title: [E-MTAB-451] somule2, 3 hours

source_name: somule2, 3 hours

value: 3 hours

value: mixed


title: [E-MTAB-315] kay 1 A

status: Public on Jul 14 2011

type: SRA

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description: Performer: DKFZ

library_source: transcriptomic

data_processing: processed data not provided

molecule: total RNA

organism: Drosophila melanogaster

growth_protocol: grow | S2 cells adjusted to growth in serum-free media (D.Mel-2, Invitrogen, Carlsbad, CA) were grown in Express Five SFM (Invitrogen, Carlsbad, CA) supplemented with 20 mM Glutamax I, 100 U/ml penicillin, 100 microgram/ml streptomycin.

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), followed by Rneasy cleanup (Qiagen, Hilden, Germany) including on-column DNAse digest. RNA integrity was verified on an Agient 2100 Bioanalyzer. mRNA was isolated with the Dynabeads mRNA DIRECT Kit (Invitrogen, Carlsbad,CA). For each sample, a library for SOLiD sequencing was prepared with the 'Whole transcriptome analysis kit' (4409491 Rev. D, Invitrogen, Carlsbad,CA). Briefly, polyA RNA was fragmented using RNAseIII, purified, hybridized and ligated to RNA adapters. Ligation products were reverse transcribed, purified and ca. 200 nt cDNA fragments selected after electrophoresis on a 6% TBE-Urea gel. cDNA was PCR amplified with SOLiD sequencing primers and purified to produce a library suitable as a template for emulsion PCR. DNA concentrations were determined using qPCR and a pooled library was generated by combining equimolar amounts from all samples.
sequencing | Emulsion PCR and sequencing with the SOLiD v.3 system was performed according to the manufacturers' protocol (Applied Biosystems, Foster City, CA).
scanning | Base calling and quality scoring done during SOLiD primary analysis. csfasta and qual files of sequencing reads were retrieved from the sequencing machine. These files were converted to srf format using solid2srf_v0.7.5.

treatment_protocol: specified_biomaterial_action | RNAi knockdown was performed by seeding 0.75 Mio cells in 1.5 ml Express-5 medium containing 20 microgram dsRNA and 8 microliter 0.4 mg/ml dimethyldioctadecylammonium bromide (DDAB) per well of a 6-well plate. Cells were incubated at 25 degr. C for 5 days and harvested by centrifugation at 1500xg for 5 min.

tag: material type

value: cell

tag: strainorline

tag: RNAi

value: kay


title: [E-MTAB-315] kay 1 B

description: Performer: DKFZ


title: [E-MTAB-315] Jra 2 B

description: Performer: DKFZ

value: Jra


title: [E-MTAB-451] somule1, 3 hours 2

description:
Performer: SC
Provider: Wellcome Trust Sanger Institute

organism: Schistosoma mansoni

source_name: somule1, 3 hours

growth_protocol: grow | A  Peurto Rican strain of S. mansoni was used in this study.  Mixed-sex worms (including female worms) were perfused from percutaneously infected Golden Syrian hamsters challenged 7-weeks earlier with cercariae and provided by Dr. Phil LoVerde (University of Texas, San Antonio, Texas, U.S.). Cercariae were shed from Biomphalaria glabrata intermediate snail hosts. Mechanically transformed schistosomula were prepared by mechanical transformation of cercariae and cultured at 37C in DMEM (Sigma, UK) supplemented with 10% foetal calf serum, 2 mM L-glutamine, and 100 ug/ml penicillin/streptomycin in an atmosphere of 5% CO2 for 3hr or 24hr. Skin transformed schistosomula were prepared by allowing cercariae to penetrate a layer of freshly excised mouse skin. After penetration, schistosomula were cultured at 37C in DMEM (Sigma, UK) supplemented with 10% foetal calf serum, 2 mM L-glutamine, and 100 ug/ml penicillin/streptomycin in an atmosphere of 5% CO2 for 24hr. Cercarial tails were obtained using the same procedure as for mechanically transformed schistosomula. (Parameters: time unit = seconds, temperature unit = C).

extract_protocol:
nucleic_acid_extraction| S. mansoni total RNA was extracted from parasites homogenised in TRIzol reagent (Invitrogen UK) using an Ultra-Turrax T10 dispersing tool (IKA-Labortechnik, Janke & Kunkel, GmbH & Co). Cercariae total RNA was isolated using a modified TRIzol/RNeasy (Invitrogen UK; Qiagen UK) procedure as previously described, RNA from the rest of the samples was extracted using  TRIzol(Invitrogen, UK)according to manufacturers instructions. All RNA was subsequently quantified with a NanoDrop ND-1000 UV-Vis spectrophotometer and visualized for quality using an Agilent 2100 bioanalyzer. (Parameters: Extracted product = total_RNA, Amplification = none)
sequencing | Total RNA was used to produce RNA-seq libraries as described in Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628 (2008). Exceptions to the protocol included: i) fragmentation of mRNA was performed by incubating the samples in a 5x fragmentation buffer (Ambion, UK) and at 70C for 5 minutes followed by removal of fragmentation buffer using sodium acetate/isopropanol precipitation of RNA; ii) after second strand cDNA synthesis, the Illumina Genomic DNA Sample Preparation Kit (Illumina, UK) was used according to manufacturer instructions and with modifications described in Quail, M. A. et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 5, 1005-1010 (2008).The samples were sequenced on an Illumina Genome Analyser II.
scanning | Image processing and base calling were done using the Illumina pipeline.

tag: age

tag: developmentalstage

value: larva

tag: Sex

value: puerto rican

tag: biosourcetype


title: [E-MTAB-599] c57xdba_Heart1

description: Performer: SC

organism: Mus musculus

source_name: c57xdba_Heart1 149873

extract_protocol:
tissue collection | Mouse tissues where obtained from 8 weeks old mice from the Jackson lab Maine USA.
nucleic_acid_extraction | Total RNA extraction using trizol as per manufacturer instructions
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.8.67.0. There were 152 cycles of sequencing with 2 reads per cluster.

