title: U87MG-cell culture [AB SOLiD]

status: Public on Jan 25 2010

first: Stanley

middle: F

last: Nelson

address: 695 Young Dr S

department: Human Genetics

description: genomic DNA library from 10ug of source DNA extracted from cultured U87MG cells

data_processing:
Alignment: We used Blat-like Fast Accurate Search Tool version 0.5.3 (BFAST http://bfast.sourceforge.net) to perform sequence alignment of the two-base encoded reads off the ABI SOLiD to the NCBI human reference genome (build 36.1). Utilizing the local alignment algorithm included in BFAST, we were able to simultaneously decode the short reads, while searching for color errors (encoding errors), base changes, insertions, and deletions. We also set parameters to use only informative keys when looking up reads in each index (BFAST parameter -K 8), and to ignore reads with too many CALs aggregated across all indexes (BFAST parameter -M 384). If reads mapped to greater than 384 locations, then they were categorized as ‘unmapped’.  We then performed local alignment for each of the returned CALs, simultaneously decoding the read from color space searching for color errors (encoding errors), base changes, insertions, and deletions. We choose the "best scoring" alignment, accepting an alignment only if it was at least the equivalent edit distance of two color errors away from the next best alignment. This is approximately similar to a ‘mapping quality’ of 20 or better from the MAQ program output, for reference. We removed duplicate reads using the alignment filtering utility found in DNAA (http://dnaa.sourceforge.net). For single-end and mate-paired reads where only one end mapped, we removed duplicates based on reads having identical stat positions. For mate-paired reads, we removed duplicates where both ends had the same start position.
Variant BED Files: Variant calls from the SAMtools pileup tool were first loaded into a SeqWare QueryEngine database and subsequently filtered to produce BED files. This filtering criteria required that a variant be seen at least 4 times and at most 60 times with an observation occurring on each strand at least once. For SNVs we further enforced the criteria that SNVs should only be called in reads lacking indels and the last 5 bases of the reads were also ignored. This reduced the likelihood that spurious mismappings were used to predict SNVs and eliminated the lowest quality bases from consideration. For small indels (<21bp) we enforced a slightly different filter by requiring that any reads supporting an indel were only allowed to contain one contiguous indel and these reads were not considered if the indel occurred on either the beginning or end of the read. These criteria, like the SNV criteria, were used to reduce the likelihood of using mismapped reads or locally misaligned reads in the variant calling algorithm. The elimination of reads with indels at the beginning or end of the read was intended to remove potential alignment artifacts caused by ambiguous gap introduction due to lack of information at the ends to guide proper alignment. Together, these filtering criteria reduced the likelihood that sequencing errors were identified as SNV or indel variants. We used scripts available in the BFAST toolset and SeqWare Pipeline to filter and annotate the variant calls. Variants passing these filters were further annotated by their overlap with dbSNP version 129. Variants were required to share the same genomic position as a dbSNP entry along with matching the allele present in the database to be considered overlapping. Mapping to dbSNP allowed us to filter out known SNPs from de novo variants.

source_name: brain tumor cell line

growth_protocol: Cells were grown in DMEM with 10% FBS.

extract_protocol: Long-Mate-Paired Library Construction: The U87MG genomic DNA 2x 50bp long mate-paired library construction was carried out using the reagents and protocol provided by Applied Biosystems (SOLiD 3 System Library Preparation Guide). Briefly, 45ug of genomic DNA was fragmented by HydroShear (Digilab Genomic Solutions Inc) to 1.0-2.5kb. The fragmented DNA was repaired by the End-It DNA End-Repair Kit (Epicentre). Subsequently, the LMP CAP adaptor was ligated to the ends. DNA Fragments between 1.2-1.7kb were selected by 1.0 % agarose gel to avoid concatamers and circularized with a biotinylated internal adaptor. Non-circularized DNA fragments were eliminated by Plasmid-Safe ATP-Dependent DNase (Epicentre) and 3ug of circularized DNA was recovered after purification. Original DNA nicks at the LMP CAP oligo/genomic insert border were translated into the target genomic DNA about 100bp by nick translation using E. coli DNA polymerase I. Fragments containing the target genomic DNA and adaptors were cleaved from the circularized DNA by single-strand specific S1 nuclease. P1 and P2 adaptors were ligated to the fragments and the ligated mixture was used to create two separate libraries with 10 cycles of PCR amplification. Finally, 250-300bp fragments were selected to generate mate paired sequencing libraries with average target genomic DNA on each end around 90bp by excision from PAGE gel and use as emulsion PCR template. Templated Beads Preparation: The templated beads preparation was performed using the reagents and protocol from the manufacturer (Applied Biosystems SOLiD 3 Templated Beads Preparation Guide).  SOLiD 3 Sequencing: The 2x50b mate-paired sequencing was performed exactly according to the Applied Biosystems SOLiD 3 System Instrument Operation Guide and using the reagents from Applied Biosystems.


