title: PrEC H3K27me3-ChIP-BS

status: Public on Jan 18 2012

city: Zuerich

first: Mark

last: Robinson

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

institute: University of Zuerich

description: Chromatin IP against H3K27me3 + Bisulphite treatment

data_processing: A custom pipeline was written for the alignment of paired-end bisulphite ChIP reads, adapted from the procedure described in Lister et al.8 (available from http://github.com/astatham/Bisulfite-seq-pipeline). Briefly, methylation information was removed from reads ('C's in read 1 replaced with 'T's; 'G's in read 2 replaced with 'A's) and reads were then mapped separately to both strands of the bisulphite converted hg18 genome using Bowtie with the following parameters (--solexa1.3- quals nomaqround n 3 l 24 e 300 y k 10). Reads from the two strands were collated and ranked by the number of mismatches against the reference; only reads with fewer than 6 mismatches that were 3 mismatches closer to the reference than the next best hit were retained as unique. Since median fragment size for our paired-end libraries (119bp PrEC and 114bp LNCaP) was less than read length (150bp), the majority of the fragment sequences overlapped in the middle; to avoid doubling up on base calls these fragments were merged into single contig reads, with disagreements between base calls decided by higher quality scores, ties were decided randomly. The number of methylated (C) and unmethylated (T) basecalls at each CpG site within the genome was then extracted imported into R for downstream analysis.  Regions of enrichment were determined using an adaptation of the ChromaBlocks algorithm for identifying both strong peaks and regions of broad enrichment, as implemented in the Repitools package.

source_name: PrEC (prostate epithelial) cell line

growth_protocol: 37 deg C with 5% CO2

extract_protocol: Five ul bisulphite-treated DNA (from above) was used in the PCR amplification step for library preparation. Triplicate 50 ul PCR reactions were set up as follows: 5 ul DNA, 1.25 ul dNTPs (10 mM) (Illumina #1000564), 1 ul PCR primer PE 1.0 (Illumina part# 1001783) and 1 ul PCR primer PE 2.0 (Illumina part # 1001784), in 1x PfuTurbo Cx reaction buffer (Stratagene #6000410) and 1 ul PfuTurbo Cx Hotstart DNA polymerase (2.5 U/ul Stratagene #600410). The PCR reaction was performed at 95°C for 5 mins, 98°C 30 seconds, followed by 14 cycles of 98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, for 14 cycles, then 72°C for 5 mins and hold at 4°C. The reactions were cleaned up following the instructions of the MinElute PCR Purification Kit, eluting each reaction in 15 ul EB buffer, and pooling the triplicate reactions to give a final volume of 45 ul. One ul was checked on Agilent Technologies 2100 Bioanalyzer. Twenty ul was sent to Illumina for cluster generation and GAIIx sequencing.

treatment_protocol: ChIP assays were carried out according to the manufacturer (Millipore). Briefly, ~ 1 x 106 cells, in a 10 cm dish, were fixed by adding formaldehyde to a final concentration of 1% and incubating for 10 minutes at 37°C. The cells were washed twice with ice cold PBS containing protease inhibitors (1 mM phenylmethylsulfonyl fluoride (PMSF), 1 ug/ml aprotinin and 1 ug/ml pepstatin A), harvested and treated with SDS lysis buffer (1%SDS, 10mM EDTA, 50mM Tris, pH 8.1) for 10 minutes on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 base pairs. The complexes were immunoprecipitated with antibodies specific for tri-methyl-histone H3(lys27) (Millipore #07-449). Ten ul of antibody were used for each immunoprecipitation according to the manufacturer. A no antibody control was included for each ChIP assay, which revealed no non-specific precipitation by quantitative Real-Time PCR analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times following the manufacturer's instructions. The immune complexes were eluted with 1 % SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 ul H2O.  H3K27me3-ChIP DNA was pooled from 3-5 ChIP assays to obtain 100 ng DNA for bisulphite treatment. The ChIP DNA was concentrated by ethanol precipitation to give a final yield of 100 ng ChIP DNA in 40 ul water. The ChIP DNA was further sonicated using a Bioruptor (High, 30 seconds on and 30 seconds off for 25 minutes) to ensure the maximum yield of DNA in the size range of 150-200 bp. End-repair and addition of 'A' bases to the 3Ã¢Â€Â² end of the DNA fragments was performed according to the 'Preparing samples for ChIP sequencing of DNA' (Part#11257047 Rev.A Illumina). Methylated paired-end adaptors undiluted (Illumina Part # 1005560) were then ligated onto the ChIP DNA using 1 ul of undiluted methylated adaptor oligo mix, 4 ul DNA ligase (Illumina Part # 1000522) in a total reaction volume of 10 ul, at room temperature for 15 minutes. The reactions were cleaned up using the MinElute PCR Purification Kit (Qiagen part # 28004) and eluted in 10 ul of EB buffer following the manufacturer's instructions. Size selection of the library was performed according to the Illumina protocol for Preparing Samples for ChIP sequencing of DNA (Illumina Part#11257047 Rev.A ). Two ul of loading buffer was added to 10 ul of DNA and the entire sample was loaded onto a single lane of the gel. A gel slice in the range of 75-225 bp was excised and eluted using the Qiagen Gel Extraction Kit (Qiagen, part # 28704) and eluted in 40 ul of EB buffer.   One ul of tRNA (10 ug/ul) was added to the 20 ul DNA in a final volume of 21 ul. 2.33 ul 3M NaOH was added to each 21 ul DNA sample and incubated for 37°C for 15 mins, 90°C for 2 mins and placed on ice and then centrifuged briefly. 208 ul of saturated sodium metabisulphite pH 5.0 (7.6 g Na2S2O5 with 464 ul of 10 M NaOH made up to 15 ml with water) and 12 ul of 10 mM quinol were added, vortexed, briefly centrifuged and incubated for 4 hours at 55°C in a PCR machine. The bisulphite reaction was cleaned up using the Microcon YM50 device (Millipore). The duplicate bisulphite reactions were combined in a new tube and 1 ul tRNA (10 ug/ul) was added before transferring to a Microcon YM50 column. The column was spun at 14000 x g for 25 mins at room temperature. The filtrate was discarded, 350 ul H2O was added to the column and spun for a further 12 mins at room temperature. This wash step was repeated. After discarding the filtrate, 350 ul of 0.1 M NaOH (freshly prepared) was added to the column for the desulphonation step and again spun at 14000 x g for 10 mins at room temperature and a final wash of 350 ul H2O followed by a 12 mins spin at room temperature at 14000 x g. The column was placed in a fresh tube, 60 ul H2O was added and gently pipetted up and down and allowed to stand for 5 mins before being inverted and spun at 1000 x g for 3 mins to transfer the bisulphite-treated DNA into the microfuge tube. The bisulphite treated DNA was stored at -20°C. The Qiagen EpiTect Bisulfite Kit (Cat.no #59104) was performed according to the manufacturer's instructions for bisulphite treatment of low concentrations of DNA. Quantitation of bisulphite-conversion and DNA yield was compared using Methylation Specific Headloop PCR (MSH-PCR)

value: prostate

value: PrEC

tag: chip antibody vendor

value: Millipore

tag: chip antibody lot#

tag: chip antibody catalog#


title: CGN1

status: Public on Jan 17 2012

type: SRA

city: Columbus

first: Dario

last: Motti

state: Ohio [OH]

address: 700 Childrens Drive

department: Research

country: USA

institute: Nationwide Children's Hospital

description: Poly-A RNAs from P8 mice CGN neurons in culture

library_source: transcriptomic

data_processing:
Alignment: Tophat software with default settings except for the following options:  –G option which supplies Tophat with gene model annotation (combined UCSC, Ensembl, and RefSeq annotations) and –i 50 which sets the minimum intron length to 50
Transcript reconstruction and expression estimation: Cufflinks software. At first Cufflinks uses the aligned reads in the dataset to describe a set of transcripts starting from the reads that span splice-junctions. We ran this step using a non-annotated reference genome because without an annotation the software will assemble novel transcripts and isoforms. After transcript assembly, normalized expression levels are estimated and reported as FPKM (Fragments Per Kilobase of exon per Million fragments mapped) together with confidence intervals. A different part of the software, named Cuffcompare (version 0.8.3) classified the reconstructed RNA-species as novel or known according to how they map back to the provided reference annotation. Cuffcompare was run twice, first with a combined reference GTF generated from crossing annotated transcripts found in the UCSC Genome, the Ensembl, and the RefSeq database.  We combined three genome annotations in an effort to minimize falsely identified novel transcripts. UCSC was used as the base since it contained the highest number of annotated RNA species; all non overlapping annotations found in the other databases were added.  We reran Cuffcompare in order to improve the accuracy of read alignment and therefore transcript expression estimation (personal communications with Cole Trapnell).  The nature of the alignment of the reconstructed RNA-specie and the annotated element is reported according to a code letter. For our purposes we isolated from the output only the “=”, “j” and “u” classes (corresponding to a “perfect match” to a known RNA-molecule, new isoforms of known active locus, and to full transcripts never identified before ). We ran Cuffcompare a 2nd time after adding annotation for unknown and novel transcripts assembled by Cufflinks.
Differential expression test: Cuffdiff. Cuffdiff determined statistical significance based on the square root of the Jensen-Shannon divergence between the relative abundance of transcripts. Significance was reported as an uncorrected p-value, and then classified as significant/not –significant after Benjamini-Hochberg correction of the p-value.
Peak data (.bedgraph files) based on mm9 genome build.

molecule: polyA RNA

organism: Mus musculus

source_name: cerebellar granular neurons (CGNs)

growth_protocol: Cells were grown on a Poly-d-lysine (100 ug/mL) and Laminin (5 ug/mL) substrate

extract_protocol: Poly-A selection. RNA was prepared for Next Generation Sequencing following the Illumina mRNA Sample Preparation Guidelines (Illumina, Cat # RS-930-1001)

tag: strain

tag: age

tag: growth

value: 16 hours in vitro

tag: cell type

value: cerebellar granular neurons (CGNs)


title: RPC1_Rep2

status: Public on Jan 19 2012

city: Lausanne

first: David

last: Bernasconi

address: Quartier Sorge, Bat. Génopode

department: CIG

country: Switzerland

institute: University of Lausanne

library_source: genomic

data_processing: Reads mapping at a unique place on the genome (uniquely matching tags) and matching without any mismatch were mapped by Eland. Reads mapping at multiple places on the reference genome (repeated tags) were aligned using “fetchGWI” (www.isrec.isb-sib.ch/tagger/). The number of matches per genome allowed was set to 500 and the reads had to map without any mismatch. ere aligned using “fetchGWI” (www.isrec.isb-sib.ch/tagger/). The number of matches per genome allowed was set to 500 and the reads had to map without any mismatch. Signal from enriched regions were converted into wig format. Genome build: NCBI37/mm9

molecule: genomic DNA

source_name: Mouse liver cells

growth_protocol: C57/BL6 male, 12-14 week old (at time of sacrifice), mice were housed in a 12h Light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.

