title: Setdb1_WT_5hmC_capture-seq

description: hmC capture and sequencing

data_processing:
Basecalls performed using CASAVA version 1.4
hmC reads were aligned to the mm9 genome assembly using Bowtie keeping only uniquely mapping reads (max number of mismatches is 2)
Non-monoclonal reads were filtered out using the Picard software
Wig files c generated by caclulating reads per 100bp bin and per million reads.
Genome_build: mm9

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA was fragmented by sonication of harvested mESCs and size selected (~300bp). The purified DNA was treated with β-glucosyltransferase (β-GT), which transfers an azide-glucose to 5-hmC. The purified products are then biotinylated by click chemistry. This allows the labelled 5hmC containing DNA fragments to be captured by using streptavidin beads. The DNA is purified and sequenced following standard protocols from Illumina.


title: LIN-42GFP_1

status: Public on Jun 03 2014

type: SRA

city: Cold Spring Harbor

first: Roberto

last: Perales

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Raw reads from the ChIP-seq and input control sequences were aligned to the ce10 version of the C elegans genome using the bowtie2 algorithm and parameters that were optimized to detect reads with approximately 3 mismatches per read and no more than 10 alignments genome-wide (-k10 -N 1)
Uniquely aligned reads were selected for input to the MACS peak calling algorithm, version 1.4, which automatically removes any duplicate sequences before calling ChIP peaks
Custom scripts were used to annotate the high confidence peaks against the Refseq list of gene models for ce10, downloaded from the UCSC genome database in April of 2013, which was supplemented with the positions of all worm microRNA genes obtained from the Wormbase genome database in April of 2013.
Genome_build: ce10
Supplementary_files_format_and_content: peaks

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Whoel animal extract

growth_protocol: Worms were grown and staged on NGM plates with bacterial OP50 food at 20º

extract_protocol:
Staged worms were washed twice with M9 buffer and freezed in liquid nitrogen. Frozan worms were crushed using a pestle and a mortar and resuspended in Chip buffer. Extracts were sonicated and precleared before ChIP experiments.
Libraires were made followinf the recommended Illumina protocol for TruSeq Chip sample preparation guide (part #15023092 Rev A, August 2012).

tag: strain

tag: tag

value: GFP

tag: antibody

value: anti GFP (abcam 290)


title: LIN-42GFP_2


title: LIN-42

value: anti LIN-42(KEA/11 Rabbit 2, PrimmBiotech)


title: Setdb1_CKO__5hmC_capture-seq

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

country: Switzerland

institute: Uiversity Hospital Zurich

description: hmC capture and sequencing

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown on gelatinized plates in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine.

treatment_protocol: Setdb1 CKO cells were treated with 800nM of 4-OHT for 4 days and further cultured without treatment for 2 days to induce Setdb1 deletion

tag: genotype

value: Setdb1 KO

tag: cell type

value: mouse embryonic stem cells


title: Input 2


title: Setdb1_WT_methylome

description: bisulfite-converted genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.4
MethylC-Seq reads were mapped as previously described (Lister et al., Nature, 2009). Briefly, reads were trimmed until encountering a base with PHRED score <= 2 and bases near the 3' end were trimmed if the adapter sequence was included. For the purpose of mapping, all cytosines were computationally converted to thymines, to be reverted back to their original state after mapping. The Bowtie program(Langmead et al. 2009) was then used to align these computationally converted reads to computationally converted copies of hg18. Non-uniquely mapping reads were discarded
Non-monoclonal reads were filtered out using the Picard software
Using the Samtools Pileup command, for each genomic position the number of reads with match and mismatch were counted in a strand sepcific manner, more specifically, the number of methylated and non-methylated reads per CpG were determined. Individual bases with Phred score < 20 were filtered out. The genome was then divided up into bins of 100 bp and the CpG methylation ratio was calculated by capturing the number of methylated CpG reads in comparison to all reads at CpG for each bin by combining the two replicates and by combining plus- and minus-strand. The methylation ratios per 100bp were used to compose bigwig files. Only bins are reported with total CpG read numbers of > 4.
Genome_build: mm9

extract_protocol:
Genomic DNA was extracted from mESCs and was spiked in with unmethylated lambda DNA (Promega). The DNA was fragmented by sonication.
The DNA was fragmented by sonication. Purified DNA fragments were end-repaired. After A-tailing reaction, fragments were ligated to paired-end cytosine-methylated adapters provided by Illumina. Size-selected adaptor-ligated DNA was treated with sodium bisulfite using the EZ DNA methylation-Gold Kit (Zymo Research). The resulting DNA molecules were enriched by PCR, purified, and sequenced following standard protocols from Illumina.

value: wildtype


title: Input replicate A (ESC)

city: New York

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were aligned to the genome (version mm9) using bowtie2 with standard parameters
The following reads were removed for down-stream analysis: mitochondrial genome, random chromosomes, mapping quality < 2, those with XS: flag in the bam file
Peak calling was performed with MACS (1.4.2), only peaks that were called in both replicates were used for downstream analyses
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage module of deepTools (https://github.com/fidelram/deepTools), normalizing to 1x coverage.

source_name: Embryonic stem cells

growth_protocol: The feeder-independent mouse male ES cell line WT26 (a kind gift from the lab of  T. Jenuwein), was grown on gelatin-coated dishes in ES cell culture media KnockOut-DMEM supplemented with 1% L-glutamine, 1% penicillin/streptavidin, 1% Non- essential amino acids, 1% Sodium Pyruvate, 1% 2-mercaptoethanol. All ESC media contained 15% FBS and 1000 U/ml (for feeder free) or 2000U/ml (for feeder-dependent) of leukemia inhibitory factor (LIF). NPC lines were derived from previously mentioned ES cell lines and cultured in N2B27 medium (StemCell Sciences) containing 10 ng/mL EGF and FGF (Preprotech) on gelatin-coated flasks. The cells were kept in a humidified incubator at 37°C and 5% CO2 and were passed when reaching 80-90% confluency.

extract_protocol:
Nuclei were isolated, resuspended in RIPA Lysis Buffer, sheared using Diagenode Bioruptor Plus Sonicator and chromatin was immunoprecipitated with the respective antibodies.
Library preparation was carried out following Illumina standard protocols for paired-end sequencing

treatment_protocol: Mouse ES cells were differentiated into neuronal progenitor cells. In brief, ESC (1x106 cells) were deprived of feeders and plated on 0.1 % gelatin-coated dishes in N2B27 medium and grown for 7 days. During that period of time, the medium was changed every day. Next, cells were dissociated from the plate using accutase and approximately 3 x 10e6 cells were plated in a petri dish to induce formation of embryoid bodies (in N2B27 medium supplemented with 10 ng/ml EGF and FGF2). After 72 hours, embryoid bodies were transferred to 0.1 % gelatin-coated dishes and allowed to attach to the bottom leading to expansion of NPC cells. NPC lines were maintained in N2B27 medium supplemented with EGF and FGF2 (10ng/ml each), on 0.1 % gelatin- coated flasks.

tag: passages

tag: chip antibody

tag: cell line


title: Setdb1_CKO_H3K9me3_ChIPSeq

description: ChIP-Seq reads were mapped by bowtie to mm9, keeping only uniquely mapping reads and discarding all but one of clonal reads. Wig files combining H3K9m3 ChIP-seq and the respective input were generated by caclulating reads per 100bp bin for ChIP and 500bp bin for Input and per million reads. The ChIP bin values were divided by the input bin values.

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie keeping only uniquely mapping reads (max number of mismatches is 2)
Non-monoclonal reads were filtered out using the Picard software
Wig files combining H3K9m3 ChIP-seq and the respective input were generated by caclulating reads per 100bp bin for ChIP and 500bp bin for Input and per million reads. The ChIP bin values were divided by the input bin values.
Genome_build: mm9

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

value: Setdb1 conditional KO

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

tag: chip antibody lot #


title: Setdb1_CKO_methylome

description: bisulfite-converted genomic DNA


title: Setdb1_WT_H3K9me3_ChIPSeq


title: DKO_RNASeq.rep2

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads trimmed to 36bp length and were aligned to the mm9 genome assembly using TopHat giving rise to bam files
BigWig files were created based on TopHat output, as Bam files were used to calculate read density file using the genomeCoverage script from the Bedtools suite. For comparability, read density numbers were normalized by a factor based on total number of reads per sample
Genome_build: mm9

molecule: total RNA

growth_protocol: mESCs were grown in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to manufacturer's instruction. Ribosomal RNA was removed using RiboMinus Eukatyote Kit (Invitrogen).
The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al. 2009).

value: Dnmt3a/3b DKO


title: DKO_RNASeq.rep1


title: H3K9me3_ChIPSeq 1

description: ChIP-Seq reads were mapped by bowtie to mm9, keeping only uniquely mapping reads and discarding all but one of clonal reads. Wig files combining H3K9m3 ChIP-seq and the respective input were generated using the SPP package for R and binning the data into non-overlapping 100bp bins.