title: Head_Dpseud_Male

status: Public on Jan 26 2010

type: SRA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

description: Deposited sequence data are high quality sequence reads that passed default parameters of the Illumina quality filter. Data were generated using Genome Analyzer I and II and various versions of the GA pipeline, see readme file on GSE19989 for details

library_source: transcriptomic

data_processing: Reads that passed default parameters of the Illumina quality filter mapped with Bowtie 0.10.0. The reference sequence used to built an index for mapping was flybase r2.4 for D. pseudoobscura. Reference index was created using the bowtie-build function with default parameters. Reads were then mapped using -v 2 -m 1 in Bowtie v. 0.10.0.

molecule: polyA RNA

organism: Drosophila pseudoobscura

source_name: head tissue

growth_protocol: D. pseudoobscura (Drosophila Species Stock Center (DSSC) 14011-0121.94) were grown at 22°C, 60% relative humidity in standard plastic vials containing banana-opuntia media. All media was purchased from the Tucson Stock Center, Tucson, Arizona (recipes: http://flyfood.arl.arizona.edu/). There were no lights inside of incubators and room lighting (standard fluorescent bulbs) was on at all times. Newly eclosed flies of both females and males were housed together in vials at normal density (60-100 flies) and aged for 7 days. On day 7, flies were anesthetized with CO2 and then females and males were sorted and placed into separate vials. Flies in same sex vials were aged an additional 24 hours then flash frozen on dry ice in 50 ml Falcon tubes and stored at -80°C until dissection.

extract_protocol:
Fly heads were immersed in 250 µl of TRIzol and thoroughly homogenized using a 1.5 ml RNAase free pestle (Kimble-Chase, Vineland, New Jersey) fitted to a Pellet Pestle Motor (Sigma-Aldrich, St. Louis, Missouri). After initial homogenization, 550 µl of TRIzol was added and the solution was further homogenized by hand. Chloroform (160 µl) was added to the homogenate and then the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The aqueous layer was removed, precipitated with isopropyl alcohol and glycogen (8 µg), then centrifuged for 10 minutes at 4°C to pellet the RNA. The supernatant was removed and the RNA pellet was washed with fresh 75% ethanol. The pellet was dried briefly and then dissolved in 50 µl DEPC treated H2O. mRNA was enriched from total RNA by poly A+ selection using a QIAGEN Oligotex mRNA kit (Valencia, California) following manufacture instructions. mRNA was eluted from small spin columns twice with hot 30 µl buffer OEB. mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer.
We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single "A" base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3' to 5' exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 200 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl primer 1.1, 1 µl primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

treatment_protocol: Frozen whole flies were placed on 10.8 x 10.8 cm ceramic plates frozen on dry ice. Forceps were used to dissect 400-500 heads/sex for subsequent RNA extraction.

tag: source

value: Drosophila Species Stock Center (DSSC) 14011-0121.94. Line MV2-25 Baylor sequencing strain (Richards et al. 2005. Comparative genome sequencing of Drosophila pseudoobscura:chromosomal, gene, and cis-element evolution. Genome Res. 15:1-18). Wild-type genotype. Collected from Anderson, Mesa Verde, Colorado in 1996. Unknown inbred generations.

tag: tissue

value: head

tag: gender

value: male


title: Mock ChIP using anti-HA antibody

status: Public on Jan 22 2010

city: Singapore

first: Mikael

last: Huss

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Anti-HA ChIP was performed for ES cells

library_source: genomic

data_processing: The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: E14 mouse ES cells, cultured under feeder-free conditions were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15 % heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon). Control shRNA and Eset shRNA knockdown samples were obtained by transfecting ES cells with the respective shRNAs using lipofectamine-2000(invitrogen). The transfected ES cells were maintained in the ES medium with 0.8ug/ml puromycin.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).

treatment_protocol: The ES cells were fixed in 1 % formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.

tag: cell type

value: embryonic stem cells

tag: dev stage

tag: antibody

value: anti-HA


title: cnv_ML-DmBG3_1 extraction1_seq1

status: Public on Jan 21 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

data_processing:
Illumina_seq_maq_processing: DM:1 protocol;
Get Illumina FASTQ files back from Duke IGSP Sequencing Facility. Their steps, briefly:
* Image analysis (SCS real time analysis software / Firecrest software)
* Base calling ( Bustard.py)
* Sequence analysis (GERALD.py) -> results in the FASTQ file that gets sent to us
* Using maq command-line tool v. 0.7.1:
* Convert Illumina FASTQ file to Sanger-style FASTQ format: maq sol2sanger $workingdir/$solfastqfilename $workingdir/$solfastqfilename.sangerfastq
* Convert Sanger FASTQ file to Binary FASTQ format: maq fastq2bfq $workingdir/$solfastqfilename.sangerfastq $workingdir/$solfastqfilename.sangerbfq
* Convert Drosophila 5.1 FASTA file to Binary FASTA format: maq fasta2bfa $workingdir/$referencefastafile $workingdir/$referencefastafile.bfa
* Map reads back to Drosophila genome allowing 3 mismatches: maq map -n 3 $workingdir/$destination_table.map $workingdir/$referencefastafile.bfa $workingdir/$solfastqfilename.sangerbfq
* Create a mapview file to import into the database: maq mapview $workingdir/$destination_table.map > $workingdir/$destination_table.mapview

Processed data are obtained using following parameters:
genome version is 5.1
read length is 36

