title: shRNA-dlg

status: Public on Mar 26 2011

city: Cold Spring Harbor

first: Benjamin

last: Czech

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description:
shRNA against dlg (discs large 1/CG1725)
small RNA sequencing

data_processing: The 36nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome, and to the genomes of Drosophila C virus, Flock house virus and Cricket paralysis virus with up to 3 mismatches. Only reads that met these conditions were subjected to further analyses. For annotations we used a combination of UCSC dm3, miRBase release 14, and Flybase r5.26 tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, shRNAs, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request). For comparison of small RNA counts between libraries, reads were normalized to the same total number after bioinformatic removal of those sequences that matched to synthetic cloning markers or assumed degradation products of abundant cellular RNAs (rRNAs, snoRNAs and tRNAs). SEQ = the sequence of the small RNA. LENGTH = the length of the small RNA. NAME = annotation name of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

organism: Drosophila melanogaster

source_name: S2-NP cells

growth_protocol: 25°C in Schneider's medium (Invitrogen) supplemented with 10% FBS and 1% pen-strep (Invitrogen)

extract_protocol: Trizol (Invirogen) extraction

treatment_protocol: ~4X10^6 S2-NP cells were transfected with 2 ug of UAS-shRNA construct and 1 ug of pMT-Gal4 plasmid. ShRNA expression in cells was induced by adding 500 uM CuSO4 two days post transfection. RNA was isolated for the production of small RNA libraries 24 hours following induction.

value: Drosophila S2-NP cells


title: shRNA-N

type: SRA

country: USA

description:
shRNA against N (Notch/CG3936)
small RNA sequencing

library_source: transcriptomic

molecule: total RNA

tag: cell type


title: ChIP-Seq for H3K9me3 in Wm451-lu melanoma cells

status: Public on Mar 25 2011

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against H3K9me3

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.

molecule: genomic DNA

organism: Homo sapiens

source_name: Melanomas

growth_protocol: Melanoma short-term cultures (STCs) were obtained from the Wistar Institute collection, and were derived from patients with metastatic disease. All lines were cultured in RPMI medium (cellgro) containing 10% FBS (cellgro) and penicillin/streptomycin (cellgro). In order to culture WM451-Lu cells, cell culture plates were pre-coated with 1% porcine gel solution (Sigma) to enhance cell adherence.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

tag: antibody catalog number

tag: antibody vendor

value: Abcam

tag: antibody lot number


title: ChIP-Seq for SetDB1 in Wm451-lu melanoma cells

description: Chromatin IP against SetDB1

value: Santa Cruz


title: MsmPS-HL3-36h-lane3

status: Public on Mar 30 2011

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University

description:
HL=high hydrogen (80%), Low Formate concentration (2.8mM);
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (36 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 2.8mM

data_processing: After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32nt barcoded samples; 33 was the minimum score used for 36-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36nt there is a large fraction of the reads that map to multiple locations within a genome or across genomes. Reads that map non-uniquely were added to each gene in proportion to each geneâ€™s fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will be scored as 0.9 count to gene A and 0.1 count to gene B). We added a pseudocount (i.e. added 1) to each gene count prior to normalization to account for differences in sampling depth, although clearly a more appropriate model-based approach to smooth lower expression values is needed in the future, particularly with mixed species samples where one or more species is clearly undersampled. Raw counts were normalized to reads/kb/million mapped reads. First column of counts files contains locus tag information.

organism: Methanobrevibacter smithii ATCC 35061

source_name: in vitro culture

growth_protocol: In vitro modified Methanobrevibacter complex medium MBC media, mid-log phase growth, 80% hydrogen, 20% CO2 gasses

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, cDNA was sonicated in a biorupter sonicator, cleaned up/concentrated through a Qiagen PCR column, and end-repaired. The blunt DNA was treated with Klenow fragment (exo minus) to add an A-overhang, and ligated to the relevant Illumina adapter sequence (either with our without a barcode).  Adaptered-DNA was then size-selected on a agarose gel and PCR amplified. The purified PCR was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: All samples were treated with RNAProtect (Qiagen) and immediately frozen at -80C.

tag: treatment

tag: genome accession

tag: strain

value: Methanobrevibacter smithii ATCC 35061

tag: sample type

value: rRNA depleted total RNA


title: ChIP-Seq for MCAF1 in WM262 melanoma cells

description: Chromatin IP against MCAF1

value: Bethyl


title: ChIP-Seq for H3K9me3 in WM262 melanoma cells

description: Chromatin IP against H3K9me3


title: shRNA-dpp

description:
shRNA against dpp (decapentaplegic/CG9885)
small RNA sequencing


title: Crop_42hrs_run1

city: Storrs

first: Joerg

last: Graf

state: CT

address: 91 North Eagleville Road

institute: University of Connectiuct

data_processing: Reads were mapped to reference genomes using CLC Genomics Workbench

organism:
Hirudo verbana
gut metagenome

source_name: Leech crop intraluminal fluid

growth_protocol: 4 leeches were fed 5 ml of sheep blood and sacrificed 42 hrs after feeding.  The intraluminal fluid, containing the bacteria, was harvested and flash frozen.

extract_protocol: 100 ng of mRNA-enriched RNA was used to construct a double stranded cDNA library using Illumina's mRNA-seq kit (RS-100-0801) following the manufacturer's instructions except that the polyT bead enrichment step was omitted.

treatment_protocol: Total RNA was extracted from the 4 leeches.  Equal amounts were pooled from each leech and then enriched for mRNA

value: Crop microbiome

tag: time after feeding

tag: tissue

value: Leech crop intraluminal fluid

tag: rna type

value: mRNA-enriched total RNA


title: Crop_42hrs_run2


title: small intestine A (Poly-A Enrichment)

status: Public on Mar 29 2011

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: RNA-Seq against polyadenylated RNA from small intestine

data_processing: Sequence reads were obtained using the Applied Biosystems Modular Analysis Pipeline (MOAP). Data is unfiltered and includes all identified beads.