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

treatment_protocol: They were then entrained with a 12h Light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off).  At each ZT02 and, as a biological replicate, ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.

tag: tissue

value: liver

tag: chip antibody

tag: chip antibody manufacturer

value: Made in our lab

tag: chip antibody catalog number

value: CS377, raised against the C-terminus of RPC1, peptide PKRPLIFDTNEFHIPLVT, see (Sepehri and Hernandez 1997)),

tag: chiip antibody lot/batch


title: DRG2

description: Poly-A RNAs from P8 mice DRG neurons in culture

source_name: dorsal root ganglia (DRG neurons)

value: 16 days in vitro

value: dorsal root ganglia (DRG neurons)


title: RPC1_Rep1


title: DRG1


title: DRG3


title: LNCaP H3K27me3-ChIP-BS

organism: Homo sapiens

source_name: LNCaP (prostate cancer) cell line

tag: cell line

value: LNCaP


title: ERα ChIP-seq 3

status: Public on Jan 16 2012

city: Boston

first: Binhua

last: Tang

state: MA

address: 10 Shattuck Street

department: BMI

institute: Harvard Medical School

data_processing:
BED: Sequence reads were obtained and mapped to the human (March, 2006) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows. Counts included.
BEDGRAPH: Peak detection was performed with BELT program
Genome Build:
t4_export.txt_unique.EE_W100_P0.96.bed: hg18
t4_export.txt_unique.EE_W100.bedgraph: hg18

source_name: Breast cancer cells

growth_protocol: MCF7 cells were maintained in a hormone-free medium (phenol red–free MEM with 2 mmol/L L-glutamine, 0.1 mmol/L nonessential amino acids, 50 units/mL penicillin, 50 Ag/mL streptomycin, 6 ng/mL insulin, and 10% charcoal-stripped FBS) for three days.

extract_protocol: The library was constructed using Illumina genomic DNA prep kit by following its protocol (Illumina, cat# FC-102-1002), clusters were generated on the Illumina cluster station (Illumina, cat# FC-103-1002), DNA samples (20 nM per sample) quantified by an Agilent Bioanalyzer, were loaded onto Illumina Genome Analyzer IIx (GAIIx) for sequencing according to the manufacturer’s protocol. Reads generated from the Illumina GAIIx pipeline were aligned to the Human Genome Assembly (NCBI build 36.1/hg18) using ELAND algorithm.

treatment_protocol: MCF7 cells were treated with DMSO (as 0 hour time point) or E2 (108 mol/L) for 1, 4 and 24 hours. 5 x 107 cells were cross-linked with 1% formaldehyde for 10 min, at which point 0.125 M glycine was used to stop the crosslinking.

tag: cell lines

tag: agent

tag: time

value: 4 hr

value: ERα, Santa Cruz Biotechnology, sc-8005 X


title: ERα ChIP-seq 1

data_processing:
BED: Sequence reads were obtained and mapped to the human (March, 2006) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows. Counts included.
BEDGRAPH: Peak detection was performed with BELT program
Genome Build:
t0_export.txt_unique.EE_W100_P0.957.bed: hg18
t0_export.txt_unique.EE_W100.bedgraph: hg18

value: DMSO

value: 0 hr


title: IgG_IMR90_ChIPseq

status: Public on Jan 13 2012

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

institute: Uiversity Hospital Zurich

data_processing: Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline. Reads were mapped to human hg18 with Illumina's Eland package.

source_name: human IMR90 fibroblasts

growth_protocol: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

extract_protocol: See the library protocol linked to the Series record.

value: fetal lung fibroblast

tag: antibody

value: IgG


title: Populus yunnanensis, males without salinity stress, leaves

status: Public on Jan 20 2012

city: chengdu

first: Hao

last: Jiang

address: CIB-CAS

country: China

institute: CIB-CAS,China

description: DGE tag profiling.

data_processing: Counts: 3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences; Empty reads removal (reads with only 3' adaptor sequences but no tags); Low quality Tags removal (Tags with unknown sequences ‘N'); Removal of Tags which are too long or too short, leaving Tags of 21nt long; Removal of Tags with a copy number of 1 (probably be sequencing error); Generate Clean Tags. Clean tags mapped to reference sequences (poplar genome: Populus trichocarpa v1.1) from multiple genes were filtered. Remaining clean tags were designated as the distinct tags for further analysis. The number of distinct tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).

molecule: total RNA

organism: Populus yunnanensis

source_name: leaf, male, no salinity stress

growth_protocol: Cuttings were planted in 10-liter plastic pots filled with 8 kg homogenized soil at normal condition for about 4 months.

extract_protocol: Total RNA was extracted from three biological replicates (three plants each) using the E.Z.N.A.TM Plant RNA Kit (Omega, USA) according to the manufacturer’s instructions. Residual genomic DNA was removed with DNase I and its integrity was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA samples from 9 individuals of a treatment were pooled with equal proportion. Double-stranded cDNA was synthesized using oligo (dT) beads. The cDNA was then digested with an anchoring restriction enzyme Nla III, which recognizes and cuts 3’ 'CATG'. The digested cDNA samples were ligated to Illumina specific adapter 'A',  containing a recognition site for enzyme Mme I. Following Mme I digestion, the Illumina specific adapter 'B' containing a 2 bp degenerated 3' overhang was ligated. The adapter-ligated cDNA tag library was then enriched by PCR primers annealing to the adaptor ends. The PCR program was as follows: 30 s at 98 °C, followed by 15 cycles of 98 °C for 10 s, 60 °C for 30 s and 72 °C for 15 s, and then 72 °C for 5 min. After gel-purification, cDNA was used for cluster generation on separated flow cell lane. Sequencing by synthesis was performed using the Illumina Genome Analyzer according to the manufacturer's protocol. Image analysis, base calling, extraction of 17 bp tags and tag counting were performed using the Illumina pipeline.

treatment_protocol: Salt-treated plants were firstly exposed to short-term low concentration salt pre-treatment (25 mM NaCl for 24 h) avoiding large osmotic shock, and then to long-term salinity (50 mM NaCl for 7 days). Control plants were kept in well-watered conditions.

tag: Sex

value: male

value: leaf

tag: development stage

value: fourth fully expanded and intact young leaves near the shoot apex of each plant

tag: treatment


title: ERα ChIP-seq 2

data_processing:
BED: Sequence reads were obtained and mapped to the human (March, 2006) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows. Counts included.
BEDGRAPH: Peak detection was performed with BELT program
Genome Build:
t1_export.txt_unique.EE_W100_P0.951.bed: hg18
t1_export.txt_unique.EE_W100.bedgraph: hg18

value: 1 hr


title: Gdown1_IMR90_ChIPseq


title: RPB2_Rep2

tag: strain

value: Santa Cruz Biotechnology


title: Input_IMR90


title: PolII_IMR90_ChIPseq

value: PolII


title: RNA Pol II Control

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing: Raw sequences generated from Illumina/Solexa sequencer were aligned using ELAND software to NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 200 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format. The complete set of RefSeq genes was downloaded from the UCSC table browser on December 1, 2010. A custom annotated RefSeq gene list was generated by merging the all TSSs for each gene that were within 500 bases of each other. Then TSSs within 1000 bp of each other (6% of the total number) were removed from the list. This list was used for further analyses. A genomic coordinate file was compiled by extending the 3’ end of each original sequence to a total of 200 bp. The number of reads within 10,000 bases of the TSS of each gene in the custom gene list was tabulated. Similar analysis was applied to the location of center of peaks generated from the peak finding algorithm for the region within 500 bp relative to the TSS. Heat maps were generated using the program R. Genes were rank ordered based on the sequence density for RNAP II from -2K to +2K from the TSS. Using this order, basepair resolution sequence density for RNAP II and Gdown1 for the top 20,000 genes was displayed without binning. A peak finding algorithm (ChIP-Seq Peak) was designed to examine the data within individual WIG files and determine precise position and height of each significant peak. This algorithm assumes that each 200 bp immunoprecipitated DNA fragment is sequenced randomly from either end and that typical peaks would be approximately 400 bases wide at the base. Peaks less than 250 bp wide were eliminated and the center of each remaining peak was determined using Gaussian curve fitting. The height was determined by the area under each peak.

source_name: RNA Pol II Control

growth_protocol: HeLa cells were maintained at 5% CO2 and 37°C in DMEM plus 10% FBS (Hyclone). Cells were grown in T-150 flasks to 90% confluence and treated for 5 or 60 minutes with Flavopiridol (final concentration 1 μM with 0.1% DMSO) or 0.1% DMSO alone for control.

extract_protocol: For each immunoprecipitation, 5 x 10^7-1 x 10^8 cells were used. 1/10 volume of fresh 11% paraformaldehyde solution was added directly into the plates and cells were cross-linked for 15 minutes at room temperature. Cross-linking was stopped by adding glycine. Cells were washed and pelleted in PBS and resuspended in ice cold Lysis Buffer 1 for 10 minutes, then pelleted and resuspended in ice cold Lysis buffer 2 for another 10 minutes, and then the cells were pelleted and resuspended in ice cold Lysis buffer 3. After sonication, DNA fragments (<500 bp) were spun to pellet debris. For each immunoprecipitation 100 μL of Protein G Dynabeads (Invitrogen) were used. The beads were washed with Block Solution three times and resuspended in 250 μL Block Solution. The beads were incubated with 10 μg of RNAP II antibody at 4°C overnight. For ChIP-Seq, the N-20 antibody (Santa Cruz, sc-899) was used which recognizes the N-terminus of Rpb1. Then the beads were washed with Block Solution three times, resuspended in 100 μL of Block Solution, and incubated with the sonicated cell lysate at 4°C overnight. After the incubation, beads were washed four times with RIPA buffer, once with a buffer containing TE and 50 mM NaCl. Immunocomplexes were eluted for 30 minutes at 65°C with Elution buffer and the beads were removed with a magnetic concentrator. Reverse crosslinking was performed for both the immunoprecipitated DNA and for the input DNA samples by an incubation at 65°C for a minimum of six hours. DNA was purified through ethanol precipitation and then used for ChIP-Seq. The DNA fragments were isolated from an agarose gel, blunt-ended, ligated to the Solexa adaptors, and sequenced using the Illumina 1G Genome Analyzer.