CNV_seq_analysis:DM:1 protocol
* Read locations are shifted:
* Positive reads are shifted downstream by half of the estimated sonication size
* Negative reads are shifted upstream by half of the estimated sonication size
* Reads with a map score (Phred) >= 35 (leading to maximum probability that a read is misaligned of ~0.03%) are then binned based on their location, with non-overlapping bins of size 1000bp covering the genome
* The total number of reads in each bin are summed across replicates

organism: Drosophila melanogaster

growth_protocol:
Cell growth protocol;
Grow 10ml of cells in 100mm dishes. For Kc and S2 cells use:  Schneider's medium (invitrogen 11720-067) 10% ModEncode serum 1% Penicillin/Streptomycin/Glutamine (PSG) (Invitrogen 10378-016). For ML-DmBG3-c2 cells use:  Schneider's medium 10% ModEncode serum 1% PSG 10ug/ml human insulin (sigma I9278). Cells are grown at 25C. Cells are happiest between 1.5X10^6 and 2.0X10^6

extract_protocol:
DNA isolation protocol;
1. Grow 10ml of cells to 1.5 x 106 in 100mm dishes
2. Harvest cells into 15ml conical tubes
3. Pellet cells at 1000g for 5 minutes
4. Wash cells once in cold 1X PBS
5. Resuspend pellet in 0.7ml 10mM Tris pH 9.5
6. Add 0.7ml NDS. Invert to mix
7. Add 0.1ml 20mg/ml Proteinase K (Amresco 0706-1G). Invert to mix
8. Inc. 37C, 2 hours
9. Add 1.5ml 1X TE. Invert to mix
10. Add 3.0ml phenol/chloroform. Invert tubes over 5 minutes
11. Centrifuge 3500 rpm for 10-12 minutes
12. Remove top layer with cut p1000 tips to a new 15ml tube
13. Repeat steps 10-12
14. Add 2.5 volumes of room temp. 100% Ethanol. Invert
15. Inc. at room temp overnight
16. Centrifuge tubes 3500-3700rpm for 10-12 minutes
17. Wash pellet with 70% Ethanol and transfer pellet to a 1.5ml tube
18. Centrifuge full speed for 5 minutes
19. Air dry pellet
20. Resusp. pellet in 250ul 1X TE
21. Add 5ul 10mg/ml RNaseA (Amresco 0675-250mg). Inc. 37C for 1h
22. Add 1/10 volume 3M NaOAc. Vortex
23. Add 2X volume cold 100% Ethanol. Vortex
24. Inc. -80C 20-30 minutes
25. Centrifuge at 4C for 15 minutes
26. Wash with 70% Ethanol
27. Air dry pellet. Resusp. in 250ul 1X TE
28. Spec DNA Shearing DNA
29. Shear DNA 3X 10 seconds with 1minute on ice in between Optional [for BrdU experiments]
30. Run 5ug on 1% agarose gel
31. Set up Southern overnight
32. Check for BrdU incorporation by western. anti-BrdU antibody (BD BioSciences 555627 ) is 1:1000 dilution in milk/TBS-T

Genomic DNA library protocol;
1. Genomic DNA was fragmented to less than 800bps by sonication
2. the library was prepared as described in the Illumina provided protocol "Preparing samples for sequencing genomic DNA" (part # 11251892 Rev. A) with the exception of an additional gel extraction (size select for 150-200bps) after the "enrich the adapter-modified DNA fragments by PCR" step.
3. Samples were submitted to the Duke University IGSP sequencing facility.

tag: cell line

value: CNS-derived cell-line

tag: developmental stage

value: third instar larval stage

tag: genotype

value: y v f mal

tag: sex

value: Unknown


title: cnv_ML-DmBG3_2 extraction2_seq1


title: cnv_Kc167_2 extraction2_seq1

source_name: cnv_Kc167_2 extraction2_seq1 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: se/e

value: Female


title: cnv_S2-DRSC_2 extraction2_seq1

value: Male


title: cnv_Kc167_1 extraction1_seq1

source_name: cnv_Kc167_1 extraction1_seq1 channel_1


title: cnv_S2-DRSC_1 extraction1_seq1


title: H3K9ac_ChIPSeq_Nipponbare

status: Public on Jan 20 2010

city: New Haven

first: guangming

last: he

state: CT

address: 165, prospect st.

department: MCDB

institute: Yale University

description: Chromatin IP against H3K9ac

data_processing: Sequencing reads from all libraries were mapped to the reference rice genome using MAQ software. Genomic regions associated with DNA methylation and histone modifications were identified using MACS software, in which default parameters were set up to call peaks representing enriched epigenetic marks.Further details found at http://www.plantcell.org/