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie keeping only uniquely mapping reads (max number of mismatches is 2)
Non-monoclonal reads were filtered out using the Picard software
wig files were generated by combining CHIP and respective Input files using SPP for R
Genome_build: mm9

value: H3K9me3 (Diagenode. Cat no. pAb-056-050, Lot# A93-0041)

value: Diagenode


title: H3K9me3_ChIPSeq 2


title: H3.3 KD + H3.2 mRNA SCNT embryos

status: Public on Jun 02 2014

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were aligned to mm9 using TopHat with default parameters
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript

source_name: 4-cell SCNT embryos

extract_protocol: Illumina TruSeq, SR 51

tag: tissue

value: 4-cell SCNT embryos

tag: treatment

value: H3.3 knockdown + H3.3mRNA


title: 4-cell NT embryos_H3.3KD

source_name: 4-cell NT embryos

value: 4-cell NT embryos

value: H3.3 knockdown


title: 4-cell NT embryos_H3.3KD+H3.3mRNA


title: Luciferase 4-cell SCNT embryos

value: luciferase


title: sRNAs from KSHV-infected BC-3 cells

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

data_processing:
Base calling was performed using CASAVA v.1.8.2
Sequencing reads were preprocessed using the Dustmasker program and FASTX-Toolkit to filter out low complexity sequences and to remove instances of the 3' adapter respectively. Degenerate bases incorporated during the library preparation protocol were also trimmed.
Remaining reads >=15 nt in length were then mapped simultaneously to the human and KSHV genomes using Bowtie 0.12.7. Up to 2 mismatches in total with no more than 1 mismatch in the first 15 nucleotides of each read were permitted. In addition, only alignments from the lowest mismatch-stratum were recorded and reads that could map to more than 50 loci were discarded.
To obtain a global overview of each library, several non-coding RNA families were successively annotated using BEDTools 2.16.2, by comparing their genomic coordinates to those of the aligned reads. Expressed human and KSHV miRNAs (miRBase19) were thus identified, followed by human rRNAs, tRNAs, snRNAs, snoRNAs and miscRNAs (UCSC repository or Ensembl r.68). During the quantification process, multiple mapped reads were weighted by the number of mapping sites in genomic features of interest.
Furthermore, two groups of hypothetical viral genomic features, antisense miRNAs (AS-miRs) and miRNA offsets (moRs), were created and submitted to the same annotation process. KSHV antisense miRNAs were defined as opposite sequences to known miRNAs, while moR-5p and moR-3p were defined as being the immediate 20 nt long flanking sequences surrounding the mature forms of each KSHV pre-miRNA.
Finally, less stringent mapping parameters were applied for the detailed analysis of KSHV miRNA isoforms. Indeed, reads with up to 9mm in total were allowed in order to detect more miRNA altered forms: full length, 3'-trimmed, 3'-tailed, 5'-trimmed, 5'-tailed and every possible combination; whether they are identical or different to the template sequence.
Genome_build: GRCh37/hg19 + NC_009333.1
Supplementary_files_format_and_content: *-annot.txt: Tab-delimited files with the detailed annotation of sequenced KSHV miRs, AS-miRs and moRs are respectively provided for each library (Genomic_Feature, Genomic_Position, Sequence_Count, Sequence, Sequence_Length, Sequence_GenomicPosition, Sequence_Category, Sequence_MmNb, Sequence_MmDescription). See Series supplementary file README-annot.txt.

organism: Homo sapiens

source_name: BC-3 cell line

growth_protocol: All cell lines were cultured in a humidified 5% CO2 atmosphere at 37°C in RPMI 1640 medium containing 10% fetal calf serum (FCS). In addition, DG-75-K10/12 were grown with 7.5 μg/mL blasticidin (for gene insert maintenance) and BC-3 media contained 50 μM mercaptoethanol.

extract_protocol:
Total RNA was extracted from cells using Tri-reagent (MRC, Inc)
Libraries were prepared as previously described with some modifications (Pfeffer, S. 2007. Identification of virally encoded microRNAs. Methods Enzymol. 427:51-63). Briefly, 10 μg of total RNA from BCBL-1, BC-3 and DG-75-K10/12 were size fractionated on a 17.5% urea denaturing polyacrylamide gel. The 19-33 nt band was excised, crushed and solved in 2 volumes of 0.3 M NaCl by overnight agitation at 4°C.
Small RNAs were sequentially ligated to degenerate 3' and 5' adapters, with T4 RNA Ligase 2 and T4 RNA Ligase 1, respectively, to minimize ligation bias due to secondary structure formation. Prior to this, the 3' adapter was adenylated using the 5' DNA adenlylation kit according to the manufacturer's recommendations (New England Biolab, #E2610S).
After each ligation step, the product was purified in denaturing polyacrylamide gel. In order to generate cDNA libraries, RNA was reverse transcribed with SuperScript III RT (Invitrogen) and primer GCCTGGCACCCGAGAATTCCA, then amplified by PCR with forward primer AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA and different reverse primers for multiplex sequencing (RPI1, RPI4 and RPI5, Illumina PCR primers) during 14 or 17 cycles (for BC-3, or DG-75-K10/12 and BCBL-1 libraries respectively) (45 sec at 94°C, 85 sec at 50°C and 60 sec at 72°C). PCR products were sent for large-scale sequencing

tag: infection

value: KSHV

value: PEL (primary effusion lymphoma) cell line


title: AR_ChIP-seq_DU145 AR C562S +FoxA1

city: Chicago

first: Hong-Jian

last: Jin

state: IL - Illinois

address: 303 E Superior St

department: Medicine

institute: Northwestern University

description:
ChIP-seq
m60

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.61
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: Columns in peaks.txt contain information about each peak:  Column 1: PeakID - a unique name for each peak.   Column 2: chr - chromosome where peak is located.   Column 3: starting position of peak.   Column 4: ending position of peak.   Column 5: Strand (+/-).   Column 6: Normalized Tag Counts - number of tags found at the peak, normalized to 10 million total mapped tags (or defined by the user).   Column 7:  Focus Ratio - fraction of tags found appropriately upstream and downstream of the peak center (see below).   Column 8: Peak score (position adjusted reads from initial peak region - reads per position may be limited).   Columns 9+: Statistics and Data from filtering.

source_name: AR_ChIP-seq_DU145 AR C562S +FoxA1

growth_protocol: DU145 cells were routinely maintained in RPMI supplemented with 10% FBS plus 1% antibiotics (penicillin and streptomycin)

extract_protocol:
Antibodies were from abcam (cat#ab23738,GR77830-1) and Millipore (cat#06-680, lot#JBC1939961) and ChIP was performed using 5e6-10e6 cells per reaction. Chromatin was fixed in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were washed twice in PBS and scraped before treatment of cell lysis buffer with protease inhibitors on ice. Pelleted nuclei were sheared to 200-700bp using an ultrasonic sonicator (Misonix). ChIP was done with 5 micrograms of antibody.  FAIRE  analysis  was  performed  according  to  the  protocol  published  by  Giresi et al .
Libraries were prepared according to Bioo Scientific's instructions accompanying the DNA Sample Kit (Part# 514101). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 or Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: DU145 AR cells were infected with LacZ or FOXA1 adenovirus for 48 hours to overexpress FOXA1 protein prior to collect cell pellets for ChIP or FAIRE experiments

value: prostate cancer cell line DU145

tag: ectopic expression

value: AR C562S + FoxA1

value: Anti-Androgen Receptor (AR) Antibody, PG-21 (Millipore, cat#06-680, lot#JBC1939961)


title: AR_ChIP-seq_DU145 AR Q640X+FoxA1

description:
ChIP-seq
m62

source_name: AR_ChIP-seq_DU145 AR Q640X+FoxA1

value: AR Q640X + FoxA1


title: sRNAs from DG-75 cells stably expressing KSHV pri-miR-K10/12

description: pri-miR-K10/12 comprises the ten KSHV intronic pre-miRNAs (pre-miR-K1 to -K9 and pre-miR-K11)

source_name: DG-75 cell line

value: DG-75 stably expressing KSHV pri-miR-K10/12

value: B-cell line


title: AR_ChIP-seq_DU145 AR C562S

description:
ChIP-seq
m57

source_name: AR_ChIP-seq_DU145 AR C562S

value: AR C562S


title: Input 1

value: GFP


title: FOXA1_ChIP-seq_DU145 AR + FoxA1 high

description:
ChIP-seq
2012-833

source_name: FOXA1_ChIP-seq_DU145 AR + FoxA1 high

value: AR wildtype + FoxA1 high

value: Anti-FOXA1 antibody (Abcam, cat#ab23738,lot# GR77830-1)


title: FOXA1_ChIP-seq_DU145 AR + FoxA1

description:
ChIP-seq
2012-831

source_name: FOXA1_ChIP-seq_DU145 AR + FoxA1

value: AR wildtype + FoxA1


title: AR_ChIP-seq_DU145 AR + FoxA1 high

description:
ChIP-seq
2012-832

source_name: AR_ChIP-seq_DU145 AR + FoxA1 high


title: FOXA1_ChIP-seq_DU145 AR

description:
ChIP-seq
2012-829

source_name: FOXA1_ChIP-seq_DU145 AR

value: AR wildtype


title: OB_H3K4me1125

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding.  Histone peaks were called with a 2-fold enrichment over input instead of 4-fold (for transcription factors) given the nature of histone chip-seq.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: mm9
Supplementary_files_format_and_content: fastq files are the raw sequence files [barcoded lanes (4 each) were concatenated for each sample for simplicity, no other modification was made], bedGraph files are for display in the UCSC genome browser, *replicate_overlap.bed are the resulting peaks found with QuEST and HOMER after normalization between both replicates

source_name: MC3T3-E1 cells differentiated for 15 days

growth_protocol: MC3T3-E1 cells were cultured in alpha MEM with 10% heat-inactivated fetal bovine serum from Hyclone (Logan, UT) and 1% penicillin-streptomycin.  Differentiated cells were cultured in complete media plus 10mM glycerol-2-phosphate and 50ug/mL ascorbic acid for 15 days, changing media every 2-3 days.

