelial cells) were maintained and grown in Dulbecco’s modified Eagle’s medium (DMEM; house-made) containing 10% fetal calf serum (FCS), sodium pyruvate, 0,1mM non-essential amino acids, and 2mM L-glutamine

extract_protocol:
Total RNA was isolated using TRIzol (Gibco Life Technologies) and the InviTrap Spin Universal RNA Mini Kit (Invitek, Isogen Life Science) according to the manufacturer’s instructions. RNA concentration was measured and quality was checked with the Agilent RNA 6000 Pico Kit (Agilent Technologies Belgium), and 5μg of RNA was sent for sequencing
Illumina truseq RNA stranded library protocol (for single end sequencing)

treatment_protocol: A549 cells were seeded in 6-well plates (0,5 x 10^6 cells/well) in DMEM. Cells were exposed to Belinostat (1µM) equal dilution of DMSO, 16 hours before Dex (10^-6M, five hours) or PBS stimulation

value: lung epithelial cells


title: WT1_RNAseq_run1


title: Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT-; Ring1A-/-)_S01670


title: Dexamethasone and Belinostat co-treated rep2


title: WT2_RNAseq_run1


title: Dexamethasone and Belinostat co-treated rep1


title: Belinostat treated rep3


title: Dexamethasone treated rep1


title: Belinostat treated rep2


title: input Atro 2


title: Untreated rep3


title: Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT+ day2; Ring1A/B-dKO)_S01668


title: Trypanosoma brucei brucei Lister 427, rep1

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

description:
Genome wide RNAi library population
extracted

data_processing:
Primer sequences were removed from the raw sequences using cutadapt (parameters: -O 10 -m 25 -n 3 -q 20; version 1.0), partitioning processed reads into terminal (primer-containing, thus trimmed) and internal (untrimmed) datasets.
Sequences were aligned to the Tbb genome (obtained from ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/ ) using bowtie2 (parameters: --very-sensitive; version: 2.0.2), piped through samtools (parameters: -bhS; version: 0.1.18), and stored in indexed BAM format.
The annotated Tbb genome was viewed using Artemis software (http://www.sanger.ac.uk/resources/software/artemis/ ; http://ukpmc.ac.uk/abstract/MED/11120685), and read depth values were extracted from the BAM files and/or viewed directly in Artemis.
Genome_build: ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/
Supplementary_files_format_and_content: Annotated read depth summary for non-zero read depth loci.

organism: Trypanosoma brucei

source_name: 2T1 T7  p’5neo5’-ESAG9 3’UTR bloodstream forms

growth_protocol: HMI-9 bloodstream culture

extract_protocol:
gDNA extraction then PCR amplificaiton of the RNAi inserts
An RNAi library population of 2x107 cells (~5 fold genome coverage) was selected in the presence of 100µM 8-pCPT-2’-O-Me-cAMP or 10µM 8-pCPT-2’-O-Me-5’-AMP22 in several replicate flasks either induced, or not, to activate RNAi.   Three cAMP-selected and five AMP-selected populations outgrew and were subject to DNA isolation and RNAi fragment insert amplification. Amplicon populations from the cAMP and AMP selections were analysed by ion torrent sequencing.   PCR amplicon primers (Forward primer: 5' TAGCCCCTCGAGGGCCAGT 3', Reverse primer: 5' GGAATTCGATATCAAGCTTGGC 3') were used to generate PCR fragments, which ranged in size up to about 2kb. These were subsequently fragmented to 250-200nt sized fragments before barcoding and sequencing.

tag: protocol

value: cultured in HMI-9

value: Lister 427


title: Untreated rep1


title: Trypanosoma brucei brucei Lister 427, rep2


title: Hypericum perforatum replicate 3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description:
BNDE-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Hypericum_perforatum.tsv
MethylC–seq

data_processing:
Data was mapped to transcriptome assemblies of each species. If a species did not have an assembled transcriptome, a closely related species (i.e., within same genus) was used.
MethylC-seq analysis were performed as described in Schmitz et al. (2013; Genome Research).
Genome_build: At the time of submission, the assembled transcriptomes used for read alignment were not publicly available. The submitter states that the transcriptomes will be made available upon release of the 1KP capstone paper.  www.onekp.com
Supplementary_files_format_and_content: Tab delimited text file. Please see metafile for column headers. The text files with the processed data are available in a tar archive on the series record.

organism: Hypericum perforatum

source_name: genomic DNA

extract_protocol:
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.
Libraries were prepared following the steps provided in Urich et al. (2015; Nature Protocols)

value: leaf

value: Wild-type


title: Lys-3

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

description: Processed data file: NaPi_vs_Lys.txt

data_processing:
Quality of the sequences was verified with FastQC 0.11.2.
EDGE-pro 1.3.1 workflow was employed for read processing. The pipeline as described by T. Magoc, et al., Evolutionary Bioinformatics, 2013, employs Bowtie2 (v2.2.3) to map reads to the reference genome (NCTC 8325), filters multimapped reads based on scoring alignments and determines read coverage for each genomic position and gene.
EDGE-pro output files were formatted using the edgeToDeseq script provided in the EDGE-pro package and used as input for DESeq2 (v1.12.4) to calculate RPKMs per gene and quantify differential expression between conditions.
Genome_build: S. aureus subsp. aureus NCTC 8325 (Assembly ASM1342v1, GCA_000013425.1, Mar 2010).
Supplementary_files_format_and_content: NaPi_vs_Lys.txt: Tab-delimited text file includes RPKM values for NCTC 8325 genes in NaPi and Lys replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.