organism: Oryza sativa

source_name: seedling shoot

growth_protocol: Rice cultivar Nipponbare, 93-11, and their reciprocal F1 hybrids (Nipponbare/93-11 and 93-11/Nipponbare) were used for all experiments in this study. Seeds were grown in soil under 16 hours light/8 hours dark conditions at 28℃ in a greenhouse. After 4 weeks, seedling shoots at the four-leaf stage were harvested, frozen in liquid nitrogen and stored at -80℃ for DNA and total RNA isolation, or processed directly after harvesting for ChIP assay.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions, and was treated with RNase-free DNase I (New England Biolabs) to remove any possible contaminating genomic DNA. mRNA was extracted from total RNA using Dynabeads Oligo(dT) (Invitrogen Dynal) following the manufacturer's directions. First-and second strand cDNA was generated using SuperscriptII reverse transcriptase (Invitrogen) and random hexamers primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the standard Illumina protocol. Small RNAs were gel isolated from total RNA, and were used to create libraries for Illumina sequencing essentially as described previously (Mi et al., 2008; Wang et al., 2009a). Genomic DNA extraction, methylated genomic DNA enrichment and construction of Illumina sequencing libraries were carried out as described previously (Li et al., 2008b; Wang et al., 2009a). Chromatin from seedling shoots was immunoprecipitated with antibodies against H3K4me3 (Upstate), H3K9ac (Upstate) or H3K27me3 (Upstate) as described previously (Gendrel et al., 2005). The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.

value: shoots from four-leaf stage

tag: cultivar

value: Nipponbare


title: H3K4me3_ChIPSeq_93-11

description: Chromatin IP against H3K4me3


title: rdp1delta_siRNA

status: Public on Feb 15 2010

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Normalised bedgraph files were created by measuring the number of reads that mapped to each base.  Each read counted 1/n towards each base that it align to, where 'n' is the number of  times a read could be aligned in the genome. .bedgraph files are give for each strand and both strands combined for the wild type and rpd1delta only.

Two additional constructs were mapped, ura4GFP (ura4 gene combined with gfp gene) and GFPHP (two gfp genes that form a hairpin).  A gff file describing these constructs and the fasta files for these contructs are included as supplementary files linked to GSE20330.

molecule: total RNA

organism: Schizosaccharomyces pombe

growth_protocol: Strains were grown in PMG complete to keep the GFP hairpin, which is under the nmt1 promoter, expressed. Standard procedures were used for growth and genetic manipulations (Moreno et al., 1991).

extract_protocol: Total small RNA was obtained by resuspending cells in RNA extraction buffer (50 mM Tris–HCl pH 7.5, 10 mM EDTA pH 8, 100 mM NaCl, 1% SDS), lysed with phenol:chloroform 5:1 and acid washed beads. The soluble fraction was extracted with phenol/chloroform. Small RNA were concentrated by precipitating away large RNAs with 10% polyethylene glycol 8000, 0.5 M NaCl and then by ethanol precipitation. For gel-purified small RNA, 10 to 30-nt siRNAs, from 400 μg of total small RNAs, were excised from a 12% polyacrylamide gel. After elution from the gel (incubation over-night in RNA extraction buffer at 4°), small RNAs were extracted with phenol/chloroform was and precipitated with ethanol, sodium acetate, and glycogen. For Ago1-associated small RNA preparation 10 g of cells were lysed in presence of liquid nitrogen using a mortar grinder (Retsch) for 30 minutes. Extracts were prepared by dilution of the crushed cells in 20 ml lysis buffer (50 mM Hepes-NaOH (pH 7.5), 150 mM NaCl, 1 mM MgCl2, 0.1% NP-40, 5mM DTT, 1x Roche EDTA-free protease inhibitors cocktail, 0.5mM PMSF, 1/100 super RNAsin (Ambion), and filtration through GD/X 1.6 μm (Whatman). Immunoprecipitations were performed using 20 μg of M2 anti-Flag antibody (Sigma F1804) coupled to 4 μL protein G Dynabeads resin (Dynal) for 15 minutes at 4 °C. RNA samples bound to Dynabeads were washed once with lysis buffer and once with lysis buffer with 2 mM MgCl2, treated with 200 ng/ml proteinase K (Sigma), extracted with phenol/chloroform and chloroform. RNA was precipitated with ethanol, sodium acetate, and glycogen. Libraries were prepared of the small RNA according to Illumina's instructions for subsequent cDNA sequencing.

tag: strain

value: rdp1::KanMX6 ars1::pREP1GFP-HP-LEU2 arg3::ura4-GFP arg11::HphMX6 ade6-210/216 leu1-32 ura4-D18

tag: purification

value: polyacrylamide gel purification

tag: molecule

value: small RNA


title: H3K27me3_ChIPSeq_Nipponbare/93-11

description: Chromatin IP against H3K27me3


title: smRNA-Seq_93-11

description: small RNA gel isolated


title: H3K27me3_ChIPSeq_93-11

description: Chromatin IP against H3K27me3


title: H3K9ac_ChIPSeq_93-11

description: Chromatin IP against H3K9ac


title: DNAmethyl_McrBCSeq_93-11/Nipponbare

description: McrBC digestion


title: smRNA-Seq_Nipponbare

description: small RNA gel isolated


title: H3K27me3_ChIPSeq_93-11/Nipponbare

description: Chromatin IP against H3K27me3


title: H3K27me3_ChIPSeq_Nipponbare

description: Chromatin IP against H3K27me3


title: H3K9ac_ChIPSeq_Nipponbare/93-11

description: Chromatin IP against H3K9ac


title: H3K4me3_ChIPSeq_Nipponbare

description: Chromatin IP against H3K4me3


title: H3K4me3_ChIPSeq_93-11/Nipponbare

description: Chromatin IP against H3K4me3


title: smRNA-Seq_Nipponbare/93-11

description: small RNA gel isolated


title: H3K9ac_ChIPSeq_93-11/Nipponbare

description: Chromatin IP against H3K9ac


title: smRNA-Seq_93-11/Nipponbare

description: small RNA gel isolated


title: H3K4me3_ChIPSeq_Nipponbare/93-11

description: Chromatin IP against H3K4me3


title: wt_siRNA

value: ars1::pREP1GFP-HP-LEU2 arg3::ura4-GFP arg11::HphMX6 his3-D1 leu1-32 ura4-D18 ade6-210/216