organism: Mus musculus

source_name: small intestine total tissue

growth_protocol: small intestine and colon from 9-10 weeks old mice were prepared and frozen in liquid nitrogen.

extract_protocol: Whole Transcriptome Analysis Kit

value: Small Intestine

tag: extract protocol

value: Whole Transcriptome Analysis Kit

tag: library selection

value: polyadenylated RNA


title: ChIP-Seq for SetDB1 in WM262 melanoma cells

description: Chromatin IP against SetDB1


title: LNCaP_PolII_Vehicle

status: Public on Mar 24 2011

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: Chromatin IP against PolII

data_processing:
Alignments: Sequence reads were generated by the Illumina analysis pipeline version 1.3.4 and 1.4.0. The two lanes of reads were combined for each sample, and aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.1, March 2008) using MAQ (Li et al., 2008). Next they were filtered  by alignment quality score, removing all reads with a MAQ score less than 20, and exact duplicate reads were removed such that no single read start position was represented more than once
Peaks: Enriched regions of the genome were identified by comparing the ChIPed samples to Input samples using two independent peak calling algorithms: MACS (Zhang et al 2008) and ChIPSeqMini (Johnson et al., 2007), taking only those regions found by both algorithms

source_name: LNCaP cell line

growth_protocol: Cells were cultured in RPMI media supplemented with 10% charcoal dextran stripped FBS for 72 before adding 1nM R1881 or 0.01% ethanol for four hours

extract_protocol:
ChIP Protocol was as described in Wilson, M.D., Barbosa-Morais, N.L., Schmidt, D., Conboy, C.M., Vanes, L., Tybulewicz, V.L., Fisher, E.M., Tavare, S., and Odom, D.T. (2008). Species-specific transcription in mice carrying human chromosome 21. Science 322, 434-438.
Genomic DNA extraction method: Genomic DNA was isolated using phenol:chloroform:isopropanol (25:24:1, Invitrogen), back-extracted with 200ul of TE, precipitated with isopropanol, washed with 75% ethanol, air-dried and resuspended in 60ul 10mM Tris-HCl pH 8
Antibodies used: 1: Santa Cruz Biotechnology, Rabbit polyclonal AR antibody, Clone number (AR(N20)X), Product code sc-816X.  2: Abcam, Mouse monoclonal RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody, Clone number 8A7, Product code ab5401.
Single-end SOLEXA sequencing libraries were prepared as previously described (Schmidt et al., 2008). Libraries were size selected by electrophoresis, excising the SYBR-safe, DNA smear between 200-300bp on a Dark Reader non-UV transilluminator, purified using a Qiagen gel-extraction  mini-elute kit, quantified using an Agilent Bioanalyser, 36bp sequence reads were generated using a Illumina (Solexa) Genome Analyzer II and these reads were mapped back to the reference human genome before peak calling

tag: condition

value: Vehicle

tag: factor

value: PolII

tag: sra accession


title: VCaP_AR_Vehicle

description: Chromatin IP against AR

source_name: VCaP cell line

value: AR


title: LNCaP_PolII_AR-stimulated

description: Chromatin IP against PolII

value: AR stimulated


title: VCaP_Input_AR-stimulated

description: Input DNA (VCaP)

value: Input


title: LNCaP_AR_Vehicle

description: Chromatin IP against AR


title: p53-pS15_ActD_ChIPSeq

city: Nijmegen

first: Marion

last: Lohrum

department: Molecular Biology

country: Netherlands

institute: NCMLS

description: Chromatin IP against p53-pS15

data_processing: 32 bp reads were aligned to the human genome (hg18) using ELAND. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peak recognition was performed using Model-based analysis of ChIP-Seq (MACS) with a p-value threshold of 1e-7. Artifacts, like spurious peaks in centromeric and telomeric regions, were removed from the list.

source_name: Chromatin IP against p53-pS15

growth_protocol: The human osteosarcoma cell line U2OS expressing endogenous wild-type p53 was maintained in Dulbecco modified Eagle medium supplemented with 10% fetal calf serum at 37ºC.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sonicated using a Bioruptor Sonicator.

treatment_protocol: The U2OS cells were treated with 5nM Actinomycin D (Sigma) or 10µM Etoposide (Sigma) for 24 hours.

tag: cell line

tag: cell type

value: osteosarcoma

tag: antibody

value: α-p53-pS15 (Cell Signaling)

tag: compound

value: Actinomycin D

tag: dose

value: 5 nM


title: VCaP_AR_AR-stimulated

description: Chromatin IP against AR


title: p53-pS46_Eto_ChIPSeq

description: Chromatin IP against p53-pS46

source_name: Chromatin IP against p53-pS46

value: Etoposide

value: 10 μM


title: p53_Eto_ChIPSeq

description: Chromatin IP against p53

source_name: Chromatin IP against p53

value: DO1 (BD PharMingen)


title: LNCaP_AR_AR-stimulated

description: Chromatin IP against AR


title: LNCaP_Input_AR-stimulated

description: Input DNA (LNCaP)


title: p53-pS46_ActD_ChIPSeq

description: Chromatin IP against p53-pS46


title: p53_ActD_ChIPSeq

description: Chromatin IP against p53


title: RNA-Seq_pEGC

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

institute: Radboud University Nijmegen, RIMLS

data_processing: ds-cDNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300bp) and limited PCR amplification (14 cycles). Quality control was made by qPCR and by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols (Illumina). Samples were sequenced to a depth of approximately 15 million mapped tags per sample. Sequences were aligned to the pig SGSC Sscrofa9.2/susScr2 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing. All sequencing analyses were conducted based on the Sus scrofa SGSC Sscrofa9.2/susScr2 genome assembly accessed from the UCSC Genome Browser (assembly Nov 2009).