tag: genotype

value: adult

tag: organismpart

value: heart

tag: biosourceprovider

value: Jackson laboratory


title: [E-MTAB-315] Jra 1 B

description: Performer: DKFZ


title: [E-MTAB-315] Jra 2 A

description: Performer: DKFZ


title: [E-MTAB-451] tail1, 0 hours

source_name: tail1, 0 hours

value: 0 hours

value: tail


title: [E-MTAB-315] bsk 2 B

description: Performer: DKFZ

value: bsk


title: [E-MTAB-315] bsk 1 B

description: Performer: DKFZ


title: [E-MTAB-315] p38b 2 B

description: Performer: DKFZ


title: [E-MTAB-315] bsk 1 A

description: Performer: DKFZ


title: [E-MTAB-315] slpr 2 A

description: Performer: DKFZ

value: slpr


title: [E-MTAB-444] Y1

description: Performer: CRI

organism: Gynandropsis gynandra

source_name: young leaf

growth_protocol: growth | standard growth condition in LD

extract_protocol: nucleic_acid_extraction | Qiagen plant RNAeasy kit. Illumina RNA-seq protocol

value: 1 month

value: young

value: leaf


title: [E-MTAB-315] slpr 1 B

description: Performer: DKFZ


title: [E-MTAB-444] O1

description: Performer: CRI

source_name: mature leaf

value: mature


title: [E-MTAB-451] cerc10a, 4 hours

source_name: cerc10a, 4 hours

value: 4 hours

value: mixed


title: [E-MTAB-513] HCT20142, kidney, female, 60 years, 2x50 paired end mRNA-seq

description:
50bp_PE_mRNA_Seq_FCB_s_6_1_sequence
2x50 paired end mRNA-seq READ1
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

organism: Homo sapiens

extract_protocol:
nucleic_acid_extraction | 1ug of total RNA was subjected to two rounds of  oligo-dT beads binding. Purified mRNA was fragmented and random primed for cDNA synthesis. cDNA fragements were end repared, added dATP, and liagted to illumina pair end sample prep adaptor. The ligated material was amplified by PCR for 15 cycles, and used for illumina sequencing.
sequencing | Illumina sequencing was performed at HiSeq 2000 at Illumina
bioassay_data_transformation | FASTQ files (Illumina format) of sequencing reads were retrieved from the sequencing machine

value: kidney

value: female

value: 60 years

tag: phenotype

value: caucasian

tag: libraryprep

value: mRNA-Seq

value: Human kidney total RNA, lot 0908002


title: [E-MTAB-513] HCT20172, 16 Tissues mixture, 100bp_Stranded_RNA_Seq_FCA_s_6_sequence

description:
100bp_Stranded_RNA_Seq_FCA_s_6_sequence
1x100 stranded total transcriptome preps; the insert size is variable; could be less than 100 bp. The linker sequence at the end of read will be ATCTCGTATGCCGTCTTCTGCTTG.
~ 0.5% phiX DNA spiked in
Performer: ILLUMINA-CA

extract_protocol:
nucleic_acid_extraction | Final product from mRNA-stranded protocol was normalized by DSN digestion and used for sequencing.
sequencing | Illumina sequencing was performed at HiSeq 2000 at Illumina
bioassay_data_transformation | FASTQ files (Illumina format) of sequencing reads were retrieved from the sequencing machine

value: 16 Tissues mixture

value: mRNA-stranded+ DSN


title: [E-MTAB-315] Cka dsRNA2 2 B

description: Performer: DKFZ

value: cell


title: [E-MTAB-315] slpr 2 B

description: Performer: DKFZ


title: [E-MTAB-444] Y3

description: Performer: CRI


title: [E-MTAB-315] slpr 1 A

description: Performer: DKFZ


title: [E-MTAB-315] Cka dsRNA2 2 A

description: Performer: DKFZ


title: [E-MTAB-444] Y2

description: Performer: CRI


title: [E-MTAB-315] Cka dsRNA2 1 A

description: Performer: DKFZ


title: [E-MTAB-444] O3

description: Performer: CRI


title: [E-MTAB-315] Cka dsRNA1 2 B

description: Performer: DKFZ


title: [E-MTAB-451] somule1, 3 hours 1

value: 3 hours

value: larva

value: puerto rican


title: [E-MTAB-315] Cka dsRNA1 1 B

description: Performer: DKFZ


title: [E-MTAB-315] Cka dsRNA1 2 A

description: Performer: DKFZ


title: [E-MTAB-315] Jra 1 A

description: Performer: DKFZ

value: Jra


title: [E-MTAB-552] Tuber cortex

description: Performer: AAU

organism: Solanum tuberosum

source_name: Tuber cortex

growth_protocol: grow | RH tubers were planted in soil-filled pots in the greenhouse. After plant emergence and several weeks of growth, non-tuberizing stolons were harvested (RH Stolon). Around one week after the first swellings were observed, small tubers were collected with a maximum size of 1cm (RH Young tuber). Around the same time, anthesis occurred and both open flowers and developing flower buds were harvested (RH flower). Around the 12th leaf stage (4 weeks after first visible swelling) various tissues were harvested, including leaves (fully expanded), shoot apex, petioles, stem, tubers (RH Mature Tuber) and roots, and immediately frozen in liquid nitrogen. Stamens were collected at the same time from fully opened flowers. All tissue samples were collected from at least five different plants. For the water-stressed leaf tissue sample, a subset of plants was denied water for 2 days after which wilting leaves were harvested (2nd - 4th fully expanded leaf). For the tuber cross section, plants were left to senescence. Tubers were then collected, and peel, cortex and pith tissues were sampled and immediately frozen in liquid nitrogen. Sprouts of previously harvested RH tubers were harvested after storage at RT in the dark for 3-4 months. RH in vitro plants were grown on standard MS medium on 2% sucrose with 16 h of light at 24C for 2 weeks, after which the whole explant, including roots, was harvested.

extract_protocol:
nucleic_acid_extraction | A total of 16 tissues was collected and RNA was isolated using the RNeasy kit (Qiagen), except for the tuber and root tissues, which were isolated using the hot-phenol method. The latter samples were than purified using the RNAeasy columns. For all samples, on-column DNAseI treatment was performed and the quality and integrity of the obtained RNA was checked using the ND-100 spectrophotometer (Nanodrop Technologies) and agarose gel-electrophoresis.
Illumina Genome Analyzer II. Analyzed with Illumina Pipeline 1.5.
scanning | All samples were base called with the standard settings. Samples RHs01.tx-RHs08.txt: CHASTITY>=0.6, using a chastity threshold of 0.6, on the first 12 cycles. Samples RHs09.tx-RHs16.txt:  failed-chastity<=1, using a chastity threshold of 0.6, on the first 25 cycles.