title: DNAmethyl_McrBCSeq_Nipponbare/93-11

description: McrBC digestion


title: mRNASeq_93-11/Nipponbare

description: polyA RNA isolated


title: DNAmethyl_McrBCSeq_93-11

description: McrBC digestion


title: mRNASeq_Nipponbare/93-11

description: polyA RNA isolated


title: DNAmethyl_McrBCSeq_Nipponbare

description: McrBC digestion


title: panicles_OSU

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: wild type B. distachyon panicle small RNA

data_processing: Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary. Only sequences that mapped perfectly to the B. distachyon genome were included in the analysis.

organism: Brachypodium distachyon

source_name: panicles

extract_protocol: Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR.  DNA amplicons were sequenced using an Ilumina Genome Analyzer.

value: panicles

value: Oregon State University

tag: growth conditions

value: Plants were grown in long-day conditions (16 h days/8 h nights) at 25°C for 28-35 days


title: mRNASeq_93-11

description: polyA RNA isolated


title: Mock ChIP-seq

status: Public on Jan 15 2010

city: Cold Spring Harbor

first: Agustin

last: Chicas

state: NY

address: One Bungtown Road

institute: Memorial Sloan Kettering

description:
Growing cells Mock ChIP-seq
Quiescent cells Mock ChIP-seq
Senescent cells Mock ChIP-seq

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the unmasked human reference genome (NCBI v36, hg18) using the Illumina Eland program. The read that could not be mapped to the genome was shortened by removing 3' terminal base pairs and was realigned using Eland, to a minimum read length of 20 bp. Only the tags uniquely mapped to the genome with at most one mismatches were kept. And to minimize the risk of ambiguous mapping, the tags which have alternative mappings when allowing one more mismatches were filtered.

organism: Homo sapiens

source_name: Chromatin IP against Mock

growth_protocol: IMR90 cells were grown in 10% FBS DMEM unless otherwise noted.

extract_protocol: RB or p130 specfic antibodies were used to immunoprecipiated paraformaldehyde crosslnked DNA from growing, quiescent or senescent IMR90 cells.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

tag: chip antibody

value: Mock

tag: growth state

value: Growing, Quiescent, Senescent


title: mRNASeq_Nipponbare

description: polyA RNA isolated


title: Quiescent cells expressing shRNA targeting RB p130 ChIP-seq

source_name: Chromatin IP against p130

value: Quiescent


title: Senescent cells expressing shRNA targeting RB p130 ChIP-seq

value: Senescent


title: Growing cells pRb ChIP-seq experiment 1, replicate 1+2

description:
Growing cells pRb ChIP-seq experiment 1, replicate 1
Growing cells pRb ChIP-seq experiment 1, replicate 2

source_name: Chromatin IP against pRb

value: pRb

value: Growing


title: Quiescent cells p130 ChIP-seq

description: Quiescent cells p130 ChIP-seq


title: Quiescent cells pRb ChIP-seq experiment 2


title: Senescent cells expressing shRNA targeting RB pRb ChIP-seq


title: Quiescent cells expressing shRNA targeting RB pRb ChIP-seq


title: Senescent cells pRb ChIP-seq experiment 1, replicate 1+2

description:
Senescent cells pRb ChIP-seq experiment 1, replicate 1
Senescent cells pRb ChIP-seq experiment 1, replicate 2


title: Quiescent cells pRb ChIP-seq experiment 1, replicate 1+2

description:
Quiescent cells pRb ChIP-seq experiment 1, replicate 1
Quiescent cells pRb ChIP-seq experiment 1, replicate 2


title: Senescent cells pRb ChIP-seq experiment 2


title: Senescent cells p130 ChIP-seq

description: Senescent cells p130 ChIP-seq


title: E0-12_HDAC-498_ChIPSeq_1 and 2

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

description:
E0-12_HDAC-498_ChIPSeq_1 and 2
corresponding input record(s): GSM499634

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software.  Signal files were generated with the R package SPP.  Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).

source_name: E0-12_HDAC-498_ChIPSeq_1 and 2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila whole animals (embryos, larvae, pupae or adults) are crushed in presence of 1.8% of formaldehyde for 15 minutes with the help of a douncer. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.

treatment_protocol: No Treatment

tag: development stage

tag: test

value: ChIP


title: Drosophila-female-input-DNAseq

status: Public on Jan 11 2010

description: DNA sequencing for chromatin structure

data_processing:
Image analysis and base calling were performed using a manufacturer-provided computational pipeline (version 0.3) including the Firecrest and Bustard applications and sequence reads were then aligned with the Drosophila melanogaster assembly (BDGP Release 5, dm3) using Bowtie (v 0.10.0). All unique mapped reads with two or fewer mismatches were retained.