molecule: polyA RNA

organism: Sus scrofa

source_name: Primordial embryonic germ cells

growth_protocol: Danish Landrace sows were artificially inseminated with semen from Yorkshire boars 3-5 days after weaning of their litters and killed at days 17-18, 20-21, 22-23, or 23-24 of pregnancy. The uteri were cut open and the embryos were removed with sterile forceps and washed in sterile PBS supplemented with 2% Knockout Serum Replacement (KSR; Invitrogen, Carlsbad, USA) and penicillin-streptomycin. Dissection was performed in the same solution and hindguts were isolated from day 17-18 pregnancies, while the medial parts of the mesonephros, including the areas of genital ridge formation, were dissected from the later stages. The tissues were disaggregated to single cells and small clumps by incubation in 0.25% trypsin-EDTA solution at 37°C for 15 min followed by pipetting. The resulting suspensions were filtered through 60 µm nylon mesh to remove large clumps, followed by centrifugation (5 min at 1200g) and re-suspension in EGC culture medium (AQ Media supplemented with 17% KSR, non-essential amino acids, penicillin-streptomycin, 10 ng/ml human recombinant LIF (Millipore, Billerica, USA), 10 ng/ml human recombinant SCF (Prospec, Rehovot, Israel), and 3 ng/ml human recombinant bFGF (Invitrogen)). The cells were seeded on mitomycin C -inactivated STO feeder cells (prepared as described in [11]) in 3.5 cm tissue culture dishes at the ratio of one embryo/dish. Culture was performed in a humidified incubator at 38.5°C and in 5% CO2 + 95% atmospheric air. For the first passage (P1) the primary culture colonies were purified from the somatic and feeder cells by digestion with 1 mg/ml Collagenase IV for 10 min at 37°C  followed by disaggregation by pipetting and filtering of the suspensions three times through 24 µm polyester mesh (Spectrum Labs, Los Angeles, USA). The EGC colonies (which are very tightly packed and could not be disaggregated by Collagenase IV treatment) were recovered by washing the mesh with PBS, disaggregated by trypsinization, and then split onto fresh feeders. At the second and all later passages the EGC colonies were split together with the feeder cells by trypsin disaggregation at ratios 1:2-1:3 every 4-5 days.

extract_protocol: 100µg total RNA was subjected to two rounds of poly(A) selection using the Oligotex mRNA Mini Kit (Qiagen), followed by DNaseI treatment (Qiagen). 100-200ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 seconds and purified using the RNAeasy Minelute Kit (Qiagen). The fragmented mRNA was used as template for cDNA synthesis using 5µg random hexamers using Superscript III Reverse Transcriptase (Invitrogen) according to the manufacturer's recommendations. Ds-cDNA was synthesized in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified using the Minelute Reaction Cleanup Kit (Qiagen). Quality control was performed by qPCR.

treatment_protocol: No specific treatments

tag: genetic background

value: Danish Landrace x Yorkshire cross pig

value: Primordial embryonic germ cells

value: fragmentented two times Poly(A) selected ds_cDNA


title: RNA-Seq_pFF

source_name: Embryonic fetal fibroblast cells

value: Embryonic fetal fibroblast cells


title: NHLF_WCE_rep2

status: Public on Mar 23 2011

city: Los Angeles

first: Jason

last: Ernst

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

data_processing: Bed files:  Any reads longer than 36 bases were first truncated to 36 bases. Reads were then aligned to the hg18 assembly using MAQ with default parameters.  The fourth column of the bed file contains the actual 36 base read sequence.

source_name: cultured NHLF cells

extract_protocol: Described in Mikkelsen et al., Nature 2007. Chromatin was fixed and sheared to 200-600 bp using Branson Sonifer. After IP and adapter ligation library fragments of ~250 bp were isolated. 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.

tag: chip antibody

value: NHLF

value: WCE


title: NHLF_H3K9ac_rep1

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number


title: NHLF_H3K4me3_rep1

value: Millipore


title: NHLF_H3K9ac_rep2


title: NHLF_WCE_rep1

tag: sample type


title: NHLF_H3K4me2_rep1


title: NHLF_H4K20me1_rep2


title: p53-pS15_Eto_ChIPSeq

description: Chromatin IP against p53-pS15


title: NHLF_H3K4me2_rep2


title: NHLF_H3K4me3_rep2


title: NHLF_H3K4me1_rep1


title: NHLF_H3K4me1_rep2


title: NHLF_H4K20me1_rep1


title: NHLF_H3K27me3_rep1


title: NHLF_H3K27ac_rep2


title: NHLF_H3K27me3_rep2


title: NHLF_H3K36me3_rep2


title: NHLF_H3K27ac_rep1


title: NHLF_CTCF_rep2

value: CTCF


title: NHEK_WCE_rep1

source_name: cultured NHEK cells

value: NHEK


title: NHLF_H3K36me3_rep1


title: NHLF_CTCF_rep1


title: NHEK_H4K20me1_rep2


title: NHEK_H3K9ac_rep1


title: NHEK_WCE_rep2


title: NHEK_H3K4me3_rep1


title: NHEK_H4K20me1_rep1


title: NHEK_H3K4me2_rep2


title: NHEK_H3K9ac_rep2


title: NHEK_H3K4me3_rep2


title: NHEK_H3K4me2_rep1


title: NHEK_H3K36me3_rep2


title: NHEK_H3K4me1_rep2


title: NHEK_H3K36me3_rep1


title: NHEK_H3K4me1_rep1


title: NHEK_H3K27me3_rep2


title: NHEK_H3K27me3_rep1


title: NHEK_CTCF_rep1


title: NHEK_CTCF_rep2


title: NHEK_H3K27ac_rep1


title: K562_H4K20me1_rep1

source_name: cultured K562 cells


title: K562_WCE_rep2


title: K562_H4K20me1_rep2


title: NHEK_H3K27ac_rep2


title: K562_H3K9me3_rep2

data_processing:
Bed files:  Any reads longer than 36 bases were first truncated to 36 bases. Reads were then aligned to the hg18 assembly using MAQ with default parameters.  The fourth column of the bed file contains the actual 36 base read sequence.
Note file update 4/20/15. Previously the hg19 version of the bed file was uploaded for the K562 H3K9me3 samples only.


