title: wild-type+sgrs

city: Wellesley

first: Brian

last: Tjaden

address: 106 Central Street

institute: Wellesley College

data_processing:
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper
Genome_build: Salmonella enterica subsp. Enterica serovar Typhimurium st. LT2 (NC_003197.1)/ASM694v1
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Total RNA from bacterial cell culture

growth_protocol: Minimal mops medium , carbon source: fructose

extract_protocol:
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910.
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit

treatment_protocol: Each of the mutant strains above were grown in min. Mops fructose medium  until cultures reached an OD600 of ~0.3. Cultures were then treated with the glucose-analog alpha-methyl glucoside (αMG), and total RNA harvested 15' after treatment

tag: growth phase

value: exponential growth

tag: treatment

value: wild-type


title: T4-PiZt-11-S mRNA-seq

status: Public on Mar 26 2013

type: SRA

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern

library_source: transcriptomic

data_processing:
mRNA-seq reads were uniquely mapped to the genome using Bowtie (Langmead et al., 2009) allowing two mismatches. For smRNA-seq reads, adapter sequences were trimmed first, and then were uniquely mapped to the genome using Bowtie allowing no mismatches, and reads were categorized by their lengths for analyses
Genome_build: MSU 6.1
Supplementary_files_format_and_content: Column 1 is the read sequence. Column 2 is the number of reads with the given sequence.

molecule: total RNA

organism: Oryza sativa

source_name: 3wk-old leaf tissue

extract_protocol: Total RNA (10 ug) for each sample was used to purify poly-A mRNA; this mRNA was used for synthesis and amplification of cDNA. The RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit from Illumina (San Diego, CA).

treatment_protocol: RNA-seq libraries were constructed from total RNA isolated using TRIzol reagent (Invitrogen, Life Technologies, USA) from leaf tissues

tag: tissue

value: leaf

tag: genotype

value: PiZt 11

tag: ecotype

value: Nipponbare

tag: rna subtype

value: polyA mRNA


title: WT protocol 1.5

state: MA

data_processing:
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper
Genome_build: Xenorhabdus nematophila ATCC 19061 (NC_014228.1)
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.

organism: Xenorhabdus nematophila

growth_protocol: LB broth. Late exponential phase.

extract_protocol:
The mirVan miRNA Isolation Kit (Ambion) was used to isolate and enrich sRNAs, 3 mg of which were used for sRNA library construction.
Libraries of sRNAs ranging from 18-200 bp were constructed by using the Small RNA Sample Prep Kit (Illumina) following the standard manufacturer's protocol (Illumina Small RNA Sample Preparation Guide).

treatment_protocol: To reduce potential interference from tRNAs and 5S rRNAs, a stable RNA depletion protocol was included.

tag: illumina protocol

value: version 1.5


title: WT

value: small RNA


title: rpoS mutant protocol 1.5

source_name: rpoS::kan mutant (HGB151)

value: rpoS::kan mutant (HGB151)


title: rpoS mutant


title: wildtype_sgrs_15

value: glucose-analog alpha-methyl glucoside

value: wildtype

tag: strain


title: T2-PiZt-11-S mRNA-seq


title: T4-PiZt-11-R mRNA-seq


title: sgrs_sgrt_mut_15

value: sgrs sgrt


title: sgrs_sgrt_mut


title: sgrs_bp_mut

value: sgrs


title: T2-PiZt-11-R mRNA-seq


title: WT2011 mRNA-seq

value: Wild type


title: T6-Spin1i-1-R smRNA-seq

extract_protocol: smRNA-seq libraries were constructed from total RNA isolated from the same tissues as described for the mRNA libraries, using the TruSeq Small RNA Sample Prep Kit from Illumina (San Diego, CA).

value: Spin1 RNAi

value: Small RNA


title: T6-Pi9-R smRNA-seq


title: sgrs_bp_mut_15


title: deltasgrS_15

value: deltasgr


title: deltasgrs_mut

value: exponential growth

value: deltasgrs


title: WT2007 mRNA-seq

value: leaf


title: T6-PiZt-11-R smRNA-seq

value: PiZt 11


title: bovine digital dermatitis full depth skin biopsy 5

city: Manchester

first: rachel

middle: anne

last: scholey

address: Oxford road

country: United Kingdom

institute: University of Manchester

data_processing:
Reads were mapped to the Bos taurus genome (Btau 4.0 accessed through http://www.ensembl.org) using Tophat (version 1.2.0 http://tophat.cbcb.umd.edu/). Across the biological replicate sets, the mean number of reads mapped for chromosomes 1-29, X and MT was for healthy skin 22,246,070 and for BDD lesions 19,801,622. Mapped regions had a median coverage of 5x and the median coverage per mapped base was approximately 3-6x.
EdgeR (Bioconductor) was used to analyse differential expression of the biological replicates (healthy skin verses digital dermatitis lesions)
The EdgeR output is available in the results file "RScholey_EdgeR common dispersion output"
Genome_build: Btau 4.0

molecule: polyA RNA

organism: Bos taurus

source_name: full depth skin biopsy

extract_protocol:
RNA was extracted using Trizol/chloroform extraction followed by Qiagen Rneasy clean up and polyA enrichment using Ambion poly A purist kit.
All PolyA supplied by was used into the RNase 3 fragmentation.  Following sscDNA synthesis these were size selected on a polyacrylamide gel, as per the SOLID Total RNA-Seqw Kit Protocol 4452437A.

tag: biopsy


title: 724R control 24h

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
Cluster generation and sequencing of the pooled RNA-seq library was carried out on an Illumina® Cluster Station and Illumina® Genome Analyzer IIx sequencer according to the manufacturer’s instructions (Illumina). The pooled library was sequenced as single-end read 84-mers using Illumina® version 4.0 sequencing kits and the standard Illumina® Genome Analyzer IIx pipeline. The Illumina® Sequencing Control Software version 2.9 and Real Time Analysis version 1.9 software packages were used for real-time tracking of the sequencing run, real-time image processing, the generation of base intensity values and base calling.
Sequence reads obtained from seven lanes of the Illumina flow cell were deconvoluted into 14 individual libraries (Raw data files) using the unique indexed barcoded adapters. A Perl script was used to screen adapter artefacts, removing any reads containing a full-length match to the 33 nucleotide Illumina® adapter sequence, allowing up to four mismatches. Read quality was then assessed using FastQC software [version 0.9] (www.bioinformatics.bbsrc.ac.uk/projects/fastqc), revealing low Phred scores at the 3' end of sequence reads. Consequently, nine nucleotides were trimmed from the 3' ends of all sequence reads using the FASTX Toolkit [version 0.0.13] (http://hannonlab.cshl.edu/fastx_toolkit) generating usable reads of 69 nucleotides.
Deconvoluted quality-checked sequence reads were aligned to the B. taurus reference genome (Btau 4.0.63 genome release) with the TopHat splice junction mapper [version 1.3.0], which aligns reads using the Bowtie aligner (version 0.12.7). The Bowtie alignment procedure was configured for strand-specific libraries and to filter only unique hits to the reference genome sequence.
To obtain raw counts per transcript, HTSeq package [version 0.5.3p1] (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) was used on alignment files in BAM format. HTSeq-count was used with option overlap resolution mode set to intersection non-empty. Counts of uniquely-mapped reads were obtained for all bovine Ensembl genes and transcripts, with separate counts obtained for sense (Processed sense data files) and antisense (Processed antisense data files) DNA strands.
Once raw counts were obtained from HTseq-count, analysis of differential expression was performed in the R statistical programming environment using the edgeR (version 2.2.5) Bioconductor package and lattice [version 0.19-30] (http://lattice.r-forge.r-project.org). First, quality checks were performed by plotting the density of counts per feature (a feature being a gene or transcript generated respectively from the sense or antisense strand) for each sample and also by generating a multidimensional scaling plot of the RNA-seq data. The edgeR software package was used to determine differential expression using the paired-sample statistical test. Filtering of lowly expressed features was performed by retaining only features with at least one count per million in three or more libraries. A normalisation factor was calculated using the default trimmed mean of M values (TMM) method, and the dispersion parameter for each feature was estimated as the Cox-Reid common dispersion method in the edgeR package. Differential expression was evaluated by fitting a negative binomial generalized linear model for each feature and then adjusting the P-value for multiple testing using the Benjamini-Hochberg correction with a false discovery rate (FDR) of 0.05.
Genome_build: Bos taurus reference genome version 4.0.63
Supplementary_files_format_and_content: Tab-delimited text files include raw count values per genes