organism: Staphylococcus aureus

source_name: Biofilm cells, LysH5

growth_protocol: Biofilms were formed for 24 hours at 25ºC, then adhered cells were treated with NaPi buffer alone or containing subinhibitory endolysin LysH5 for 30 minutes and subsequently harvested for RNA purification.

extract_protocol:
Bacterial cells were harvested, treated with RNA protect (Qiagen) and kept at -80ºC until RNA purification. RNA was obtained by mechanical disruption in the presence of acid phenol and subsequent purification was carried out with illustra RNA spin minikit (GE Healthcare).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: IPLA 1

value: Biofilm

value: NaPi buffer + LysH5


title: Hypericum perforatum replicate 1


title: Hypericum perforatum replicate 5


title: input Atro 1


title: Hypericum perforatum replicate 2


title: Dexamethasone treated rep3


title: Untreated rep2


title: Aristolochia grandiflora replicate 5

description:
PAWA-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Aristolochia_grandiflora.tsv
MethylC–seq

organism: Aristolochia grandiflora


title: Dexamethasone treated rep2


title: Lys-1

description: Processed data file: NaPi_vs_Lys.txt


title: Lys-2

description: Processed data file: NaPi_vs_Lys.txt


title: NaPi-2

description: Processed data file: NaPi_vs_Lys.txt

source_name: Biofilm cells, control

value: NaPi buffer


title: Aristolochia grandiflora replicate 8


title: Aristolochia grandiflora replicate 6


title: Aristolochia grandiflora replicate 1


title: NaPi-3

description: Processed data file: NaPi_vs_Lys.txt


title: Aristolochia grandiflora replicate 4


title: NaPi-1

description: Processed data file: NaPi_vs_Lys.txt


title: Aristolochia grandiflora replicate 2


title: Belinostat treated rep1


title: Hypericum perforatum replicate 4


title: Amentotaxus argotaenia replicate 1

description:
IAJW-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Amentotaxus_argotaenia.tsv
MethylC–seq

organism: Amentotaxus argotaenia


title: Urtica dioica replicate 5

description:
WKCY-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Urtica_dioica.tsv
MethylC–seq

organism: Urtica dioica


title: Araucaria  replicate 8

description:
ACWS-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Araucaria_sp.tsv
MethylC–seq

organism: Araucaria


title: Urtica dioica replicate 3


title: Urtica dioica replicate 4


title: Aristolochia grandiflora replicate 7


title: Araucaria  replicate 6


title: Araucaria  replicate 5


title: 2xlink IgG ChIP-seq rep 3, 3-19-14

first: Helen

last: McNeill

address: 600 University Ave.

institute: Lunenfeld Tanenbaum Research Institute

description: bam file was generated from fastq files

data_processing:
Base calling done with MiSeq (Illumina RTA version 1.18.54)
Reads aligned with BWA (v0.6.1), done using default parameters
Genome_build: BDGP release 5 (dm3)
Supplementary_files_format_and_content: wig files were generated from bam files

source_name: S2_2xlink IgG ChIP-seq

extract_protocol:
Cells were sonicated and cleared of cellular debris.  Lysates were immunoprecipitated with the corresponding antibodies
Briefly, DNA ends were repaired with T4 DNA polymerase, Klenow Large Fragment DNA polyermerase and T4 polynclease kinase.  DNA was purified with PEG bead slurry.  Illumina short sequencing adaptor was ligated to DNA overnight.  Library was purified with PEG beads

treatment_protocol: Crosslinked with ethylene glycol bis(succinimidyl succinate) and then crosslinked with formaldehyde

value: S2 cells

value: Normal rabbit IgG

tag: chip antibody information

value: Cell Signaling, catalog number 2729

tag: crosslinker

value: 2mM ethylene glycol bis(succinimidyl succinate) and 1% formaldehyde


title: 2xlink Atro ChIP-seq rep 3, 3-19-14

description: bam file was generated from fastq files

source_name: S2_2xlink Atro ChIP-seq

value: Rabbit anti-Atro sera (SG2524)

value: raised in rabbit, against Atro (amino acids 121-134)


title: Urtica dioica replicate 2


title: Aristolochia grandiflora replicate 3


title: Araucaria  replicate 3


title: Araucaria  replicate 4


title: Urtica dioica replicate 1


title: 2xlink Atro ChIP-seq rep 2, 3-13-14

description: bam file was generated from fastq files


title: Thuja sutchuenensis replicate 5

description:
VFYZ-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Thuja_sutchuenensis.tsv
MethylC–seq

organism: Thuja sutchuenensis


title: Thuja sutchuenensis replicate 4


title: 2xlink Atro ChIP-seq rep 1, 3-11-14

description: bam file was generated from fastq files


title: Thuja sutchuenensis replicate 3


title: Araucaria  replicate 1


title: Araucaria  replicate 2


title: Psilotum sp. replicate 8

description:
QVMR-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Psilotum_sp.tsv
MethylC–seq

organism: Psilotum


title: Amentotaxus formosania replicate 1

description:
IAJW-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Amentotaxus_formosania.tsv
MethylC–seq

organism: Amentotaxus formosana


title: Araucaria  replicate 7


title: Pereskia grandiflora replicate 5

description:
JLOV-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Pereskia_grandiflora.tsv
MethylC–seq