title: K562_H3K9me3_rep1


title: K562_H3K9ac_rep2


title: K562_H3K9ac_rep1


title: K562_H3K4me3_rep2


title: K562_H3K4me2_rep2


title: K562_H3K4me3_rep1


title: K562_H3K4me2_rep1


title: K562_H3K4me1_rep1


title: K562_H3K4me1_rep2


title: K562_H3K27me3_rep1


title: K562_H3K36me3_rep1


title: K562_H3K27ac_rep1


title: K562_H3K27ac_rep2


title: K562_H3K27me3_rep2


title: K562_WCE_rep1


title: K562_CTCF_rep1


title: K562_CTCF_rep2


title: Huvec_WCE_rep2

source_name: cultured HUVEC cells

value: HUVEC


title: Huvec_WCE_rep1


title: Huvec_H4K20me1_rep2


title: Huvec_H3K9ac_rep1


title: Huvec_H3K9ac_rep2


title: Huvec_H4K20me1_rep1


title: Huvec_H3K4me3_rep2


title: Huvec_H3K4me2_rep1


title: K562_H3K36me3_rep2


title: Huvec_H3K4me1_rep2


title: Huvec_H3K4me3_rep1


title: Huvec_H3K36me3_rep2


title: Huvec_H3K4me1_rep1


title: Huvec_H3K36me3_rep1


title: Huvec_H3K27me3_rep2


title: Huvec_H3K27me3_rep1


title: Huvec_CTCF_rep2


title: Huvec_H3K27ac_rep2


title: Huvec_CTCF_rep1


title: HSMM_WCE_rep1

source_name: cultured HSMM cells

value: HSMM


title: Testis tissue small RNA

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: Nine male were pooled.

data_processing: Sequenced sequences were processed using the Pipeline software from the Genome Analyzer GA-1 instrument (Illumina Inc.) at first, then were subject to a series of data filtration steps to obtain "mappable sequences", which are sequences satisfy the following criteria from the statistics of miRBbase 15.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing not only A and C or G and T, (5) containing no stretches of A7, C8, G6, or T7; (6) being longer than 14 nt and shorter than 27 nt; (7) not containing 10 repeats of any dimer, 6 repeats of any trimer, or 5 repeats of any tetramer; (8) been observed more than two times; and (9) not originating from porcine known classes of RNAs (i.e., mRNA in NCBI database; rRNA, tRNA, snRNA and snoRNA in Rfam database; and repetitive sequence elements in Repbase database). Further data analysis of the "mappable sequences" mainly used ACGT101-miR, o ur own development software for discovering miRNAs from next-generation sequencing (NGS) data (to be published separately), based on the databases of pig genome (Sscrofa9, April 2009) sequences and mammalian konwn miRNA genes in miRBase 15.0.

source_name: Testis

extract_protocol: Tibetan pigs (a black, Chinese indigenous breed) were used to harvest tissues. Ovaries and testes from nine female and male Tibetan pigs (210-days-old) respectively, and were isolated and immediately frozen in liquid nitrogen and stored at -80℃. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) following the manufacturer’s procedure. The total RNA quantity and purity passed the analysis of NanoDrop ND-1000 spectrophotometer (Nano Drop) at 260/280 nm (ratio > 2.0). The integrity of total RNA also passed the analysis of Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent) with RIN number > 6.0. The sequencing RNA samples were prepared as follows: for each individual, equal quantities (5 µg) of small RNA isolated from nine female or male pigs were pooled. Approximately 45 µg of small RNA representing ovaries or testes was used for library preparation and sequencing. In brief, the sequencing was performed as follows: the small RNA fraction between 10-40 nt was isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). The short RNAs were then converted to cDNA by RT-PCR and the cDNA was sequenced on the Genome Analyzer GA-I (Illumina) following the vendor’s recommended protocol for small RNA sequencing.

tag: breed

tag: developmental stage

value: adult (210-days-old)

tag: gender

value: male

tag: tissue

value: Testis


title: HSMM_WCE_rep2


title: HSMM_H4K20me1_rep1


title: HSMM_H4K20me1_rep2


title: Huvec_H3K4me2_rep2


title: Ovary tissue small RNA

description: Nine female were pooled.

source_name: Ovary

value: Tibetan pigs (a black, Chinese indigenous breed)