value: tuber cortex


title: [E-MTAB-444] O2

description: Performer: CRI

value: 1 month

value: mature

value: leaf


title: [E-MTAB-315] Cka dsRNA1 1 A

description: Performer: DKFZ


title: [E-MTAB-315] bsk 2 A

description: Performer: DKFZ

value: bsk


title: [E-MTAB-315] msk 2 B

description: Performer: DKFZ

value: msk


title: [E-MTAB-315] msk 2 A

description: Performer: DKFZ


title: [E-MTAB-315] msk 1 B

description: Performer: DKFZ


title: [E-MTAB-552] Tuber sprout

description: Performer: AAU

source_name: Tuber sprout

value: tuber sprout


title: [E-MTAB-315] msk 1 A

description: Performer: DKFZ


title: [E-MTAB-315] pnt 2 B

description: Performer: DKFZ

value: pnt


title: [E-MTAB-552] Whole in vitro plant

description: Performer: AAU

source_name: Whole in vitro plant

value: whole plant

tag: growthcondition

value: in vitro


title: [E-MTAB-552] Tuber pith

description: Performer: AAU

source_name: Tuber pith

value: tuber pith


title: [E-MTAB-552] Water stressed leaf

description: Performer: AAU

source_name: Water stressed leaf

value: water stressed


title: [E-MTAB-315] pnt 1 B

description: Performer: DKFZ

value: cell


title: [E-MTAB-315] pnt 2 A

description: Performer: DKFZ


title: [E-MTAB-706] rpoN2

description: Performer: SC

organism: Campylobacter jejuni

growth_protocol: grow | C. jejuni strains were cultured for 48 hours on MH blood agar plates with antibiotics added as appropriate. Bacterial lawns were harvested in 1 ml BHI broth, 50 ul of which was inoculated into 10 ml BHI broth in a 50 ml Falcon centrifuge tube with a loosened cap, and grown for 16 h at 42C under microaerobic conditions with agitation at 150 rpm to generate a starter culture. The optical density at 600nm (OD600) of starter cultures was taken using a 6305 UV/Visible Spectrophotometer (Jenway, Dunmow, U.K.). Starter cultures were diluted appropriately in BHI broth and used to inoculate 10 ml of BHI broth containing 10 ug/ml trimethoprim in a 50 ml falcon tube (previously equilibrated at 42C in microaerobic conditions for 16 h) to a calculated OD600 of 0.00002. Cultures were grown at 42C under microaerobic conditions with shaking at 150 rpm for 24 h. Growth was monitored by recording OD600, and by determining viable colony forming units (CFU/ml) by serial 10-fold dilution of cultures in BHI broth and plating onto MH agar. Plates were incubated microaerobically at 42C for 48 h before colonies were counted.

extract_protocol:
nucleic_acid_extraction | C. jejuni cultures were fixed with 2 volumes of RNA protect Bacteria (Qiagen) and harvested. RNA was isolated from the pellet using the SV RNA isolation kit (Promega) according to the manufacturers instructions. 23S and 16S rRNAs were depleted using a MicrobExpress kit (Ambion). Genomic DNA was removed with two digestions, using Amplification grade DNAse I (Invitrogen), to below PCR-detectable levels. RNA was reverse transcribed using random primers (Invitrogen) and Superscript III (Invitrogen) at 45C for 3 h and denatured at 70C for 15 min. leuB (using primers QJAW084 5 GCAAGTATAGATGCTTATGGAGTG 3 and QJAW085 5 CTCTTTCAGGTCTTTGATCTATGG 3), aroA (using primers QJAW092 5 GCTTTGGCTAAGGGTAAATCTAGT 3 and QJAW093 5 ATCAAGTTCTCTAGCTTCAACACC 3), lpxD (using primers QJAW104 5 GGAGCTTATATAGGCGATAATGTC 3 and QJAW105 5 CAAAACCGTCACTTCCTATTACAC 3) and guaB (using primers QJAW108 5 GGGTGTTGATGTTGTTGTGC 3 and QJAW109 5 GGCGATATTTCCTGCGATAA 3) were used as targets for a PCR as a positive control for reverse transcription.
sequencing | Sequencing libraries for the Illumina GA platform were constructed by shearing the enriched cDNA by nebulisation (35psi, 6 min) followed by end-repair with Klenow polymerase, T4 DNA polymerase and T4 polynucleotide kinase (to blunt-end the DNA fragments). A single 3 adenosine moiety was added to the cDNA using Klenow exo- and dATP. The Illumina adapters (containing primer sites for sequencing and flowcell surface annealing) were ligated onto the repaired ends on the cDNA and gel-electrophoresis was used to separate library DNA fragments from unligated adapters by selecting cDNA fragments between 200â250 bps in size. Fragmentation followed by gel-electrophoresis were used to separate library DNA fragments and size fragments were recovered following gel extraction at room temperature to ensure representation of AT rich sequences. Ligated cDNA fragments were recovered following gel extraction at room temperature to ensure representation of AT rich sequences. Libraries were amplified by 18 cycles of PCR with Phusion polymerase. Sequencing libraries were denatured with sodium hydroxide and diluted to 3.5 pM in hybridisation buffer for loading onto a single lane of an Illumina GA flowcell. Cluster formation, primer hybridisation and single-end, 36 cycle sequencing were performed using proprietary reagents according to manufacturers' recommended protocol (https://icom.illumina.com/). The efficacy of each stage of library construction was ascertained in a quality control step that involved measuring the adapter-cDNA on a Agilent DNA 1000 chip. A final dilution of 2 nM of the library was loaded onto the sequencing machine.