source_name: Monocyte-derived macrophages

growth_protocol: Seven age-matched (three-year old) Holstein-Friesian females were used. All animals were maintained under uniform housing conditions and nutritional regimens at the UCD Lyons Research Farm (Newcastle, County Kildare, Ireland). The animals were selected from an experimental herd without a recent history of bovine tuberculosis infection. This was confirmed using the single intradermal tuberculin test (SICTT) and the BoviGAM® IFN-g enzyme linked immunosorbent assay (ELISA; Prionics AG, Schlieren-Zurich, Switzerland) with all animals testing negative. These cattle also tested negative for Brucella abortus, M. avium subsp. paratuberculosis, Salmonella typhimurium, bovine herpesvirus 1 and bovine viral diarrhoea (BVD) virus. For monocyte isolation, 300 ml of whole blood was collected in acid citrate dextrose buffer (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) in sterile bottles. Blood was layered onto Accuspin™ tubes containing Histopaque® 1077 (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and following density gradient centrifugation, peripheral blood mononuclear cells (PBMC) were collected. Contaminating red blood cells (RBC) were removed following resuspension and subsequent incubation of the PBMC in RBC lysis buffer (10mM KHCO3, 150mM NH4Cl, 0.1mM EDTA pH 8.0) for 5 minutes at room temperature. After incubation, PBMC were washed twice with phosphate-buffered saline (PBS) before resuspending cells in phosphate-buffered saline (PBS) containing 1% bovine serum albumin (BSA, Sigma-Aldrich Ireland Ltd., Dublin, Ireland). Monocytes were then isolated using the MACS® protocol and a human anti-CD14 antibody (Miltenyi Biotec Ltd., Surrey, UK), which has been shown to be cross-reactive with bovine monocytes. All procedures were carried out according to the manufacturers’ instructions. The identity and purity of monocytes was confirmed by flow cytometry using an anti-CD14 FITC labelled antibody. Purified monocytes were seeded at 1 × 106/ml in 24-well tissue culture plates in RPMI 1640 medium (Invitrogen Ltd., Paisley, UK) containing 15% heat inactivated foetal calf serum (FCS; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), 1% non-essential amino acids (NEAA; Sigma-Aldrich Ireland Ltd., Dublin, Ireland), gentamicin (5 µg/ml; Sigma-Aldrich Ireland Ltd., Dublin, Ireland) and incubated at 37°C, 5% CO2. Following 24 hours incubation (day one) the media was replaced with 1ml fresh antibiotic-containing media to remove any non-adhered cells. On day three, media was replaced with 1 ml antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only). To ensure that the same number of MDM were subjected to different treatments between experiments, cells were dissociated on day five using a non-enzymatic cell dissociation solution (Sigma-Aldrich Ireland Ltd., Dublin, Ireland), counted and then re-seeded at 2 × 105 cells/well in 24-well tissue culture plates (Sarstedt, County Wexford, Ireland) using antibiotic-free culture media. By day eight, 80-100% confluent monolayers of MDM were generated that displayed the characteristic macrophage morphology as confirmed by Giemsa staining (data not shown). Day eight MDM were used for the in vitro challenge experiments with M. bovis.