value: female

value: Ovary


title: HSMM_H3K9ac_rep1


title: HSMM_H3K9ac_rep2


title: HSMM_H3K4me3_rep1


title: HSMM_H3K36me3_rep1


title: HSMM_H3K27me3_rep1


title: HSMM_H3K4me1_rep2


title: HSMM_H3K36me3_rep2


title: HSMM_H3K27me3_rep2


title: HSMM_H3K27ac_rep1


title: HSMM_H3K4me1_rep1


title: HSMM_H3K4me2_rep2


title: HSMM_CTCF_rep1


title: HSMM_H3K4me2_rep1


title: HMEC_H4K20me1_rep2

source_name: cultured HMEC cells

value: HMEC


title: HMEC_WCE_rep1


title: HSMM_H3K27ac_rep2


title: HMEC_WCE_rep2


title: HSMM_CTCF_rep2


title: HMEC_H4K20me1_rep1


title: HMEC_H3K9ac_rep2


title: HMEC_H3K9ac_rep1


title: HMEC_H3K4me2_rep2


title: HMEC_H3K4me3_rep1


title: HMEC_H3K4me2_rep1


title: HMEC_H3K27me3_rep2


title: Huvec_H3K27ac_rep1


title: HMEC_H3K4me3_rep2


title: HMEC_H3K4me1_rep1


title: HMEC_H3K36me3_rep2


title: HMEC_H3K36me3_rep1


title: HSMM_H3K4me3_rep2


title: HMEC_H3K27me3_rep1


title: HMEC_H3K27ac_rep2


title: HMEC_H3K27ac_rep1


title: HepG2_WCE_rep2

source_name: cultured HepG2 cells


title: HMEC_CTCF_rep2


title: HMEC_CTCF_rep1


title: HepG2_H4K20me1_rep2


title: HepG2_H3K9ac_rep1


title: HMEC_H3K4me1_rep2


title: HepG2_H3K4me3_rep2


title: HepG2_H3K4me2_rep1


title: HepG2_H3K4me2_rep2


title: HepG2_H3K27ac_rep2


title: HepG2_H3K27me3_rep1


title: HepG2_H4K20me1_rep1


title: HepG2_H3K4me3_rep1


title: HepG2_WCE_rep1


title: HepG2_H3K4me1_rep1


title: HepG2_H3K9ac_rep2


title: HepG2_CTCF_rep1


title: HepG2_CTCF_rep2


title: H1_WCE_rep2

source_name: cultured H1 cells


title: H1_WCE_rep1


title: H1_H4K20me1_rep2


title: H1_H3K9ac_rep2


title: H1_H4K20me1_rep1


title: H1_H3K9ac_rep1


title: HepG2_H3K36me3_rep2


title: H1_H3K4me3_rep2


title: H1_H3K4me3_rep1


title: HepG2_H3K27me3_rep2


title: H1_H3K4me2_rep2


title: HepG2_H3K36me3_rep1


title: H1_H3K4me2_rep1


title: H1_H3K4me1_rep1


title: H1_H3K36me3_rep1


title: H1_H3K36me3_rep2


title: H1_H3K4me1_rep2


title: H1_H3K27me3_rep2


title: H1_H3K27ac_rep1


title: HepG2_H3K27ac_rep1


title: GM12878_WCE_rep1

source_name: cultured GM12878 cells


title: H1_H3K27me3_rep1


title: GM12878_H3K4me3_rep1


title: GM12878_H3K9ac_rep2


title: H1_CTCF_rep1


title: GM12878_H3K4me2_rep1


title: GM12878_H4K20me1_rep1


title: GM12878_H3K4me3_rep2


title: GM12878_WCE_rep2


title: GM12878_H3K9ac_rep1


title: GM12878_H3K4me2_rep2


title: GM12878_H3K4me1_rep1


title: GM12878_H3K4me1_rep2


title: GM12878_H3K36me3_rep1


title: GM12878_H3K36me3_rep2


title: GM12878_H3K27me3_rep1


title: H1_CTCF_rep2


title: GM12878_H3K27me3_rep2


title: GM12878_H4K20me1_rep2


title: GM12878_H3K27ac_rep1


title: GM12878_H3K27ac_rep2


title: GM12878_CTCF_rep1


title: GM12878_CTCF_rep2


title: Whole_Dsim_251.011_Female_Rep1

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: droSim1 (no chrU)+ERCC Spike-In Controls

organism: Drosophila simulans

source_name: Whole tissue

growth_protocol: Adult flies were growth 5-7 days post eclosion. See GSE6640 for details.

extract_protocol: See GSE6640 for RNA extraction methods. We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA, 1 ng of ERCC spike-in controls, and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single "A" base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3' to 5' exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 300 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl primer 1.1, 1 µl primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

treatment_protocol: Flies were raised in incubators with no photoperiod at 22 C and 60% humidity. See GSE6640 for details.

tag: strain

value: Drosophila Species Stock Center (DSSC) 14021-0251.011. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Whole flies

value: Adult

tag: sex

value: Female

tag: age

value: 5-7 days post eclosion


title: Whole_Dyak_261.01_Female_Rep2

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: droYak2+ERCC Spike-In Controls

organism: Drosophila yakuba

value: Drosophila Species Stock Center (DSSC) 14021-0261.01. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Whole_Dpse_111.94_Male_Rep2

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: dp4+ERCC Spike-In Controls

organism: Drosophila pseudoobscura

value: Drosophila Species Stock Center (DSSC) 14011-0121.94. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Male


title: Whole_Dpse_111.94_Female_Rep2


title: Whole_Dmoj_1352.22_Female_Rep2

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: droMoj3+ERCC Spike-In Controls

organism: Drosophila mojavensis

value: Drosophila Species Stock Center (DSSC) 15081-1352.22. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Whole_Dana_371.13_Female_Rep2

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: droAna3+ERCC Spike-In Controls

organism: Drosophila ananassae

value: Drosophila Species Stock Center (DSSC) 14024-0371.13. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Whole_Dana_371.13_Female_Rep1


title: Whole_Dsim_251.198_Male_Rep1

value: Drosophila Species Stock Center (DSSC) 14021-0251.198. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Whole_Dsim_251.198_Female_Rep1


title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC.H1.09.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK57
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6053
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667642_UCSD.H1.Input.AK57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H1.09.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library AK57 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6277
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 30
FINDPEAKS_SCORE: 0.0078
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1786
POISSON_PERCENTILE: 93

**********************************************************************

ANALYSIS FILE NAME: GSM667642_UCSD.H1.Input.AK57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H1.09.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library AK57 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6619
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H1 Input 57
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library AK57 EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 30
FINDPEAKS_SCORE: 0.0078
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1786
POISSON_PERCENTILE: 93