value: HeLa

value: N-20 antibody (Santa Cruz, sc-899)


title: RNA Pol II siRNA Control

source_name: RNA Pol II siRNA Control


title: RNA Pol II Flavo 5min

source_name: RNA Pol II Flavo 5min

value: 5min flavopiridol treatment


title: Gdown1 Control

source_name: Gdown1 Control

value: Gdown1 antibody (in-house)


title: MEF_STAT5-OE-IP_repeat

status: Public on Jan 12 2012

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

description: processed data files: mm9_OE-GH2_repeat_STAT5_Peaks.bed, mm9_OE-GH2_repeat_STAT5_Peaks.bedgraph (available as Series supplementary files)

data_processing: Experimental data sets came from wild type (WT-GH), Stat5-/- (KO-GH) and Stat5-/-overexpressing STAT5A (OE-GH) MEFs upon GH stimulation. The mapped tags of STAT5 antibodies and IgG samples were analyzed using the MACS program (http://liulab.dfci.harvard.edu/MACS/) with the following parameters; -mfold = 10,20 -g mm -p 1.0e-4 (p-value cutoff). The identified peaks were further split by using PeakSplitter (http://www.ebi.ac.uk/bertone/software.html). ChIP-seq data obtained from GH-treated Stat5-/- MEFs (Transfected with an empty vector, KO-empty-GH) served as negative controls and were independently processed with the same parameters. We utilized the GAS motif information to accurately identify bona fide STAT5 binding sites. The FIMO DNA motif identification tool (http://meme.nbcr.net/meme/cgi-bin/fimo.cgi) was used to scan the peak regions with a STAT5 position-specific scoring matrix (p-value threshold: 1e-3). The peaks including at least one GAS motif within their peak regions were regarded as bona fide STAT5 binding and used in this study.

growth_protocol: Stat5+/- mice were bred into the C57BL/6 background. Stat5+/- mice were intercrossed and mouse embryonic fibroblasts (MEFs) were isolated from 12.5-13.5-day fetuses. MEFs were expanded in DMEM with high glucose supplements and 15% fetal bovine serum (FBS). MEFs of passage 9-10 were used for experiments.

extract_protocol: After 5-hour starvation, WT, Stat5-/-, or STAT5A-Stat5-/- MEFs were stimulated with or without 1 ug/ml GH for 45 min. MEFs were then cross-linked with 1% formaldehyde for 10 min. Chromatin from 5 × 10^6 cells was used for each ChIP experiment. Antibodies against STAT5 (sc-835, Santa Cruz, California) and IgG (AB-105C, R&D System) were used. The ChIP DNA fragments were blunt-ended, ligated to the Solexa paired-end adaptors, and sequenced with the Illumina Hi-seq 2000 genome analyzer.

treatment_protocol: After 5 hours starvation in serum free medium with 0.1% of BSA, MEFs were treated with growth hormone for indicated time period.

tag: background strain

tag: genotype/variation

value: STAT5 overexpression; STAT5A-Stat5-/-

tag: tissue origin

value: 12.5-13.5-day fetuses

value: mouse embryonic fibroblasts (MEFs)

tag: passages

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: MEF_STAT5-KO-empty-GH-IgG

value: STAT5 KO; Stat5-/-

tag: cell type

tag: stimulated with

value: 1 ug/ml growth hormone (GH) for 45 min

tag: chip antibody

value: IgG control

value: R&D System


title: Gdown1 Flavo

source_name: Gdown1 Flavo

tag: cell line

value: 60min flavopiridol treatment


title: MEF_STAT5-OE-GH-IgG

description: processed data files: mm9_OE-GH_STAT5_Peaks.bed, mm9_OE-GH_STAT5_Peaks.bedgraph (available as Series supplementary files)


title: RNA Pol II Flavo 60min

source_name: RNA Pol II Flavo 60min


title: MEF_STAT5-KO-GH-IP


title: Rice_root-time_point_2-replicate_2

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

data_processing: Reads were mapped to the Oryza sativa subsp. Japonica reference genome (build MSU6.0) in two phases using TopHat (v 1.3.1) and Cufflinks (v 1.0.3). This software requires Samtools (v 0.1.12a) which was downloaded from “http://samtools.sourceforge.net/”. The Bowtie index was constructed with the ‘bowtie-build’ command (v 0.12.7) from the chromosomal fasta files at “ftp://ftp.ensemblgenomes.org/pub/release-10/plants/fasta/oryza_sativa/dna/”. In the first phase the reads from all samples were mapped together using TopHat, maximising sensitivity, to create the input file for Cufflinks. The Ensembl reference annotation in GTF format (“ftp://ftp.ensemblgenomes.org/pub/release-10/plants/gtf/oryza_sativa/”) was used to provide established junctions via the ‘–G’ option. Further standard parameters were used with exception of following options: --bowtie-n, --initial-read-mismatches 1, -g 10, -a 10, -m 1, -i 30, --solexa1.3-quals. The next step consisted of applying Cufflinks to construct a minimal set of transcripts using reference annotation based transcript (RABT) assembly, again based on the Ensembl MSU6 GTF annotation file. Standard settings were used with the exception of following options:  -u, -I 500000, --min-intron-length 30. In the second phase all samples were remapped separately using the same TopHat settings with the following two exceptions: the ‘transcripts.gtf’ output from Cufflinks was used to supply junctions and ‘--no-novel-juncs’ was added to prevent TopHat from introducing new sample specific junctions that weren’t detected in the first phase.  All mapped reads were summed per gene (indiscriminate of splice variants) and per sample to represent expression values. Genes for which  5' or 3'  extensions were detected, are marked with the suffix "-ext". Putative nTARs are also included in this summary count table (see publication for nTAR methods). Genes without mapped tags in any of the samples are not included.

organism: Oryza sativa Japonica Group

source_name: Rice root

growth_protocol: Seeds were germinated in the dark on wet filter paper at 30°C for five days and then transferred to SAP-substrate (Reversat et al. 1999) and further grown at 26°C under a 12h/12h light-regime (150 µmol/m² s). When the seedlings were 12 days old they were transferred to a hydroponic system containing Hoagland solution, and the whole plant was exposed to light. At 2 days and 6 days after transfer to hydroponics root tissues were sampled.

extract_protocol: RNA was extracted using the RNeasy Plant Mini Kit (Qiagen), with an additional sonication step after addition of buffer RLT (Qiagen).  Approximately two microgram of total RNA from rice roots and rice root tips were used for mRNA-Seq library construction according to the manufacturer’s recommendations (Illumina). The mRNA was isolated from the total RNA using oligo dT-attached magnetic beads and subsequently fragmented using divalent cations under elevated temperature. First-strand cDNA was generated with reverse transcriptase and random primers. After second-strand cDNA synthesis and adaptor ligation, cDNA fragments of approximately 200 bp were isolated by gel electrophoresis. cDNA fragments were amplified by 18 cycles of PCR using the multiplexing primers from the ‘Multiplexing sample preparation kit’.

treatment_protocol: The root tips, encompassing the meristem and the elongation zone, were excised with a scalpel from the remaining root system (‘mature root’). Multiple independent biological replicates, each containing a pool of 6 different plants, were sampled.

tag: tissue

value: root

value: cv. Nipponbare (GSOR-100)

tag: growth conditions

value: hydroponic culture for 6 days


title: MEF_STAT5-OE-GH-IP


title: Rice_root-time_point_2-replicate_1


title: MEF_STAT5-OE-IP

description: processed data files: mm9_OE_STAT5_Peaks.bedgraph (available as Series supplementary files)


title: MEF_STAT5-WT-GH-IgG

description: processed data files: mm9_WT-GH_STAT5_Peaks.bed, mm9_WT-GH_STAT5_Peaks.bedgraph (available as Series supplementary files)

value: STAT5 wild type


title: MEF_STAT5-WT-GH-IP


title: Rice_root-time_point_1-replicate_1

value: hydroponic culture for 2 days


title: RNA Pol II siRNA Gdown1

source_name: RNA Pol II siRNA Gdown1

value: HeLa

value: N-20 antibody (Santa Cruz, sc-899)

value: Gdown1 siRNA treatment


title: Rice_root_tip-time_point_2-replicate_2

source_name: Rice root tip

value: root tip


title: Rice_root_tip-time_point_2-replicate_3


title: ERα ChIP-seq 4

data_processing:
BED: Sequence reads were obtained and mapped to the human (March, 2006) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows. Counts included.
BEDGRAPH: Peak detection was performed with BELT program
Genome Build:
t24_export.txt_unique.EE_W100_P0.951.bed: hg18
t24_export.txt_unique.EE_W100.bedgraph: hg18

tag: cell lines

tag: agent

tag: time

value: 24 hr

value: ERα, Santa Cruz Biotechnology, sc-8005 X


title: Rice_root_tip-time_point_2-replicate_1


title: poly(A)+ RNAs from 8-cell embryos derived from from Cvi-0 x Col-0 crosses

city: Cambridge

first: Michael

middle: D

last: Nodine

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing: After removing adaptor sequences, reads were mapped to both the A. thaliana genome and transcript models (Col-0 genome reference, TAIR10) with the Bowtie short-read aligner. Reads were also mapped to a ‘pseudo’ Cvi-0 genome and Cvi-0 transcript models, in which SNPs in the Col-0 genome and transcript models were replaced with Cvi-0 variants (ftp://ftp.arabidopsis.org/home/tair/Sequences/Ecker_Cvi_snps.txt) generated by the 1,001 Genomes Project. Reads that both perfectly and uniquely matched either the genomes or transcript models were retained, and those overlapping transcribed regions of annotated genes were evaluated for overlap with SNPs. To normalize for differences in library sizes, the numbers of reads representing each transcript were divided by the total number of reads matching the genome and transcript models. SNP-overlapping reads were assigned to one of the parental genomes and tallied for each transcript, combining tallies for multiple SNPs within the same transcript.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown at 22° C in a Conviron growth chamber with a 16-h light/8-h dark cycle.

extract_protocol: Strand-specific mRNA-Seq libraries were generated as described by Guo et al. (Nature, 2010)

treatment_protocol: Flowers were emasculated one day before crossing, and pools of twenty 1-cell/2-cell, 8-cell and ~32-cell embryos were hand-dissected approximately 40, 64 and 78 hours after pollination, respectively. Embryo dissections, RNA isolation and linear amplification of poly(A) RNA was as described (Nodine and Bartel, 2010, Genes & Development), except that embryos were extensively washed prior to RNA isolation.