extract_protocol:
All RNA extractions were performed in the CL3 laboratory using an RNeasy kit incorporating an on-column DNase treatment step (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions. RNA quantity and quality was assessed using both the NanoDropTM 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Cork, Ireland). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) greater than 8.5.
In total, 14 strand-specific RNA libraries for high-throughput sequencing were prepared (seven libraries for each treatment: M. bovis-infected and control samples) using 200 ng of total RNA. Total RNA was first heated at 65°C for 5 min to disrupt any secondary structure. Purification of poly(A) RNA was performed using a Dynabeads® mRNA DIRECTTM Micro Kit according to the manufacturer’s instructions (Invitrogen™/Life Technologies Ltd., Paisley, UK). Purified poly(A) RNA was then fragmented using 1× RNA Fragmentation Reagent (Ambion®/Life Technologies Corporation, Warrington, UK) for 5 min at 70°C and precipitated using 68 mM sodium acetate pH 5.2 (Ambion), 227 ng/μl glycogen (Ambion) and 30 μl of 100% ethanol (Sigma-Aldrich Ltd., Dublin, Ireland). Pellets were washed with 80% ethanol, air-dried for 10 min at room temperature and re-suspended in 10.5 µl DNase- and RNase-free water. Synthesis of first strand cDNA was performed by incubating fragmented RNA with 261 mM Random Hexamer Primers (Invitrogen), 1× first strand buffer (Invitrogen); 10 mM DTT (Invitrogen); 0.5 mM dNTPs; 20 U RNaseOUTTM Recombinant Ribonuclease Inhibitor; and 200 U SuperScript® II Reverse Transcriptase (Invitrogen) at 25°C for 10 min, at 42°C for 50 min, and 70°C for 15 min. First strand synthesis reaction mixtures were purified using MicroSpinTM G-50 columns according to the manufacturer’s instructions (GE Healthcare UK Ltd., Little Chalfont, Buckinghamshire, UK). Second strand cDNA synthesis, involving the incorporation of uracil, was performed by adding the first strand cDNA synthesis reaction to a second strand reaction mix consisting of 0.065× first strand buffer (Invitrogen); 1× second strand buffer (Invitrogen); a dNTP mix consisting of a final concentration of 0.3 mM dATP, dCTP, dGTP (Sigma-Aldrich) and 0.3 mM dUTP (Bioline Reagents Ltd., London, UK); 1 mM DTT (Invitrogen); 2 U RNase H (Invitrogen) and 50 U E. coli DNA Polymerase I (Invitrogen). Reactions were incubated at 16°C for 2.5 h. The double stranded cDNA was subsequently purified using a QIAquick PCR Purification kit (Qiagen) according to the manufacturer’s instructions and eluted in 30 µl of the provided elution buffer. Blunt-end repair of cDNA was performed in a 100 µl reaction containing 1× T4 DNA ligase buffer with 10 mM dATP (New England Biolabs® Inc., MA, USA), 0.4 mM of each dNTP (Invitrogen), 15 U T4 DNA polymerase (New England Biolabs), 5 U DNA Polymerase I Large [Klenow] Fragment (New England Biolabs) and 50 U T4 polynucleotide kinase (New England Biolabs). Reactions were incubated at 20°C for 30 min and the cDNA was then purified using a QIAquick PCR Purification Kit (Qiagen) according to the manufacturer’s instructions and eluted in 32 µl of the provided elution buffer. To facilitate Illumina® GA adaptor ligation, a single ‘A’ base was added to the 3' ends of the blunt-end repaired cDNA samples. 32 µl of purified phosphorylated blunt end-repaired cDNA was included in a final 50 µl reaction mixture containing: 1× Klenow fragment buffer (New England Biolabs); 0.2 mM dATP (Invitrogen), and 15 U Klenow fragment with 3'-to-5' exonuclease activity (New England Biolabs). Reactions were incubated at 37°C for 30 min, after which cDNA was purified using a QIAquick MinElute Kit (Qiagen) according to the manufacturer’s instructions and eluted in 21 µl of the provided elution buffer. Illumina® RNA-seq adaptor ligation reactions (50 µl volumes) involved incubation of 21 µl of phosphorylated blunt-ended cDNA containing a 3'-dATP overhang with 1× Quick DNA ligase buffer (New England Biolabs); 30 nM custom indexed single-read adaptors (see Samples_barcode.xlsx) and 15 U T4 DNA ligase (Invitrogen). Reaction mixes were incubated at room temperature for 15 min and purified using a QIAquick MinElute Kit according to the manufacturer’s instructions (Qiagen) and eluted in 10 µl of the provided elution buffer. Adaptor-ligated cDNA was gel-purified using 2.5% agarose gels stained with 1 μg/ml ethidium bromide (Invitrogen). Gels were electrophoresed at 100 Volts using 1× TAE buffer (Invitrogen) for 75 min at room temperature. Size fractionated bands corresponding to 200 bp (+50 bp) were excised from each sample and purified using a QIAquick Gel Extraction kit (Qiagen) according to the manufacturer’s instructions and eluted in 30 µl of elution buffer. To generate strand-specific RNA-seq libraries, the second strand of the gel-purified adapter-ligated cDNA containing uracil was digested enzymatically in 30 µl reaction volumes containing 1× Uracil-DNA Glycosylase buffer and 1 U Uracil-DNA Glycosylase (Bioline). Reactions were incubated at 37°C for 15 min followed by 94°C for 10 min. PCR enrichment amplifications (50 µl) containing 15 μl of second strand-digested, adaptor-ligated cDNA; 1× Phusion® High-Fidelity DNA polymerase buffer (New England Biolabs); 334 nM each Illumina® PCR primer (Illumina® Inc., San Diego, CA, USA); 0.4 mM each of dATP, dCTP, DGTP and dTTP (Invitrogen) and 1 U Phusion® High-Fidelity DNA polymerase (New England Biolabs). PCR amplification reactions consisted of an initial denaturation step of 98°C for 30 seconds, 18 cycles of 98°C for 10 seconds, 65°C for 30 seconds and 72°C for 30 seconds, followed by a final extension step of 72°C for 5 min. PCR products were visualised following electrophoresis on a 2% agarose gel stained with ethidium bromide (0.6 µg/ml; Invitrogen) and purified to remove PCR-generated adaptor-dimers using an Agencourt AMPure XP kit (Beckman Coulter Genomics, Danvers, MA, USA) according to the manufacturer’s instructions with final elution in 30 μl of 1× TE buffer. All RNA-seq libraries were quantified using a Qubit® Fluorometer and Qubit® double stranded DNA High Sensitivity Assay Kit (Invitrogen). RNA-seq library quality was assessed using an Agilent Bioanalyzer and Agilent High sensitivity DNA chip (Agilent) and confirmed that library insert sizes were ~200-250 bp for all individual libraries. Individual RNA-seq libraries were standardised and pooled in equimolar quantities (10 µM for each individual library). The quantity and quality of the final pooled library was assessed as described above prior to sequencing.

treatment_protocol: Culturing of M. bovis was performed in a Biosafety Containment Level 3 (CL3) laboratory and conformed to the national guidelines on the use of Hazard Group 3 infectious organisms. A clinical isolate of M. bovis, obtained from an infected Irish animal was supplied by Dr. Eamon Costello (Department of Agriculture, Fisheries and Food, Backweston, County Kildare) was used in the current study. M. bovis stocks for MDM-challenge experiments were cultured in Middlebrook 7H9 medium (DifcoTM, Becton-Dickinson, Dublin, Ireland) containing 10% (volume/volume) Middlebrook albumin-dextrose-catalase (ADC) enrichment (DifcoTM, Becton-Dickinson, Dublin, Ireland), 0.05% Tween 80 (Sigma-Aldrich, Dublin, Ireland) and 0.40% (weight/volume) sodium pyruvate (Sigma-Aldrich, Dublin, Ireland) at 37°C. For colony forming unit (cfu) counting Middlebrook 7H11 medium (DifcoTM, Becton-Dickinson, Dublin, Ireland) containing 0.40% (volume per volume) sodium pyruvate and 10% (volume/volume) Middlebrook (ADC) enrichment. Bacterial cultures were grown to mid-logarithmic phase as determined by spectrophotometric analysis prior to the challenge experiments using the purified bovine MDM. All challenge experiments including the preparation of non-challenge control samples were performed in the CL3 laboratory. MDM samples (seeded at 2 × 105 cells per well) were challenged with M. bovis (4 × 105 cells/well; based on bacterial cell counts performed using a Petroff Hausser chamber (Fisher-Scientific, Dublin, Ireland) [multiplicity of infection 2:1] and incubated at 37°C, 5% CO2 for 24 hours. For the non-challenged control samples at 24 hours, antibiotic-free culture media (RPMI 1640 medium containing 15% heat inactivated FCS and 1% NEAA only) was added to each well. After 2 hours post-challenge, the media from all 24 hours challenge experiments was replaced with 0.5 ml fresh antibiotic-free culture media per well and re-incubated at 37°C, 5% CO2 until MDM were required for harvesting. Challenged and non-challenged control MDMs were lysed and harvested using RLT/1% β-mercaptoethanol buffer (Qiagen Ltd., Crawley, UK) at the designated time points. For each treatment, MDM lysates from two culture plate wells were pooled and stored at ‑80°C until required for RNA extraction.

value: Holstein-Friesian

tag: Sex

value: Female

tag: age

value: Four years old

tag: animal id

tag: cell type

value: Monocyte-derived macrophages

tag: infection status

value: Control uninfected


title: T4-PiZt-11-R smRNA-seq

value: Nipponbare


title: bovine digital dermatitis full depth skin biopsy 3


title: bovine digital dermatitis full depth skin biopsy 4


title: bovine digital dermatitis full depth skin biopsy 2


title: normal bovine foot digital skin full depth biopsy 5


title: WT2003 smRNA-seq


title: normal bovine foot digital skin full depth biopsy 4


title: WT2011 smRNA-seq


title: normal bovine foot digital skin full depth biopsy 3


title: WT2011 (replicate) BS-seq

description: Bisulfite-treated genomic DNA_Sample 18

library_source: genomic

data_processing:
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to MSU6.1 chr1..12, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Identical reads were collapsed into single reads.
Genome_build: MSU 6.1
Supplementary_files_format_and_content: Column 1 is chromosome (1..12).  Column 2 is the coordinate of the genomic cytosine. Column 3 is genomic strand (+/-) of the cytosine. Column 4 is context (CG, CHG, or CHH) of the genomic cytosine. Column 5 is #Cs. Column 6 is #Ts.

molecule: genomic DNA

extract_protocol: Fragmented genomic DNA library as described in Cokus et al., Nature 2008, except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 for further information)

treatment_protocol: Genomic DNA was extracted using Qiagen Plant DNeasy Maxi Kit.

tag: genotype/variation

value: 3wk-old leaf tissue


title: WT2007 smRNA-seq


title: normal bovine foot digital skin full depth biopsy 2


title: normal bovine foot digital skin full depth biopsy 1


title: WT_plus_2DG_3

data_processing:
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.