extract_protocol: Chromatin immunoprecipitation was performed as described previously (Meyer MB. Mol Endo. 2012).  Briefly, MC3T3-E1 cells were treated for 3 hrs with vehicle or 100nM 1,25(OH)2D3.  Samples were subjected to immunoprecipitation using either a control IgG antibody or the indicated experimental antibody (VDR, RXR, C/EBPβ, RUNX2, H3K5Ac, H3K9Ac, H3K4me1, H3K4me3, or H3K36me3).  For differentiated cells, there was substantial mineralized matrix.  To remove the matrix from the assay, the cell/matrix mix was subjected to 3x 15s pulses with a Polytron Homogenizer (Power Gen 125, Fisher Scientific) while in NCP 1 buffer (Hepes 10mM pH 6.5, EDTA 10mM, EGTA 0.5mM, Triton X-100 0.25%).  The resulting homogenate was centrifuged (200 x g) through a 10% sucrose buffer at a 1:1 ratio (10mM Tris-HCl, 15mM NaCl, 60mM KCl, 1mM EDTA, 10% Sucrose).  Resulting cell pellet was resuspended in NCP 2 buffer (Hepes 10mM pH 6.5, EDTA 1mM, EGTA 0.5mM, NaCl 200mM) and remainder of protocol was followed (Meyer MB. Mol Endo. 2012).  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.  ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols. ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina GAIIx [for all samples sequenced before June, 2011] or the Illumina HiSeq2000 [after June, 2011] sequencers by the University of Wisconsin - Madison DNA Sequencing Facility in the University of Wisconsin- Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver. 3) on an Illumina cBot (Illumina) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver. 3).  Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  Each ChIP sample was repeated in biological replicate in the same manner (minimum of 2 replicates).  Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Cells were treated with 100nM 1,25(OH)2D3 [125] or with ethanol vehicle [Veh] for 3 hours prior to ChIP assay

tag: passage number

value: MC3T3-E1 differentiated for 15 days


title: OB_H3K36me3125


title: OB_H3K9Ac125


title: OB_H3K4me3125


title: AR_ChIP-seq_DU145 AR + FoxA1

description:
ChIP-seq
2012-830

source_name: AR_ChIP-seq_DU145 AR + FoxA1


title: FOXA1_ChIP-seq_DU145 AR C562S+FoxA1

description:
ChIP-seq
m58

source_name: FOXA1_ChIP-seq_DU145 AR C562S+FoxA1

value: AR C562S +FoxA1


title: OB_Runx2125

value: RUNX2 (Santa Cruz, M-70, sc10758, lot# D1411)


title: AR_ChIP-seq_DU145 AR

description:
ChIP-seq
2012-828

source_name: AR_ChIP-seq_DU145 AR


title: 4-cell NT embryos

value: 4-cell NT embryos


title: Input_DU145 Empty Vector

description:
ChIP-seq
2012-1044

source_name: Input_DU145 Empty Vector

value: empty vector

value: none (input)


title: OB_H4K5Ac125


title: sRNAs from KSHV-infected BCBL-1 cells

source_name: BCBL-1 cell line

value: KSHV

value: PEL (primary effusion lymphoma) cell line


title: OB_RXR125

value: RXR (Santa Cruz, ΔN-197, sc-774, lot# G2310)


title: OB_VDR125

value: VDR (Santa Cruz, C-20, sc-1008, lot# A0912)


title: OB_RXRVeh

value: ethanol vehicle


title: FOXA1_ChIP-seq_DU145 AR Q640X+FoxA1

description:
ChIP-seq
m59

source_name: FOXA1_ChIP-seq_DU145 AR Q640X+FoxA1

value: prostate cancer cell line DU145

value: AR Q640X + FoxA1


title: POB_H3K36me3125

source_name: MC3T3-E1 cells


title: AR_ChIP-seq_DU145 AR Q640X

description:
ChIP-seq
m61

source_name: AR_ChIP-seq_DU145 AR Q640X

value: AR Q640X

value: Anti-Androgen Receptor (AR) Antibody, PG-21 (Millipore, cat#06-680, lot#JBC1939961)


title: POB_H3K9Ac125


title: POB_H3K4me3125


title: POB_H3K4me1125


title: POB_Runx2125


title: POB_CEBPb125

value: C/EBPβ (Santa Cruz, C-19, sc-150, lot# F3011)


title: OB_CEBPb125


title: FAIRE_DU145 AR

description:
FAIRE-seq
m98

source_name: FAIRE_DU145 AR

value: AR wildtype


title: FAIRE_DU145 AR + FoxA1

description:
FAIRE-seq
m99

source_name: FAIRE_DU145 AR + FoxA1

value: AR wildtype + FoxA1


title: FAIRE_DU145 AR + FoxA1 high

description:
FAIRE-seq
m100

source_name: FAIRE_DU145 AR + FoxA1 high

value: AR wildtype + FoxA1 high


title: POB_RXR125


title: POB_RXRVeh


title: POB_VDR125


title: AR_ChIP-seq_DU145 AR G568W+FoxA1

description:
ChIP-seq
m84

source_name: AR_ChIP-seq_DU145 AR G568W+FoxA1

value: AR G568W +FoxA1


title: AR_ChIP-seq_DU145 AR G568W

description:
ChIP-seq
m83

source_name: AR_ChIP-seq_DU145 AR G568W

value: AR G568W


title: POB_VDRVeh


title: WT  [ChIP-Seq] 2

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

institute: University of Bern

data_processing:
Basecalls performed using CASAVA version 1.5
Sequence reads were aligned to the M. tuberculosis H37Rv genome (NCBI accession NC_000962.2) using Bowtie with options “-l 28 -best -strata”.
Peaks were analysed using MACS v.1.4 with parameters “-bw 200 -m 10100”.
To determine the level of ChIP-seq enrichment for each feature, an enrichment ratio (ER) was calculated by dividing the read count for the ChIP-seq sample in the wild type strain by the read count for the mutant (control) sample.
Genome_build: ASM19595v1, NC_000962.2

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria

growth_protocol: M. tuberculosis cultures were grown to exponential phase (optical density at 600 nm of 0.4) and cross-linked with 1% formaldehyde for ten minutes at 37°C.

extract_protocol:
Cross-linking was quenched by addition of glycine (125 mM). Cells were then washed twice with Tris-buffered saline (TBS, 20 mM Tris-HCl pH 7.5, 150 mM NaCl), resuspended in 4 ml immunoprecipitation (IP) buffer (50 mM Hepes-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, protease inhibitor cocktail from Roche) and sonicated to shear DNA using Bioruptor (Diagenode). Cell debris was removed by centrifugation and the supernatant used in IP experiments. Nucleo-protein extracts were incubated with 50 μl of rabbit polyclonal anti-PhoP antibodies at 4°C for 2 days on a rotating wheel. Complexes were subsequently precipitated with Dynabeads (Dynal, anti-rabbit, Invitrogen) for three hours at 4°C. Beads were washed twice with IP buffer, once with IP buffer plus 500 mM NaCl, once with buffer III (10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% sodium deoxycholate), once with Tris-EDTA buffer pH 7.5. Elution was performed in 50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS for 40 minutes at 65°C. Samples were finally treated with RNAse A for one hour at 37°C and cross-links were reversed by incubation for two hours at 50°C and for eight hours at 65°C in 0.5x elution buffer with 50 μg Proteinase K (Eurogentec). DNA was purified by phenol-chloroform extraction and quantified by Nanodrop and Qubit fluorometer according to the manufacturer’s recommendations (Invitrogen).
ChIP-Seq Sample Preparation Kit (Illumina), according to the protocol provided by the manufacturer

tag: genotype/variation

value: wild type

value: rabbit polyclonal anti-PhoP

tag: antibody manufacturer

value: Z.E.U. INMUNOTEC S.L.


title: delta-phoP mutant   [ChIP-Seq]

value: isogenic phoP mutant

tag: strain


title: FoxA1_ChIP-seq_shCtrl_R1881

description: Chromatin IP against FoxA1

data_processing:
Reads were aligned to the hg19 reference genome using Eland software (Illumina)
Peak-calling by HOMER v3.8
Genome_build: hg19
Supplementary_files_format_and_content: Columns in peaks.txt contain information about each peak:
Column 1: PeakID - a unique name for each peak
Column 2: chr - chromosome where peak is located
Column 3: starting position of peak
Column 4: ending position of peak
Column 5: Strand (+/-)
Column 6: Normalized Tag Counts - number of tags found at the peak, normalized to 10 million total mapped tags (or defined by the user)
Column 7:  Focus Ratio - fraction of tags found appropriately upstream and downstream of the peak center. (see below)
Column 8: Peak score (position adjusted reads from initial peak region - reads per position may be limited)
Columns 9 +: Statistics and Data from filtering    The bedGraph format is described http://genome.ucsc.edu/goldenPath/help/bedgraph.html

source_name: LNCaP

growth_protocol: LNCaP lines were maintained in RPMI supplemented with 10% FBS.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions.

treatment_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

value: LNCaP

value: control

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#

tag: chip antibody lot#


title: WT  [ChIP-Seq] 1

tag: antibody


title: POB_H4K5Ac125


title: FoxA1_ChIP-seq_shFoxA1_R1881

description: Chromatin IP against FoxA1

value: FoxA1 knockdown

tag: chip antibody


title: WT [RNA-Seq]

description: wild type

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequences were aligned to the M. tuberculosis H37Rv genome (NCBI accession NC_000962.2) using Bowtie2 with default parameters. Read count for all annotated features were obtained with htseq-count program. Regions where genes overlapped were excluded from counting. Reads spanning more than one feature were counted for each feature. Since the RNA library was strand-specific, the orientation of sequence reads had to correspond to the orientation of annotated features to be counted.
Analysis of differential gene expression was carried out using the DESeq package.
Genome_build: ASM19595v1, NC_000962.2
Supplementary_files_format_and_content: Differenctial gene expression results from DESeq.

growth_protocol: Bacteria were grown at 37°C in 7H9 medium (Difco) supplemented with 0.05% Tween 80 and 10% albumin-dextrose-catalase (ADC, Middlebrook) or on 7H10 plates supplemented with 10% ADC. Mycobacterial cultures were grown to exponential phase (OD600=0.5-0.6) and pelleted by centrifugation.