value: rpoN::cat mutant


title: [E-MTAB-552] Root

description: Performer: AAU

source_name: Root

value: root


title: [E-MTAB-315] rl 1 B

description: Performer: DKFZ

source_name: rl

value: rl


title: [E-MTAB-552] Stamen

description: Performer: AAU

source_name: Stamen

value: stamen


title: [E-MTAB-706] rpoN1

description: Performer: SC


title: [E-MTAB-315] rl 1 A

description: Performer: DKFZ


title: [E-MTAB-315] aop 2 B

description: Performer: DKFZ

value: aop


title: [E-MTAB-706] wt1

description: Performer: SC


title: [E-MTAB-550] 3_1DayTG_tachyzoites_vc_RNA

description: Performer: SC

organism: Toxoplasma gondii

growth_protocol: grow | Toxoplasma gondii-VEG strain tachyzoites were maintained as described previously (Cohen et al. 2002). Briefly,  parasites were cultured by twice weekly passage into African Green Monkey Kidney Fibroblasts (Vero cells) using Iscove's Modified Dulbecco's Medium (IMDM, Lonza, Walkersville, USA) supplemented with 5% (v/v) foetal calf serum (FCS, Labtech international, UK) and 100Uml-1 penicillin/100Âµgml-1 streptomycin (Sigma-Aldrich). Parasites were harvested 2, 3, 4 or 6 days post-infection in aliquots of 108 tachyzoites and stored at -20oC either resuspended in TRIÂ® Reagent (Sigma-Aldrich) for RNA extraction or as pellets for proteomics. Further T.gondii-VEG were maintained in Human Foreskin Fibroblasts by twice weekly passage into 70-90% confluent cell cultures, maintained in Dulbecco's Modified Eagle's Medium (DMEM, Sigma-Aldrich) supplemented with 2 mM L-Glutamine (Sigma-Aldrich), 10% (v/v) FCS and 100Uml-1 penicillin/100Âµgml-1 streptomycin. Otherwise cultivation was identical to parasites grown in Vero cells. Cohen, A.M., Rumpel, K., Coombs, G.H. & Wastling, J.M. (2002) 'Characterisation of global protein expression by two-dimensional electrophoresis and mass spectrometry: proteomics of Toxoplasma gondii', Int J Parasitol, vol. 32, no. 1, pp. 39-51.

extract_protocol:
nucleic_acid_extraction | RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.6.0a14. There were 152 cycles of sequencing with 2 reads per cluster.

tag: cellline

value: 3 days post infection


title: [E-MTAB-550] 4_1DayTG_tachyzoites_vc_RNA

description: Performer: SC

value: African Green Monkey Kidney Fibroblasts (Vero cells)

value: 4 days post infection


title: [E-MTAB-550] 6DayTG_tachyzoites_vc_RNA

description: Performer: SC

value: 6 days post infection


title: [E-MTAB-315] aop 2 A

description: Performer: DKFZ


title: [E-MTAB-315] Cka dsRNA2 1 B

description: Performer: DKFZ


title: [E-MTAB-550] 6_1DayTG_tachyzoites_vc_RNA

description: Performer: SC


title: [E-MTAB-552] Tuber peel

description: Performer: AAU

source_name: Tuber peel

value: tuber peel


title: [E-MTAB-315] aop 1 B

description: Performer: DKFZ


title: [E-MTAB-550] 4DayTG_tachyzoites_vc_RNA

description: Performer: SC


title: [E-MTAB-636] Mut(KO)v2_RNA

description: Performer: SC

organism: Plasmodium yoelii

growth_protocol: grow | Groups of 5 Balb/c mice were infected i.v. on day 0 with either 200, 1000, or 5000 WT or PY01365-KO parasitized erythrocytes. Blood smears from each mouse were made daily from D3, stained with Giemsa's reagent and infected cells counted to monitor the course of infection.

extract_protocol:
P-MTAB-20359
specified_biomaterial_action | Erythrocytes containing late stage parasites, were harvested at 20 to 25% parasitaemia and schizonts were purified by centrifugation for 25 min at 600 g at room temperature (RT) on a 55% Nycodenz (Nycoprep) cushion (NYCOMED Pharma AS). 5_107 schizonts were mixed with 90 ul AMAXA nucleofactor T-cell solution (plus supplements) and 5 ug of targeting construct DNA was added. These parasites were transfected using AMAXA Nucleofector programme U33. Immediately, 100 ul of RPMI 1640 medium containing 20% foetal calf serum (FCS) was added to the transfected parasites and the suspension injected intravenously (i.v.) into the tail vein of a single mouse. Electroporation of parasites with targeting construct and injection into individual mice was carried out twice independently using the above conditions. Pyrimethamine-resistant parasites were verified by PCR and Southern blot analysis and the transgenic parasite line was cloned by limiting dilution.
nucleic_acid_extraction | Parasites were purified using a MACS type-D depletion column with a SuperMACS II magnetic separator (Miltenyi Biotec GmbH). Total RNA was prepared from leukocyte-depleted, Percoll-purified late stage WT and PY01365-KO parasitized erythrocytes using Trizol (Invitrogen Life Technologies). RNA samples were first treated with RNase-Free DNase I (Quiagen) and cleaned up using RNeasy MiniElute to remove contaminating gDNA. RNA of both samples was depleted of ribosomal RNAs with exonuclease and  and libraries were created using the Illumina RNA-seq protocol.
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.6.0a14. There were 152 cycles of sequencing with 2 reads per cluster.

tag: geneticmodification

value: YM

value: py235ebp-1 knock out

value: David Walliker, University of Edinburgh


title: [E-MTAB-550] 4.1DayTG_tachyzoites_RNA 1

description: Performer: SC

source_name: 4.1DayTG_tachyzoites_RNA 1

value: Human Foreskin Fibroblasts


title: [E-MTAB-636] WT_RNA

description: Performer: SC

extract_protocol:
P-MTAB-20359
specified_biomaterial_action | Erythrocytes containing late stage parasites, were harvested at 20 to 25% parasitaemia and schizonts were purified by centrifugation for 25 min at 600 g at room temperature (RT) on a 55% Nycodenz (Nycoprep) cushion (NYCOMED Pharma AS). 5_107 schizonts were mixed with 90 ul AMAXA nucleofactor T-cell solution (plus supplements) and 5 ug of targeting construct DNA was added. These parasites were transfected using AMAXA Nucleofector programme U33. Immediately, 100 ul of RPMI 1640 medium containing 20% foetal calf serum (FCS) was added to the transfected parasites and the suspension injected intravenously (i.v.) into the tail vein of a single mouse. Electroporation of parasites with targeting construct and injection into individual mice was carried out twice independently using the above conditions. Pyrimethamine-resistant parasites were verified by PCR and Southern blot analysis and the transgenic parasite line was cloned by limiting dilution.
nucleic_acid_extraction | Parasites were purified using a MACS type-D depletion column with a SuperMACS II magnetic separator (Miltenyi Biotec GmbH). Total RNA was prepared from leukocyte-depleted, Percoll-purified late stage WT and PY01365-KO parasitized erythrocytes using Trizol (Invitrogen Life Technologies). RNA samples were first treated with RNase-Free DNase I (Quiagen) and cleaned up using RNeasy MiniElute to remove contaminating gDNA. RNA of both samples was depleted of ribosomal RNAs with exonuclease and  and libraries were created using the Illumina RNA-seq protocol.
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.3. There were 108 cycles of sequencing with 2 reads per cluster.