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.Input.hESC.H1.09.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

value: H1 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

tag: medium

value: mTeSER

tag: Sex

tag: batch

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Whole_Dsim_251.011_Female_Rep2

value: Drosophila Species Stock Center (DSSC) 14021-0251.011. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Whole flies

value: Adult

value: Female

value: 5-7 days post eclosion


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in hESC H9 Cells; renlab.H4K91ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx and HiSeq 2000 platforms.
Library name: SK287
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5999
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667639_UCSD.H9.H4K91ac.SK287.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on the H9 Cell Line, Library SK287 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6276
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0233
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1802
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.704
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3022
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM667639_UCSD.H9.H4K91ac.SK287.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the H9 Cell Line, Library SK287 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6618
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H4K91ac 87
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H4K91ac Library SK287 EA Release 3

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0233
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1802
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.704
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3022
POISSON_PERCENTILE: 100

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H4K91ac.hESC.H9.01.01

value: H9 Cell Line

value: Between 30 and 50

value: Histone H4K91ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Whole_Dsim_251.011_Male_Rep2

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in hESC H9 Cells; renlab.H4K91ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK332
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6060
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6006
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667640_UCSD.H9.H4K91ac.SK332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on the H9 Cell Line, Library SK332 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6296
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0144
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1165
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.61
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2691
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM667640_UCSD.H9.H4K91ac.SK332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the H9 Cell Line, Library SK332 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6638
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H4K91ac 32
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H4K91ac Library SK332 EA Release 3

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0144
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1165
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.61
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2691
POISSON_PERCENTILE: 50

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H4K91ac.hESC.H9.02.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in hESC H9 Cells; renlab.H4K8ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx and HiSeq 2000 platforms.
Library name: SK283
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5966
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667638_UCSD.H9.H4K8ac.SK283.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on the H9 Cell Line, Library SK283 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6281
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0131
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1166
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.5504
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2539
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM667638_UCSD.H9.H4K8ac.SK283.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the H9 Cell Line, Library SK283 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6623
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H4K8ac 83
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H4K8ac Library SK283 EA Release 3

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0131
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1166
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.5504
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2539
POISSON_PERCENTILE: 50

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H4K8ac.hESC.H9.02.01

value: Histone H4K8ac

value: Biorupter

value: 500 micrograms

value: Millipore


title: Whole_Dsim_251.011_Male_Rep1

value: Drosophila Species Stock Center (DSSC) 14021-0251.011. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Whole flies

value: Adult

value: 5-7 days post eclosion


title: Whole_Dyak_261.01_Female_Rep1_2

value: Drosophila Species Stock Center (DSSC) 14021-0261.01. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Female


title: Whole_Dmoj_1352.22_Male_Rep2

value: Drosophila Species Stock Center (DSSC) 15081-1352.22. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Reference Epigenome: ChIP-Seq Input from hESC H9 Cells; renlab.Input.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SKH9-4
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5993
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667643_UCSD.H9.Input.SKH9-4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H9 Cell Line, Library SKH9-4 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6286
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 30
FINDPEAKS_SCORE: 0.0124
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.0778
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9959
IROC_PERCENTILE: 59
POISSON_SCORE: 0.0966
POISSON_PERCENTILE: 87

**********************************************************************

ANALYSIS FILE NAME: GSM667643_UCSD.H9.Input.SKH9-4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H9 Cell Line, Library SKH9-4 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6628
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 Input 4
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line ChIP-Seq Input Library SKH9-4 EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 30
FINDPEAKS_SCORE: 0.0124
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.0778
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9959
IROC_PERCENTILE: 59
POISSON_SCORE: 0.0966
POISSON_PERCENTILE: 87

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.Input.hESC.H9.01.01

value: H9 Cell Line

value: Between 30 and 50

value: ChIP-Seq Input

value: Input


title: Whole_Dvir_1051.87_Female_Rep1

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: droVir3+ERCC Spike-In Controls

organism: Drosophila virilis

value: Drosophila Species Stock Center (DSSC) 15010-1051.87. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Cl8 CNV extraction1_seq1 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: In this experiment, there is no ChIP step. Simply separate the polytene dna from the tissue (cell line) and seq them, if more reads (than other regions) then they are the CNV regions.

data_processing: Illumina_sequencing:DM:1 protocol. Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).  Processed data are obtained using following parameters: read length is 36   Illumina_seq_maq_processing:DM:1 protocol. Illumina seq maq processing protocol;  * Get Illumina FASTQ files back from Duke IGSP Sequencing Facility. Their steps, briefly: * Image analysis (SCS real time analysis software / Firecrest software) * Base calling ( Bustard.py) * Sequence analysis (GERALD.py) -> results in the FASTQ file that gets sent to us. * Using maq command-line tool v. 0.7.1: * Convert Illumina FASTQ file to Sanger-style FASTQ format: maq sol2sanger $workingdir/$solfastqfilename $workingdir/$solfastqfilename.sangerfastq  * Convert Sanger FASTQ file to Binary FASTQ format: maq fastq2bfq $workingdir/$solfastqfilename.sangerfastq $workingdir/$solfastqfilename.sangerbfq  * Convert Drosophila 5.1 FASTA file to Binary FASTA format: maq fasta2bfa $workingdir/$referencefastafile $workingdir/$referencefastafile.bfa  * Map reads back to Drosophila genome allowing 3 mismatches: maq map -n 3 $workingdir/$destination_table.map $workingdir/$referencefastafile.bfa $workingdir/$solfastqfilename.sangerbfq  * Create a mapview file to import into the database: maq mapview $workingdir/$destination_table.map > $workingdir/$destination_table.mapview * Processed data are obtained using following parameters: genome version is 5.1   CNV_seq_analysis:DM:1 protocol. CNV seq analysis protocol;  * Read locations are shifted: * Positive reads are shifted downstream by half of the estimated sonication size. * Negative reads are shifted upstream by half of the estimated sonication size. * Reads with a map score (Phred) >= 35 (leading to maximum probability that a read is misaligned of ~0.03%) are then binned based on their location, with non-overlapping bins of size 1000bp covering the genome. * The total number of reads in each bin are summed across replicates.