Like DNase hypersensitivity assays, mechanically sheared chromatin breaks preferentially at some sites to provide information about chromatin structure genome-wide. Thus, we measured differential shearing accessibility in genome-wide experiments by deep DNA sequencing and increased mapped read density correlates with regions of preferential shearing. We are particularly interested in shearing and chromatin structure at gene models and different gene features to detect chromatin alternations associated with transcription.
Detailed analysis is included in the accompanying publication.

File description for *_bowtiealign.txt processed data files: sequence reads mapped to unique portion of the genome with two or fewer mismatches using Bowtie (v 0.10.0)
Column descriptions for *_bowtiealign.txt files:
Sequence: sequence of the aligned reads
Chromosome: chromosome reads mapped to
Location: chromosomal position where alignment starts
Strand: forward or reverse strand the reads mapped to

source_name: ChIP input from Drosophila melanogaster adult female

growth_protocol: Flies were grown at 25 °C on standard cornmeal media.

extract_protocol:
Wild type flies (y1w67c) for chromatin immunoprecipitaion were aged for 5-7 days post-eclosion, sexed and flash frozen. About 0.5 g of sex-sorted adult flies was cross-linked with 1.8% for 20 minutes at room temperature. After washing, the flies were completely homogenized and the cells were disrupted by cell lysis and nuclei lysis. The nuclear extraction was then sheared to 200-1000bp by sonication using a Misonix Sonicator 3000 and the soluble chromatin was collected.
300 ng of DNA derived from sheared chromatin of female and male adult flies was prepared as ChIP input controls.

tag: gender

value: female


title: Drosophila-male-input-DNAseq

description: DNA sequencing for chromatin structure

source_name: ChIP input from Drosophila melanogaster adult male

value: male


title: Drosophila-S2-msl2RNAi-RNAseq1

description:
Gene expression profile of msl2 RNAi treated S2 cells
Processed_data_file: RNA-S2-msl2-1_align.txt
Processed_data_file: RNA-S2-msl2-1_geneRPKM.txt
Raw_data_file: run12-s_4_sequence.fastq
Raw_data_file: run18-s_2_sequence.fastq

data_processing:
Alignment: Sequence reads were mapped to the Drosophila reference genome [i.e., the April 2006 Drosophila melanogaster draft assembly (BDGP Release 5, dm3)] using the Illumina Genome Analyzer Pipeline. All unique mapped reads with two or fewer mismatches were retained.
GeneRPKM: Then we counted the number of unique mapped reads landed within any unique exons of Drosophila Flybase Release 5.12 annotation (Oct. 2008) and calculated the number of reads per kilobase of exon model per million mapped reads (RPKM) for all the genes.

source_name: Drosophila S2 cell

growth_protocol: Drosophila S2 cells were grown at 25°C in Schneider's Drosophila Medium (Invitrogen, Carlsbad, CA) supplemented with 10% Fetal Bovine serum (SAFC Biosciences, Lenexa, KS) and Penicillin-Streptomycin.

extract_protocol: Total RNA from S2 cells with dsRNA or mock treatment was extracted using Trizol (Invitrogen, Carlsbad, CA) and followed by mRNA isolation using Oligotex poly(A) extraction kit (Qiagen, Valencia CA).

treatment_protocol: S2 cells were mock or RNAi treatment with dsRNA using standard procedure.

tag: cell type

value: S2 cells

tag: protocol

value: msl2 knockdown, RNAi-mediated


title: Drosophila-S2-msl2RNAi-RNAseq2

description:
Gene expression profile of msl2 RNAi treated S2 cells
Processed_data_file: RNA-S2-msl2-2_align.txt
Processed_data_file: RNA-S2-msl2-2_geneRPKM.txt
Raw_data_file: run12-s_7_sequence.fastq
Raw_data_file: run17-s_7_sequence.fastq


title: Drosophila-S2-mofRNAi-RNAseq1

description:
Gene expression profile of mof RNAi treated S2 cells
Processed_data_file: RNA-S2-mof-1_align.txt
Processed_data_file: RNA-S2-mof-1_geneRPKM.txt
Raw_data_file: run12-s_5_sequence.fastq
Raw_data_file: run18-s_3_sequence.fastq

value: mof knockdown, RNAi-mediated


title: STAT3 bound pre IL21 in IRF4 KO mice, second exp

status: Public on Jan 08 2010

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 E Duarte Rd.

institute: City of Hope

description: Chromatin IP against STAT3

data_processing: To align sequence tags, analyze their clustering, identify binding motifs, and display results, new code was developed in C language as extensions of the AceView project (Thierry-Mieg and Thierry-Mieg, 2006). Each Solexa 25-mer tag was mapped on the mouse reference genome (version 37), allowing up to 2 mismatches (single base insertion, deletion, or substitution), and retained only if it had a single best position genome-wide. Each tag was shifted downstream by half the effective length of the sonicated sequenced fragments, measured as the maximum of the genome-wide correlation function between hits to the sense and antisense strands of the chromosomes, and represented by an elementary Gaussian with an area of 1 and s of 100 bp, which dampens the sampling fluctuations and introduces a controlled level of fuzziness and “smoothness”. Summing these elementary Gaussians yields a smoothed tag density. Regions where the density locally exceeds a given threshold are analyzed. The number of tags was measured after subtracting the local tags from the matched IgG experiment. If the tag number exceeded a second threshold, it was scored as a peak. Regions with an IgG peak were considered non-specific and eliminated. The peak height indicates the strength of protein binding. The position of the maximum of the peak (i.e., the maximum of the probability of binding the protein) is expected to coincide with the binding motif. The width covered by the peak (typically 200-600 bp) is the region protected by the protein or protein complex. Often, in large peaks, one can distinguish sub-peaks that are expected to correspond to the binding of multiple proteins. When multiple proteins bind to overlapping sequences, their peaks are clustered to generate a broader composite binding site.