extract_protocol:
Bacteria were resuspended in 1 ml RNA Protect Bacteria Reagent (Qiagen), incubated for 5 min at room temperature and then centrifuged. Bacterial pellets were resuspended in 0.4 ml lysis buffer (0.5% SDS, 20 mM NaAc, 0.1 mM EDTA) and 1 ml phenol:chloroform (pH=4.5) 1:1. Suspensions were transferred to tubes containing glass beads (Qbiogene) and lysed using a ribolyser (Fast-prep instrument) with a three-cycle program (15 sec at speed 6.5 m) including cooling the samples on ice for 5 min between pulses. Samples were then centrifuged and the homogenate was removed from the beads and transferred to a tube containing chloroform:isoamylalcohol 24:1. Tubes were inverted carefully before centrifugation and the upper (aqueous) phase was then transferred to a fresh tube containing 0.3 M Na-acetate (pH=5.5) and isopropanol. Precipitated nucleic acids were collected by centrifugation. The pellets were rinsed with 70% ethanol and air dried before being re-dissolved in RNase-free water. DNA was removed from RNA samples using Turbo DNA free (Ambion) by incubation at 37°C for 1 h. RNA integrity was assessed by agarose gel electrophoresis and absence of contaminating DNA was checked by lack of amplification products after 30 PCR cycles. 10 μg total RNA were treated with 10 U of Terminal 5’-phosphate dependent Exonuclease (Epicentre) for 24 h at 30°C followed by phenol extraction and isopropanol precipitation. Successful preparation of primary transcriptome was confirmed by lack of 23S/16S rRNA bands and presence of intact 5S rRNA  in agarose gels.
100 ng of total RNA were mixed with 5x Fragmentation buffer (Applied Biosystems), incubated for 4 minutes at 70°C and then transferred immediately on ice. RNA was purified using RNAClean XP beads (Beckman Coulter), according to the manufacturer’s recommendations, and subsequently treated with Antarctic phosphatase (New England Biolabs). RNA was then re-phosphorylated at the 5’-end with polynucleotide kinase (New England Biolabs) and purified with Qiagen RNeasy MinElute columns. In order to ensure strand-specificity, v1.5 sRNA adapters (Illumina) were ligated at the 5’- and 3’-ends using RNA ligase. Reverse transcription was carried out using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). Twelve cycles of PCR amplification using Phusion DNA polymerase were then performed and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (2.5 ml) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer prior to sequencing on Illumina HiSeq 2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3.


title: LNCaP Input

description: ChIP input

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.61
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: Columns in peaks.txt contain information about each peak:  Column 1: PeakID - a unique name for each peak   Column 2: chr - chromosome where peak is located  Column 3: starting position of peak  Column 4: ending position of peak  Column 5: Strand (+/-)  Column 6: Normalized Tag Counts - number of tags found at the peak, normalized to 10 million total mapped tags (or defined by the user)  Column 7:  Focus Ratio - fraction of tags found appropriately upstream and downstream of the peak center. (see below)  Column 8: Peak score (position adjusted reads from initial peak region - reads per position may be limited)  Columns 9+: Statistics and Data from filtering    The bedGraph format is described http://genome.ucsc.edu/goldenPath/help/bedgraph.html

growth_protocol: LNCaP cellss were maintained in RPMI supplemented with 10% FBS.

extract_protocol:
Antibodies were from abcam (cat#ab23738,GR77830-1) and Millipore (cat#06-680, lot#JBC1939961) and ChIP was performed using 5e6-10e6 cells per reaction. Chromatin was fixed in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were washed twice in PBS and scraped before treatment of cell lysis buffer with protease inhibitors on ice. Pelleted nuclei were sheared to 200-700bp using an ultrasonic sonicator (Misonix). ChIP was done with 5 micrograms of antibody.  FAIRE  analysis  was  performed  according  to  the  protocol  published  by  Giresi et al .
Libraries were prepared according to Bioo Scientific's instructions accompanying the DNA Sample Kit (Part# 514101). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiScan following the manufacturer's protocols.

tag: cell line

value: none (input)


title: AR_ChIP-seq_shFoxA1_R1881, biological replicate 2

description: Chromatin IP against AR

value: anti-AR

value: Millipore


title: OB_VDRVeh

value: VDR (Santa Cruz, C-20, sc-1008, lot# A0912)

value: MC3T3-E1 differentiated for 15 days

value: ethanol vehicle


title: phoP-KO [RNA-Seq]

description: delta-phoP-mutant


title: AR_ChIP-seq_shCtrl_R1881, biological replicate 2

description: Chromatin IP against AR


title: AR_ChIP-seq_shFoxA1_R1881, biological replicate 1

description: Chromatin IP against AR

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions.
Instrument name: Illumina HiScan.


title: AR_ChIP-seq_shCtrl_R1881, biological replicate 1

description: Chromatin IP against AR


title: AR_ChIP-seq_shCtrl_hormone-deprived

description: Chromatin IP against AR

data_processing:
Reads were aligned to the reference genome using Eland software (Illumina)
Peak-calling by HOMER v3.8
Genome_build: hg19
Supplementary_files_format_and_content: Columns in peaks.txt contain information about each peak:
Column 1: PeakID - a unique name for each peak
Column 2: chr - chromosome where peak is located
Column 3: starting position of peak
Column 4: ending position of peak
Column 5: Strand (+/-)
Column 6: Normalized Tag Counts - number of tags found at the peak, normalized to 10 million total mapped tags (or defined by the user)
Column 7: Focus Ratio - fraction of tags found appropriately upstream and downstream of the peak center. (see below)
Column 8: Peak score (position adjusted reads from initial peak region - reads per position may be limited)
Columns 9 +: Statistics and Data from filtering
The bedGraph format is described http://genome.ucsc.edu/goldenPath/help/bedgraph.html

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions

tag: treatment protocol

value: hormone-deprived


title: AR_ChIP-seq_shFoxA1_hormone-deprived

description: Chromatin IP against AR


title: cac1 mutant biorep1 (521-1)

status: Public on Jun 01 2014

city: Boston

first: Steve

last: Buratowski

state: MA

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: nascent, Pol II associated RNA

data_processing:
data analysis protocol: see Churchman et al, Nature  2011
data analysis code and resources: https://github.com/churchmanlab/NET-seq
strip_primer_tails
filter_tRNA_rRNA
align_to_genome
shard_alignments_by_chr
analyze_shards
collapse_shards
calculate RPKM from ORF-T definitions
calculate RPKM from ncRNA definitions
Genome_build: S.cerevisae transcriptome GFF (no build)
Supplementary_files_format_and_content: RPKM

organism: Saccharomyces cerevisiae

source_name: cac1 mutant biorep1 (521-1)

growth_protocol: YPD media, mid-log growth of S. cerevisiae strains

extract_protocol:
see Churchman et al, Nature  2011
see Churchman et al, Nature  2011

tag: growth phase

value: mid-log

value: YSB3062 Rpb3-FLAG cac1Δ


title: cac3 mutant biorep2 (511-2)

description: nascent, Pol II associated RNA

source_name: cac3 mutant biorep2 (511-2)

value: YSB3064 Rpb3-FLAG cac3Δ


title: cac3 mutant biorep1 (511-1)

description: nascent, Pol II associated RNA

source_name: cac3 mutant biorep1 (511-1)


title: cac2 mutant biorep1 (522-1)

description: nascent, Pol II associated RNA

source_name: cac2 mutant biorep1 (522-1)

value: YSB3063 Rpb3-FLAG cac2Δ


title: wild-type biorep1 (490-1)

description: nascent, Pol II associated RNA

source_name: wild-type biorep1 (490-1)

value: YSC0001 Rpb3-FLAG


title: cac2 mutant biorep2 (522-2)

description: nascent, Pol II associated RNA

source_name: cac2 mutant biorep2 (522-2)


title: cac1 mutant biorep2 (521-2)

description: nascent, Pol II associated RNA

source_name: cac1 mutant biorep2 (521-2)


title: wild-type biorep2 (490-2)

description: nascent, Pol II associated RNA

source_name: wild-type biorep2 (490-2)


title: DBVPG1373_FAIRE_replicate1

city: Worcester

first: Caitlin

middle: F

last: Connelly

address: 364 Plantation Street, LRB

department: Biochemistry & Molecular Pharmacology

institute: University of Massachusetts Medical School

description: Sample 3

data_processing:
library strategy: FAIRE-seq
Basecalls performed using CASAVA
Reads were aligned to the S. cerevisiae UWOPS05_217_3 and DBVPG1373 strain assemblies from Skelly et al. Genome Research 2011, and to the S. paradoxus CBS432 assembly from Liti et al. Nature 2009 using bwa
Reads were summed at divergent sites between the two species across each Nucleosome-free region (for FAIRE samples), or each gene (for RNA samples).
Genome_build: sacCer3
Supplementary_files_format_and_content: bed files contain the positional information for each NFR (for FAIRE data) or gene (for RNA data), and the score column contains the summed counts at divergent sites between the two species.  Note that for CBS432 samples, there are two processed files for each sample, one summing across the divergent sites between CBS432 and DBVPG1373 (DBVdivsites files) and one summing across the divergent sites between CBS432 and UWOPS05_217_3 (UWdivsites files).

growth_protocol: 65 ml of yeast was grown in YEPD to mid-log phase. 50 ml was used for FAIRE (Formaldehyde-assisted Isolation of Regulatory Elements).

extract_protocol:
The protocol was followed as described in Simon et al., Curr Protoc Mol Biol, 2013, with minor changes.  Briefly, cells were suspended in cold lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA) and 2 g glass beads were added to the tube.  Cells were vortexed for 30 seconds 8 times, cooling on ice for 30 seconds in between each pulse.  The cell lysates were sonicated using the Fisher Scientific Sonic Dismembrator Model 100 for three cycles of 15 one-second bursts with 1 second rest in between, keeping the cells on ice for at least 30 seconds between cycles. The remainder of the protocol was followed as in Simon et al. 2013.  Briefly, cells were pelleted at 20,000g for 5 minutes to remove cell debris.  2 phenol/chloroform extractions were performed, isolating the aqueous layer, followed by a chloroform extraction.  Samples were ethanol precipitated, and resuspended in water.  Samples were then treated with RNaseA for 30 minutes, followed by treatment with Proteinase K overnight.  Samples were then purified using Zymo spin columns.
Libraries were constructed for the FAIRE samples using the Illumina TruSeq DNA kit, starting with approximately 200 ng FAIRE DNA, following their standard kit protocol but omitting the fragmentation step.

treatment_protocol: The cells were fixed with 1% formaldehyde for 35 minutes with mixing and quenched with 125 mM glycine, as in Simon et al., Curr Protoc Mol Biol, 2013.