tag: ecotype

value: Cvi-0/Col-0 hybrids

value: embryos

tag: developmental stage

value: 8-cell embryo proper


title: MEF_STAT5-OE-GH-IP_repeat

tag: background strain

value: STAT5 overexpression; STAT5A-Stat5-/-

value: 12.5-13.5-day fetuses

value: mouse embryonic fibroblasts (MEFs)

value: 1 ug/ml growth hormone (GH) for 45 min

value: Santa Cruz


title: MEF_STAT5-KO-empty-GH-IP

tag: genotype/variation

value: STAT5 KO; Stat5-/-


title: MEF_STAT5-KO-GH-IgG

tag: tissue origin

value: IgG control

value: R&D System


title: poly(A)+ RNAs from 1-cell/2-cell embryos derived from from Cvi-0 x Col-0 crosses

value: 1-cell/2-cell embryo proper


title: Rice_root_tip-time_point_1-replicate_3

tag: strain

value: cv. Nipponbare (GSOR-100)

value: hydroponic culture for 2 days


title: Rice_root_tip-time_point_1-replicate_2

value: root tip


title: poly(A)+ RNAs from 1-cell/2-cell embryos derived from from Col-0 x Cvi-0 crosses

value: Col-0/Cvi-0 hybrids


title: PolII Chip-Seq

city: Kansas City

first: Marco

last: Blanchette

institute: Stowers Institute for Medical Research

data_processing: ALIGNMENT: Prinary sequencing results (fastq files) were aligned to the human genome (hg19) with bowtie using the following options “-S -a -p6 -m1 -n2 --best –strata” and the resulting alignments were converted to binary sorted alignments in BAM format using the SamTools {Li, 2009 #740}.

source_name: Cell culture

growth_protocol: HCT116 cells were seeded in 100-mm-diameter plates and grown in normal conditions (10% FBS, DMEM).

extract_protocol: ChIP-Seq DNA Sample Prep Kit (Illumina)

treatment_protocol: When cells reach 70-80% confluence they were fixed with 1% formaldehyde to crosslink the chromatin and were incubated at room temperature for 10 min. Subsequently, the cells were washed two times with ice-cold phosphate-buffered saline (PBS).  Chromatin IP were performed with antibody H-224 against RNA pol II (sc-9001, Santa Cruz Biotechnology) using the procedure described in Svotelis et al., 2009. (Svotelis A, Gévry N, Gaudreau L. Methods Mol Biol. 2009;543:243-51)

value: anti-RNAPII H-224

tag: vendor

value: Santa Cruz Biotechnology

tag: catalog


title: Rice_root-time_point_1-replicate_2

value: root


title: poly(A)+ RNAs from ~32-cell embryos derived from from Col-0 x Cvi-0 crosses

value: embryos

value: ~32-cell embryo proper


title: BrCaCohort-87

status: Public on Jan 11 2012

first: Fei

last: Gu

state: Ohio

department: Molecular Virology, Immunology & Medical Genetics

institute: The Ohio State University

description:
MBDCap
library strategy: MBDCap-seq
library selection: MBDCap-seq

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) hg18 genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: Human breast cells

growth_protocol: Endometrial samples and Breast cohorts: N/A. Breast cells: Breast cells were routinely cultured in dishes and changed medium every 3 days.

extract_protocol:
Genomic DNA was isolated by standard methods or by the QIAamp DNA Mini Kit (Qiagen) following the manufacturer's protocol.
Methylated DNA was eluted by the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer's instructions. Briefly, one microgram of genomic DNA was sonicated and captured by MBD proteins. The methylated DNA was eluted in 1 M salt buffer. DNA in each eluted fraction was precipitated by glycogen, sodium acetate and ethanol, and was resuspended in TE buffer. Eluted DNA was used to generate libraries for sequencing following the standard protocols from Illumina. MBDCap-seq libraries were sequenced using the Illumina Genome Analyzer II as per manufacturer's instructions.
Illumina ChIP protocol

treatment_protocol: Endometrial samples and Breast cohorts: N/A. Breast cells: No treatment.

value: Human breast cells

tag: cell type

value: primary tissues

tag: disease status

value: Breast cancer cohort

tag: chromatin selection

value: MBD protein


title: BrCaCohort-80


title: BrCaCohort-83


title: BrCaCohort-82


title: BrCaCohort-81


title: BrCaCohort-84


title: BrCaCohort-79


title: BrCaCohort-78


title: BrCaCohort-76


title: MEF_STAT5-OE-IgG

value: STAT5 overexpression; STAT5A-Stat5-/-

value: 12.5-13.5-day fetuses

value: mouse embryonic fibroblasts (MEFs)

tag: passages

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #


title: BrCaCohort-75

tag: tissue


title: BrCaCohort-73


title: BrCaCohort-77


title: BrCaCohort-74


title: BrCaCohort-72


title: BrCaCohort-70


title: poly(A)+ RNAs from 8-cell embryos derived from from Col-0 x Cvi-0 crosses

value: 8-cell embryo proper


title: Rice_root_tip-time_point_1-replicate_1

value: cv. Nipponbare (GSOR-100)

tag: growth conditions


title: BrCaCohort-85


title: BrCaCohort-69


title: BrCaCohort-86


title: BrCaCohort-68


title: BrCaCohort-71


title: BrCaCohort-67


title: BrCaCohort-66


title: BrCaCohort-64


title: BrCaCohort-63


title: poly(A)+ RNAs from ~32-cell embryos derived from from Cvi-0 x Col-0 crosses

tag: ecotype

value: Cvi-0/Col-0 hybrids


title: BrCaCohort-65


title: BrCaCohort-59


title: BrCaCohort-62


title: BrCaCohort-61


title: BrCaCohort-60


title: BrCaCohort-57


title: BrCaCohort-56


title: BrCaCohort-55


title: BrCaCohort-54


title: BrCaCohort-53


title: BrCaCohort-58


title: BrCaCohort-51


title: BrCaCohort-50


title: BrCaCohort-52


title: BrCaCohort-49


title: BrCaCohort-48


title: BrCaCohort-46


title: BrCaCohort-47


title: BrCaCohort-45


title: BrCaCohort-41


title: BrCaCohort-44


title: BrCaCohort-40


title: BrCaCohort-39


title: BrCaCohort-38


title: BrCaCohort-37


title: BrCaCohort-36


title: BrCaCohort-34


title: BrCaCohort-35


title: BrCaCohort-33


title: BrCaCohort-31


title: BrCaCohort-29


title: BrCaCohort-32


title: BrCaCohort-27


title: BrCaCohort-28


title: BrCaCohort-26


title: BrCaCohort-24


title: BrCaCohort-25


title: BrCaCohort-20


title: BrCaCohort-21


title: BrCaCohort-22


title: BrCaCohort-42


title: BrCaCohort-19


title: BrCaCohort-16


title: BrCaCohort-43


title: BrCaCohort-17


title: BrCaCohort-15


title: BrCaCohort-18


title: BrCaCohort-14


title: BrCaCohort-13


title: BrCaCohort-11


title: BrCaCohort-10


title: BrCaCohort-30


title: BrCaCohort-8


title: BrCaCohort-7


title: BrCaCohort-6


title: BrCaCohort-5


title: BrCaCohort-9


title: BrCaCohort-4


title: BrCaCohort-23


title: BrCaCohort-2


title: BrCaCohort-1


title: Breast normal 3

description:
MBDCap using MethylMiner Methylated DNA Enrichment Kit (Invitrogen, ME 10025)
library strategy: Endometrial samples: MBDCao-seq. Breast cells: MBDCap-seq.
library selection: Endometrial samples: MBDCap. Breast cells: MBDCap-seq.

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

growth_protocol: Endometrial samples: N/A. Breast cells: Breast cells were routinely cultured in dishes and changed medium every 3 days.

treatment_protocol: Endometrial samples: N/A. Breast cells: No treatment.