organism: Pereskia grandiflora


title: Pereskia grandiflora replicate 4


title: Psilotum sp. replicate 7


title: 2xlink IgG ChIP-seq rep 1, 3-11-14

description: bam file was generated from fastq files


title: 2xlink IgG ChIP-seq rep 2, 3-13-14

description: bam file was generated from fastq files


title: Thuja sutchuenensis replicate 2


title: Pereskia grandiflora replicate 3


title: Thuja sutchuenensis replicate 1


title: Psilotum sp. replicate 6


title: Psilotum sp. replicate 5


title: Pereskia grandiflora replicate 2


title: Psilotum sp. replicate 4


title: Pereskia grandiflora replicate 1


title: Nepenthes bicalcarata replicate 8

description:
WQUF-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Nepenthes_bicalcarata.tsv
MethylC–seq

organism: Nepenthes bicalcarata


title: Psilotum sp. replicate 3


title: LMP1/2a_mouse5_Bcell

city: Boston

first: Benjamin

last: Gewurz

state: Massachusetts

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

description:
Ribosomal RNA depleted RNA
Raw_counts.txt
Normalized_counts.txt
LMP1,2a_vs_GFP.txt

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the mouse GRCm38.86 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 10 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between LMP1/2a group and the GFP group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCm38.86
Supplementary_files_format_and_content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively

source_name: Spleen

growth_protocol: Mature B cells or B220+ B cells from splenocytes were purified using the magnetic cell sorting-based B-cell isolation kit or B220 MicroBeads, according to the manufacturer’s protocol (Miltenyi Biotec). The cells were cultured in RPMI 1640 medium containing 10% (vol/vol) FBS, streptomycin/penicillin, 2-mercaptoethanol, and minimal essential medium (MEM) Nonessential Amino Acid Solution (all obtained from GIBCO).

extract_protocol:
Total RNAs were isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 500 ng total RNA was used for ribosomal RNA depletion, followed by library construction using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (#634874, Clontech Laboratories, Inc., CA).

value: B220+ B splenocytes

tag: strain


title: Psilotum sp. replicate 2

tag: genotype


title: Psilotum sp. replicate 1


title: cf. Cyathea sp. replicate 8

description:
GANB-SOAPdenovo-Trans-assembly.fa
processed data file: allc_cf_Cyathea_sp.tsv
MethylC–seq

organism: Cyathea


title: Nepenthes bicalcarata replicate 6


title: Nepenthes bicalcarata replicate 7


title: LMP1/2a_mouse4_Bcell


title: GFP_mouse2_Bcell


title: Nepenthes bicalcarata replicate 5


title: cf. Cyathea sp. replicate 7


title: Nepenthes bicalcarata replicate 4


title: Synsepalum dulcificum replicate 1

description:
WRPP-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Synsepalum_dulcificum.tsv
MethylC–seq

organism: Synsepalum dulcificum


title: cf. Cyathea sp. replicate 6


title: GFP_mouse1_Bcell


title: Nepenthes bicalcarata replicate 3


title: Selaginella kraussiana replicate 4

description:
ZFGK-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Selaginella_kraussiana.tsv
MethylC–seq

organism: Selaginella kraussiana


title: Nepenthes bicalcarata replicate 2


title: cf. Cyathea sp. replicate 5


title: Selaginella kraussiana replicate 3


title: cf. Cyathea sp. replicate 3


title: cf. Cyathea sp. replicate 4


title: cf. Cyathea sp. replicate 2


title: Nepenthes bicalcarata replicate 1


title: cf. Cyathea sp. replicate 1


title: Selaginella kraussiana replicate 1


title: Gnetum gnemon replicate 8

description:
GTHK-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Gnetum_gnemon.tsv
MethylC–seq

organism: Gnetum gnemon


title: Polypodium punctatum replicate 8

description:
CJNT-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Polypodium_punctatum.tsv
MethylC–seq

organism: Microsorum punctatum


title: Gnetum gnemon replicate 6


title: Lupinus angustifolius replicate 8

description:
TTRG-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Lupinus_angustifolius.tsv
MethylC–seq

organism: Lupinus angustifolius


title: Gnetum gnemon replicate 7


title: Polypodium punctatum replicate 7


title: Gnetum gnemon replicate 5


title: Polypodium punctatum replicate 6


title: Lupinus angustifolius replicate 6


title: Lupinus angustifolius replicate 7


title: Polypodium punctatum replicate 5


title: Gnetum gnemon replicate 4


title: Gnetum gnemon replicate 3


title: Gnetum gnemon replicate 2


title: Polypodium punctatum replicate 4


title: Equisetum sp. replicate 4

description:
JVSZ-SOAPdenovo-Trans-assembly.fa
processed data file: allc__sp.tsv
MethylC–seq

organism: Equisetum


title: Lupinus angustifolius replicate 5


title: Gnetum gnemon replicate 1


title: Lupinus angustifolius replicate 4


title: Polypodium punctatum replicate 3


title: Selaginella kraussiana replicate 2


title: Polypodium punctatum replicate 2


title: Equisetum sp. replicate 3


title: Celtis occidentalis replicate 4

description:
KYAD-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Celtis_occidentalis.tsv
MethylC–seq

organism: Celtis occidentalis


title: Lupinus angustifolius replicate 3


title: Diplazium proliferum replicate 5

description:
IZGN-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Diplazium_proliferum.tsv
MethylC–seq