tag: ploidy

value: haploid

value: log-phase


title: UWOPS05_217_3_FAIRE_replicate1

description: Sample 1


title: DBVPG1373_RNA_replicate2

description: Sample 14

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the S. cerevisiae UWOPS05_217_3 and DBVPG1373 strain assemblies from Skelly et al. Genome Research 2011, and to the S. paradoxus CBS432 assembly from Liti et al. Nature 2009 using bwa
Reads were summed at divergent sites between the two species across each Nucleosome-free region (for FAIRE samples), or each gene (for RNA samples).
Genome_build: sacCer3
Supplementary_files_format_and_content: bed files contain the positional information for each NFR (for FAIRE data) or gene (for RNA data), and the score column contains the summed counts at divergent sites between the two species.  Note that for CBS432 samples, there are two processed files for each sample, one summing across the divergent sites between CBS432 and DBVPG1373 (DBVdivsites files) and one summing across the divergent sites between CBS432 and UWOPS05_217_3 (UWdivsites files).

molecule: polyA RNA

growth_protocol: 65 ml of yeast was grown in YEPD to mid-log phase. 15 ml was used for RNA-seq.

extract_protocol:
RNA was isolated using the hot phenol method (Rose MD et al., Methods in yeast genetics: A laboratory course manual, 1990).  Total RNA was treated with Turbo DNase-free prior to library construction.
RNA libraries were prepared using the Illumina TruSeq RNA kit, following their standard protocol.


title: UWOPS05_217_3_RNA_replicate2

description: Sample 12


title: DBVPG1373_FAIRE_replicate2

description: Sample 4


title: CBS432_FAIRE_replicate2

description: Sample 6


title: CBS432_RNA_replicate1

description: Sample 15


title: DBVPG1373_RNA_replicate1

description: Sample 13


title: CBS432_FAIRE_replicate1

description: Sample 5


title: CBS432_RNA_replicate2

description: Sample 16


title: UWOPS05_217_3_RNA_replicate1

description: Sample 11


title: GFP ChIP-Seq

city: Stanford

first: Eunkyoo

last: Oh

state: CA

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

description: Chromatin IP against GFP transcription factor

data_processing:
ARF6 binding peaks were identified using ChIP-Seq analysis R (CSAR) software with parameters (backg=10, norm=-1, test="Ratio", times=1e6, digits=2) (Muino et al., 2011)
Genome_build: TAIR9

organism: Arabidopsis thaliana

source_name: Etiolated 35S::GFP-Myc seedlings

growth_protocol: Transgenic plants expressiong ARF6-Myc driven by native ARF6 promoter (ARF6p::ARF6-Myc) are grown in the dark for 5 days.

extract_protocol: Lysates were clarified from sonicated nuclei and ARF6-Myc-DNA complexes were isolated with anti-Myc antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

tag: tissue

value: Etiolated seedlings

value: anti-myc antibody


title: rif1 delta replicate 2

city: Los Angeles

first: Jared

middle: M

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

description: Barcode: ACTGT

data_processing:
PE reads were joined and barcodes split using the Fast-X tool. After splitting barcodes for each sample, PE reads were split from each other.
Split paired end reads were aligned using Bowtie2 to S. cerevisiae release r.64 after trimming the first 10 bps to account for the barcode sequence.
Aligned reads were binned into 50 bp windows using the Bedtools
Binned samples were median smooth over 1kb, quantile normalized between samples, average between replicates and smoothed a second time over 1kb using R.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Processed data file is in tab delimited .txt format. Columns include Chromosome, Coordinate (50 bp bin), and final normalized seq count for WT, rif1 delta

source_name: BrdU IP DNA from S. cerevisiae

growth_protocol: Cells were grown in YEPD to OD ~0.5

extract_protocol:
Genomic DNA was extracted from 25ml of culture using standard phenol chloroform extraction
Standard Illumina Indexed Library prep with additional barcode in adapter

treatment_protocol: Cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor and then released into fresh media containing 0.2 Hydroxyurea, 200ug/ml Pronase, 400 ug/ml BrdU.  At 45 minutes post releasem,  50 ml of culture were harvested for DNA extraction.

value: rif1 delta

tag: drug

value: HU

tag: time point

value: 45 minutes

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)


title: WT replicate2

description: Barcode: ACTGT

value: WT


title: rif1 delta replicate 1

description: Barcode: ACTGT


title: WT replicate1

description: Barcode: ACTGT


title: WT YPEG Rep1

city: Tianjin

first: Huifeng

last: Jiang

address: #32XiQiDao Tianjin airport economic park

country: China

institute: Tianjin Institute of Industrial Biotechnology

description:
RNA-seq
Sample 1

data_processing:
SOAP2 were used to map reads onto genome (allowing two or less mismatches) and to calculate RPKMs.
Genome_build: S288C_reference_genome_R64-1-1
Supplementary_files_format_and_content: In the .bed file, RPKM of each gene was calculated by summing the number of reads on the gene location

source_name: BY4742 YPEG

growth_protocol: Both the PUF3 deletion strain and wild type BY4742 (MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0) strain were cultured overnight in YPD media. 0.01 OD cells were transferred into fresh YPEG media until 1.0 OD.

extract_protocol:
Total RNA was extracted by the standard Trizol protocol. mRNA was then purified using oligo-dT DynaBeads.
cDNA sequencing library was constructed according to the protocol described by Wang et al.

tag: media

value: YPEG


title: PUF3del YPEG Rep2

description:
RNA-seq
Sample 4

source_name: PUF3del YPEG


title: WT YPEG Rep2

description:
RNA-seq
Sample 2


title: PUF3del YPEG Rep1

description:
RNA-seq
Sample 3


title: T_Liver

city: Exeter

first: Ronny

last: van Aerle

state: Devon

address: Stocker Road

department: Biosciences, College of Life and Environmental Sciences

country: United Kingdom

institute: University of Exeter

description: Sample 10

data_processing:
The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) was used to clip Illumina adapter sequences and to trim the first 12 bp at the 5’ end to remove bias caused by random hexamer priming (Hansen et al 2010).
Quality trimming of the 3' end of the reads using a sliding window at the first base with a quality Phred score of < 20 was performed (http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.slidingWindow.pl) and reads shorter than 30 bp were discarded
Paired reads were separated from orphan reads for each of the adult tissue libraries using the script from https://github.com/lexnederbragt/denovo-assembly-tutorial/blob/master/scripts/pair_up_reads.py
Interleaved paired and orphan sequences for adult tissues were assembled de novo using Velvet (version 1.2.08; Zerbino and Birney, 2008) and Oases (version 0.2.08; Schulz et al, 2012). An initial assembly was created using a k-mer of 73 (using ins_length 50 -ins_length_sd 200). Subsequent assemblies were created using k-mers ranging from 65 to 41  (with steps of 8), such that the transcripts generated by the previous assembly were used as a –long input for the next assembly.
Transcripts were annotated using Blast and all available Ensembl cDNA sequences for zebrafish (Danio rerio), medaka (Oryzias latipes), nile tilapia (Oreochromis niloticus), stickleback (Gasterosteus aculeatus), human and mouse (Release 69; October 2012), (non-human) vertebrate RefSeq RNA and protein sequences (Database of 2012-11-09), non-redundant nucleotides (nt) and proteins (nr) databases and EST (others). Top hits with an e-value of < 1e-15 were retained and annotations were assigned in the following preferential order: zebrafish, medaka, nile tilapia, stickleback, human, mouse (Ensembl cDNA), RefSeq vertebrates RNA, nt, RefSeq vertebrates proteins, nr and EST sequences. When no annotation could be found, the Locus_ID of the transcript was given.
Gene expression was determined in the gill, gut, kidney and liver of fish inhabiting the metal-contaminated river Hayle and the reference river Teign using RSEM (Li and Dewey, 2011), using the Accession numbers of the various annotations as gene ID and the transcript names generated by Oases as transcript IDs.
Genome_build: n/a
Supplementary_files_format_and_content: Processed data files are RSEM output files with gene-level expression estimates for each of the tissue samples, containing the Gene_IDs (GI identifiers) and all corresponding Transcript_IDs, length, effective length, expected count, TPM and FPKM values.

organism: Salmo trutta

source_name: Teign liver

growth_protocol: Fertilised brown trout eggs were obtained from a trout farm and maintained in 8 °C flow through-water on gravel beds. Wild adult brown trout were caught by electric fishing from the river Hayle and river Teign (control).

extract_protocol:
Individual tissues from wild fish were snap frozen in liquid nitrogen. RNA was extracted with TRI reagent.
Libraries were constructed with Illumina TruSeq RNA sample preparation kit.

tag: developmental stage

value: adult

value: liver

tag: river

value: :Teign

tag: treatment

value: control

tag: adaptor sequence


title: H_Liver

description: Sample 5

source_name: Hayle liver

value: :Hayle

value: chronic metal exposure


title: T_Gut

description: Sample 8

source_name: Teign gut

value: stomach and intestine


title: T_Gill

description: Sample 7

source_name: Teign gill

value: gill


title: iaa3 + BR RNA-Seq replicate 1

description: RNA-Seq of iaa3 + BR replicate 1

data_processing:
Basecalls performed using CASAVA version 1.?
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome_build: TAIR9

source_name: Etiolated iaa3 seedlings treated with 100 nM brassinolide

growth_protocol: Seedlings were grown on medium containing 2 µM propiconazole (PPZ) in the dark for 5 days and treated with mock or 100 nM BL for 4 hr before harvesting.

extract_protocol: Total RNA was extracted by using the Spectrum Plant Total RNA kit (Sigma, USA). Libraries were constructed using TruSeqTM RNA Sample Preparation Kit (Illumina) according to the manufacturer’s procedure.


title: H_Kidney

description: Sample 4

source_name: Hayle kidney

value: trunk kidney


title: T_Kidney

description: Sample 9

source_name: Teign kidney


title: UWOPS05_217_3_FAIRE_replicate2

description: Sample 2

tag: strain

value: haploid

value: log-phase


title: H_Gut

description: Sample 3

source_name: Hayle gut


title: H_Gill

description: Sample 2

source_name: Hayle gill


title: myd88+/+_M. marinum infected

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

country: Netherlands

institute: Institute of Biology, Leiden University

data_processing:
Image analysis and base calling was done by the Illumina HCS version 1.15.1; raw data from 2 (sample 20) and 3 sequencing runs (samples 19, 21, and 22) were combined  to generate the tsv files and to calculate average insert sizes and standard deviations for paired end experiments.
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Zv9_67) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Danio_rerio.Zv9.67.dna.toplevel / Danio_rerio.Zv9.67.cdna.all.fa (http://www.ensembl.org/info/data/ftp/index.html )
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: wild type siblings (myd88+/+), M.marinum infected, 4 dpi

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
A total of 3 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 2 x 50 nucleotides.