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

source_name: Total RNA from bacterial culture

growth_protocol: Aerobic growth at 37°C  in specified media

treatment_protocol: Cells treated during mid-exponential growth phase

tag: media

value: Defined MOPS Minimal + 0.4% Glycerol +0.5% 2-DG

value: WT


title: WT regenerated from tissue culture 3 BS-seq

description: Bisulfite-treated genomic DNA_Sample 17

value: Wild type


title: WT regenerated from tissue culture 1 BS-seq

description: Bisulfite-treated genomic DNA_Sample 15


title: WT Callus 2 BS-seq

description: Bisulfite-treated genomic DNA_Sample 14

source_name: callus

value: callus


title: WT_plus_2DG_2


title: WT_plus_2DG_1


title: WT Callus 1 BS-seq

description: Bisulfite-treated genomic DNA_Sample 13


title: T2-PiZt-839-8-S ( Non functional PiZt) BS-seq

description: Bisulfite-treated genomic DNA_Sample 12


title: WT_minus_2DG_3

value: Defined MOPS Minimal + 0.4% Glycerol


title: WT_minus_2DG_1


title: T2-PiZt-839-8-R BS-seq

description: Bisulfite-treated genomic DNA_Sample 11


title: bovine digital dermatitis full depth skin biopsy 1


title: T2-PiZt-11-R smRNA-seq

value: Small RNA


title: T6-Spin1i-1-R BS-seq

description: Bisulfite-treated genomic DNA_Sample 10

value: Spin1 RNAi


title: MG1655_plus_aMG_3

value: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG


title: T4-PiZt-11-S BS-seq

description: Bisulfite-treated genomic DNA_Sample 7


title: MG1655_plus_aMG_2


title: T6-Pi9-R BS-seq

description: Bisulfite-treated genomic DNA_Sample 9


title: T4-PiZt-11-S smRNA-seq

value: leaf


title: T2-PiZt-11-S smRNA-seq

value: PiZt 11


title: T6-PiZt-11-R BS-seq

description: Bisulfite-treated genomic DNA_Sample 8


title: T4-PiZt-11-R BS-seq

description: Bisulfite-treated genomic DNA_Sample 6


title: MG1655_minus_aMG_1


title: MG1655_minus_aMG_3


title: T2-PiZt-11-R BS-seq

description: Bisulfite-treated genomic DNA_Sample 4


title: WT2011 BS-seq

description: Bisulfite-treated genomic DNA_Sample 3


title: T2-PiZt-11-S BS-seq

description: Bisulfite-treated genomic DNA_Sample 5


title: MG1655_minus_aMG_2


title: MG1655_plus_aMG_1


title: miwi.mut.17.rnaseq

city: Worcester

first: Christian

last: Roy

state: Massachusetts

address: 364 Plantation St

institute: Umass Med

data_processing:
De novo transcriptome assembly from three biological replicates of strand-specific RNA-seq data from adult testes was performed using Trinity (r2012-06-08) with default parameters (Grabherr et al., 2011). The assembled RNA sequences were aligned to the mouse genome (mm9) with BLAT (Kent, 2002), and the alignments with more than 95% of sequence length mapped and fewer than 1% mismatches retained. We extracted novel junctions from Trinity (i.e., reads with [0-9]+M[0-9]+N[0-9]+M pattern in the CIGAR string of SAM output), and re-mapped all RNA-seq reads to these junctions, rescuing 1,402,444 reads in three replicates. Rescued reads were combined with TopHat alignments (supplied with "–max-multihits 100" to assembly through repetitive regions) and used as input for reference-based assembly. We used Cufflinks v2.0.2 (Trapnell et al., 2010) with parameters of “-u -j 0.2 --min-frags-per-transfrag 40” to assemble transcripts. To join small transcript fragments caused by insufficient read coverage or embedded repetitive elements, two different gap-joining distance cutoffs were used for the assembly of genes (“--overlap-radius 100”) and piRNA loci (“--overlap-radius 250”). We used Cuffcompare v2.0.2 (Trapnell et al., 2010) to annotate the 49,840 Cufflinks-assembled transcripts using parameters optimized for genic conditions (“--overlap-radius 100”). A final list of 50,081 transcripts (including correct piRNA loci) are provided here.
RNA-seq reads were aligned to the genome (NCBI 37/mm9) using TopHat 2.0.4 (Trapnell et al., 2009). Reads were mapped uniquely using the ‘-g 1’ switch. We assembled the mouse testes transcriptome. For genes with multiple isoforms, the transcript with the highest average rpkm value among the three replicates of adult testes was selected for further analysis. Fragments with both reads mapped within a transcript, or to piRNA precursor transcripts, were counted using BEDTools (Quinlan and Hall, 2010). The sum of the reads aligning to the top quartile of expressed transcripts per library was used to calibrate the samples. The number of reads per transcript was normalized by length, divided by the library-specific calibration factor, and reported as rpkm with a pseudo count of 0.001.
Genome_build: mm9
Supplementary_files_format_and_content: bed file containing assembled transcripts and csv file containing rpkm values available on Series record

organism: Mus musculus

source_name: testes

extract_protocol:
Mice were maintained and used according to the guidelines of the Institutional Animal Care and Use Committee of the University of Massachusetts Medical School.
Strand-specific RNA-seq libraries via Incorporation of dUTP in second strand synthesis (Zhang et al., 2012) using Ribo-Zero Gold (Epicentre Biotechnologies, Madison, WI, USA) were sequenced using the paired-end protocol on a HiSeq 2000.

tag: developmental stage

value: miwi mut

value: testes


title: CV108_plus_aMG_3


title: CV108_plus_aMG_1


title: CV108_plus_aMG_2


title: WT2007 BS-seq

description: Bisulfite-treated genomic DNA_Sample 2


title: WT regenerated from tissue culture 2 BS-seq

description: Bisulfite-treated genomic DNA_Sample 16


title: miwi.het.14.rnaseq

value: miwi het


title: amyb.mut.17.rnaseq

value: amyb mut


title: CV108_minus_aMG_3


title: miwi.het.17.rnaseq


title: WT_minus_2DG_2


title: CV108_minus_aMG_1


title: amyb.het.17.rnaseq

value: amyb het


title: wt_un_3

value: Defined MOPS Rich+ 0.4% Glycerol


title: amyb.mut.14.rnaseq


title: CV108_minus_aMG_2


title: wt_un_2


title: wt_T_2

value: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG


title: wt_un_1


title: wild.type.20.rnaseq

value: wild type


title: wt_T_1

value: WT


title: wild.type.12.rnaseq


title: wild.type.10.rnaseq


title: amyb.het.14.rnaseq


title: WT2003 BS-seq

description: Bisulfite-treated genomic DNA_Sample 1

value: Nipponbare

value: Wild type

value: 3wk-old leaf tissue


title: wild.type.14.rnaseq


title: wild.type.17.rnaseq


title: WT_3

value: LB + 0.5% aMG


title: wild.type.42.rnaseq

value: 6 weeks


title: wt_T_3


title: sgrS_un_3

value: sgrS


title: miwi.mut.14.rnaseq


title: Mouse Pol II ChIPSeq

data_processing:
ChIP-seq reads were aligned to the genome (mouse mm9, chicken gg3) using Bowtie version 0.12.7 (Langmead et al., 2009). Reads were mapped uniquely using the '-M 1 --best --strata' switches and one mismatch was allowed (-v 1).
ChIP peaks were identified using MACS version 1.4.1 (Zhang et al., 2008) using default arguments, input as control, and a cutoff p-value = 10-25 was used. Peaks of all p-values are supplied here.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BED files containing called peaks (all p-values).