organism: Diplazium proliferum


title: Celtis occidentalis replicate 5


title: Kalanchoe tomentosa replicate 5

description:
DRIL-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Kalanchoe_tomentosa.tsv
MethylC–seq

organism: Kalanchoe tomentosa


title: Cephalotaxus harringtonia replicate 1

description:
WYAJ-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Cephalotaxus_harringtonii.tsv
MethylC–seq

organism: Cephalotaxus harringtonia


title: Lupinus angustifolius replicate 2


title: Lupinus angustifolius replicate 1


title: Equisetum sp. replicate 1


title: Kalanchoe tomentosa replicate 4


title: Polypodium punctatum replicate 1


title: Diplazium proliferum replicate 3


title: Diplazium proliferum replicate 4


title: Celtis occidentalis replicate 1


title: Yucca brevifolia replicate 2

description:
YBML-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Yucca_brevifolia.tsv
MethylC–seq

organism: Yucca brevifolia


title: Kalanchoe tomentosa replicate 3


title: Diplazium proliferum replicate 2


title: Celtis occidentalis replicate 2


title: Yucca brevifolia replicate 1


title: Kalanchoe tomentosa replicate 2


title: Diplazium proliferum replicate 1


title: Torreya taxifolia replicate 2

description:
EFMS-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Torreya_taxifolia.tsv
MethylC–seq

organism: Torreya taxifolia


title: Equisetum sp. replicate 2


title: Dacrydium balansae replicate 2

description:
IZGN-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Dacrydium_balansae.tsv
MethylC–seq

organism: Dacrydium balansae


title: Aloe vera replicate 3

description:
JVBR-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Aloe_vera.tsv
MethylC–seq

organism: Aloe vera


title: Torreya taxifolia replicate 1


title: Kalanchoe tomentosa replicate 1


title: Juniperus virginiana replicate 5

description:
XMGP-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Juniperus_virginiana.tsv
MethylC–seq

organism: Juniperus virginiana


title: Dacrydium balansae replicate 1


title: Aloe vera replicate 2


title: Aloe vera replicate 1


title: Papuacedrus papuana replicate 1

description:
SOAPdenovo-Trans-assembly.fa
processed data file: allc_Papuacedrus_papuana.tsv
MethylC–seq

organism: Papuacedrus papuana


title: Celtis occidentalis replicate 3


title: Dacrycarpus compactus replicate 1

description:
FMWZ-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Dacrycarpus_compactus.tsv
MethylC–seq

organism: Dacrycarpus compactus


title: Juniperus virginiana replicate 4


title: Manoao colensoi replicate 2

description:
CDFR-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Manoao_colensoi.tsv
MethylC–seq

organism: Manoao colensoi


title: Juniperus virginiana replicate 3


title: Manoao colensoi replicate 1


title: Trypanosoma brucei AnTata1.1 REG9.1 RNAi line uninduced, rep2

description: No Tet

data_processing:
Raw sequence quality was assessed using FASTQC software
Reads were aligned to the reference using bowtie v2 with parameters “--very-sensitive -p 12 --no-unal --no-discordant --trim5 10”, version 2.0.2), piped through samtools (parameters: -bhS; version: 0.1.18), and stored in indexed BAM format
Bedtools software was used to extract read counts for the genes from the bam file data
Gene counts were scale normalised by total gene counts in the R environment
Genome_build: ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/
Supplementary_files_format_and_content: Tab-delimited text file containing raw tag counts for all sample replicates

organism: Trypanosoma brucei

extract_protocol:
QIA gen RNAeasy
Library construction and sequencing was carried out by BGI-Hong Kong using the Illumina® TruSeq™ RNA Sample Preparation Kit.

tag: Stage

value: bloodstream forms


title: Cyperus papyrus replicate 8

description:
PWSG-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Cyperus_papyrus.tsv
MethylC–seq

organism: Cyperus papyrus


title: Trypanosoma brucei AnTata1.1 REG9.1 RNAi line induced, rep2

description: Plus Tet


title: Juniperus virginiana replicate 2


title: Fokienia hodginsii replicate 1

description:
UEVI-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Fokienia_hodginsii.tsv
MethylC–seq

organism: Chamaecyparis hodginsii


title: Aloe vera replicate 4


title: Cyperus papyrus replicate 7


title: Trypanosoma brucei AnTata1.1 REG9.1 RNAi line induced, rep1

description: Plus Tet


title: Juniperus virginiana replicate 1


title: Cyperus papyrus replicate 6


title: Encephalartos horridus replicate 1

description:
GNQG-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Encephalartos_horridus.tsv
MethylC–seq

organism: Encephalartos horridus


title: Trypanosoma brucei AnTata1.1 REG9.1 RNAi line uninduced, rep1

description: No Tet


title: Cissus quadrangularis replicate 5

description:
BGZG-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Cissus_quadrangularis.tsv
MethylC–seq

organism: Cissus quadrangularis


title: Cissus quadrangularis replicate 4


title: Impatiens niamniamensis replicate 4

description:
JEXA-SOAPdenovo-Trans-assembly.fa
processed data file: allc_Impatiens_niamniamensis.tsv
MethylC–seq