title: [E-MTAB-550] 3DayTG_tachyzoites_vc_RNA

description: Performer: SC


title: [E-MTAB-315] pnt 1 A

description: Performer: DKFZ

value: pnt


title: [E-MTAB-315] aop 1 A

description: Performer: DKFZ


title: [E-MTAB-636] MutPyoelii_RNA

description: Performer: SC


title: [E-MTAB-315] Ras85D 2 B

description: Performer: DKFZ


title: [E-MTAB-706] wt2

description: Performer: SC


title: [E-MTAB-636] Mut_RNA

description: Performer: SC


title: [E-MTAB-610] Pachycladon fastigiatum - PF3

description: Performer: AWCGS

organism: Pachycladon fastigiatum

extract_protocol:
nucleic_acid_extraction | RNA from three native populations of P. enysii and P. fastigiatum was isolated as described in Voelckel et al. 2008. Replicate RNAs of each species were pooled and underwent sample preparation according to manufacturer instructions (DGE-Tag Profiling DpnII Sample Prep Kit, Illumina Inc., San Diego, USA). mRNA was isolated from total RNA and DpnII-restricted to generate 16 bp tags. DpnII-anchored tags were then enriched for sequencing. After tag library construction, libraries were titrated resulting in three flow cell lanes being loaded for each species.
sequencing | Cluster generation and sequencing were conducted according to Illumina protocols (DGE-Tag Profiling DpnII Cluster Generation Kit, 18 Cycle Solexa Sequencing Kit, Illumina Inc., San Diego, USA).
scanning: FASTQ files of sequencing reads were retrieved from the sequencing machine.

tag: population

tag: tissue

value: 14 leaves

value: middle-aged, rosette-stage


title: [E-MTAB-550] 3.1DayTG_tachyzoites_RNA 1

description: Performer: SC

source_name: 3.1DayTG_tachyzoites_RNA 1

tag: material type


title: [E-MTAB-315] Ras85D 1 B

description: Performer: DKFZ

value: cell

tag: strainorline


title: [E-MTAB-315] Ras85D 2 A

description: Performer: DKFZ

tag: RNAi


title: [E-MTAB-550] 6.1DayTG_tachyzoites_RNA 1

description: Performer: SC

source_name: 6.1DayTG_tachyzoites_RNA 1


title: [E-MTAB-315] Ras85D 1 A

description: Performer: DKFZ


title: [E-MTAB-610] Pachycladon fastigiatum - PF2

description: Performer: AWCGS

value: 16 leaves

tag: age


title: [E-MTAB-610] Pachycladon fastigiatum - PF1

description: Performer: AWCGS


title: [E-MTAB-550] 6DayTG_tachyzoites_RNA 1

description: Performer: SC

source_name: 6DayTG_tachyzoites_RNA 1

tag: developmentalstage


title: [E-MTAB-315] Dsor1 2 B

description: Performer: DKFZ


title: [E-MTAB-636] WTPyoelii_RNA

description: Performer: SC


title: [E-MTAB-315] Dsor1 2 A

description: Performer: DKFZ


title: [E-MTAB-550] 3DayTG_tachyzoites_RNA 1

description: Performer: SC

source_name: 3DayTG_tachyzoites_RNA 1

extract_protocol:
nucleic_acid_extraction | RNA was extracted from Trizol with chloroform (as per the Invitrogen protocol), ethanol precipitated and then resuspended in RNAse free water. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection followed by metal ion hydrolysis fragmentation with the Ambion RNA fragmentation kit. 1st strand cDNA is synthesized using randomly primed oligos followed by 2nd strand synthesis to produce dscDNA. This was followed by end repair with T4 and Klenow DNA polymerases and T4 polynucleotide kinase to blunt-end the DNA fragments. A single 3' A nucleotide was added to the repaired ends using Klenow exo- and dATP to deter concatemerization of templates, limit adapter dimers and increase the efficiency of adapter ligation. Adapters were then ligated (containing primer sites for sequencing). Ligated fragments were run on an agarose gel, size selected for 200-250bp inserts and DNA extracted as per Qiagen gel extraction kit protocol but with dissolution of gel slices at room temperature (rather than 50oC) to avoid heat induced bias. Libraries were then amplified by PCR to enrich for properly ligated template strands, to generate enough DNA and to add primers for flowcell surface annealing followed by a clean up with AMPure SPRI beads. These libraries were quantified using Agilent Bioanalyser chip and Kapa Illumina SYBR Fast qPCR kit.
scanning | The samples were sequenced on an Illumina Genome Analyser II.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina GApipeline v1.3. There were 152 cycles of sequencing with 2 reads per cluster.


title: [E-MTAB-550] 2DayTG_tachyzoites_RNA 1

description: Performer: SC

source_name: 2DayTG_tachyzoites_RNA 1

value: 2 days post infection


title: [E-MTAB-315] Dsor1 1 B

description: Performer: DKFZ


title: [E-MTAB-550] 4Day_TG_tachyzoites_RNA 1

description: Performer: SC

source_name: 4Day_TG_tachyzoites_RNA 1


title: [E-MTAB-315] Dsor1 1 A

description: Performer: DKFZ


title: [E-MTAB-550] 2.1DayTG_tachyzoites_RNA 1

description: Performer: SC

source_name: 2.1DayTG_tachyzoites_RNA 1


title: CSHL_RnaSeq_K562_cell_longNonPolyA (superseded by GSE90231)

status: Public on Jul 13 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
****************************
GSM758577 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90231
****************************

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 76 nt directed reads

tag: replicate

tag: spikeinpool

tag: localization description

value: Whole cell


title: CSHL_RnaSeq_HSMM_cell_longPolyA (superseded by GSE78587)

description:
****************************
GSM758578 record metadata submitted on July 11, 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78587
****************************

molecule: polyA RNA

source_name: HSMM

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt


title: CSHL_RnaSeq_HMEC_cell_longPolyA (superseded by GSE78586)

description:
****************************
GSM758571 record metadata submitted on July 11, 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78586
****************************

source_name: HMEC

tag: cell karyotype

value: normal


title: CSHL_RnaSeq_H1-hESC_nucleus_longPolyA (superseded by GSE90227)

description:
****************************
GSM758574 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90227
****************************