source_name: Testes, Pol II ChIP

extract_protocol:
ChIP was performed as described (Chen et al., 2008) except that testes were macerated on ice and then fixed with 1.5% (w/v) formaldehyde for 20 min. Samples were then further crushed using 20 strokes with a 'B' pestle in a Dounce homogenizer (Kimble-Chase, Vineland, NJ, USA). Chromatin was sheared by sonication and immunoprecipitated using anti-A-MYB (HPA008791; Sigma, St. Louis, MO, USA), anti-H3K4me3 (ab8580; Abcam, Cambridge, MA, USA), or anti-RNA polymerase II antibody (N20, sc899, Santa Cruz Biotechnology, Santa Cruz, CA, USA); immunoglobulin G (IgG; Sigma, item 2729) served as a control.
ChIP-seq libraries were prepared following the Illumina ChIP-seq protocol and sequenced on a HiSeq 2000 (50 nt reads).

tag: chip antibody

value: anti-RNA polymerase II


title: WT_1


title: Mouse H3K4me3_ChIPSeq

source_name: Testes, H3K4me3_ChIP


title: WT_2


title: Mouse Input DNA ChIPSeq

source_name: Testes, input

value: immunoglobulin G


title: sgrS_T_3


title: sgrS_un_1


title: sgrS_T_2


title: Mouse A-MYB ChIPSeq

source_name: Testes, A-MYB ChIP

value: anti-A-MYB


title: SgrR_1

value: SgrR


title: sgrS_T_1


title: SgrR_3


title: SgrR_2


title: N. gonorrhoeae grown in KSFM Rep 3

data_processing:
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper
Genome_build: FA 1090 genome (NC_002946.2)/ASM16353v1
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.

organism: Neisseria gonorrhoeae F62

source_name: N. gonorrhoeae grown in KSFM

growth_protocol: Grown for 120 mInutes in KSFM, static with 5% CO2

extract_protocol:
RNA was extracted with TRIzol (phenol/chloroform) according to instructions
Libraries were constructed with BioChain's mRNA Sample Prep Kit

tag: specific growth conditions


title: MG1655+aMG_3


title: N. gonorrhoeae grown in KSFM Rep 2

value: Grown for 120 mInutes in KSFM, static with 5% CO2


title: N. gonorrhoeae grown in KSFM Rep 1


title: MG1655-aMG_2

value: LB


title: MG1655-aMG_1


title: pLCV1_3

value: Defined MOPS Rich + 0.2% Glucose


title: pLCV1_1


title: pHDB3_3


title: pHDB3_2


title: Galaxy5-[CV104_pLCV1_20.txt]


title: Galaxy4-[CV104_pHDB3_20.txt]


title: Galaxy3-[CV104_pLCV1_10.txt]


title: sgrS_un_2

value: Defined MOPS Rich+ 0.4% Glycerol


title: Galaxy1-[CV104_pHDB3_5.txt]


title: Galaxy6-[CV104_pHDB3_10.txt]


title: Bcell_Brg1

status: Public on Mar 25 2013

city: Memphis

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads mapped to hg18 using bowtie 0.12.7, with -m 1 allowing one location per read
Mapped reads filtered to allow one read per position
Pol II and p300 binding sites calculated using MACS 1.4.1, -s hg, --p-value=1e-8
H2AZ analyzed with SICER using -w 200 -g 400 -t 0.68 -e 100 -f 150 -p 1e-5
H3K4 analyzed with SICER using -w 200 -g 200 -t 0.68 -e 100 -f 150 -p 1e-5
Brg1 analyzed with SICER using -w 200 -g 600 -t 0.68 -e 100 -f 150 -p 1e-5
H3K27 analyzed with SICER using predicted -w -I 150 -t 0.68 -e 100 -g 0 -f 150 -p 1e-5,
Outermost windows of H3K27 islands were trimmed to maximize the difference between island and non-island bins of 50bp
Genome_build: hg18
Supplementary_files_format_and_content: BED: chromosome, start, end, ReadID, number of mapping locations of read, strand
Supplementary_files_format_and_content: Island: chromosome, start, end, reads in island in control, reads in island in test, pvalue, normalized fold change, FDR
Supplementary_files_format_and_content: bsites (Peak): chromosome, start, end, peak ID, -10(log10(pvalue))

organism: Homo sapiens

source_name: Blood

extract_protocol:
Purified from whole blood using human Naive B cell isolation kit II kits (Miltenvi #130-091-150)
As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).

tag: tissue

value: Blood

value: Adult

value: Bcell

tag: chip antibody details


title: Bcell_PolII

value: wild type

value: Abcam, ab5408


title: Bcell_H3K4me3

value: Abcam, ab8580


title: Bcell_H3K27me3

value: Upstate, 07-449


title: Bcell_H3K4me1

value: Abcam, ab8895


title: Bcell_input


title: MG1655+aMG_2

value: LB + 0.5% aMG

tag: genotype


title: CD36_Brg1

extract_protocol:
Treated as described in SRP000801.  To examine the changes of chromatin modifications before and after differentiation, we fragmented the chromatin from CD36+ cells using micrococcal nuclease (MNase) digestion and performed ChIP-Seq analysis as described previously (Barski et al., 2007 A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837.
As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).


title: Bcell_H3K27me1

value: Upstate, 07-448


title: Bcell_H2A.Z


title: HSC_p300

extract_protocol:
Treated as described in SRP000801.  To examine the changes of chromatin modifications before and after differentiation, we fragmented the chromatin from CD133+ cells using micrococcal nuclease (MNase) digestion and performed ChIP-Seq analysis as described previously (Barski et al., 2007 A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837.
As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).

value: HSC

value: Santa Cruz, SC-585X, lot D1509


title: pLCV1_2


title: MG1655+aMG_1


title: HSC_Brg1


title: CD4_Brg1

extract_protocol:
CD4 cells isolated and treated as in SRP000201.  CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi). The cells were digested with MNase to generate mainly mononucleosomes with minor fraction of dinucleosomes for histone modification mapping. For mapping enzyme target sites, the cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2.0E+7 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3' A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer following manufacturer protocols.
As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).


title: B cell polyA RNA-Seq

description: Purified from whole blood using human Naive B cell isolation kit II kits (Miltenvi #130-091-150).