organism: Impatiens niamniamensis


title: Cyperus papyrus replicate 4


title: Trypanosoma brucei AnTata1.1 REG9.1 over-expressor line induced, rep2

description:
pLEW ectopic expression
Plus Tet


title: Cyperus papyrus replicate 3


title: Impatiens niamniamensis replicate 3


title: Cissus quadrangularis replicate 3


title: Trypanosoma brucei AnTata1.1 REG9.1 over-expressor line induced, rep1

description:
pLEW ectopic expression
Plus Tet


title: Impatiens niamniamensis replicate 2


title: Trypanosoma brucei AnTata1.1 REG9.1 over-expressor line uninduced, rep2

description:
pLEW ectopic expression
No Tet


title: Cyperus papyrus replicate 2


title: Cissus quadrangularis replicate 2


title: Cyperus papyrus replicate 1


title: Impatiens niamniamensis replicate 1


title: Trypanosoma brucei AnTata1.1 REG9.1 over expressor line uninduced, rep1

description:
pLEW ectopic expression
No Tet


title: ChIP:LOUCY_Input_052615 [lab: Look-DFCI]

status: Public on Mar 15 2017

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
genome build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

organism: Homo sapiens

source_name: T-ALL

growth_protocol: Cells were maintained under typical conditions in RPMI +10% FBS.

extract_protocol:
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: Loucy

tag: system

value: Blood


title: ChIP: MYB_ab45150_DU.528_032615 [lab: Look-DFCI]

description: antibody: MYB (Abcam ab45150)

growth_protocol: According to ATCC guidelines


title: ChIP: MYB_ab45150_PF-382_032615 [lab: Look-DFCI]

description: antibody: MYB (Abcam ab45150)


title: Pcf11-PAR-CLIP

city: Göttingen

first: Carlo

last: Bäjen

address: Am Fassberg 11

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

data_processing:
library strategy: PAR-CLIP
PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools.
ChIP-seq: Paired-end reads were aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 2.2.3) with options: ––p 8 --no-discordant. SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped. Duplicate reads were removed. The BEDTools toolset was used to obtain coverage tracks that were subsequently imported into R/Bioconductor where further processing of the data was carried out.
4tU-seq: Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0). SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further processing of the RNA-Seq data was carried out using the R/Bioconductor environment
Readthrough index (RI): Was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of our analysis. We then compared the RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) to characterize the amount of termination defects.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content:
*.bed: Paired-end reads were aligned using Bowtie (2.2.3) and filtered with SAMTools. Alignments with MAPQ smaller than 7 were skipped and BEDTools was used to obtain coverage tracks.
*normalized_q95.table: Reads were aligned using Bowtie (1.1.1.). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. The P-value calculation was performed for any genomic T site, given the total number of reads covering the site (”coverage”) and given the fraction of these reads which show the T-to-C mismatch (P-value cut-off of 0.005 and a minimum coverage threshold of 4). The frequency of T-to-C transitions was subsequently normalized by RNA-seq.
*fragmentcoverageRatiotable_*.txt:  The readthrough index (RI) was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of the analysis.The RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) were finally compared to characterize the amount of termination defects.

organism: Saccharomyces cerevisiae

source_name: Yeast cell extract

growth_protocol: Cells expressing the TAP-tagged or FRB-tagged protein were grown at 30 °C and 160 rpm. While ChIP and 4tU-seq were performed in YPD, the PAR-CLIP experiments were carried out in CSM minimal medium (Formedium) supplemented with 10 mg/l uracil, 100 µM 4-thiouracil and 2 % glucose.

extract_protocol:
CLIP and ChIP: Cells were lysed by bead beating and the lysate was sonicated in a Covaris S220 system. Immunoprecipitation was performed at 4 °C with rabbit IgG-conjugated Protein G magnetic Dynabeads.
4tU-seq: Total RNA was extracted and labeled RNA purified. 100 ng of labeled RNA was used as input for the Ovation Universal RNA-Seq System Library Kit (NuGen) and processed following the manufacturer’s protocol. ChIP-seq: Purified DNA from IP and input samples was RNase digested and used for ChIP-seq library perparation with the NEB-Next ChIP-seq Library Reagent Set for Illumina Sequencing (NEB) in combination with Multiplex Oligos (NEB) according to the manufacturers protocol.

treatment_protocol: ChIP: 1% formaldehyde for 20 min at 20°C and subsequently quenched with 375 mM glycine for 10 min. PAR-CLIP: 900 µM 4-thiouracil were added and cells were grown further for 4 h before they were UV-irradiated with an energy dose of 12 J/cm2 at 365 nm. 4tU-seq: the cultures were supplemented with rapamycin (1 μg/ml) and labeled for 60 min.

tag: strain background

value: expressing the TAP-tagged protein

tag: molecule subtype

value: crosslinked RNA


title: ChIP:MYB_ab45150_LOUCY_052615 [lab: Look-DFCI]

description: antibody: MYB (Abcam ab45150)

tag: cell line


title: ChIP:JURKAT_Input_052616 [lab: Look-DFCI]

description: antibody: None

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

value: Jurkat


title: ChIP-seq analysis of p65 in Huh7 cells ( control )

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings using ChIP sample as treatment file and input as control.
Enhancers were identified by calculating the union of H3K4me1 and H3K27ac peaks across all experimental conditions (supplementary files: enhancers.bed).
Genome_build: hg19
Supplementary_files_format_and_content: coverage Wiggle files were generated with Mscs1.4 at 10 bp resolution. Wig files were converted to bigwig using the wigToBigWig utility (UCSC)

source_name: HuH7 cells

growth_protocol: Approximately 10*10^6 Cells were seeded in culture vessels in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal calf serum and 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, 100 U/ml penicillin, 100 μg/ml streptomycin GibcoBRL. Afterwards cells were infected with the human coronavirus 229E at 33°C, 5%CO2 - incubation for 24h.