growth_protocol: missing

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: C_AN10028_41

status: Public on Jul 12 2011

city: Cambridge

first: Xinchen

last: Wang

state: MA

address: 32 Vassar St, D514

institute: MIT

description: RNA-Seq

data_processing:
We generate alternative splice junctions using sequences from three exons: C1 (upstream constitutively spliced exon), A (alternatively spliced exon) and C2 (downstream constitutively spliced exon). Quantification of alternative exon usage is determined by the percentage of reads aligning to inclusion junctions (C1-A and A-C2) relative to all junctions (C1-A, A-C2 and C1-C2).
Additional details: RNA sequencing and data analysis.  73-nucleotide reads were generated using an Illumina GAII sequencer according to the manufacturer's protocol. To generate sufficient read coverage for the quantitative analysis of alternative splicing events, reads for ASD and control brain samples were separately pooled and aligned to an existing database of EST and cDNA-derived alternative splicing junctions using the Basic Local Alignment Tool (BLAT) as described previously35, 36. Reads were considered properly aligned to a splice junction if at least 71 of the 73 nucleotides matched and at least 5 nucleotides mapped to each of the two exons forming the splice junction. Alternative exon inclusion values ('%inc'), representing the proportion of messenger RNA transcripts with the alternatively spliced exon included, were calculated for each mRNA pool as the ratio of reads aligning to the C1-A or A-C2 junctions against reads aligning against all three possible junctions as previously described35 (C1-A, A-C2, C1-C2, see Supplementary Fig. 3). Calculated %inc values were considered reliable if at least one of the included junctions as well as the skipped junctions were covered by at least 20 reads. %inc values were compared across samples using Fisher's exact test and the BonferroniâHochberg correction to identify differentially spliced exons associated with autism. Differential splicing events were considered significant if they fulfilled both criteria of FDR < 0.1 and %inc difference between autism and controls >15%.

source_name: postmortem brain tissue

extract_protocol: Standard library preparation protocol for high throughput DNA sequencing on  Illumina Genome Analyzer was performed at the Yale Center for Genome Analysis (detailed protocol at: http://medicine.yale.edu/keck/ycga/sequencing/protocols/index.aspx). Briefly, poly-A containing mRNA was purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented using divalent cations under elevated temperature. The cleaved RNA fragments were revers-transcribed using random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH.  cDNA fragments were then end-repaired by the addition of a single âAâ base, followed by ligation of the adapters. Finally, these products were purified and PCR-amplified to create the final cDNA library.

tag: tissue

value: brain region BA41 (temporal cortex)

tag: sample status

value: Control


title: A_AN19511_09

description: RNA-Seq

value: brain region BA09 (frontal cortex)

value: Autism


title: CSHL_RnaSeq_HepG2_cell_longPolyA (superseded by GSE86659)

description:
****************************
GSM758575 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86659
****************************

tag: cell description

value: hepatocellular carcinoma


title: CSHL_RnaSeq_HepG2_cell_longNonPolyA (superseded by GSE90229)

description:
****************************
GSM758567 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90229
****************************


title: CSHL_RnaSeq_H1-hESC_cell_longPolyA (superseded by GSE90225)

description:
****************************
GSM758566 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90225
****************************


title: CSHL_RnaSeq_HUVEC_nucleus_longPolyA (superseded by GSE78590)

description:
****************************
GSM758565 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78590
****************************

source_name: HUVEC


title: CSHL_RnaSeq_GM12878_cell_longNonPolyA (superseded by GSE90223)

description:
****************************
GSM758572 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90223
****************************

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus


title: CSHL_RnaSeq_HUVEC_cytosol_longPolyA (superseded by GSE78589)

description:
****************************
GSM758569 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78589
****************************

value: RnaSeq

value: The fluid between the cells outer membrane and the nucleus


title: CSHL_RnaSeq_BJ_cell_longPolyA (superseded by GSE90221)

description:
****************************
GSM758562 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90221
****************************

source_name: BJ

value: Sequencing analysis of RNA expression

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID:9916803)


title: CSHL_RnaSeq_A549_cell_longPolyA (superseded by GSE86657)

description:
****************************
GSM758564 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86657
****************************

value: immortalized cell line

tag: line

value: iIDR


title: CSHL_RnaSeq_H1-hESC_cytosol_longPolyA (superseded by GSE90226)

description:
****************************
GSM758570 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90226
****************************

tag: datatype

value: Paired 76 nt directed reads


title: C_AN00142_09

description: RNA-Seq


title: CSHL_RnaSeq_HUVEC_cell_longPolyA (superseded by GSE78588)

description:
****************************
GSM758563 record metadata submitted on July 11, 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78588
****************************

tag: datatype description

value: longPolyA

value: Whole cell


title: CSHL_RnaSeq_GM12878_cell_longPolyA (superseded by GSE86658)

description:
****************************
GSM758559 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86658
****************************

tag: rnaextract

value: Poly(A)+ RNA longer than 200 nt


title: CSHL_RnaSeq_HepG2_nucleus_longPolyA (superseded by GSE90228)

description:
****************************
GSM758568 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90228
****************************

tag: rnaextract description


title: CSHL_RnaSeq_H1-hESC_cell_longNonPolyA (superseded by GSE90224)

description:
****************************
GSM758573 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90224
****************************

value: longNonPolyA

value: Poly(A)- RNA longer than 200 nt

tag: biorep


title: CSHL_RnaSeq_GM12878_cytosol_longPolyA (superseded by GSE90222)

description:
****************************
GSM758560 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90222
****************************

tag: labexpid


title: Max ChIP-Seq

status: Public on Jul 09 2011

city: New Haven

first: Joel

last: Rozowsky

state: CT

address: 266 Whitney Ave, Bass 437

department: Molecular Biophysics & Biochemistry

institute: Yale University

description: Chromatin IP against Max

library_source: genomic

data_processing: Peaks: Peak detection was performed with PeakSeq v1.01 (http://www.gersteinlab.org/proj/PeakSeq/)

molecule: genomic DNA

source_name: Lymphoblastoid cell-line

growth_protocol: GM12878 cells were obtained from American Type Culture Collection (Expansion A for GM12878) and cultured by using standard conditions. GM12878 cells were grown in RPMI media containing 15% FBS

extract_protocol:
Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) GM12878 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250.
Libraries were prepared according to Illumina's protocols using reagents purchased from different vendors. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (Epicenter). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) (New England Biolab, NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation (LigaFast, Promega) DNA was PCR amplified (Phusion polymerase, NEB) with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Antibodies for RNA Pol II (8WG16) [Manufacturer/Source: Covance; Catalog Lot/Batch Number: MMS-126R /  14922701], cFos [Manufacturer/Source: Santa Cruz Biotech; Catalog Lot/Batch Number: sc-7202], cMyc [Manufacturer/Source: Santa Cruz Biotech; Catalog Lot/Batch Number: sc-764 / H0107], JunD [Manufacturer/Source: Santa Cruz Biotech; Catalog Lot/Batch Number: sc-74] and Max [Manufacturer/Source: Santa Cruz Biotech; Catalog Lot/Batch Number: sc-197] were validated by IP/Western. ChIP DNA and matching input DNA control for each biological replicate was prepared from 5 Ã 107 formaldehyde cross-linked GM12878 cells, except after RNase and Proteinase-K digestion, ChIP DNA was purified by using QIAquick PCR Purification Kit (Qiagen).