value: Epithelial cells

value: normal


title: Breast normal 2


title: Breast normal 1


title: BrCa-70

value: BrCa


title: BrCa-72


title: BrCa-59


title: BrCa-60


title: BrCaCohort-12


title: BrCa-55


title: BrCa-51


title: BrCa-63


title: BrCa-44


title: BrCa-49


title: BrCa-65


title: BrCa-50


title: BrCa-43


title: BrCa-41


title: BrCa-40


title: BrCaCohort-3


title: BrCa-37


title: BrCa-38


title: BrCa-25


title: BrCa-32


title: BrCa-33


title: BrCa-23


title: BrCa-20


title: BrCa-68


title: BrCa-17


title: BrCa-67


title: BrCa-16


title: BrCa-15


title: BrCa-12


title: BrCa-11


title: BrCa-10


title: BrCa-09


title: BrCa-08


title: BrCa-06


title: BrCa-07


title: BrCa-03


title: BrCa-02


title: BrCa-01


title: Endometrial Recurrent 14 redo

source_name: Human endometrial specimen

value: Human endometrial specimen

value: Recurrent


title: Endometrial Non-recurrent 28 redo

value: Non-recurrent


title: Endometrial Non-recurrent 51 redo


title: BrCa-05


title: Endometrial Non-recurrent 47 redo


title: Endometrial Recurrent 13 redo


title: Endometrial Non-recurrent 46 redo


title: Endometrial Recurrent 2 redo


title: Endometrial Normal 8

value: Normal


title: Endometrial Non-recurrent 5 redo


title: Endometrial Non-recurrent 31 redo


title: Endometrial Non-recurrent 2 redo


title: Endometrial Normal 12


title: Endometrial Normal 11


title: Endometrial Normal 5


title: Endometrial Normal 4


title: Endometrial Normal 3


title: Endometrial Normal 10


title: BrCa-14

value: Human breast cells


title: Endometrial Normal 1

value: primary tissues


title: Endometrial Normal 9


title: Endometrial Recurrent 20


title: Endometrial Normal 2


title: Endometrial Recurrent 21


title: Endometrial Recurrent 19


title: Endometrial Recurrent 18


title: Endometrial Recurrent 16


title: Endometrial Recurrent 17


title: Endometrial Non-recurrent 3 redo


title: Endometrial Recurrent 14


title: Endometrial Recurrent 12


title: Endometrial Recurrent 10


title: Endometrial Recurrent 13


title: Endometrial Recurrent 11


title: Endometrial Normal 6


title: Endometrial Recurrent 9


title: Endometrial Normal 7


title: Endometrial Recurrent 7


title: Endometrial Recurrent 4


title: Endometrial Recurrent 6


title: Endometrial Recurrent 8


title: Endometrial Recurrent 2


title: Endometrial Recurrent 3


title: Endometrial Recurrent 1


title: Endometrial Recurrent 5


title: Endometrial Non-recurrent 71


title: Endometrial Non-recurrent 70


title: Endometrial Non-recurrent 66


title: Endometrial Recurrent 15


title: Endometrial Non-recurrent 64


title: Endometrial Non-recurrent 63


title: Endometrial Non-recurrent 69


title: Endometrial Non-recurrent 65


title: Endometrial Non-recurrent 61


title: Endometrial Non-recurrent 62


title: Endometrial Non-recurrent 57


title: Endometrial Non-recurrent 59


title: Endometrial Non-recurrent 55


title: Endometrial Non-recurrent 56


title: Endometrial Non-recurrent 54


title: Endometrial Non-recurrent 60


title: Endometrial Non-recurrent 51


title: Endometrial Non-recurrent 52


title: Endometrial Non-recurrent 53


title: Endometrial Non-recurrent 50


title: Endometrial Non-recurrent 47


title: Endometrial Non-recurrent 49


title: Endometrial Non-recurrent 48


title: Endometrial Non-recurrent 46


title: Endometrial Non-recurrent 45


title: Endometrial Non-recurrent 43


title: Endometrial Non-recurrent 67


title: Endometrial Non-recurrent 68


title: Endometrial Non-recurrent 42


title: Endometrial Non-recurrent 41


title: Endometrial Non-recurrent 39


title: Endometrial Non-recurrent 40


title: Endometrial Non-recurrent 58


title: Endometrial Non-recurrent 35


title: Endometrial Non-recurrent 36


title: Endometrial Non-recurrent 34


title: Endometrial Non-recurrent 37


title: Endometrial Non-recurrent 30


title: Endometrial Non-recurrent 31


title: Endometrial Non-recurrent 29


title: Endometrial Non-recurrent 26


title: Endometrial Non-recurrent 25


title: Endometrial Non-recurrent 44


title: Endometrial Non-recurrent 24


title: Endometrial Non-recurrent 22


title: Endometrial Non-recurrent 21


title: Endometrial Non-recurrent 23


title: Endometrial Non-recurrent 19


title: Endometrial Non-recurrent 18


title: Endometrial Non-recurrent 38


title: Endometrial Non-recurrent 11


title: Endometrial Non-recurrent 12


title: Endometrial Non-recurrent 17


title: Endometrial Non-recurrent 13


title: Endometrial Non-recurrent 15


title: Endometrial Non-recurrent 33


title: Endometrial Non-recurrent 16


title: Endometrial Non-recurrent 28


title: Endometrial Non-recurrent 7


title: Endometrial Non-recurrent 10


title: Endometrial Non-recurrent 9


title: Endometrial Non-recurrent 4


title: Endometrial Non-recurrent 5


title: Seedling A [SL68]

status: Public on Jan 10 2012

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description:
Samples name: SL68
small RNA sequencing

data_processing:
Sequences were called using the standard Illumina pipeline.
Reads were trimmed using perfect matching to adaptor sequences.
Alignment to the A. thaliana genome [TAIR 10 (NCBI build Arabidopsis thaliana 9.1)] was performed with the PatMaN algorithm with no mismatches permitted.

source_name: Seedling tissue sRNAs

extract_protocol: Illumina small RNA cloning kit, version 1.

value: Seedling

tag: lab

value: UEA


title: Endometrial Non-recurrent 20

value: MBD protein


title: Silique B [SL90_1]

description:
Samples name: SL90_1
small RNA sequencing

source_name: Silique tissue sRNAs

value: Silique

value: University of Cambridge


title: Endometrial Non-recurrent 3


title: Endometrial Non-recurrent 14


title: Seedling A [SL69]

description:
Samples name: SL69
small RNA sequencing


title: Endometrial Non-recurrent 1


title: Endometrial Non-recurrent 8


title: Leaf B [SL161]

description:
Samples name: SL161
small RNA sequencing

source_name: Leaf tissue sRNAs

value: Leaf


title: Endometrial Non-recurrent 2


title: Seedling A [SL96]

description:
Samples name: SL96
small RNA sequencing


title: Floral B [SL335]

description:
Samples name: SL335
small RNA sequencing

source_name: Floral tissue sRNAs

value: Floral


title: Floral B [SL334]

description:
Samples name: SL334
small RNA sequencing


title: Floral A (SL30_124) [SL30_4]

description:
Samples name: SL30_4
small RNA sequencing


title: Floral B  [SL99]

description:
Samples name: SL99
small RNA sequencing


title: Floral A [SL31]

description:
Samples name: SL31
small RNA sequencing


title: Floral A (SL30_124) [SL30_1]

description:
Samples name: SL30_1
small RNA sequencing


title: Floral A (SL30_124) [SL30_2]

description:
Samples name: SL30_2
small RNA sequencing


title: T-ALL Notch1

city: Yorktown Heights

first: Aristotelis

last: Tsirigos

state: NY

address: 1101 Kitchawan Road, Route 134

department: Computational Biology Center

institute: IBM Research

description: ChIP-Seq analysis for Notch1 in T-ALL cells

data_processing:
We aligned the sequenced reads to the genome (mouse assembly NCBIM37/mm9) using Burrows-Wheeler Alignment (BWA) with maximum two mismatches. The ChIP-seq reads were validated regarding the reproducibility of the replicates, and the sensitivity and specificity of each activating and repressive histone mark in classifying genes of high versus low expression and average read profiles of genes of high expression versus genes of low expression were constructed in TSSs flanked by 10 kb.
We determined epigenetic changes between the double-positive and T-ALL samples by evaluating sliding windows across the genome using an approach adapted from PeakSeq. We performed all ChIP-seq read data manipulations using GenomicTools (http://code.google.com/p/ibm-cbc-genomic-tools/), and the algorithm for identifying epigenetic changes in T-ALL compared to double-positive was implemented in R language. Notch1 ChIP-seq peaks in T-ALL were determined using MACS.

source_name: T-ALL Notch1

extract_protocol: ChIP-seq libraries were generated using standard Illumina kit and protocol. We started preparing libraries using 5 to 10ngs of DNA. We sequenced 6.5 pmoles of library preparation using GAII illumina sequencer. We performed 36bp (34bp after processing) single-end run.

treatment_protocol: We fixed the cells with 1% formaldehyde for 10 min at 25oC and mononucleosomal particles were generated using micrococcal nuclease (from USB). We stopped the reaction with the addition of EDTA (20 mM), and the nuclei were lysed using the ‘Nuclei lysis buffer’ (50 mM Tris-HCl pH 8.0), 10 mM EDTA (pH 8.0) and 1% SDS) followed by sonication (2.5 min in total) using the bioruptor from Diagenode and addition of nine volumes of ‘IP dilution’ buffer  (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA (pH 8.0), 16.7 mM Tris-HCl pH 8.0 and 167 mM NaCl) and addition of magnetic Dynal beads (preclearing of chromatin). For the ChIP of Notch1, we fixed the cells with 1% formaldehyde for 10 min at 25oC and lysed them using the ‘cell lysis’ buffer (5 mM HEPES pH 8.0, 85 mM KCl and 0.5% NP-40). We lysed the nuclei using the Nuclei lysis buffer (50 mM Tris-HCl pH 8.0), 10 mM EDTA (pH 8.0) and 1% SDS) followed by sonication (40 min in total) using the bioruptor from Diagenode and addition of nine volumes of IP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA pH 8.0, 16.7 mM Tris-HCl pH8.0 and 167 mM NaCl) and addition of magnetic Dynal beads (preclearing of chromatin). We used standard ChIP procedures adapted to our cell numbers (~1–5 ´ 106 cells) for ChIP.

value: Notch1-IC over-expressing tumors (T-ALL)


title: T-ALL mnase input replicate 2

description: ChIP-Seq analysis for input in T-ALL cells replicate 2

source_name: T-ALL mnase input

value: none (input)


title: Endometrial Non-recurrent 6


title: T-ALL mnase input replicate 1

description: ChIP-Seq analysis for input in T-ALL cells replicate 1


title: T-ALL sonicated input

description: ChIP-Seq analysis for sonicated input in T-ALL cells

source_name: T-ALL sonicated input


title: T-ALL H3K4me3 replicate 2

description: ChIP-Seq analysis for H3K4me3 in T-ALL cells replicate 2

source_name: T-ALL H3K4me3


title: T-ALL H3K9ac replicate 1

description: ChIP-Seq analysis for H3K9ac3 in T-ALL cells replicate 1

source_name: T-ALL H3K9ac


title: T-ALL H3K9ac replicate 2

description: ChIP-Seq analysis for H3K9ac3 in T-ALL cells replicate 2


title: T-ALL H3K4me3 replicate 1

description: ChIP-Seq analysis for H3K4me3 in T-ALL cells replicate 1


title: Leaf A [SL382_H]

description:
Samples name: SL382_H
small RNA sequencing


title: T-ALL H3K27me3 replicate 2

description: ChIP-Seq analysis for H3K27me3 in T-ALL cells replicate 2

source_name: T-ALL H3K27me3


title: DP mnase input replicate 1

description: ChIP-Seq analysis for Micrococcal Nuclease-treated input in Normal DP cells replicate 1

source_name: DP mnase input

value: CD4+/8+ Double Positive (DP) cells


title: DP H3K9ac replicate 1

description: ChIP-Seq analysis for H3K9ac in Normal DP cells replicate 1

source_name: DP H3K9ac


title: DP H3K9ac replicate 2

description: ChIP-Seq analysis for H3K9ac in Normal DP cells replicate 2


title: DP H3K27me3 replicate 2

description: ChIP-Seq analysis for H3K27me3 in Normal DP cells replicate 2

source_name: DP H3K27me3


title: DP mnase input replicate 2

description: ChIP-Seq analysis for Micrococcal Nuclease-treated input in Normal DP cells replicate 2


title: Leaf A [SL381_A]

description:
Samples name: SL381_A
small RNA sequencing


title: T-ALL H3K27me3 replicate 1

description: ChIP-Seq analysis for H3K27me3 in T-ALL cells replicate 1


title: DP H3K27me3 replicate 1

description: ChIP-Seq analysis for H3K27me3 in Normal DP cells replicate 1


title: DP H3K4me3 replicate 2

description: ChIP-Seq analysis for H3K4me3 in Normal DP cells replicate 2

source_name: DP H3K4me3


title: E_coli_transcriptome_1

status: Public on Jan 07 2012

first: Tony

middle: Z

last: Jia

address: 12 Oxford St.