extract_protocol:
ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1, 1mM PMSF, Roche protease inhibitor mix), followed by IP and purification of DNA
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions

treatment_protocol: For the infection cells were incubated with DMEM containing the virus at a multiplicity of infection (MOI) of 1. The cells were further incubated at 33°C for 24h with either the CoV-229E or with the heat-inactivated virus. Control cells were left untreated, but were also incubated at 33°C. As positive control another sample of cells was treated with IL-1 (10 ng/ml) for 1h at 33°C .

tag: treatment

tag: antibody

value: p65 (Santa Cruz, C-20, sc-372)


title: ChIP-seq analysis of p65 in Huh7 cells ( IL-1 )

description: ChIP-seq

value: 10ng/ml IL-1alpha for 1 h


title: Impatiens niamniamensis replicate 5

tag: tissue

value: leaf

value: Wild-type


title: Cyperus papyrus replicate 5


title: ChIP-seq analysis of p(S5) PolII in Huh7 cells ( CoV )

description: ChIP-seq

value: DMEM containing CoV-229E at MOI = 1

value: P(S5)-pol II (Abcam, ab5131)


title: ChIP-seq analysis of p(S5) PolII in Huh7 cells ( IL-1 )

description: ChIP-seq


title: ChIP-seq analysis of p(S5) PolII in Huh7 cells ( control )

description: ChIP-seq


title: ChIP-seq analysis of Input in Huh7 cells ( control )

description: ChIP-seq


title: ChIP-seq analysis of Input in Huh7 cells ( IL-1 )

description: ChIP-seq


title: ChIP-seq analysis of H4K5ac in Huh7 cells ( CoV )

description: ChIP-seq

value: H4K5ac (Millipore, 17-10045)


title: ChIP-seq analysis of H4K5ac in Huh7 cells ( control )

description: ChIP-seq


title: ChIP-seq analysis of H4K5ac in Huh7 cells ( IL-1 )

description: ChIP-seq


title: ChIP-seq analysis of H3K9ac in Huh7 cells ( IL-1 )

description: ChIP-seq

value: H3K9ac (Millipore, 07-352)


title: Cissus quadrangularis replicate 1


title: ChIP-seq analysis of H3K9ac in Huh7 cells ( control )

description: ChIP-seq


title: ChIP-seq analysis of H3K4me1 in Huh7 cells ( IL-1 )

description: ChIP-seq

value: H3K4me1 (Abcam, ab8895)


title: ChIP-seq analysis of H3K36ac in Huh7 cells ( IL-1 )

description: ChIP-seq

value: H3K36ac (Diagenode, C154 10307)


title: ChIP-seq analysis of H3K4me1 in Huh7 cells ( control )

description: ChIP-seq


title: ChIP-seq analysis of H3K36ac in Huh7 cells ( control )

description: ChIP-seq


title: ChIP-seq analysis of H3K27ac in Huh7 cells ( IL-1 )

description: ChIP-seq

value: H3K27ac (Diagenode, 174-050)


title: ChIP-seq analysis of H3K27ac in Huh7 cells ( CoV )

description: ChIP-seq


title: ChIP-seq analysis of p65 in Huh7 cells ( CoV )

description: ChIP-seq


title: ChIP-seq analysis of H3K27ac in Huh7 cells ( control )

description: ChIP-seq


title: ChIP-seq analysis of H3K9ac in Huh7 cells ( CoV )

description: ChIP-seq


title: F2 Sample 6 (Technical Replicate 2)

city: Salt Lake City

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2000 instrument, a 50 cycle single-end sequence run was performed, and the resulting reads were aligned to the A. thaliana TAIR 10 reference genome and annotation using the Bowtie2 (2.1.0.0) and TopHat 2 (2.0.8b) mapping pipeline. Reads were sorted using SAMtools 0.1.18.0.
Read counts for genes in the TAIR 10 annotation were obtained using HTSeq 0.6.0 with --stranded no.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab-delimited text files with counts of reads per gene from alignments as assessed with HTSeq 0.6.0.

organism: Arabidopsis thaliana

source_name: aerial shoot

growth_protocol: F2 seeds were stratified for 5 days in 0.1 % agarose at 4°C. Plants were germinated and grown 2 plants per pot in 8 cm2 pots on Sunshine LA4P Mix (Sun Gro Horticulture, Bellevue, WA, USA) at 16°C constant temperature with a 16 hour light photoperiod. Plants were thinned to one plant per pot at the 5 true leaf stage and aerial portions of the plants were harvested at the 9 true leaf stage between 7.5 and 8.5 hours into the photoperiod.