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. At 5 days post fertilization (4 d post infection) pools of 20 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: sample type

value: wild type zebrafish embryos injected with M. marinum at 28 hpf; RNA isolated at 4 dpi

value: injected with M. marinum

tag: genotype

value: wild type

value: embryo


title: myd88+/+_uninfected

source_name: wild type siblings (myd88+/+), not-infected

value: wild type zebrafish embryos mock-injected with PBS at 28 hpf; RNA isolated at 4 dpi

value: PBS


title: myd88-/-_uninfected

source_name: myd88 mutant (myd88-/-), not-infected

value: myd88 mutant zebrafish embryos mock-injected with PBS at 28 hpf; RNA isolated at 4 dpi

value: myd88 mutant


title: myd88-/-_M. marinum infected

source_name: myd88 mutant (myd88-/-), M.marinum infected, 4 dpi

value: myd88 mutant zebrafish embryos injected with M. marinum at 28 hpf; RNA isolated at 4 dpi


title: NCCIT - EC cell line - H3K27ac

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

institute: Erasmus MC

data_processing: Image acquisition, bead processing, quality metrics and base calling was performed using SOLiD™ Instrument Control Software and SOLiD™ Experiment Track System (http://www.lifetechnologies.com/au/en/home/technical-resources/software-downloads/solid-software.html)

source_name: mediastinal germ cell tumor (embryonal carcinoma) (Teshima et al. 1988)

growth_protocol: Cells (wild type) were cultured in DMEM medium (Life Technologies, #31966-021) containing 10% fetal calf serum (FCS, Hyclone) in T75 cm2 flasks to 75-90% confluence.

extract_protocol:
The ChIP assay was performed according to the low cell number ChIP protocol from Diagenode (Liege, Belgium), with minor modifications. In brief, 1x10e6 cells were cross-linked for eight minutes by addition of formaldehyde to a final concentration of 1%, followed by neutralization with 1.25M glycine. The cells were then lysed, and chromatin was sheared to ~500 bp fragments using the Covaris sonicator under the following conditions; duty cycle 20%, peak incident power 200 watts, cycles/burst 200, time 5min, temperature 4ᵒC. Protein A-coated Dynabeads (Invitrogen) were incubated with 7 µg of the following antibodies: H3K4me3 (Diagenode pAb-003-050) or H3K27ac (Abcam Ab4729). The beads were combined with chromatin from 1x106 cells overnight on a rotating wheel. The immunobeads were washed, and DNA was purified using the iPure DNA purification kit (Diagenode AL-100-0100) according to manufacturer’s instructions. DNA fragments were sheared a second time using a Covaris sonicator (duty cycle 10%, peak incidence power 175 watts, cycles/burst 200, time 5 minutes, temperature 4ᵒC). Average sequence length was 300nt.
According to the manufacturer's instructions

tag: histological_subtype_primary tumor

value: non-seminoma including an embryonal carcinoma component

tag: anatomical localisation

value: mediastinum

tag: antibody

value: H3K27ac (Abcam Ab4729)

value: NCCIT


title: Pachytene_spermatocytes_RNA-seq_rep1

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

description: Male Sprague-Dawley rats

data_processing:
Comprehensive database of known transcripts: Transcript annotations from public databases (Ensembl and NCBI (release RGSC3.4), AceView (43), and mRNAs from UCSC rn4) were merged into a combined set of non-redundant known transcript annotations using Cuffcompare. This comprehensive database of known transcripts and EST alignments (from UCSC) were used to define an additional junction set (AJS) that will be used to aid read mapping.
Mapping reads: RNA-seq-derived reads from each sample were aligned independently to the Rattus norvegicus genome (rn4) with TopHat (version 1.4.1). Briefly, to aid these alignments, the database of additional junctions (DAJ) were used for each TopHat run. The junction outputs from individual TopHat runs were pooled and added to the DAJ to allow TopHat to use junction information from all samples. TopHat was run again on each sample using the resulting DAJ. The output of this second run comprised the final alignment. tophat options: --min-anchor 5 --library-type fr-unstranded --solexa1.3-quals --max-multihits 10 --coverage-search --microexon-search --raw-juncs [DAJFile] --GTF [KnownTranscriptsFromEnsemblAceViewNCBIAndUCSCFile] --prefilter-multihits. The resulting .bam files were subsequently converted into .bed files using the genomeCoverageBed tool (BEDTools 2.12.0).
ab initio Transcriptome assembly: Individual cell type-specific transcriptomes were assembled with Cufflinks (version 1.2.0). cufflinks settings: --library-type fr-unstranded --upper-quartile-norm --multi-read-correct
Merging and classification of transcript fragments: The Cuffcompare program (cufflinks 1.2.0) was used to merge the individual transfrags into a combined set (non-redundant "union" of all transcript fragments that share all introns and exons), and to classify the 122,262 resulting transcripts according to the known transcript annotation database (Ensembl and NCBI (release RGSC3.4), AceView (43), and mRNAs from UCSC rn4)  into several classes.
Transcriptome quantification and pre-processing: The isoform-level abundances (expression level) were assessed using Cuffdiff (cufflinks 1.2.0) for each sample with upper quantile normalization. Abundance was measured in Fragments per Kilobase of exon model per Million reads mapped (FPKM). A matrix of FPKM expression values was then prepared based on the resulting transcriptome quantification. Expression data were subsequently log2-transformed after adding 0.05 to all FPKM values. Finally, the data were quantile normalized to reduce systematic effects and thus to allow direct comparison of the individual samples.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: .bed files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "genomeCoverageBed" utility in BEDTools (release 2.12.0); .gtf file contains the reconstructed transcripts obtained with cufflinks and subsequently classified with cuffcompare in the cufflinks suite of tools (release 1.2.0); .FPKM file contains the log2(FPKM) expression levels quantified with Cufflinks for each transfrag and each sample; the columns are tab-separated.

organism: Rattus norvegicus

source_name: Pachytene spermatocytes

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA integrity was measured using an Agilent 2100 Bioanalyzer, and only samples with a RIN score >7.0 were further processed.
The RNA-seq libraries were prepared using "mRNA-seq sample prep kit" (#RS-100-0801, Illumina Inc.) following Illumina's protocol with some modifications. Briefly, 10 µg of total RNA were hybridized with eukaryote rRNA sequence-specific 5'biotin labeled oligonucleotide probes to selectively deplete abundant ribosomal RNA. The rRNA/5'biotin labeled probe hybrid was removed from the sample with streptavidin-coated magnetic beads ("Ribominus Eukaryote kit for RNA-seq", #A10837-08, Invitrogen). Then, 250 ng of rRNA-depleted RNA were fragmented using divalent cations at 95°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers and SuperScript II reverse transcriptase (# 18064-014, Invitrogen). This was followed by second strand cDNA synthesis using Polymerase I and RNase H. The double stranded cDNA fragments were end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were separated by 2% agarose gel electrophoresis and ~200-220bp fragments were excised and purified using QIAquick Gel Extraction Kit (Qiagen) and enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 13 cycles; 5 min at 72°C). After PCR amplification, surplus PCR primers were removed by purification using Agencourt AMPure XP beads (#A63881, Beckman). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). Each library was loaded in two lanes of the flowcell at 5pM concentration and clusters were generated using the cluster station and sequenced on the Illumina Genome Analyzer II as paired-end 2x60 base reads. Image analysis and base calling were performed using the Illumina Pipeline version 1.6.

value: Sprague-Dawley

tag: Sex

value: Male

tag: cell type

value: Pachytene spermatocytes

value: testis

tag: age

value: 90 days


title: Round_spermatids_RNA-seq_rep2

description: Male Sprague-Dawley rats

source_name: Round spermatids

value: Round spermatids

tag: tissue


title: Spermatogonia_RNA-seq_rep2

description: Male Sprague-Dawley rats

source_name: Spermatogonia

value: Spermatogonia

value: 9 days


title: Spermatogonia_RNA-seq_rep1

description: Male Sprague-Dawley rats


title: Round_spermatids_RNA-seq_rep1

description: Male Sprague-Dawley rats


title: Sertoli_cells_RNA-seq_rep1

description: Male Sprague-Dawley rats

source_name: Sertoli cells

value: Sertoli cells

value: 20 days


title: Sertoli_cells_RNA-seq_rep2

description: Male Sprague-Dawley rats


title: TCam-2 - SE cell line - H3K4me3

source_name: testicular seminoma (Mizuno et al, 1993, de Jong et al,2008)

value: seminoma

value: H3K4me3 (Diagenode pAb-003-050)

tag: cell line


title: DBVPG1373-CBS432_RNA_replicate1

description: Sample 19

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

tag: ploidy

value: diploid (hybrid between DBVPG1373 and CBS432)

tag: growth phase

value: log-phase


title: morc6_Bisulfite-Seq

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

institute: University of Washington

data_processing:
BS-seq reads for 131216 libraries were mapped with BSmap (Xi Y, Li W, 2009 BMC Bioinformatics) allowing up to 2 mismatches and retaining only uniquely mapping reads..
Genome_build: TAIR10
Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced). Only cytosines with 5X coverage were plotted.  Note: No strand information given for cytosines.

source_name: adult leaf tissue

growth_protocol: All plants were grown at 22 degrees celsius in constant light.