tag: cell-type

tag: description

value: lymphoblastoid cell-line derived from NA12878

tag: antibody

value: Max


title: A_AN17777_41

description: RNA-Seq

value: brain region BA41 (temporal cortex)

value: Autism


title: A_AN09730_22

description: RNA-Seq

value: brain region BA22 (temporal cortex)


title: cMyc ChIP-Seq

description: Chromatin IP against cMyc

value: c-Myc


title: CSHL_RnaSeq_AG04450_cell_longPolyA (superseded by GSE78585)

description:
****************************
GSM758561 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78585
****************************

value: RnaSeq

tag: labversion

tag: readtype

tag: readtype description

tag: replicate


title: C_AN12240_41

description: RNA-Seq

tag: tissue

value: Control


title: Pol II ChIP-Seq

description: Chromatin IP against Pol II


title: cFos ChIP-Seq

description: Chromatin IP against cFos

value: c-Fos


title: RNA-Seq

description:
cDNA reverse transcribed from polyA RNA
RNA-Seq for GM12878

data_processing: RNA-Seq reads were aligned using Bowtie against hg18. RNA-Seq data was processed for allele-specific expression using the AlleleSeq pipeline (alleleseq.gersteinlab.org)

extract_protocol:
Total RNA was extracted from GM12878 cells using TRIzol reagents (Invitrogen) following the manufacturerâs protocol. A spike-in control RNA was synthesize by in vitrotranscriptionof pTRImouse Î²-actinDNAusingT7RNApolymerase.The RNA was purified after DNase I digestion. Ribosomal RNAs were removed from total RNA by using RiboMinus Eukaryote Kit (Invitrogen) and polyA RNA was purified from Ribo(-) RNA fraction using the Applied Biosystem (Ambion) MicroPoly(A) Purist kit.
Then, the desired fragment size products (200 bp or 300 bp) were retrieved from the gel and subjected to PCR amplification using universal primer sites present at the end of the ligated adapters. The library was then subjected to quality control steps such as verification of fragment size and concentration measurements using the DNA 1000 Kit (Agilent Technologies) on an Agilent 2100 Bioanalyzer. All samples were sequenced using an Illumina Genome Analyzer II (GAII). Since the experiments were performed over several months as Illumina introduced advances to the GAII platform, the total number of reads and the read length vary (see Table 1). However, all samples were prepared following the same protocol.

treatment_protocol: The samples were prepared in accordance with the Illumina RNA sample preparation protocol (Part # 1004898 Rev. A September 2008). Briefly, mRNAs were fragmented at elevated temperature using divalent cations and transcribed into cDNA thereby generating a library of cDNA fragments. RNA-Seq adapters are then ligated to the blunt ends of the cDNA fragments. The library of cDNA fragments subsequently underwent a size-selection step in which cDNAs were first electrophoresed through a 2.5% agarose gel in TAE buffer.

tag: rna-type

value: poly(A) selected RNA


title: JunD ChIP-Seq

description: Chromatin IP against JunD

value: Jun-D


title: CSHL_RnaSeq_HepG2_cytosol_longPolyA (superseded by GSE90230)

description:
****************************
GSM758576 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90230
****************************

value: Sequencing analysis of RNA expression

tag: cell description

value: hepatocellular carcinoma

value: iIDR

value: Paired 76 nt directed reads

tag: spikeinpool


title: HeLa ELAV1/HuR sRNA siRNA1

status: Public on Jul 07 2011

city: Berlin

first: Marvin

last: Jens

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

data_processing: Adapters were removed with FAR 1.81. Reads were aligned to MirBASE 15 precursors. Read counts were used to compute normalized log2 fold-changes using a custom perl-script.

source_name: HeLa cell culture

extract_protocol: see Lebedeva et. Al 2011

tag: cell line

value: HeLa

tag: knockdown

value: ELAVL1/HuR siRNA1 (see Lebedeva et. Al 2011)


title: HeLa sRNA mock sRNA


title: Chromatin accessibility assay of Breast_vHMEC; DS18438

status: Public on Jul 06 2011

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18438
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7552
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.2872
****************
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: GSM753974_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18438.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Breast vHMEC Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Breast vHMEC, Donor RM035, Library DS18438 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.7697
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,557,534
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3782
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4762
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9967
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5169
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM753974_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18438.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Breast vHMEC, Donor RM035, Library DS18438 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.7751
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: Bv DNase 35 38
BROWSER_TRACK_DESCRIPTION: UW Breast vHMEC DNase Hypersensitivity Donor RM035 Library DS18438 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,557,534
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3782
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4762
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9967
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5169
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Breast, vHMEC, RM035; DS18438

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: Breast vHMEC RM035

tag: sample common name

value: Breast, vHMEC

tag: molecule

value: genomic DNA

tag: disease

value: Tlsty Lab, University of California, San Francisco

value: Primary Cell Culture

value: Variant Human Mammary Epithelial Cells

tag: markers

value: spilt 1:5 in MEGM medium (Lonza Inc.)

value: Disease Free

value: Female

value: Caucasian

tag: karyotype

tag: parity

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: HeLa ELAV1/HuR sRNA siRNA2


title: Reference Epigenome: ChIP-Seq Input from BMP4 Mesendoderm Cells; renlab.Input.BMP4M.02.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK149
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7836
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
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: GSM753447_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4M.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK149, 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.10458
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,257,256
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.06
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM753447_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4M.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK149, 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.10531
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 5
BROWSER_TRACK_NAME: HBDM Input 49
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK149 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,257,256
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.06
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.Input.BMP4M.02.01