source_name: Cl8 CNV extraction1_seq1 channel_1

growth_protocol: Cell growth protocol;  Grow 10ml of cells in 100mm dishes For Kc and S2 cells use :  Schneider's medium (invitrogen 11720-067) 10% ModEncode serum 1% Penicillin/Streptomycin/Glutamine (PSG) (Invitrogen 10378-016) small edit For ML-DmBG3-c2 cells use:  Schneider's medium 10% ModEncode serum 1% PSG 10ug/ml human insulin (sigma I9278)) Cells are grown at 25C. Cells are happiest between 1.5X106 and 2.0X106

extract_protocol:
DNA isolation protocol;  1.Grow 10ml of cells to 1.5 x 106 in 100mm dishes 2.Harvest cells into 15ml conical tubes. 3.Pellet cells at 1000g for 5 minutes 4.Wash cells once in cold 1X PBS 5.Resuspend pellet in 0.7ml 10mM Tris pH 9.5 6.Add 0.7ml NDS. Invert to mix 7.Add 0.1ml 20mg/ml Proteinase K (Amresco 0706-1G). Invert to mix 8.Inc. 37C, 2 hours. 9.Add 1.5ml 1X TE. Invert to mix 10.Add 3.0ml phenol/chloroform. Invert tubes over 5 minutes 11.Centrifuge 3500 rpm for 10-12 minutes 12.Remove top layer with cut p1000 tips to a new 15ml tube 13.Repeat steps 10-12. 14.Add 2.5 volumes of room temp. 100% Ethanol. Invert 15.Inc. at room temp overnight 16.Centrifuge tubes 3500-3700rpm for 10-12 minutes 17.Wash pellet with 70% Ethanol and transfer pellet to a 1.5ml tube 18.Centrifuge full speed for 5 minutes 19.Air dry pellet 20.Resusp. pellet in 250ul 1X TE 21.Add 5ul 10mg/ml RNaseA (Amresco 0675-250mg). Inc. 37C for 1h 22.Add 1/10 volume 3M NaOAc. Vortex 23.Add 2X volume cold 100% Ethanol. Vortex 24.Inc. -80C 20-30 minutes 25.Centrifuge at 4C for 15 minutes 26.Wash with 70% Ethanol 27.Air dry pellet. Resusp. in 250ul 1X TE 28.Spec DNA Shearing DNA 29.Shear DNA 3X 10 seconds with 1minute on ice in between.
Genomic DNA library protocol;  Genomic DNA Library 1. Genomic DNA was fragmented to less than 800bps by sonication 2. the library was prepared as described in the Illumina provided protocol "Preparing samples for sequencing genomic DNA" (part # 11251892 Rev. A) with the exception of an additional gel extraction (size select for 150-200bps) after the "enrich the adapter-modified DNA fragments by PCR" step. 3. Samples were submitted to the Duke University IGSP sequencing facility.

tag: cell line

value: dorsal mesothoracic disc

value: third instar larval stage

value: Male


title: Cl8 CNV extraction1_seq2 aliquote 1

source_name: Cl8 CNV extraction1_seq2 channel_1

tag: developmental stage


title: Whole_Dsim_251.198_Male_Rep2

value: Drosophila Species Stock Center (DSSC) 14021-0251.198. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Whole_Dmoj_1352.22_Male_Rep1


title: Reference Epigenome: ChIP-Seq Analysis of H4K20me1 in hESC H9 Cells; renlab.H4K20me1.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K20me1 in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK286
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6002
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667634_UCSD.H9.H4K20me1.SK286.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K20me1 ChIP-Seq on the H9 Cell Line, Library SK286 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6282
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H4K20me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0246
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.194
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6795
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2836
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM667634_UCSD.H9.H4K20me1.SK286.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K20me1 ChIP-Seq read mappings from the H9 Cell Line, Library SK286 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6624
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H4K20me1 86
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H4K20me1 Library SK286 EA Release 3

QUALITY SCORES:
NUMBER_OF_H4K20me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0246
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.194
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6795
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2836
POISSON_PERCENTILE: 100

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H4K20me1.hESC.H9.01.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Histone H4K20me1

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Whole_Dsim_251.198_Female_Rep2

value: Whole flies

value: Adult

value: Female

value: 5-7 days post eclosion


title: Reference Epigenome: ChIP-Seq Analysis of H4K5ac in hESC H9 Cells; renlab.H4K5ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K5ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx and HiSeq 2000 platforms.
Library name: SK282
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5961
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667636_UCSD.H9.H4K5ac.SK282.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K5ac ChIP-Seq on the H9 Cell Line, Library SK282 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6272
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0134
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1016
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2344
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM667636_UCSD.H9.H4K5ac.SK282.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K5ac ChIP-Seq read mappings from the H9 Cell Line, Library SK282 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6614
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H4K5ac 82
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H4K5ac Library SK282 EA Release 3

QUALITY SCORES:
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0134
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1016
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2344
POISSON_PERCENTILE: 50

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H4K5ac.hESC.H9.02.01

value: H9 Cell Line

value: Between 30 and 50

value: Histone H4K5ac

value: Millipore


title: Whole_Dvir_1051.87_Female_Rep2

value: Drosophila Species Stock Center (DSSC) 15010-1051.87. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: Whole_Dmoj_1352.22_Female_Rep1

value: Drosophila Species Stock Center (DSSC) 15081-1352.22. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.


title: SG Orc ChIP-Seq extraction2_seq1 aliquote 2

description: channel ch2 is input DNA;