extract_protocol:
DNA was extracted by Qiagen DNeasy Plant Mini Prep kit
libraries were prepared using LT Illumina TruSeq kit followed by bisulfite conversion with Qiagen Epitect Bisulfite conversion and subsequent PCR amplification

value: leaf

tag: developmental stage

value: adult


title: WT_Bisulfite-Seq

value: Wild type

tag: cultivar

value: Columbia


title: DBVPG1373-CBS432_RNA_replicate2

description: Sample 20


title: UWOPS05_217_3-CBS432_RNA_replicate2

description: Sample 18

value: diploid (hybrid between UWOPS05_217_3 and CBS432)


title: mom1morc6_Bisulfite-Seq

value: mom1-2 morc6-3


title: UWOPS05_217_3-CBS432_RNA_replicate1

description: Sample 17


title: mom1_Bisulfite-Seq


title: DBVPG1373-CBS432_FAIRE_replicate2

description: Sample 10


title: Set_2_bio_replicate_2-mom1

description:
biological replicate 2
Total RNA Trizol extracted from leaf tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane

data_processing:
RNA-seq -- Reads were filtered for full-length (50bp) reads.  Reads containing adapter were discarded. Reads were mapped with Tophat2 (Kim et al. 2011 Genome Bio) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read.
Genome_build: TAIR10
Concatenated per-chromosome plain text UCSC Genome Browser wiggle files with UNIX-style line endings, compressed with GNU gzip, values represent RPKM within a given step
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)

extract_protocol:
Standard Trizol method
Libraries were prepared using LT Illumina TruSeq RNA kit


title: DBVPG1373-CBS432_FAIRE_replicate1

description: Sample 9


title: UWOPS05_217_3-CBS432_FAIRE_replicate2

description: Sample 8


title: Set_2_bio_replicate_2-morc6


title: Set_2_bio_replicate_2-morc6mom1


title: NCCIT - EC cell line - H3K4me3

value: non-seminoma including an embryonal carcinoma component

value: mediastinum

value: NCCIT


title: Set_2_bio_replicate_2-WT_Col

tag: ecotype


title: UWOPS05_217_3-CBS432_FAIRE_replicate1

description: Sample 7


title: Set_1_bio_replicate_2-morc1morc2morc6_triple

value: atmorc1-2 atmorc2-1 morc6-3 (crt1-2 crh1-1 atmorc6-3)


title: Pachytene_Spermatocytes_RNA-seq_rep2

description: Male Sprague-Dawley rats

value: Sprague-Dawley

value: Male

value: Pachytene spermatocytes

value: testis

value: 90 days


title: TCam-2 - SE cell line - H3K27ac

source_name: testicular seminoma (Mizuno et al, 1993, De Jong et al,2008)

value: seminoma

value: H3K27ac (Abcam Ab4729)


title: Set_1_bio_replicate_2-morc1morc2_double

value: atmorc1-2 atmorc2-1 (crt1-2 crh1-1)

value: leaf


title: Set_1_bio_replicate_2-morc6

value: adult


title: Set_1_bio_replicate_2-morc1

value: atmorc1-2 (crt1-2)


title: Set_1_bio_replicate_2-morc2

value: atmorc2-1 (crh1-1)


title: Set_2_bio_replicate_1-morc6mom1

description:
biological replicate 1
Total RNA Trizol extracted from leaf tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane

value: mom1-2 morc6-3


title: Set_1_bio_replicate_1-morc1

description:
biological replicate 1
Total RNA Trizol extracted from leaf tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/10 lane


title: Set_1_bio_replicate_1-morc1morc2_double


title: Set_2_bio_replicate_1-morc6


title: Set_1_bio_replicate_1-morc1morc2morc6_triple


title: Set_2_bio_replicate_1-WT_Col

value: Wild type

value: Columbia


title: Set_1_bio_replicate_1-morc6


title: Set_1_bio_replicate_1-morc2


title: Set_1_bio_replicate_1-WT_Col


title: Diffuse large B cell lymphoma biopsy, patient 2038

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Sequenced reads were trimmed for adapter sequence, then mapped to miRBase 19 precursors using bowtie-0.12.7 with parameters –color --col-keepends -f --all --maqerr 400 --seedmms 2 --norc –seedlen 20
Custom software to remove poorly matched reads and then assemble reads into clusters
Clusters were trimmed to give a core region mapped by the majority of reads in a cluster
Consensus sequences were formed from the most abundant bases at each position in each cluster
Consensus clusters were overlapped with miRBase 19 mature sequences to annotate
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files including normalized miRNA expression for each sample

source_name: GC-derived lymphomas

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's indications. The small RNA fraction was enriched by flashPAGE fractionation (Ambion).
small RNA libraries were generated using the SOLiD Small RNA Expression Kit (Applied Biosystems).

treatment_protocol: The frozen tissue was homogeneized in Trizol reagent.

value: Diffuse large B cell lymphoma bioptic tissue


title: Diffuse large B cell lymphoma biopsy, patient 2104


title: Diffuse large B cell lymphoma biopsy, patient 2157


title: Diffuse large B cell lymphoma biopsy, patient 2134


title: Diffuse large B cell lymphoma biopsy, patient 2189


title: Diffuse large B cell lymphoma biopsy, patient 2147


title: Diffuse large B cell lymphoma biopsy, patient 2125


title: Diffuse large B cell lymphoma biopsy, patient 2100


title: Diffuse large B cell lymphoma biopsy, patient 2126


title: Diffuse large B cell lymphoma biopsy, patient 2032


title: Set_2_bio_replicate_1-mom1


title: Set_1_bio_replicate_2-WT_Col


title: Diffuse large B cell lymphoma biopsy, patient 2152


title: Diffuse large B cell lymphoma biopsy, patient 2044


title: Diffuse large B cell lymphoma biopsy, patient 2017


title: Diffuse large B cell lymphoma biopsy, patient 2180


title: Diffuse large B cell lymphoma biopsy, patient 2132


title: Diffuse large B cell lymphoma biopsy, patient 2183


title: Diffuse large B cell lymphoma biopsy, patient 2063


title: Diffuse large B cell lymphoma biopsy, patient 2043


title: Diffuse large B cell lymphoma biopsy, patient 2025


title: Diffuse large B cell lymphoma biopsy, patient 2091


title: Diffuse large B cell lymphoma biopsy, patient 2019


title: Germinal Center Centroblasts, sample 093008

source_name: normal mature germinal center (GC) B cells

treatment_protocol: Upon magnetic cell sorting cells were lysated in Trizol Reagent (Invitrogen) and frozen

value: CD77-positive B-cells from human tonsil


title: Germinal Center Centroblasts, sample 092308


title: Diffuse large B cell lymphoma biopsy, patient 2034


title: Diffuse large B cell lymphoma biopsy, patient 2089


title: Mice_mammary_SA1_smallRNA

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

data_processing:
Small 35 nt RNA reads were produced using an Illumina GAIIx Genome Analyzer. Low quality reads were trimmed using NGSQC Tool kit.
After elimination of redundancy, sequences ≥ 18 nt were mapped to the mouse genome build Mm9. Sequences that perfectly matched the genome along their entire length were considered for subsequent analyses.
Genome sequences and annotations of the mouse genome (Mm9) were downloaded from NCBI. Sequences matching mouse rRNA, tRNA, snRNA and snoRNA deposited at the NCBI GenBank database or overlapping with rRNA and tRNA annotations of the genome were discarded. Repeat overlapping sequences were annotated as repeat-associated small RNAs. The majority of sequences overlapping with predicted exons were excluded from further analysis in view of the possibility that they were derived from messenger RNAs, and only those with precursors presenting p-values below 0.01 were collected.
All Small RNA was quantified and normalized using RPKM Method
Differential Small RNA expression was done by calcualting Fold change based on Log base 2 of RPKM
Genome_build: NCBI mouse genome (Mm9)
Supplementary_files_format_and_content: Text Tab delimited file with RPKM values of sample 1, Sample 2 and Sample 3

source_name: Lactating mice mammary tissue for S. aureus-infected mouse

extract_protocol:
Total RNA was isolated with Trizol reagent following manufacturer's protocol.total RNA of each sample was size-fractionated on a 15% PAGE gel, and a 16-30 nt fraction was collected. The 5' RNA adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3') was ligated to the RNA pool with T4 RNA ligase. Ligated RNA was size-fractionated on a 15% agarose gel, and a 40-60 nt fraction excised. The 3'RNA adapter (5'-pUCGUAUGCCGUCUUCUGCUUGidT-3'; p, phosphate; idT, inverted deoxythymidine) was subsequently ligated to precipitated RNA using T4 RNA ligase. Ligated RNA was size-fractionated on a 10% agarose gel, and the 70-90 nt fraction (small RNA + adaptors) excised. Small RNAs ligated with adaptors were subjected to RT-PCR (Superscript II reverse transcriptase, 15 cycles of amplification) to produce sequencing libraries. PCR products were purified and small RNA libraries were sequenced using Illumina GAIIx, a massively parallel sequencing technology.
Small RNAs ligated with adaptors were subjected to RT-PCR (Superscript II reverse transcriptase, 15 cycles of amplification) to produce sequencing libraries. PCR products were purified and small RNA libraries were sequenced using Illumina GAIIx, a massively parallel sequencing technology.

treatment_protocol: Lactating mice mammary tissue was innoculated with S.aureus culture and incubated for 24 hr.