department: Chemistry and Chemical Biology

institute: Harvard University

data_processing:
Using a combination of python (3.2.1) and bowtie(0.12.7), from the raw sequencing data, we isolated reads which contained barcode sequences that corresponded to our original list of single molecule barcodes in both forward and reverse reads for each sequence pair that had at most one mismatch. We then aligned the first 28 bases (26 bases for the second sequencing run) of the targeted sequence of both the forward and reverse reads of each cluster to the E. coli genome and kept the sequences that uniquely align fewer than three mismatches and where the two reads did not map to the same sense or antisense strand of the genome.  We used a detailed filtering process to determine the identity of closely-mapped reads. Mapped sequence fragments with a length of at least 1,000 bases were discarded.  All sequences within the same transcription unit that had the same unique tag were analyzed further. We determined that more than one sequence with the same unique tag were identical if the distance between their center positions was less than four base-pairs and if the difference in length was less than 9 base-pairs. Then for each unique sequence, we counted the number of unique barcode tags that appeared to determine the copy number of each sequence and mapped each of them to genes. We include indexed genome viewer files (.sam and .sai) for both experiments using both the conventional method and the digital method.
Genome build: E. coli [K-12 MG1655 strain (U00096.2)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: RNA from Escherichia coli

growth_protocol: E. coli [K-12 MG1655 strain (U00096.2)] was grown overnight at 30 °C in LB medium.  The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35.

extract_protocol: Standard Paired-End Illumina Library Construction Protocol was used with modified adapters containing optimized 20 bp barcode sequences (see original paper).  Samples with barcoded adapters were sequenced on an Illumina HiSeq 2000 with a 2x101 (for the first sequencing run) and 2x51 (for the second) base paired-end reads in one lane.

treatment_protocol: RNA was purified by a standard protocol using Phenol Chloroform.  Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria) (Epicentre, Illumina).  Then, the conventional Illumina protocol for mRNA Sequencing Sample Preparation was applied with a few modifications (see original paper).

tag: reference genome

tag: genotype

value: F-, lambda-, rph-1


title: CCL-125 CHIKV

status: Public on Jan 06 2012

city: Blacksburg

first: Kevin

last: Myles

state: VA

address: Fralin Biotechnology Center

department: Fralin Life Science Institute

institute: Virginia Tech

data_processing: After removal of adaptor sequences and non-coding RNA sequences (rRNAs, tRNAs, snoRNAs, etc.) processed reads were mapped to the CHIKV genome (strain 37997) using Bowtie (v-mode, permitting 1 mismatch). In order to compare small RNA reads between libraries we normalized using the TMM method implemented by the edgeR software package (http://www.bioconductor.org). Differential expression analysis between normalized read counts was done using the A-C statistic. We generated Weblogo 3 (http://weblogo.threeplusone.com) plots to analyze the frequency of nucleotide usage in small RNA reads of an identical size class.

organism: Aedes aegypti

source_name: larva

extract_protocol: As described in Illumina's Small RNA sample preparation guide (Cat# FC-102-1009)

tag: infection

value: CCL-125 CHIKV

value: larva

tag: days post infection


title: E_coli_transcriptome_2

tag: strain


title: DP H3K4me3 replicate 1

description: ChIP-Seq analysis for H3K4me3 in Normal DP cells replicate 1


title: C6/36 CHIK B2 (FHV) c44a rep2 (truSeq)

organism: Aedes albopictus

extract_protocol: total and viral RNA, As described in Illumina's Small RNA sample preparation guide (Cat# FC-102-1009)

value: C6/36 CHIK B2 (FHV) c44a


title: Aag2 CHIKV

source_name: embryos

value: Aag2 CHIKV

value: embryos


title: C6/36 CHIK B2 (FHV) c44a rep3 (truSeq)


title: C6/36 CHIK B2 (FHV) c44a rep1 (truSeq)


title: Ae. aegypti WB CHIKV

source_name: Whole body

value: WB CHIKV

value: Whole body


title: C6/36 CHIKV B2(FHV) rep1 (truSeq)

value: C6/36 CHIKV B2(FHV)


title: C6/36 B2 (FHV) c44y


title: C6/36 CHIKV B2(FHV) rep3 (truSeq)


title: C6/36 CHIKV B2(FHV) rep2 (truSeq)


title: C6/36 B2 (FHV) r54q


title: C7-10 CHIKV

value: C7-10 CHIKV


title: U4.4 CHIKV

value: U4.4 CHIKV


title: C6/36 CHIKV

value: C6/36 CHIKV


title: C6/36 CHIKV B2(FHV)


title: Ae. albopictus HT CHIKV-B2(FHV)

source_name: head and thorax

value: HT CHIKV-B2(FHV)

value: head and thorax


title: Ae. albopictus HT CHIKV

value: HT CHIKV


title: Ae. albopictus HT CHIKV-ΔB2(NOV)

value: HT CHIKV-ΔB2(NOV)


title: Ae. albopictus WB CHIKV


title: small RNA sequencing from wild type C. elegans from a  a time-course RNAi experiment, 4 hours

city: Piscataway

first: Sam

middle: Guoping

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
SG0511_lib8.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

organism: Caenorhabditis elegans

source_name: larval L4 stage C. elegans

growth_protocol: RNAi by feeding was carried out as previously described (Timmons, L. & Fire, A. Specific interference by ingested dsRNA. Nature 395, 854 (1998).)

extract_protocol: Libraries of small RNAs were prepared using a protocol similar to one previously described for miRNA cloning (LAU, N. C., L. P. LIM, E. G. WEINSTEIN and D. P. BARTEL, 2001 An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858–862.), in which small RNA species were flanked by adapter sequences to allow for PCR and sequencing. We modified the original protocol at several key steps to allow for capture of triphosphorylated species and for sequencing with the Illumina genome analyzer system. To remove the bias for 5′ monophosphorylated species but preserve the bias toward 3′ hydroxylated species, we removed both monophosphates and polyphosphates from the 5′-end of the small RNA with Antarctic Phosphatase (New England Biolabs) following the addition of the 3′ adapter with T4 RNA ligase 1 (New England Biolabs). The resulting hydroxylated 5′-ends were phosphorylated by treatment with T4 polynucleotide kinase (New England Biolabs) and ATP to form a subtrate for T4 RNA ligase 1-mediated addition of the 5′ adapter. T4 polynucleotide kinase treatment after addition of the 3′ adapter is important because of its 3′ phosphatase and 2′,3′ cyclic phosphodiesterase activity, which can convert unwanted RNA degradation products into a substrate for the 3′ adapter ligation reaction. After ligation of both the 3′ and 5′ adapters, the adapters were extended during the reverse transcription and PCR steps to include complete primer binding sites for subsequent amplification and sequencing reactions. To protect against cross-contamination and to allow for pooling of samples, we modified the 5′ adapter sequence to include the Illumina genomic sequencing primer immediately followed by a 4-nt barcode. The samples were PAGE purified at three stages: after initial RNA extraction and after each ligation step (except with the isolated spermatogenic cell sample, where the first PAGE purification was skipped to conserve material).  The following oligos were used:    3′ adapter (IDT linker-1 with 5′ adenylation and 3′ dideoxyC): rAppCTGTAGGCACCATCAATC;    5′ adapter (i.e., AF-PP-341 DNA/RNA hybrid oligo with a 5′ amino modifier and 4-nt barcode at the 3′-end): ACGCTCTTCCGATCTrGrUrUrA;    Dual reverse transcription primer and PCR primer (AF-JIG-37, complementary to IDT linker-1): CAAGCAGAAGACGGCATACGAattgatggtgcctacag;    PCR primer (AF-JIG-40, containing 5′ adapter sequence): AATGATACGGCGACCACCGACACTCTTTCCCTACACGACGCTCTTCCGATCT.

treatment_protocol: Small RNA was extracted from frozen tissue samples with the mirVana microRNA (miRNA) isolation kit (Ambion).

tag: genetic background

value: wild type

tag: developmental stage

value: larval L4 stage

tag: barcode (first 3 nt for fastq files of chip-seq libraries, first 4 nt for fastq files of small rna libraries)

value: GGGT

tag: RNAi target


title: small RNA sequencing from wild type C. elegans from a  a time-course RNAi experiment, 24 hours

data_processing:
SG0511_lib7.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: CGTC


title: small RNA sequencing from wild type C. elegans from a multigenerational RNAi experiment, F3 generation

data_processing:
SG0511_lib11.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

source_name: adult C. elegans

tag: generation

value: adult


title: footprints for the V timepoint of the traditional timecourse

city: San Francisco

first: Gloria

last: Brar

state: CA

address: 1700 4th Street, BH404

institute: UCSF

description:
Ribosome-protected mRNA
s_tV_fp_100917_l2.txt

data_processing: Alignments were performed using the first 25 nt of each read.  mRNA  wiggle files are generated using location assignment that is  distributed along the length of the read ('coverage' mapping), while  footprint wiggle files are generated using a single location  assignment to a position 13 nt from the 5' end of the read ('start' mapping; corresponding to the ribosome P-site position). csv files  describe annotated uORF and AUG units and include RPKM quantitation of  genome-wide expression of annotated genes using the included SK1 gff  file [Yassour et al., Genome Biol 11, R87 (2010)]. All the processed data files are available on Series records [processed_wig_files.tar.gz].

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae sporulation media

extract_protocol: Small RNA fragments were size selected via gel purification,  dephosphorylated, polyA tailed, and reverse transcribed. The resulting  cDNA was circulizarized and PCR amplified [Ingolia et al.,n, Science,  (Mar 12, 2009)]. More at  Brar et al, PMID 22194413.


title: footprints for the 18 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t18-fp_090827_l3


title: footprints for mata/a strain, fig s6a

description:
Ribosome-protected mRNA
s_mataa_4.5hr_fp_101203_l4.txt


title: small RNA sequencing from wild type C. elegans from a multigenerational RNAi experiment, F1 generation

data_processing:
SG0511_lib9.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: ACTT


title: footprints for the 15 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t15-fp_090901_l3


title: footprints for the 13 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t13-fp_091022_l7


title: footprints for the 12 timepoint of the ndt80 release timecourse (the first lane of this)

description:
Ribosome-protected mRNA
s_t12-fp_090706_l7


title: H3K9me3 nucleosome-IP from wild type C. elegans from a multigenerational RNAi experiment, F2 generation

data_processing:
SG0411_lib32.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

extract_protocol: DNA was treated with 0.5 U/μl T4 polynucleotide kinase (NEB) in 1x T4 DNA ligase buffer (NEB, containing 1 mM ATP) at 37°C for 1 hour to phosphorylate 5’ ends and dephosphorylate 3’ ends.  Ends were then blunted in a reaction containing 0.75 U/μl of T4 DNA polymerase (NEB), dNTP (100 μM each, Roche), and 1x NEB buffer 1 at 12°C for 15 min.  Nucleosome core DNA was then ligated to previously annealed DNA oligos 5’ Pi-/barcode/-AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG-OH 3’ and 5’ OH-CCCTACACGACGCTCTTCCGATCT-/barcode/-OH 3’) (NEB Quick Ligation Kit).  Nucleosome core DNA captured by linker oligos was purified using 6 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea, followed by PCR amplification with primers AF-SG-135 (5’ OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-OH 3’) and AF-SG-137 (5’ OH-CAAGCAGAAGACGGCATACGAGCT-OH 3’).  A series of PCR reactions with increasing cycle numbers were then carried out; we carefully choose cycle numbers for which product levels have not saturated (i.e. product levels still able to increase substantially with additional cycles); this ensures that the majority of amplified segments are still annealed to a true complement and avoids reannealing-distortion in the resulting sequence libraries. After separating PCR products on 2 % agarose gels, DNA bands of the expected size (~210-240 bp) were extracted (QIAchange® Gel Extraction Kit (Invitrogen); omitting the 50°C heating step) and used for Illumina GAIIx.