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned using TopHat 1.3.1 on top of Bowtie 0.12.7 to the hg18 genome with default parameters
accepted_hits file was converted to BED using SAMtools.  For graph-making and RPKM calculations, and all subsequent analyses, chromosome Y reads were discarded as some sources in study were female.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Hu et al 2011.  Briefly reads in RefSeq gene exons were counted and normalized by total genic exon size and library size.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample with columns: RefSeq ID, RPKM, exon base pair count, read count, unique ID, num genes w/ ID
Supplementary_files_format_and_content: BED file of TopHat mapped reads

extract_protocol: As in Chepelev et al, Nucleic Acids Research, 2009.

value: blood

value: in vivo differentiated B cell


title: MG1655-aMG_3

value: LB


title: Galaxy2-[CV104_pLCV1_5.txt]

value: Defined MOPS Rich + 0.2% Glucose


title: Wild Type Behavior - Replicate 2436

status: Public on Mar 24 2013

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description:
WTBH_2436
Tissue harvested 30min following behavior

data_processing:
Basecalling performed using RTA version 1.13.48
Demultiplexing performed using CASAVA version 1.8.2
Alignments to reference assembly mm9 performed using ELAND v2e and bowtie version 0.12.8
Filtering and selection performed using in-house tools
Expression analysis performed using CASAVA version 1.8.2
Differential analysis performed using CyberT: http://cybert.ics.uci.edu
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for each replicate have been combined in a single text file (RPKM_Values.txt), the differential analysis results from CyberT have been summarized and annotated in a single excel file (Differential_Analysis.xls)

source_name: WildType_Behavior_dosal hippocampus

extract_protocol:
RNA was isolated from bilateral, dorsal hippocampus using the using RNeasy minikit (Qiagen, 74104).
cDNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina).
Samples were multiplexed so that each behavioral group was represented in each flow cell of the sequencer. 10nM of each library was pooled together in four multiplex libraries and sequenced on an IlluminaHiSeq 2000 instrument during a single-end 50 cycles sequencing run by the Genomics High-Throughput Facility (GHTF) at the University of California, Irvine.

tag: strain background

tag: sample group

value: behavior; sacrificed thirty minutes following Object Location Memory training

value: dorsal hippocampus


title: Tr.rp

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: ribosome-protected fragments

data_processing:
Reads were aligned to a reference set of human transcripts using Bowtie
Number of reads mapping to each transcript was counted and normalized to FPKMs
Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads

source_name: Immortalized primary fibroblasts

growth_protocol: Immortalized human BJ primary fibroblast cells (by hTERT expression) were cultured in DMEM supplemented with 10% heat-inactivated fetal calf serum (FCS) in 5% CO2 at 37 °C.

extract_protocol:
Cells were treated with cycloheximide (100 μg/ml) for 8-10 minutes, washed with ice-cold PBS (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml cycloheximide, 1x complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7%-47%) using the SW-41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in monosomes were polled and treated wih proteinase K (Roche) in 1%SDS. Released RNA fragments were purified using trizol and precipitated in the presence of glycogen.
RNA from the pooled monosomes was gel-purified on a denaturing 10% polyacrylamide urea (7M) gel. A section corresponding to 30-33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted, and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 PNK (NEB) for 6 h at 37 °C in MES buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (NEB) for 2.5h at 37°C. Ligation products were 5′-phosphorylated with T4 PNK for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18h at 22°C.

tag: cell line

value: BJ cells

tag: condition

value: Transformed cells (induced by RASG12V in the background of stable p53 and p16INK4A kds)

tag: protocol

value: BJ cells expressing hTERT, p16INK4A-KD, p53-KD and SV40 small T were retrovirally transduced with pBabe-puro-RASG12V


title: Wild Type Homecage - Replicate 2404

description:
WTHC_2404
Tissue harvested directly from home cage

source_name: WildType_Homecage_dosal hippocampus

value: wild type

value: homecage; sacrificed directly from the animal's cage


title: Wild Type Homecage - Replicate 2425

description:
WTHC_2425
Tissue harvested directly from home cage


title: C3.rp

description: ribosome-protected fragments

value: Senescence; 14 dys after RASG12V induction

value: BJ cells expressing hTERT and tamoxifen-inducible RASG12V were cultured in the presence of 10-7M 4-OHT-Tamoxifen for 14 days


title: Wild Type Homecage - Replicate 2402

description:
WTHC_2402
Tissue harvested directly from home cage


title: Wild Type Homecage - Replicate 2418

description:
WTHC_2418
Tissue harvested directly from home cage


title: Wild Type Homecage - Replicate 2430

description:
WTHC_2430
Tissue harvested directly from home cage


title: Wild Type Behavior - Replicate 2433

description:
WTBH_2433
Tissue harvested 30min following behavior


title: Wild Type Behavior - Replicate 2421

description:
WTBH_2421
Tissue harvested 30min following behavior


title: pHDB3_1

extract_protocol:
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910.
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit

tag: strain


title: Wild Type Behavior - Replicate 2407

description:
WTBH_2407
Tissue harvested 30min following behavior


title: preS.rp

description: ribosome-protected fragments

value: pre-senescence; 5 dys after RASG12V induction

value: BJ cells expressing hTERT and tamoxifen-inducible RASG12V were cultured in the presence of 10-7M 4-OHT-Tamoxifen for 5 days


title: S.rp

description: ribosome-protected fragments

value: Proliferation, normal conditions


title: Wild Type Behavior - Replicate 2403

description:
WTBH_2403
Tissue harvested 30min following behavior


title: C1.rp

description: ribosome-protected fragments


title: Baf53b+/- Homecage - Replicate 2417

description:
MUHC_2417
Tissue harvested directly from home cage

source_name: Baf53b_Het_Homecage_dosal hippocampus

value: Baf53b+/- mutant


title: Baf53b+/- Homecage - Replicate 2415

description:
MUHC_2415
Tissue harvested directly from home cage


title: Q2.rp

description: ribosome-protected fragments

value: Quiescence induced by serum depletion


title: Tr.rna

data_processing:
Reads were aligned to a reference set of human transcripts using Bowtie
Number of reads mapping to each transcript was counted and normalized to FPKMs
Genome build: hg19
Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen), following the  manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the  manufacturer's instructions.


title: Baf53b+/- Homecage - Replicate 2422

description:
MUHC_2422
Tissue harvested directly from home cage


title: Q1.rp

description: ribosome-protected fragments


title: Baf53b+/- Homecage - Replicate 2401

description:
MUHC_2401
Tissue harvested directly from home cage


title: S.rna


title: C3.rna


title: Wild Type Homecage - Replicate 2405

description:
WTHC_2405
Tissue harvested directly from home cage


title: CD36_p300

value: Blood

value: Adult

value: Santa Cruz, SC-585X, lot D1509


title: preS2.rna


title: Wild Type Behavior - Replicate 2412

description:
WTBH_2412
Tissue harvested 30min following behavior

value: behavior; sacrificed thirty minutes following Object Location Memory training


title: Baf53b+/- Behavior - Replicate 2416

description:
MUBH_2416
Tissue harvested 30min following behavior

source_name: Baf53b_Het_Behavior_dosal hippocampus

value: dorsal hippocampus


title: preS1.rna

value: BJ cells


title: Baf53b+/- Behavior - Replicate 2414

description:
MUBH_2414
Tissue harvested 30min following behavior


title: C2.rna


title: Baf53b+/- Behavior - Replicate 2429

description:
MUBH_2429
Tissue harvested 30min following behavior


title: Baf53b+/- Behavior - Replicate 2435

description:
MUBH_2435
Tissue harvested 30min following behavior


title: Baf53b+/- Behavior - Replicate 2410

description:
MUBH_2410
Tissue harvested 30min following behavior


title: Baf53b+/- Behavior - Replicate 2409

description:
MUBH_2409
Tissue harvested 30min following behavior


title: Baf53b+/- Homecage - Replicate 2424

description:
MUHC_2424
Tissue harvested directly from home cage


title: C1.rna


title: C2.rp

description: ribosome-protected fragments


title: RUNX1

status: Public on Mar 22 2013

city: Rechovot

first: Ram

last: Jaschek

address: P.O Box 26

institute: Weizmann Institute of Science

description: Chromatin IP against Runx1.