source_name: murine Irf4 deficient CD4+ T

growth_protocol: CD4+ T cells were isolated from mouse spleen using anti-CD4-magnetic beads (Miltenyi). For pre-activation of CD4+ T cells, cells were stimulated with 3 μg/ml plate-bound anti-CD3 and 1 μg/ml soluble anti-CD28 for 3 days, and rested for 24 h in fresh RPMI medium.

extract_protocol: Chromatin from approximately 2x10^7 cells were used for each ChIP experiment. End repair for ChIP fragments was performed using PNK and Klenow enzyme, followed by treatment with Taq polymerase.  Sequencing adaptors were ligated to the repaired ends and ChIP DNA was amplified using adaptor primers for 17 cycles.  Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.

treatment_protocol: CD4+ T cells were treated with IL-21 (100ng/ml) for 1 hour.

tag: antibody

tag: stimulation

value: pre IL21

tag: genotype/variation

value: IRF4 KO


title: Drosophila-S2-RNAseq2

description:
Gene expression profile of WT S2 cells
Processed_data_file: RNA-S2-WT-2_align.txt
Processed_data_file: RNA-S2-WT-2_geneRPKM.txt
Raw_data_file: run12-s_6_sequence.fastq
Raw_data_file: run18-s_4_sequence.fastq

value: control (WT)


title: STAT3 bound pre IL21 in IRF4 KO mice, first exp

description: Chromatin IP against STAT3


title: IRF4 bound post IL21 in IRF4 KO mice

description: Chromatin IP against IRF4

value: post IL21


title: Drosophila-S2-RNAseq1

description:
Gene expression profile of WT S2 cells
Processed_data_file: RNA-S2-WT-1_align.txt
Processed_data_file: RNA-S2-WT-1_geneRPKM.txt
Raw_data_file: run12-s_3_sequence.fastq
Raw_data_file: run18-s_1_sequence.fastq


title: GIgG bound post IL6

description: Chromatin IP against IgG

source_name: murine CD4+ T

value: wildtype

value: GIgG

value: post IL6


title: CMV delta2b in rdr1/2/6 mutant of Arabidopsis thaliana, replicate

city: Riverside

first: Qingfa

last: Wu

address: 900 University Ave

institute: UC Riverside

description:
total small RNAs in systemically infected leaves of A. thaliana
barcode: TAC

library_source: viral RNA

data_processing: All sequences containing perfect match 5' barcode (ATC/CGT/TAC) and at least 6 sucessive perfect-matched nucleotides of  the 3' linker ( CTGTAGGCACCATCAAT / CACTCGGGCACCAAGGA) were kept for later analysis. The barcode and linker sequences were computationally removed by in-house perl script. All trimmed sequences in length of 17~30nt were aligned with CMV genome and the perfect matched reads were used for all further analysis.

organism:
Arabidopsis thaliana
Cucumber mosaic virus (strain FNY)

source_name: leaves of mutant Arabidopsis thaliana infected with CMVf-Δ2b

extract_protocol: Small RNAs of 18- to 28-nt extracted by Trizol from the systemically infected leaves 14 days after inoculation with CMVf-Δ2b were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3′-linker used for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to the 5′ Solexa linker (GUU CAG AGU UCU ACA GUC CGA CGA UC) by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3′-linker (CTGTAGGCACCATCAAT OR CACTCGGGCACCAAGGA ) and the cDNA pool was amplified by PCR and sent for sequencing by the Solexa technology (Illumina). Duplicate libraries were constructed from two independent RNA samples from WT, rdr1, and rdr1 rdr2 rdr6 plants and sequenced by the Solexa platform in Illumina, Inc, and the University of California–Riverside Core Facility, respectively.

tag: a.thaliana genotype

value: rdr1/2/6 mutant

tag: a.thaliana tissue

value: leaves

tag: cmv genotype/variation

tag: cmv strain

value: FNY

tag: collected time

value: 14 days after inoculation


title: STAT3 bound post IL21 in IRF4 KO mice

description: Chromatin IP against STAT3


title: STAT3 bound post IL21 in IRF4 KO mice, second exp

description: Chromatin IP against STAT3


title: STAT3 bound post IL21 in IRF4 KO mice, third exp

description: Chromatin IP against STAT3


title: GIgG bound post IL21 in B cells

description: Chromatin IP against IgG

source_name: B cells


title: IRF4 bound pre IL21 in IRF4 KO mice

description: Chromatin IP against IRF4


title: Drosophila-S2-DNAseq

description:
DNA sequencing for copy number variation
Processed data file: DNA-S2_align.txt
Raw file: run19-s_5_sequence.fastq
Raw file: run19-s_6_sequence.fastq
Raw file: run19-s_7_sequence.fastq
Raw file: run19-s_8_sequence.fastq

data_processing: Alignment: Sequence reads were mapped to the Drosophila reference genome [i.e., the April 2006 Drosophila melanogaster draft assembly (BDGP Release 5, dm3)] using the Illumina Genome Analyzer Pipeline. All unique mapped reads with two or fewer mismatches were retained.