treatment_protocol: 50-100 μl frozen embryo pellets or 100 - 200 μl frozen adult worm pellets were used for each nucleosome immunoprecipitation experiment.  Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1 ml buffer A (15 mM Hepes-Na, pH 7.5, 60 mM KCl, 15 mM NaCl, 0.15 mM beta-mecaptoethonal, 0.15 mM spermine, 0.15 mM spermidine, 0.34 M sucrose, 1x HALT protease and phosphatase inhibitor cocktail (Thermo Scientific)). To crosslink, formaldehyde was added to the resulting crude extract to a final concentration of 2%, followed by incubation at room temperature for 15 min. 0.1 ml 1 M Tris.Cl (pH 7.5) was then added to quench formaldehyde. Lysate was spun (15,000xg for 1 min). Pellets were washed with ice-cold buffer A and then resuspended in 0.3 ml buffer A with 2 mM CaCl2. Micrococcal nuclease (Roche) was added to the lysate to a final concentration of 0.3 U/μl, followed by 5 minutes incubation at 37°C (inverting the tube several times per minute). Micrococcal Nuclease (MNase) digestion was optimized so that approximately 70% of DNA entered the mono-nucleosome band, with the remainder predominantly in di- and trinucleosome bands.  Digestion reactions were stopped by adding EGTA to a final concentration of 20 mM. After centrifugation (15,000xg, 1 min) pellets were washed with ice-cold RIPA buffer (1xPBS, 1% NP40, 0.5% Sodium Deoxycholate, 0.1% SDS, 1x HALT protease and phophatase inhibitor and 2 mM EGTA), resuspended in 0.8 ml ice-cold RIPA buffer, and solubilized by sonication (Microson TM XL 2000 sonicating machine with a micro tip, output level: 5, three times of 30-second sonication). Sonication was used here to efficiently solubilize crosslinked chromatin without further fragmenting the chromatin (data not shown). Crude lysate was cleared by centrifugation at 15,000xg for 2 min. 80 μl of the supernatant was used to make "IP input" nucleosome libraries.  The remaining supernatant was used for IP, adding 2 μg of anti-H3K9me3 antibody (Abcam, ab8898) and agitating gently at 4°C overnight before 50 μl of protein A Dynabeads (10% slurry in 1x PBS buffer) was added and the resulting mixture shaken for 2hr at 4°C . The beads were then washed four times (four minutes each) with ice-cold 600 μl LiCl washing buffer (100mM Tris.Cl, pH 7.5, 500mM LiCl, 1%NP-40, 1% Sodium deoxycholate), transferring to a new tube after the first wash. To elute the immunoprecipitated nucleosome and reverse crosslinks, beads were incubated with 450 μl worm lysis buffer (0.1M Tris.Cl, pH 8.5, 100 mM NaCl, 1% SDS) containing 200 μg/ml protease K at 65°C for four hours with agitation every 30 minutes (total nucleosome aliquots were treated similarly to reverse crosslink), followed by organic extraction and DNA precipitation.

tag: chip antibody

value: anti-H3K9me3 antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

value: TGA


title: H3K9me3 nucleosome-IP from wild type C. elegans from a time-course RNAi experiment, 4 hours

data_processing:
SG0411_lib16.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: larval L4 stage C. elegans

value: GCT


title: Ae. albopictus HT CHIKV-B2(NOV)

value: HT CHIKV-B2(NOV)

tag: tissue


title: H3K9me3 nucleosome-IP from wild type C. elegans from a multigenerational RNAi experiment, P0 generation

data_processing:
SG0411_lib28.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: TAG


title: Endometrial Non-recurrent 32

description:
MBDCap using MethylMiner Methylated DNA Enrichment Kit (Invitrogen, ME 10025)
library strategy: Endometrial samples: MBDCao-seq. Breast cells: MBDCap-seq.
library selection: Endometrial samples: MBDCap. Breast cells: MBDCap-seq.

source_name: Human endometrial specimen

value: Human endometrial specimen

tag: cell type

value: primary tissues

tag: disease status

value: Non-recurrent

tag: chromatin selection

value: MBD protein


title: footprints for the 11 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t11-fp_090807_l7


title: footprints for the 9 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t9-fp_090623_l6


title: small RNA sequencing from nrde-2(gg091) mutant C. elegans that underwent smg-1 (center region) RNAi

data_processing:
SG0511_lib1.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: small RNA sequencing from  rde-1(ne300) mutant C. elegans that underwent smg-1 (center region) RNAi

data_processing:
AF_SOL_389.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: TATG


title: footprints for the 7 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t7-fp_090827_l2


title: footprints for the 10 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t10-fp_090919_l7


title: footprints for the 8 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t8-fp_090811_l7


title: footprints for the 6 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t6-fp_090807_l6


title: small RNA sequencing from  wild type C. elegans that underwent smg-1 (center region) RNAi

data_processing:
AF_SOL_385.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: wild type

value: AGCG


title: footprints for the 5 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t5-fp_090623_l4


title: small RNA sequencing from  MAGO C. elegans that underwent smg-1 (center region) RNAi

data_processing:
AF_SOL_388.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: GTTA


title: H3K9me3 nucleosome-IP from wild type C. elegans from a multigenerational RNAi experiment, F3 generation

data_processing:
SG0411_lib34.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: adult

value: AGC


title: H3K9me3 nucleosome-IP from wild type C. elegans from a time-course RNAi experiment, 24 hours

data_processing:
SG0411_lib14.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: anti-H3K9me3 antibody

value: CTA


title: small RNA sequencing from wild type C. elegans from a multigenerational RNAi experiment, F2 generation

data_processing:
SG0511_lib10.bed; genome build: C. elegans, May 2008 (WS190/ce6)
For each 36-nt sequence tag, remove the 4-nt barcode from the 5' end and removing sequences that correspond the linker sequence (CTG TAG GCA CCA TCA AT) from the 3' end. The remaining sequence was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: ACTT


title: footprints for the 12 timepoint of the ndt80 release timecourse (the second lane of this)

description:
Ribosome-protected mRNA
s_t12*2-fp_100306_l7_sequence


title: footprints for the 4 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t4-fp_090827_l1


title: H3K9me3 nucleosome-IP from wild type C. elegans from a multigenerational RNAi experiment, F1 generation

data_processing:
SG0411_lib30.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: Abcam

value: ACG


title: footprints for the 3 timepoint of the ndt80 release timecourse

description:
Ribosome-protected mRNA
s_t3-fp_090919_l6


title: footprints for the 1 timepoint of the ndt80 release timecourse (premeiotic)

description:
Ribosome-protected mRNA
s_t1-fp_090807_l4


title: H3K9me3 nucleosome-IP from MAGO C. elegans that underwent smg-1 (center region) RNAi

data_processing:
SG0211_23lib.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: TGA


title: footprints for the O timepoint of the traditional timecourse

description:
Ribosome-protected mRNA
s_tO-fp_100306_l3_sequence


title: footprints for the K timepoint of the traditional timecourse

description:
Ribosome-protected mRNA
s_tK-fp_100211_l1_sequence


title: footprints for the L timepoint of the traditional timecourse

description:
Ribosome-protected mRNA
s_tL-fp_100306_l1_sequence


title: H3K9me3 nucleosome-IP from rrf-3 (pk1426) mutant C. elegans that underwent smg-1 (center region) RNAi

data_processing:
SG0111_9lib_CAT.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: CAT


title: footprints for the i timepoint of the traditional timecourse

description:
Ribosome-protected mRNA
s_ti-fp_100216_l2_sequence


title: footprints for the G timepoint of the traditional timecourse (the second lane of this)

description:
Ribosome-protected mRNA
s_tG2-fp_100306_l6_sequence


title: footprints for the G timepoint of the traditional timecourse (the first lane of this)

description:
Ribosome-protected mRNA
s_tG-fp_100115_l4_sequence


title: H3K9me3 nucleosome-IP from nrde-2(gg091) mutant C. elegans that underwent smg-1 (center region) RNAi

data_processing:
SG0411_lib61.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: footprints for the F timepoint of the traditional timecourse

description:
Ribosome-protected mRNA
s_tF-fp_091231_l7_sequence


title: footprints for the E timepoint of the traditional timecourse (first lane of this)

description:
Ribosome-protected mRNA
s_tE-fp_100130_l2_sequence


title: footprints for the E timepoint of the traditional timecourse (second lane of this)

description:
Ribosome-protected mRNA
s_tE2-fp_100130_l3_sequence


title: H3K9me3 nucleosome-IP from wild type C. elegans that underwent smg-1 (5' end) RNAi

data_processing:
SG0411_lib52.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: footprints for the B timepoint of the traditional timecourse

description:
Ribosome-protected mRNA
s_tB-fp_100211_l5_sequence

data_processing: Alignments were performed using the first 25 nt of each read.  mRNA  wiggle files are generated using location assignment that is  distributed along the length of the read ('coverage' mapping), while  footprint wiggle files are generated using a single location  assignment to a position 13 nt from the 5' end of the read ('start' mapping; corresponding to the ribosome P-site position). csv files  describe annotated uORF and AUG units and include RPKM quantitation of  genome-wide expression of annotated genes using the included SK1 gff  file [Yassour et al., Genome Biol 11, R87 (2010)]. All the processed data files are available on Series records [processed_wig_files.tar.gz].