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  WIG Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

source_name: SG Orc ChIP-Seq extraction2_seq1 channel_2

growth_protocol:
From a Drosophila culture, manually remove larvea of selected type.
Collection and dissection of biologicial tissues, to include:embryo 0-2hfollicle cellsnurse cellsadult fat bodysalivary gland

extract_protocol:
Cross linking and chromatin extraction protocol for Drosophila ChIP experiments.
Chromatin IP of a chromatin extract with an antibody.
Generation of a genomic library suitable for Illumina sequencing, using the standard Illumina protocol.  This includes a 150-200bp size selection step.
Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: salivary gland

value: L3 stage wandering larvae

tag: genotype

value: wild type


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in hESC H9 Cells; renlab.H3K9me3.hESC.H9.03.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK40
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5981
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667633_UCSD.H9.H3K9me3.AK40.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H9.03.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H9 Cell Line, Library AK40 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6273
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.0402
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1465
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.7488
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3359
POISSON_PERCENTILE: 62

**********************************************************************

ANALYSIS FILE NAME: GSM667633_UCSD.H9.H3K9me3.AK40.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H9.03.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H9 Cell Line, Library AK40 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6615
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H3K9me3 40
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K9me3 Library AK40 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.0402
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1465
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.7488
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3359
POISSON_PERCENTILE: 62

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K9me3.hESC.H9.03.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Histone H3K9me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: SG Orc ChIP-Seq extraction2_seq1 aliquote 1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: dORC2 target name: Drosophila ORC2p host: Rabbit antigen: purified full length protein clonal: Polyclonal purified: Crude company: Lab catalog: Stephen P. Bell MIT reference: Austin et al 1999

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

source_name: SG Orc ChIP-Seq extraction2_seq1 channel_1

value: SuUR - Orr-Weaver(official name :SuUR genotype :SuUR mutant outcross :3 tags :Transposon tag :GFP description :SuUR mutant as maintained by the Orr-Weaver lab. made_by :Orr-Weaver )

tag: tissue

value: SuUR mutant


title: SG Orc ChIP-Seq extraction1_seq1 aliquote 2

description: channel ch2 is ChIP DNA; Antibody information listed below: official name: dORC2 target name: Drosophila ORC2p host: Rabbit antigen: purified full length protein clonal: Polyclonal purified: Crude company: Lab catalog: Stephen P. Bell MIT reference: Austin et al 1999

source_name: SG Orc ChIP-Seq extraction1_seq1 channel_2

tag: strain


title: Whole_Dmel_yw_Male_Rep1

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: dm3 (no chrUextra)+ERCC Spike-In Controls

value: Whole flies

value: Adult

tag: sex

value: Male

value: 5-7 days post eclosion


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in hESC H9 Cells; renlab.H3K79me1.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK329
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6072
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6006
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667629_UCSD.H9.H3K79me1.SK329.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the H9 Cell Line, Library SK329 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6267
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0198
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1293
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.748
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2661
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM667629_UCSD.H9.H3K79me1.SK329.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H9 Cell Line, Library SK329 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6609
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H3K79me1 29
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K79me1 Library SK329 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0198
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1293
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.748
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2661
POISSON_PERCENTILE: 100

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K79me1.hESC.H9.01.01

value: H9 Cell Line

value: Between 30 and 50

value: Female

value: Histone H3K79me1

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K56ac in hESC H1 Cells; renlab.H3K56ac.hESC.H1.02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K56ac in hESC H1 Cells. Sequencing was done on the Illumina Genome Analyzer IIx and HiSeq 2000 platforms.
Library name: SK300
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6022
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667627_UCSD.H1.H3K56ac.SK300.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC.H1.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K56ac ChIP-Seq on the H1 Cell Line, Library SK300 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6274
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0141
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0979
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.7711
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1696
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM667627_UCSD.H1.H3K56ac.SK300.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC.H1.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K56ac ChIP-Seq read mappings from the H1 Cell Line, Library SK300 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6616
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H1 H3K56ac 00
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K56ac Library SK300 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0141
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0979
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.7711
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1696
POISSON_PERCENTILE: 50

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K56ac.hESC.H1.02.01

value: H1 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Histone H3K56ac

value: Millipore


title: SG Orc ChIP-Seq extraction1_seq1 aliquote 1

source_name: SG Orc ChIP-Seq extraction1_seq1 channel_1

value: SuUR - Orr-Weaver(official name :SuUR genotype :SuUR mutant outcross :3 tags :Transposon tag :GFP description :SuUR mutant as maintained by the Orr-Weaver lab. made_by :Orr-Weaver )

value: salivary gland

value: L3 stage wandering larvae

value: SuUR mutant


title: 0-24h Embryo PolII ChIP-Seq extraction2_seq1 aliquote 1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name:Anti-RNA polymerase II, clone CTD4H8 ; aliases:Upstate 05-623 target name: RNA polymerase II; species:D. melanogaster;host: Mouse;purified: Protein A/G; clonal: Monoclonal;company:Upstate-Millipore;catalog:05-623 short description:   Anti-RNA polymerase II, clone CTD4H8. Peptide containing 10 repeats of YSPT[pS]PS corresponding to the carboxyl-terminal domain of RNA polymerase II. Purified mouse IgG1 in buffer containing 0.02 M phosphate buffer, pH 7.6, 0.25 M NaCl, and 0.1% Sodium Azide before the addition of glycerol to 30%.

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

source_name: 0-24h Embryo PolII ChIP-Seq extraction2_seq1 channel_1

growth_protocol: Embryo collection protocol

value: Mixed Embryos 0-24h


title: Whole_Dmel_yw_Female_Rep1

source_name: Whole tissue

value: Whole flies

value: Adult

value: Female

tag: age

value: 5-7 days post eclosion