data_processing:
Base-calling: CASAVA_1.6
Alignment: Bowtie. Genome build mm9.
Peak-calling: Genomic stretches at a resolution of 50bp showing coverage in the top 0.1% of the genome for P300 or RUNX1 and not showing NIS in the top 1% of the genome.
Genome_build: MGSCv37

source_name: MK Cells, Runx1 ChIP

growth_protocol: Culture in DMEM.

extract_protocol:
ChIP samples were prepared using 5*10^7 cells per sample. Chromatin was prepared as described in Ainbinder et. Al Mol Cell Biol. 2002 (PMID 12192035).
Antibodies used: NIS - non-immune serum was taken from our rabbits; RUNX1- our home-made antibody, described in Aziz-Aloya RB, Levanon D, Karn H, et al. Expression of AML1-d, a short human AML1 isoform, in embryonic stem cells suppresses in vivo tumor growth and differentiation. Cell Death Differ. 1998;5(9):765-773 (PMID 10200536); and P300 - C-20:rabbit polyclonal IgG, Santa Cruz Biotechnology sc-585, lot #E2010.
ChIP libraries were created following the Illumina sample preparation protocol from 10ng of DNA. Following end-repair and A-base addition, primers were ligated and samples were size selected on a 2% agarose gel. Fragments of 200bp were excised and purified using the Qiagen gel-extraction kit with gel melting at room temperature. Enrichment was carried out using 18 cycles of amplification. Library yield was quantified using Qubit (Invitrogen), while final fragment sizes were determined using Agilent BioAnalyzer. The ChIP-seq libraries were run on an Illumina GAIIx at the Department of Biological Services at WIS, using Illumina cluster generation kits and sequencing reagents.

treatment_protocol: Murine FL-derived mature MKs were produced essentially as previously described by Shivdasani RA, Schulze H (2005) Culture, expansion, and differentiation of murine megakaryocytes. Curr Protoc Immunol Chapter 22: Unit 22F 26. Briefly, FL cells were derived from E14.5 embryos and cultured in DMEM medium supplemented with 10% FBS (Gibco, US), 2mM L-glutamine and penicillin/streptomycin and TPO (50ng ml-1) at 37ºC and 10% CO2. After 7 days in culture, mature MKs were isolated by two sequential 2%-4% BSA gradients.

tag: strain/background

value: WT

value: megakaryocyte cells


title: INPUT

description: Non-immune serum.

source_name: MK Cells, input

tag: cell type

value: non-immune serum


title: CX137 input DNA 1

city: Buffalo

first: Robert

middle: William

last: Leach

state: NY

address: 701 Ellicott Street

department: Center for Computational Research

institute: Center of Excellence in Bioinformatics

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.7 with parameters -n 1 -m 1 -e 70 -l 28 -k 1 -t -p 8 -q -S —best
Control bam files were merged using bamtools merge, version 1.0.2 using default parameters
Peaks were called using PeakRanger, version 1.16, with parameters ccat --format bam -l 300
Genome_build: hg19
Supplementary_files_format_and_content: The *summit.bed files are tab delimited text files containing coordinates of peak summits of androgen receptor binding sites in the absence/presence of curaxin
Supplementary_files_format_and_content: The *region.bed files are tab delimited text files containing coordinates of peak regions of androgen receptor binding sites in the absence/presence of curaxin

source_name: HT1080 human fibrosarcoma cells

growth_protocol: HT1080 cells were maintaned in DMEM with 10% FBS, 1% pen-strep, used at a confluency 80%

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with SSRP1 antibody.
ChIP isolated DNA was treated using the standard ChIP-seq protocol from Illumina with the following modification.  After adaptor ligation the library was separated on a 2% agarose gel and the 150 to 500 bp region was excised and purified.  This larger excision region allows successfully sequencing libraries from low quality (< 10 ng) ChIP samples.

treatment_protocol: HT1080 cells were treated with 3 uM CX 137 for 1 hour

tag: tissue origin

value: derived from biopsy of fibrosarcoma of Human male

tag: treatment

value: curaxin

tag: antibody

value: none, input


title: input DNA 3


title: CX137 input DNA 2


title: CX137 input DNA 3


title: input DNA 1


title: CX137_SSRP1_ChIPSeq 2

value: SSRP1 (Biolegend, cat#609702, clone:10D1)


title: CX137_SSRP1_ChIPSeq 1


title: SSRP1_ChIPSeq 3


title: SSRP1_ChIPSeq 2


title: Q1.rna


title: SSRP1_ChIPSeq 1


title: Q2.rna


title: ChIP-Seq Input of CD14 Primary Cells; Histone.DS21627

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21627
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15743
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6962
****************
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: GSM1102807_UW.CD14_Primary_Cells.Input.RO_01701.Histone.DS21627.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21627-Histone.DS21627.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD14 Primary Cells, Donor RO 01701, 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.16804
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,584,100
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.0392
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9722
IROC_PERCENTILE: 67
POISSON_SCORE: 0.094
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102807_UW.CD14_Primary_Cells.Input.RO_01701.Histone.DS21627.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21627-Histone.DS21627.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01701, 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.16900
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 9
BROWSER_TRACK_NAME: CD14 Input 01 27
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells ChIP-Seq Input Donor RO 01701 Library Histone.DS21627 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,584,100
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.0392
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9722
IROC_PERCENTILE: 67
POISSON_SCORE: 0.094
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD14+ Cells, year 37; Histone.DS21627

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD14 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Male

value: Hispanic

value: ChIP-Seq Input

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Input


title: ChIP-Seq Input of CD4 Primary Cells; Histone.DS21541

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21541
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15773
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
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: GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21541-Histone.DS21541.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4 Primary Cells, Donor RO 01679, 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.16807
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,969,799
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0028
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.025
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21541-Histone.DS21541.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4 Primary Cells, Donor RO 01679, 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.16903
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 9
BROWSER_TRACK_NAME: CD4 Input 79 41
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells ChIP-Seq Input Donor RO 01679 Library Histone.DS21541 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,969,799
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0028
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.025
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD4+ Cells,year 21; Histone.DS21541

value: CD4 Primary Cells

value: year 21

value: Caucasian


title: ChIP-Seq Input of Fetal Stomach; Histone.DS22596

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS22596
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15695
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15694
****************
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: GSM1102808_UW.Fetal_Stomach.Input.H-24639.Histone.DS22596.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22596-Histone.DS22596.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Stomach, Donor H-24639, 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.16823
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,363,181
FINDPEAKS_SCORE: 0.0032
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0284
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102808_UW.Fetal_Stomach.Input.H-24639.Histone.DS22596.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22596-Histone.DS22596.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Stomach, Donor H-24639, 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.16919
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 9
BROWSER_TRACK_NAME: FS Input 39 96
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach ChIP-Seq Input Donor H-24639 Library Histone.DS22596 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,363,181
FINDPEAKS_SCORE: 0.0032
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0284
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Stomach primary tissue, day 98; Histone.DS22596

value: Fetal Stomach

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 98

value: Female


title: Histone H3K9me3 ChIP-Seq of CD8 Primary Cells; Histone.DS22908

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22908
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15753
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7035
****************
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: GSM1102803_UW.CD8_Primary_Cells.H3K9me3.RO_01701.Histone.DS22908.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22908-Histone.DS22908-Histone.DS22908.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD8 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD8 Primary Cells, Donor RO 01701, 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.16885
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,541,477
FINDPEAKS_SCORE: 0.0537
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.1461
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.7505
IROC_PERCENTILE: 36
POISSON_SCORE: 0.2936
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102803_UW.CD8_Primary_Cells.H3K9me3.RO_01701.Histone.DS22908.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22908-Histone.DS22908-Histone.DS22908.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD8 Primary Cells, Donor RO 01701, 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.16981
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 9
BROWSER_TRACK_NAME: CD8 H3K9me3 01 08
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells Histone H3K9me3 Donor RO 01701 Library Histone.DS22908 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,541,477
FINDPEAKS_SCORE: 0.0537
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.1461
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.7505
IROC_PERCENTILE: 36
POISSON_SCORE: 0.2936
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD8+ Cells, year 37; Histone.DS22908

value: CD8 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Histone H3K9me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K9me3 ChIP-Seq of Fetal Intestine, Small; Histone.DS22902