value: Swiss albino

value: mammary


title: Mice_mammary_PBS_smallRNA

source_name: Lactating mice mammary tissue


title: input replicate3

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

description:
input
inputreplicate1_2_3_4_Scaled.wig

data_processing:
In brief, all samples were sequenced on an Illumina Genome Analyzer (GAIIx for ChIP-seq and RNA-seq, or HIseq2000 for MNase-seq). Quality assessment and filtering of ChIP-seq and MNase-seq sequences were performed using either the Integrated Eland software or FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) to pre-process FastQ files. Quality score and nucleotide composition at each position of the sequenced tags were assessed by box and bar plotting using FastX-Toolkit standard functions. Quality controls (QC) and filtering of RNA samples were performed using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), FASTX-toolkit and Cutadapt (http://code.google.com/p/cutadapt/). Adapters were removed (Cutadapt) and a QC report was generated (fastQC). Sequences were further trimmed at nucleotide 55 and quality filtered as for DNA sample (FASTX-toolkit).
All samples were aligned to human genome (hg19, GRCh37) using Bowtie aligner (allowing 2 mismatches, keeping uniquely aligned reads only)
Piles of tags with same coordinates, due to artifacts of PCR or unannotated regions of the genome were removed according to a thresholding method, except for RNA-seq experiment
Uniquely aligned tags were further elongated after estimating optimal elongation size in silico and enabling to use the original fragment length for further processing.
For ChIP-seq experiments, all samples were input subtracted and signals were scaled so that the same number of units appeared in each experiment after merging of the replicates.
For nucleosome mapping, MNAse-seq experiment in Raji was sequenced in paired-end with higher depth than ChIP-seq in Hiseq2000. Two types of analyses were applied to this data: nucleosomes density and nucleosomes midpoint  that allow to score more specifically for depletion or positioning, respectively. For nucleosome density, paired tags were processed so to be directly connected and to retrieve original fragments (orphan tags were connected to the corresponding pairs using the estimated elongation size computed as described above). The input subtraction step was omitted. For nucleosomes midpoint analyses, the middle of elongated fragments was set as reference allowing locating the maximum signal approximately at the midpoint of the nucleosomes (dyads).
For all experiments, the number of tags covering each nucleotide of the genome was computed and averaged in bins of 50 nucleotides. The scores of bins were rescaled (after input subtraction when applicable) to reduce over-representation of particular genomic regions and signal/noise ratio.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: wig, contains score of binding, nucleosomes occupancy and short RNAs expression.
Supplementary_files_format_and_content: raw.txt.gz, Eland processed file

source_name: Raji B-cell line

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100U/ml penicillin, 100mg/ml streptomycin and 2mM L-glutamine (Gibco/Invitrogen) at 37°C and 5% CO2. For the removal of Pol II, cells were treated with 2.5 μg/ml of α-amanitin for the indicated time points for the WT Raji cells.

extract_protocol: Total RNA was extracted from 1x107 Raji cells using TRIzol (Life Technologies, USA) according to the manufacturer’s instructions with some modifications to ensure higher recovery rates of small RNAs. This was achieved by addition of 10μg of linear acrylamide (Life Technologies, USA) before RNA precipitation. DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment as per manufacturer’s instructions. RNA quantity was measured on a Qubit apparatus (Life Technologies, USA) using RNA assay kit the quality was verified using RNA pico chips on a 2100 Bioanalyzer (Agilent Technologies, USA).  Before preparation of sequencing libraries, small RNAs were enriched from 10µg total RNA by using mirVana RNA Isolation kit (Life Technologies, USA) using manufacturer’s protocol for small RNA enrichment. Strand specific RNA-seq library was constructed with ScriptMiner Small RNA-seq Library Preparation Kit (Epicenter, USA) according to manufacturer’s recommended protocol. Briefly, after both 5’ and 3’ adapter ligation, resulting cDNA library was PCR amplified with 14 amplification cycles. Purified library DNA was run on a 10% TBE-PAGE gel and library DNA corresponding to transcripts between 15nt-50nt was cut from the gel and transferred into 0.5mL tubes with punctured bottoms which were in turn placed in 2mL collection tubes. Gel slices were crushed into 2mL tubes by a 2 minutes centrifugation at 14000g. For library DNA elution by soaking, 0.4ml of 0.3M NaCl was added to each tube, before a 4 hour rotation at room temperature. After removal of gel particles using 0.22μm cellulose acetate filters, 10μg of linear acrylamide (Life Technologies, USA) and 2.5 volumes (approximately 1ml) of ice-cold absolute ethanol were added. After 30 minutes incubation at -80°C, the eluted cDNA was precipitated by centrifugation at 4°C and maximum speed for 45 minutes. The pellet was washed with 1ml of cold 80% ethanol, air dried and resuspended in 20μl of water. The size-selected small RNA library DNA was quantified using a Qubit apparatus with dsDNA High Sensitivity kit (Life Technologies, USA) and verified using DNA High Sensitivity 2100 Bioanalyzer chips (Agilent Technologies, USA).

value: Raji B


title: Mice_mammary_SA2_smallRNA


title: shortRNA

description: short strand specific RNA


title: input replicate2

description:
input
inputreplicate1_2_3_4_Scaled.wig


title: Diffuse large B cell lymphoma biopsy, patient 2194

city: New York


title: input replicate1

description:
input
inputreplicate1_2_3_4_Scaled.wig


title: Tyr1P8G5 replicate1

description:
protein associated DNA
Tyr1P3D12_replicate1_replicate2_Scaled_BGSub.wig

value: Tyr1P 8G5


title: Tyr1P3D12 replicate2

value: Tyr1P 3D12


title: H3K27me3_ChIPSeq-miR155-KO

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Reads from ChIP-seq were mapped to the mouse genome (NCBI 37, mm9) using the short read, memory efficient aligner Bowtie (version-0.12.7) with option -p 8 --chunkmbs 256 -a --best --strata -m 20
Unique reads are considered by instructing Bowtie to refrain from reporting any alignments for reads that have more than 20 reportable alignments
Reads from ChIP-exo were mapped by Peconic (State College, PA) to the mouse genome (NCBI 37, mm9) using BWA (version 0.5.9) with default options allowing one gap open and a maximum number of three alignments for any read that aligned across the genome.
Sub-module of SICER (version-1.1) was used on BED files containing the unique reads to determine window size. The window sizes for each ChIP-seq were as follows: c-Maf was 137bp; Suz12 was 397bp; Jarid2 was 2102bp; while H3K27me3 had a window size of 2852bp. SICER-df.sh was used for c-Maf, Suz12, Jarid2 and H3K27me3 analysis with a gap size of 274bp for c-Maf and a gap size of 0 for Jarid2, Suz12, and H3K27me3. All SICER-df.sh analysis had an FDR cutoff of 0.01.
For ChIP-exo analysis, SICER-rb.sh was used to find enriched Jarid2 and Suz12 islands with an E value cut-off of 0.1, a window size of 50 and a gap size of 100.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle files were generated from BAM files generated by Bowtie

source_name: Primary CD4+ Th cells

growth_protocol: CD4+ T cells were co-cultured with irradiated (3000 Rads) T cell-depleted splenocytes in presence of 1 μg/ml of anti-CD3 (145-2C11) and 1μg/ml of anti-CD28 (37.51) for 4 days with combinations of antibodies and cytokines that included 10 ng/ml of IL-6, 10 ng/ml of IL-21, and 0.5 ng/ml of TGFβ with 10 μg/ml of anti-IL-4 (11B11), anti-IL-12 (C17.8), and anti-IFNγ (XMG1.2)  for Th17.

extract_protocol:
10 million Th17 cells were fixed, lysed and sonicated to 200 base pairs. Then, histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Activated CD4+ T cells skewed towards a Th17 subset.

tag: chip antibody

value: H3K27me3 (Millipore, 07-449)

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: H3K27me3_ChIPSeq-miR155-WT

tag: strain

tag: genotype


title: Suz12_ChIPSeq-miR155-KO

value: Suz12 (Cell Signaling, D39F6)

value: Cell Signaling


title: c_Maf_ChIPSeq-miR155-WT

value: c-Maf  (Santa Cruz, M-153)

value: Santa Cruz


title: Suz12_ChIPSeq-miR155-WT


title: Ser2P replicate2

description:
protein associated DNA
Ser2P_replicate1_replicate2_Scaled_BGSub.wig


title: Suz12_ChIPExo-Jarid2-fl_fl-CD4cre

data_processing: Reads from ChIP-exo were mapped by Peconic LLC (State College, PA) to the mouse genome (NCBI 37, mm9) using BWA (version 0.5.9) with default options allowing one gap open and a maximum number of three alignments for any read that aligned across the genome.

growth_protocol: CD4+ T cells were co-cultured with irradiated (3000 Rads) T cell-depleted splenocytes in presence of 1 μg/ml of anti-CD3 (145-2C11) and 1μg/ml of anti-CD28 (37.51) for 4 days with combinations of antibodies and cytokines that included 10 ng/ml of IL-6, 10 ng/ml of IL-21, and 0.5 ng/ml of TGFβ with 10 μg/ml of anti-IL-4 (11B11), anti-IL-12 (C17.8), and anti-IFNγ (XMG1.2)  for Th17 differentiation.

extract_protocol: In brief, 10 million Th17 cells were fixed, lysed and sonicated to 200 base pairs. Sheared chromatin was submitted to Peconic LLC (http://www.peconicgenomics.com/) along with antibodies for ChIP-exo.

value: Jarid2fl/fl; CD4cre


title: Ser2P replicate1


title: c_Maf_ChIPSeq-miR155-KO


title: Pol II replicate3

description:
protein associated DNA
polII_replicate1_replicate2_replicate3_Scaled_BGSub.wig

tag: antibody vendor/catalog

value: Santa Cruz (sc-899x)

value: Pol II


title: Jarid2_ChIPSeq-miR155-KO

value: Jarid2 (Abcam, ab48137)

value: Abcam


title: Diffuse large B cell lymphoma biopsy, patient 2056

value: Diffuse large B cell lymphoma bioptic tissue


title: Input_DNA-miR155-WT


title: Jarid2_ChIPSeq-miR155-WT


title: Input_DNA-miR155-KO


title: Germinal Center Centroblasts, sample 012307

value: CD77-positive B-cells from human tonsil


title: Germinal Center Centroblasts, sample 010907_T2


title: Pol II replicate2

value: Raji B

tag: antibody


title: Pol II replicate1


title: H3K4me3 replicate2

description:
protein associated DNA
H3K4me3_replicate1_replicate2_Scaled_BGSub.wig

value: Abcam (ab8580)


title: GM12878-ZBTB33-Rep1-Robotic-SL46187

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
base calling: Casava1.8
read alignment: Bowtie 0.12.7
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

growth_protocol: GM12878 cells were grown under the standard ENCODE protocols (http://genome.ucsc.edu/encode/protocols/cell/human/Jurkat_protocol.pdf and http://genome.ucsc.edu/encode/protocols/cell/human/GM12878_protocol.pdf)

extract_protocol:
Cells were fixed using 1% formaldehyde or 1% formaldehyde at 37C
Libraries were generated following Illumina's DNA Sample Prep Kit protocol

tag: chip-antibody

value: mouse monoclonal Kaiso/ZBTB33, Santa Cruz sc-23871


title: GM12878-ZBTB33-Rep2-Robotic-SL46188


title: GM12878-ZBTB33-Rep2-Manual-SL45081