extract_protocol:
Briefly, individual frozen plants were ground in liquid nitrogen using a mortar and pestle and RNA was isolated using PureLink Plant RNA Reagent (#12322-012, Invitrogen, Carlsbad, CA, USA) following the manufacturers instructions. Precipitated RNA was resuspended in RNAsecure Resuspension Solution (#AM7010, Ambion; Life Technologies, Carlsbad, CA, USA) following manufacturers guidelines to prevent RNA degradation. Contaminating genomic DNA was removed by incubating samples with Turbo DNase (#AM2238, Ambion) for 15 min at 37°C. Finally, RNA was precipitated using 2.5 vol 100% ethanol, 0.1 volume 5M Ammonium Acetate and 1µl glycogen (5 mg/ml) and resuspended in RNase-free water.
RNA-seq libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit V2 (# 15026495 Rev. C). Briefly, poly-A mRNA was purified from 1 µg of isolated total RNA using poly-T oligo-attached magnetic beads. Purified RNA was fragmented into 120-210 bp fragments (average size ~155 bp) using divalent cations at 94°C for 8 minutes. After fragmentation, first strand cDNA synthesis was performed using random primers and reverse transcriptase, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments then went through end repair and overhang A addition reactions followed by the ligation of the RNA Adapters. Finally, the products were purified and enriched using 12 PCR cycles to create the final cDNA sequencing library.

value: 9 true leaves

tag: accession

value: F2:8230 x 6195 (female x male)

value: aerial shoot


title: F2 Sample 10 (Technical Replicate 2)


title: F2 Sample 98 (Technical Replicate 2)


title: F2 Sample 85 (Technical Replicate 2)


title: F2 Sample 182


title: F2 Sample 29 (Technical Replicate 2)


title: F2 Sample 108 (Technical Replicate 2)


title: F2 Sample 183


title: F2 Sample 181


title: ChIP-seq analysis of H3K4me1 in Huh7 cells ( CoV )

description: ChIP-seq


title: PFC_individual_1

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: MD

address: 855 N. Wolfe St., Rangos 570

department: Center for Epigenetics

institute: Johns Hopkins

description:
SAMN04568232
SRP072071
SRX1648239

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
ITEX
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format. Diverse content: output from processing pipeline described in manuscript

source_name: pre frontal cortex

extract_protocol:
Epicentre DNA extraction kit
Illumina TruSeq, NEBNext

tag: cancer / normal

value: normal

tag: passage


title: PFC_individual_2

description:
SAMN04568233
SRP072071
SRX1652938


title: F2 Sample 179 (Technical Replicate 1)


title: F2 Sample 180


title: ChIP-seq analysis of H3K36ac in Huh7 cells ( CoV )

description: ChIP-seq


title: F2 Sample 178


title: F2 Sample 174


title: F2 Sample 175


title: F2 Sample 176


title: F2 Sample 173


title: F2 Sample 172


title: F2 Sample 177


title: F2 Sample 171


title: F2 Sample 179 (Technical Replicate 2)


title: F2 Sample 13 (Technical Replicate 2)


title: F2 Sample 168 (Technical Replicate 2)


title: F2 Sample 102 (Technical Replicate 2)


title: F2 Sample 162


title: F2 Sample 169


title: F2 Sample 165


title: F2 Sample 167


title: F2 Sample 163


title: F2 Sample 160


title: F2 Sample 158


title: F2 Sample 159


title: F2 Sample 166


title: F2 Sample 168 (Technical Replicate 1)


title: F2 Sample 164


title: F2 Sample 161


title: F2 Sample 170


title: F2 Sample 157


title: F2 Sample 155


title: F2 Sample 156


title: F2 Sample 151


title: F2 Sample 150


title: F2 Sample 152


title: F2 Sample 154


title: F2 Sample 153


title: F2 Sample 149


title: F2 Sample 147


title: F2 Sample 148


title: F2 Sample 144


title: F2 Sample 146


title: F2 Sample 143


title: F2 Sample 145


title: F2 Sample 142


title: F2 Sample 141


title: F2 Sample 140


title: F2 Sample 139


title: F2 Sample 138


title: F2 Sample 137


title: F2 Sample 133


title: F2 Sample 134


title: F2 Sample 131


title: F2 Sample 132


title: F2 Sample 135


title: F2 Sample 123


title: F2 Sample 128


title: F2 Sample 122


title: F2 Sample 136


title: F2 Sample 127


title: F2 Sample 126


title: F2 Sample 130


title: F2 Sample 120


title: F2 Sample 119


title: F2 Sample 121


title: F2 Sample 116


title: F2 Sample 124


title: F2 Sample 117


title: F2 Sample 115


title: F2 Sample 125


title: F2 Sample 114


title: F2 Sample 118


title: F2 Sample 113


title: F2 Sample 112


title: F2 Sample 129


title: F2 Sample 111


title: F2 Sample 110


title: F2 Sample 106


title: F2 Sample 108 (Technical Replicate 1)


title: F2 Sample 107


title: F2 Sample 104


title: F2 Sample 101


title: F2 Sample 103


title: F2 Sample 105


title: F2 Sample 100


title: F2 Sample 97


title: F2 Sample 95


title: F2 Sample 98 (Technical Replicate 1)


title: F2 Sample 99


title: F2 Sample 94


title: F2 Sample 92


title: F2 Sample 91


title: F2 Sample 93


title: F2 Sample 87


title: F2 Sample 86


title: F2 Sample 85 (Technical Replicate 1)


title: F2 Sample 84


title: F2 Sample 83


title: F2 Sample 109


title: F2 Sample 82


title: F2 Sample 81


title: F2 Sample 102 (Technical Replicate 1)