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

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: passage

value: Between 20 and 30

tag: medium

tag: Sex

value: Male

tag: batch

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Input from BMP4 Trophoblast Cells; renlab.Input.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK457
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7860
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7840
****************
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: GSM753448_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Input.SK457.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4T.01.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK457, 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.10473
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,442,419
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.08
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM753448_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Input.SK457.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4T.01.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK457, 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.10546
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 5
BROWSER_TRACK_NAME: HBDT Input 57
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library SK457 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,442,419
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.08
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.Input.BMP4T.01.01

value: genomic DNA

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in hESC H1 Cells; renlab.H4K91ac.hESC.H1.02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 and Illumina Genome Analyzer IIx platforms.
Library name: SK303
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7619
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM752991_UCSD.H1.H4K91ac.SK303.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC.H1.02.01-renlab.H4K91ac.hESC.H1.02.01-renlab.H4K91ac.hESC.H1.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on H1 Cell Line, Library SK303, 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.10485
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,718,358
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.03
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.75
IROC_PERCENTILE: 100
POISSON_SCORE: 0.28
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM752991_UCSD.H1.H4K91ac.SK303.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC.H1.02.01-renlab.H4K91ac.hESC.H1.02.01-renlab.H4K91ac.hESC.H1.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the H1 Cell Line, Library SK303, 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.10558
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 5
BROWSER_TRACK_NAME: H1 H4K91ac 03
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H4K91ac Library SK303 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,718,358
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.03
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.75
IROC_PERCENTILE: 100
POISSON_SCORE: 0.28
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H4K91ac.hESC.H1.02.01

value: H1 Cell Line

value: James Thompson Laboratory

value: mTeSER

value: Histone H4K91ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H4K5ac in hESC H1 Cells; renlab.H4K5ac.hESC.H1.03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K5ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 and Illumina Genome Analyzer IIx platforms.
Library name: SK302
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7623
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM752990_UCSD.H1.H4K5ac.SK302.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.hESC.H1.03.01-renlab.H4K5ac.hESC.H1.03.01-renlab.H4K5ac.hESC.H1.03.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K5ac ChIP-Seq on H1 Cell Line, Library SK302, 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.10488
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,705,736
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.12
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.65
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

ANALYSIS FILE NAME: GSM752990_UCSD.H1.H4K5ac.SK302.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.hESC.H1.03.01-renlab.H4K5ac.hESC.H1.03.01-renlab.H4K5ac.hESC.H1.03.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K5ac ChIP-Seq read mappings from the H1 Cell Line, Library SK302, 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.10561
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 5
BROWSER_TRACK_NAME: H1 H4K5ac 02
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H4K5ac Library SK302 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,705,736
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.12
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.65
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H4K5ac.hESC.H1.03.01

value: Cell Line

value: Embryonic Stem Cell

value: Histone H4K5ac

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in BMP4 Mesendoderm Cells; renlab.H3K36me3.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK137
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7806
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
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: GSM752972_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K36me3.AK137.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.BMP4M.01.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK137, 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.10469
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 62,490,509
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.08
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM752972_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K36me3.AK137.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.BMP4M.01.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK137, 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.10542
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 5
BROWSER_TRACK_NAME: HBDM H3K36me3 37
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K36me3 Library AK137 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 62,490,509
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.08
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K36me3.BMP4M.01.01

value: James Thomson Laboratory

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 20 and 30

value: Male

value: Histone H3K36me3

value: Biorupter


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in iPS 19.11 Cells; renlab.H3K27me3.iPS-19.11.02.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in iPS 19.11 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK435
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7662
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7659
****************
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: GSM752970_UCSD.iPS_DF_19.11.H3K27me3.SK435.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.iPS-19.11.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on iPS DF 19.11 Cell Line, Library SK435, 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.10449
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,084,496
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.05
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.08
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.15
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

ANALYSIS FILE NAME: GSM752970_UCSD.iPS_DF_19.11.H3K27me3.SK435.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.iPS-19.11.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS DF 19.11 Cell Line, Library SK435, 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.10522
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 5
BROWSER_TRACK_NAME: iD19.11 H3K27me3 35
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Histone H3K27me3 Library SK435 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,084,496
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.05
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.08
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.15
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K27me3.iPS-19.11.02.01

value: iPS DF 19.11 Cell Line

value: genomic DNA

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: mTeSR

value: Histone H3K27me3

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in BMP4 Trophoblast Cells; renlab.H3K4me2.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK497
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7869
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7840
****************
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: GSM753438_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me2.SK497.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.BMP4T.01.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK497, 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.10504
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,104,623
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.18
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM753438_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me2.SK497.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.BMP4T.01.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK497, 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.10577
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 5
BROWSER_TRACK_NAME: HBDT H3K4me2 97
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me2 Library SK497 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,104,623
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.18
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K4me2.BMP4T.01.01

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Histone H3K4me2

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in iPS 6.9 Cells; renlab.H3K9me3.iPS-6.9.02.01

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in iPS 6.9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK503
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7795
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7666
****************
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: GSM752989_UCSD.iPS_DF_6.9.H3K9me3.SK503.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.iPS-6.9.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on iPS DF 6.9 Cell Line, Library SK503, 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.10448
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 66,582,755
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.03
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.17
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM752989_UCSD.iPS_DF_6.9.H3K9me3.SK503.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.iPS-6.9.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS DF 6.9 Cell Line, Library SK503, 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.10521
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 5
BROWSER_TRACK_NAME: iD6.9 H3K9me3 03
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Histone H3K9me3 Library SK503 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 66,582,755
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.03
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.17
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K9me3.iPS-6.9.02.01

value: iPS DF 6.9 Cell Line

value: James Thomson Laboratory

value: iPS 6.9

value: Male

value: Histone H3K9me3

value: Biorupter


title: Chromatin accessibility assay of Breast_vHMEC; DS18406

description:
sample_term_id: CL_0002327
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18406
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7555
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.2872
****************
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: GSM753973_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18406.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Breast vHMEC Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Breast vHMEC, Donor RM035, Library DS18406 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.7687
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,386,613
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3982
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4808
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5033
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM753973_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18406.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Breast vHMEC, Donor RM035, Library DS18406 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.7741
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: Bv DNase 35 06
BROWSER_TRACK_DESCRIPTION: UW Breast vHMEC DNase Hypersensitivity Donor RM035 Library DS18406 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,386,613
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3982
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4808
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5033
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Breast, vHMEC, RM035; DS18406

value: Breast vHMEC RM035

value: Breast, vHMEC

value: genomic DNA

value: Tlsty Lab, University of California, San Francisco

value: Primary Cell Culture

value: Variant Human Mammary Epithelial Cells

value: spilt 1:5 in MEGM medium (Lonza Inc.)

value: Disease Free

value: Female

value: Caucasian

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)