title: H3K9me3 nucleosome-IP from wild type C. elegans that underwent smg-1 (center region) RNAi

data_processing:
SG0411_lib20.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: GTC


title: footprints for the D timepoint of the traditional timecourse

description:
Ribosome-protected mRNA
s_tD-fp_100211_l7_sequence


title: H3K9me3 nucleosome-IP from wild type C. elegans that underwent smg-1 (3'-UTR) RNAi

data_processing:
SG0411_lib54.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: footprints for the A timepoint of the traditional timecourse (premeiotic)

description:
Ribosome-protected mRNA
s_tA-fp_100211_l3_sequence


title: footprints for exponential vegetative cells of the strain gb15 (used for the traditional timecourse)

description:
Ribosome-protected mRNA
s_gb15exp(veg)-fp_100219_l4_sequence

source_name: S. cerevisiae vegetative


title: footprints for exponential vegetative cells of the strain 14201 (used for the ndt80 release timecourse)

description:
Ribosome-protected mRNA
s_14201exp(veg)-fp_100219_l6_sequence


title: H3K9me3 nucleosome-IP from eri-1(mg366) mutant C. elegans as control for no RNAi

data_processing:
V74_7IPmix_ACG.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

source_name: embryonic C. elegans

value: embryo


title: mRNA-seq for the 18 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t18_20090827_l7


title: H3K9me3 nucleosome-IP from rde-1(ne300) mutant C. elegans that underwent smg-1 (center region) RNAi

data_processing:
SG0211_24lib.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: mRNA-seq for the V timepoint of the traditional timecourse

description:
mRNA
s_tV_mrna_100917_l3.txt


title: mRNA-seq for mata/a strain, fig s6a

description:
mRNA
s_mataa_4.5hr_mrna_101205_l4.txt


title: H3K9me3 nucleosome-IP from eri-1(mg366) mutant C. elegans that underwent smg-1 (center region) RNAi

data_processing:
SG0910_6lib.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: H3K9me3 nucleosome-IP from eri-1(mg366) mutant C. elegans that underwent lin-15B RNAi

data_processing:
V74_7IPmix_CAT.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: H3K9me3 nucleosome-IP from eri-1(mg366) mutant C. elegans that underwent lir-1 RNAi

data_processing:
SG0810_15lib.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.


title: mRNA-seq for the 15 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t15_20090901_l1


title: mRNA-seq for the 8 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t8_090811_l6


title: H3K9me3 nucleosome-IP from eri-1(mg366) mutant C. elegans that underwent ego-1 RNAi

data_processing:
SG0910_4lib.bed; genome build: C. elegans, May 2008 (WS190/ce6)
After removing the 3-nt barcode, the first 25-nt sequence for each tag was used to align to the C. elegans genome (WS190 version) using Bowtie 0.12.7. Only perfect alignments were included in the bed file.

value: GCT


title: mRNA-seq for the 13 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t13_20091022_l6


title: mRNA-seq for the 4 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t4_20090827_l4


title: mRNA-seq for the 5 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t5_20090718_l5


title: mRNA-seq for the 12 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t12_20090827_l6


title: mRNA-seq for the 11 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t11_20090718_l7


title: mRNA-seq for the 1 timepoint of the ndt80 release timecourse (premeiotic)

description:
mRNA
mrna_t1_20090811_l5


title: mRNA-seq for the 9 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t9_20090718_l6


title: mRNA-seq for the 10 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t10_20090901_l2


title: mRNA-seq for the 7 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t7_20090827_l5


title: mRNA-seq for the O timepoint of the traditional timecourse

description:
mRNA
s_tO-mrna_100306_l4_sequence


title: mRNA-seq for the 6 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t6_20090807_l5


title: mRNA-seq for the F timepoint of the traditional timecourse

description:
mRNA
s_tF-mrna_091211_l4_sequence


title: mRNA-seq for the 3 timepoint of the ndt80 release timecourse

description:
mRNA
mrna_t3_20090919_l5


title: mRNA-seq for the i timepoint of the traditional timecourse (the second lane of this)

description:
mRNA
s_ti2-mrna_100306_l5_sequence


title: mRNA-seq for the G timepoint of the traditional timecourse

description:
mRNA
s_tG-mrna_091211_l3_sequence


title: mRNA-seq for the L timepoint of the traditional timecourse

description:
mRNA
s_tL-mrna_100306_l2_sequence


title: mRNA-seq for the i timepoint of the traditional timecourse (the first lane of this)

description:
mRNA
s_ti-mrna_100130_l4_sequence


title: mRNA-seq for the B timepoint of the traditional timecourse

description:
mRNA
s_tB-mrna_100211_l4_sequence


title: mRNA-seq for the A timepoint of the traditional timecourse (premeiotic)

description:
mRNA
s_tA-mrna_100211_l2_sequence


title: mRNA-seq for exponential vegetative cells of the strain gb15 (used for the traditional timecourse)

description:
mRNA
s_gb15exp(veg)-mrna_100219_l5_sequence


title: LANA_2_BCBL1_ChIP-Seq

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: BCBL1 cells per IP with LANA  monoclonal antibody

data_processing:
Lana_ChIP-Seq_TotalPeak_2.bed; genome build: hg18
Tag_Lana_2_ChIP-Seq_hg18_align_exp.bed; genome build: hg18
Alignment: Alignment was performed using BOWTIE
Solexa ChIP-Seq experiments were performed with 2x106 BCLB1 cells per IP with either LANA monoclonal antibody or control mouse IgG.  BCBL1cells are KSHV positive human Pleural Effusion Lymphoma (PEL) cell line.  For Peak calling, A combination of fold ratio and Poisson model for the tag distribution was used to define peaks as follows: (i) Identification of genomic regions (of length 1000bp) enriched with ChIP-seq sequence tags using fold ratio – A genomic region is considered as sequence enriched if the fold ratio, calculated using number of reads normalized to the total reads within that region in ChIP (antibody treatment) sample divided by the number of reads normalized to the total reads in control sample (IgG control) in the same region, is higher than the given cutoff. Nearby enriched regions were merged to make broader enriched genomic regions. A cutoff of 3 was applied to find the initial genomic regions of enrichment at this stage. (ii) Creating the read overlapping profile for each identified region from step 1, by extending the sequence reads from the 5’ end to the 3’ end of the reads up to 300 bps (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol) for the experiment sample. (iii) Peak identification, by using Poisson model – by counting the number of overlapped reads at each nucleotide position and defining the genomic position with the highest number as the peak position within the significant region.  Finally, only those genomic regions that have fold ratio > 10 and peak score > 8 and p value < 0.001 (as determined by Poisson background model) are considered as statistically significant.   Peak score is calculated as the average value of raw counts within a given region of significant fold enrichment relative to control IgG levels.  The average is measured for overlapping tags at every base after extending the tags to their average tag length within the significant region.

source_name: BCBL1 Pleural Effusion Lymphoma (PEL)cell line

growth_protocol: 10% FBS in RPMI with antibiotics

extract_protocol: Illumina Library Preparation Protocol

treatment_protocol: No treatment

tag: cell line

tag: genotype/variation

value: KSHV positive PEL

tag: chip-antibody

value: LANA rat monoclonal antibody


title: mRNA-seq for the D timepoint of the traditional timecourse

description:
mRNA
s_tD-mrna_100211_l6_sequence


title: IgG_2_BCBL1_ChIP-Seq

description: BCBL1 cells per IP with IgG control  monoclonal antibody

data_processing:
Tag_Lana_2_ChIP-Seq_hg18_align_IgG.bed; genome build: hg18
Alignment: Alignment was performed using BOWTIE
Solexa ChIP-Seq experiments were performed with 2x106 BCLB1 cells per IP with either LANA monoclonal antibody or control mouse IgG.  BCBL1cells are KSHV positive human Pleural Effusion Lymphoma (PEL) cell line.  For Peak calling, A combination of fold ratio and Poisson model for the tag distribution was used to define peaks as follows: (i) Identification of genomic regions (of length 1000bp) enriched with ChIP-seq sequence tags using fold ratio – A genomic region is considered as sequence enriched if the fold ratio, calculated using number of reads normalized to the total reads within that region in ChIP (antibody treatment) sample divided by the number of reads normalized to the total reads in control sample (IgG control) in the same region, is higher than the given cutoff. Nearby enriched regions were merged to make broader enriched genomic regions. A cutoff of 3 was applied to find the initial genomic regions of enrichment at this stage. (ii) Creating the read overlapping profile for each identified region from step 1, by extending the sequence reads from the 5’ end to the 3’ end of the reads up to 300 bps (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol) for the experiment sample. (iii) Peak identification, by using Poisson model – by counting the number of overlapped reads at each nucleotide position and defining the genomic position with the highest number as the peak position within the significant region.  Finally, only those genomic regions that have fold ratio > 10 and peak score > 8 and p value < 0.001 (as determined by Poisson background model) are considered as statistically significant.   Peak score is calculated as the average value of raw counts within a given region of significant fold enrichment relative to control IgG levels.  The average is measured for overlapping tags at every base after extending the tags to their average tag length within the significant region.

value: purified IgG


title: mRNA-seq for the E timepoint of the traditional timecourse

description:
mRNA
s_tE-mrna_100130_l1_sequence


title: LANA_1_BCBL1_ChIP-Seq

data_processing:
Lana_ChIP-Seq_TotalPeak_1.bed; genome build: hg18
Lana_1_2_Peak_overlap_pm250bp.bed; genome build: hg18
Tag_Lana_1_ChIP-Seq_hg18_align_exp.bed; genome build: hg18
Alignment: Alignment was performed using BOWTIE
Solexa ChIP-Seq experiments were performed with 2x106 BCLB1 cells per IP with either LANA monoclonal antibody or control mouse IgG.  BCBL1cells are KSHV positive human Pleural Effusion Lymphoma (PEL) cell line.  For Peak calling, A combination of fold ratio and Poisson model for the tag distribution was used to define peaks as follows: (i) Identification of genomic regions (of length 1000bp) enriched with ChIP-seq sequence tags using fold ratio – A genomic region is considered as sequence enriched if the fold ratio, calculated using number of reads normalized to the total reads within that region in ChIP (antibody treatment) sample divided by the number of reads normalized to the total reads in control sample (IgG control) in the same region, is higher than the given cutoff. Nearby enriched regions were merged to make broader enriched genomic regions. A cutoff of 3 was applied to find the initial genomic regions of enrichment at this stage. (ii) Creating the read overlapping profile for each identified region from step 1, by extending the sequence reads from the 5’ end to the 3’ end of the reads up to 300 bps (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol) for the experiment sample. (iii) Peak identification, by using Poisson model – by counting the number of overlapped reads at each nucleotide position and defining the genomic position with the highest number as the peak position within the significant region.  Finally, only those genomic regions that have fold ratio > 10 and peak score > 8 and p value < 0.001 (as determined by Poisson background model) are considered as statistically significant.   Peak score is calculated as the average value of raw counts within a given region of significant fold enrichment relative to control IgG levels.  The average is measured for overlapping tags at every base after extending the tags to their average tag length within the significant region.