title: F2 Sample 80


title: F2 Sample 78


title: F2 Sample 79


title: F2 Sample 96


title: F2 Sample 76


title: F2 Sample 90


title: F2 Sample 88


title: F2 Sample 74


title: F2 Sample 73


title: F2 Sample 89


title: F2 Sample 70


title: F2 Sample 72


title: F2 Sample 68


title: F2 Sample 67


title: F2 Sample 64


title: F2 Sample 65


title: F2 Sample 69


title: F2 Sample 63


title: F2 Sample 62


title: F2 Sample 61


title: Input R3

city: Shanghai

first: Hongxing

last: Yang

address: 3888 Chenhua Rd, Songjiang District

institute: Shanghai Chenshan Botanical Garden

description: Input DNA

data_processing:
Raw reads were preprocessed to remove adapters, as well as to filter out low-quality and short (<50bp) reads.
Processed reads were aligned against the Arabidopsis thaliana reference genome using Bowtie (version 2.2.3), with only uniquely aligned reads retained and duplication redundancy removed.
Peak-calling were performed using MACS (version 1.4.2) (Zhang et al., 2008), and between-sample differential bindings were evaluated using MAnorm (Shao et al., 2012).
Significant peak regions were defined as those showing >2-fold increase in binding strength (as measured by normalized M values) in the heat-stressed samples compared with controls, and with p-values <0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files, read coverage across genomic regions

source_name: 13d-old seedlings

growth_protocol: Seeds were sow directly on 1/2 MS medium (with 1.2% sucrose and 0.7% agar, PH5.7) and stratified at 4 0C for two days, then transferred to illumination incubator with stable condition (22 0C, 16/8 h day/night photoperiod).

extract_protocol:
Protein A agarose beads (Millipore) with MYC antibody (Sigma) were used to precipitate the DNA.
The ChIP-DNA and input-DNA libraries were constructed and sequenced with Illumina HiSeq3000.

treatment_protocol: 13-day-old seedlings of 35S::MYC-bZIP28 plants were subjected to heat stress (42 0C for 1 hour). The stressed materials and non-stressed controls were fixed with 1% Formaldehyde solution for 2 times, 10 min each time, then glycine was added to a concentration of 0.125M to stop the reaction.

value: treated at 42C for 1h

value: seedlings

tag: developmental stage

value: 13 day old

tag: ecotype


title: Heat R3

description: Protein A agarose beads (Millipore) with MYC antibody (Sigma) were used to precipitate the DNA.


title: F2 Sample 77


title: F2 Sample 59


title: F2 Sample 58


title: F2 Sample 75


title: Heat R2


title: F2 Sample 71


title: Heat R1


title: Input R2

description: Input DNA


title: F2 Sample 55


title: F2 Sample 66


title: Control

value: control


title: Input R1

description: Input DNA


title: F2 Sample 52


title: F2 Sample 50


title: bzip28bzip60 LF3h rep2

data_processing:
RNA-seq reads were aligned to the Arabidopsis thaliana reference genome using TopHat (version 2.0.13)
Uniquely aligned reads were counted for each annotated gene using the program htseq-count from the python package HTSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_readCount.txt: Tab-delimited text file with each row representing a gene and each column a sample; sample names were shown on the head line (Abbr.: RL, rosette leaf; EF, early flower; LF, late flower)

source_name: flower buds at stages 10-12

growth_protocol: Seeds were sown into soil before stratified at 4 0C for two days, and cultivated under standard growth conditions (22 0C, 16/8 h day/night photoperiod, 60% humidity).

extract_protocol:
Plant materials were ground in liquid nitrogen, and total RNA was extracted with Trizol.
The cDNA libraries were constructed and sequenced with Illumina HiSeq3000.

treatment_protocol: Flowering plants were treated at 37 0C for 3 hours, and the control were taken at 22C. After heat shock, early flower (EF), late flower (LF) and rosette leaf (RL) were collected immediately and put into the liquid nitrogen.

value: bzip28 bzip60

value: treated at 37C for 3h

value: flower bud

value: flower stages 10-12


title: bzip28bzip60 LF3h rep3


title: F2 Sample 54


title: F2 Sample 53


title: F2 Sample 49


title: bzip28bzip60 LF0h rep3


title: bzip28bzip60 LF0h rep2


title: F2 Sample 51


title: bzip28bzip60 LF3h rep1


title: F2 Sample 47


title: F2 Sample 46


title: F2 Sample 45


title: bzip28bzip60 EF3h rep2

source_name: flower buds at stages 1-9

value: flower stages 1-9


title: bzip28bzip60 EF3h rep1


title: F2 Sample 44


title: F2 Sample 56


title: bzip28bzip60 EF3h rep3


title: F2 Sample 48


title: bzip28bzip60 EF0h rep3


title: F2 Sample 43


title: F2 Sample 42


title: bzip28bzip60 EF0h rep2


title: F2 Sample 41


title: bzip28bzip60 RL3h rep3

source_name: rosette leaves at flower stages 1-9

value: rosette leaf


title: bzip28bzip60 EF0h rep1


title: F2 Sample 40


title: bzip28bzip60 LF0h rep1


title: bzip28bzip60 RL3h rep2


title: bzip28bzip60 RL3h rep1


title: F2 Sample 39


title: F2 Sample 38


title: F2 Sample 37


title: bzip28bzip60 RL0h rep3


title: F2 Sample 35


title: bzip28bzip60 RL0h rep1


title: WT LF3h rep3

value: Wild-type


title: F2 Sample 34


title: F2 Sample 36


title: F2 Sample 60


title: F2 Sample 31


title: WT LF0h rep3


title: WT LF0h rep2


title: WT LF3h rep2


title: bzip28bzip60 RL0h rep2


title: F2 Sample 30


title: F2 Sample 32


title: WT EF3h rep3


title: WT LF0h rep1