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22902
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15746
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14909
****************
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: GSM1102802_UW.Fetal_Intestine_Small.H3K9me3.H-24595.Histone.DS22902.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22902-Histone.DS22902.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Intestine Small, Donor H-24595, 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.16842
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,188,818
FINDPEAKS_SCORE: 0.1719
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.2452
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9375
IROC_PERCENTILE: 92
POISSON_SCORE: 0.3483
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102802_UW.Fetal_Intestine_Small.H3K9me3.H-24595.Histone.DS22902.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22902-Histone.DS22902.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Intestine Small, Donor H-24595, 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.16938
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 9
BROWSER_TRACK_NAME: FIS H3K9me3 95 02
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small Histone H3K9me3 Donor H-24595 Library Histone.DS22902 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,188,818
FINDPEAKS_SCORE: 0.1719
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.2452
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9375
IROC_PERCENTILE: 92
POISSON_SCORE: 0.3483
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Small primary tissue, day 108; Histone.DS22902

value: Fetal Intestine, Small

value: day 108

value: Male

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


title: Histone H3K9me3 ChIP-Seq of CD14 Primary Cells; Histone.DS22404

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22404
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15729
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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: GSM1102801_UW.CD14_Primary_Cells.H3K9me3.RO_01721.Histone.DS22404.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22404-Histone.DS22404-Histone.DS22404.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD14 Primary Cells, Donor RO 01721, 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.16831
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,467,677
FINDPEAKS_SCORE: 0.3908
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4307
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9809
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5248
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102801_UW.CD14_Primary_Cells.H3K9me3.RO_01721.Histone.DS22404.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22404-Histone.DS22404-Histone.DS22404.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01721, 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.16927
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 9
BROWSER_TRACK_NAME: CD14 H3K9me3 21 04
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells Histone H3K9me3 Donor RO 01721 Library Histone.DS22404 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,467,677
FINDPEAKS_SCORE: 0.3908
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4307
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9809
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5248
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD14+ Cells,year 21; Histone.DS22404

value: CD14 Primary Cells

value: year 21

value: Caucasian


title: Histone H3K4me3 ChIP-Seq of CD4 Primary Cells; Histone.DS21776

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21776
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15770
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
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: GSM1102798_UW.CD4_Primary_Cells.H3K4me3.RO_01679.Histone.DS21776.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21776-Histone.DS21776.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4 Primary Cells, Donor RO 01679, 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.16875
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,998,792
FINDPEAKS_SCORE: 0.556
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5523
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9998
IROC_PERCENTILE: 29
POISSON_SCORE: 0.5498
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102798_UW.CD4_Primary_Cells.H3K4me3.RO_01679.Histone.DS21776.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21776-Histone.DS21776.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4 Primary Cells, Donor RO 01679, 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.16971
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 9
BROWSER_TRACK_NAME: CD4 H3K4me3 79 76
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells Histone H3K4me3 Donor RO 01679 Library Histone.DS21776 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,998,792
FINDPEAKS_SCORE: 0.556
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5523
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9998
IROC_PERCENTILE: 29
POISSON_SCORE: 0.5498
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD4+ Cells,year 21; Histone.DS21776

value: CD4 Primary Cells

value: Histone H3K4me3

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2


title: Histone H3K9me3 ChIP-Seq of Fetal Stomach; Histone.DS22928

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22928
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15698
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15701
****************
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: GSM1102804_UW.Fetal_Stomach.H3K9me3.H-24754.Histone.DS22928.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22928-Histone.DS22928.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Stomach, Donor H-24754, 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.16867
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,491,408
FINDPEAKS_SCORE: 0.1865
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2619
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9008
IROC_PERCENTILE: 78
POISSON_SCORE: 0.3763
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102804_UW.Fetal_Stomach.H3K9me3.H-24754.Histone.DS22928.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22928-Histone.DS22928.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Stomach, Donor H-24754, 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.16963
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 9
BROWSER_TRACK_NAME: FS H3K9me3 54 28
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach Histone H3K9me3 Donor H-24754 Library Histone.DS22928 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,491,408
FINDPEAKS_SCORE: 0.1865
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2619
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9008
IROC_PERCENTILE: 78
POISSON_SCORE: 0.3763
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Stomach primary tissue, day 96; Histone.DS22928

value: Fetal Stomach

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 96

value: Female

value: Histone H3K9me3


title: P300

description: Chromatin IP against P300.

source_name: MK Cells, P300 ChIP

tag: genotype

value: WT

value: megakaryocyte cells

tag: chip antibody


title: Histone H3K4me3 ChIP-Seq of CD14 Primary Cells; Histone.DS21707

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21707
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15740
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6962
****************
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: GSM1102797_UW.CD14_Primary_Cells.H3K4me3.RO_01701.Histone.DS21707.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21707-Histone.DS21707.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD14 Primary Cells, Donor RO 01701, 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.16798
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,014,496
FINDPEAKS_SCORE: 0.458
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4585
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4494
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102797_UW.CD14_Primary_Cells.H3K4me3.RO_01701.Histone.DS21707.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21707-Histone.DS21707.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01701, 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.16894
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 9
BROWSER_TRACK_NAME: CD14 H3K4me3 01 07
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells Histone H3K4me3 Donor RO 01701 Library Histone.DS21707 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,014,496
FINDPEAKS_SCORE: 0.458
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4585
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4494
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD14+ Cells, year 37; Histone.DS21707

value: CD14 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Male

value: Hispanic

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


title: Histone H3K4me3 ChIP-Seq of CD8 Primary Cells; Histone.DS21778

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21778
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15760
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352
****************
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: GSM1102799_UW.CD8_Primary_Cells.H3K4me3.RO_01679.Histone.DS21778.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21778.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD8 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD8 Primary Cells, Donor RO 01679, 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.16882
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,841,918
FINDPEAKS_SCORE: 0.4817
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.4815
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.477
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102799_UW.CD8_Primary_Cells.H3K4me3.RO_01679.Histone.DS21778.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21778.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD8 Primary Cells, Donor RO 01679, 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.16978
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 9
BROWSER_TRACK_NAME: CD8 H3K4me3 79 78
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells Histone H3K4me3 Donor RO 01679 Library Histone.DS21778 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,841,918
FINDPEAKS_SCORE: 0.4817
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.4815
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.477
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD8+ Cells,year 21; Histone.DS21778

value: CD8 Primary Cells

value: genomic DNA

value: year 21

value: Caucasian

value: Histone H3K4me3

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2