extract_protocol: Genomic DNA from wild type S2 cells was extracted using Qiagen genomic DNA kit (Qiagen, Valencia CA). Approximately 2 µg of purified genomic DNA was randomly fragmented to less than 1000b bp using the bioruptor UCD 200 (Diagenode, Sparta NJ).

tag: strain

value: WT


title: IgG bound post IL21 in WT, quar

description: Chromatin IP against IgG

value: IgG


title: IgG bound post IL21 in B cells

description: Chromatin IP against IgG


title: IgG bound post IL21, ter

description: Chromatin IP against IgG


title: Drosophila-S2-mofRNAi-RNAseq2

description:
Gene expression profile of mof RNAi treated S2 cells
Processed_data_file: RNA-S2-mof-2_align.txt
Processed_data_file: RNA-S2-mof-2_geneRPKM.txt
Raw_data_file: run12-s_8_sequence.fastq
Raw_data_file: run17-s_8_sequence.fastq


title: Small RNAs from Miscanthus leaves

status: Public on Jan 27 2010

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

description:
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.
MGI1

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5'-TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artefacts.

organism: Miscanthus x giganteus

source_name: Leaves

extract_protocol: Total RNA was extracted with the Plant RNA Purification Reagent (Invitrogen). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).

tag: tissue


title: STAT3 bound post IL21 in WT, quar

description: Chromatin IP against STAT3


title: STAT3 bound post IL21 in WT, cinq

description: Chromatin IP against STAT3


title: IgG bound post IL2 dup

description: Chromatin IP against IgG

value: post IL2


title: IgG bound post IL6

description: Chromatin IP against IgG


title: STAT3 bound post IL21 dup, seq 2

description: Chromatin IP against STAT3


title: STAT3 bound pre IL21 in WT, 4th experiment

description: Chromatin IP against STAT3


title: STAT3 bound pre IL21 dup, seq 1

description: Chromatin IP against STAT3


title: STAT3 bound pre IL21 in WT, ter

description: Chromatin IP against STAT3


title: STAT3 bound pre IL21 dup, seq 2

description: Chromatin IP against STAT3


title: STAT3 bound pre IL21, seq 2

description: Chromatin IP against STAT3


title: STAT3 bound post IL21 in WT, ter

description: Chromatin IP against STAT3


title: STAT3 bound post IL21, seq 1

description: Chromatin IP against STAT3


title: IRF4 bound post IL21 dup, seq 2

description: Chromatin IP against IRF4


title: STAT3 bound pre IL21, seq 1

description: Chromatin IP against STAT3


title: Small RNAs from Miscanthus flowers

description:
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.
MGI2

source_name: Flowers

value: flower


title: Small RNAs from Miscanthus rhizomes

description:
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.
MGI3

source_name: Rhizomes

value: rhizomes (apical tip portion)


title: STAT3 bound post IL21, seq 2

description: Chromatin IP against STAT3


title: STAT3 bound post IL21 dup, seq 1

description: Chromatin IP against STAT3


title: IRF4 bound post IL21 dup, seq 1

description: Chromatin IP against IRF4


title: IRF4 bound post IL21, seq 2

description: Chromatin IP against IRF4


title: IRF4 bound pre IL21 dup, seq 2

description: Chromatin IP against IRF4


title: IRF4 bound post IL21, seq 1

description: Chromatin IP against IRF4


title: IRF4 bound pre IL21 dup, seq 1

description: Chromatin IP against IRF4


title: CMV delta2b in rdr1 mutant of Arabidopsis thaliana

description:
total small RNAs in systemically infected leaves of A. thaliana
barcode: CGT

value: rdr1 mutant


title: IRF4 bound pre IL21, seq 1

description: Chromatin IP against IRF4

value: pre IL21


title: IRF4 bound pre IL21, seq 2

description: Chromatin IP against IRF4


status: Public on Jan 07 2010

city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: MRE-Seq analysis of breast progenitor enriched cell from RM035 (HS1283) using Illumina Genome Analyzer II
library name: HS1283
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: N/A ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-400 bp
****************
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: GSM493626_Breast_Stem_Cells_Individual_2.mre-seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast_Stem_Cells_Individual_2.MRE-Seq.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells, Individual 2, MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in Breast Stem Cells, Individual 2, 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.1881
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM493626_UCSF-UBC.Breast_Stem_Cells.MRE-Seq.RM035.bed
ANALYSIS ALIAS: HS1283-2_3061PAAXX-HS1283-2_305Y8AAXX-HS1283-2_42ENEAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Stem Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Breast Stem Cells, Donor RM035 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.4199
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 96.86
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 28

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

ANALYSIS FILE NAME: GSM493626_UCSF-UBC.Breast_Stem_Cells.MRE-Seq.RM035.wig
ANALYSIS ALIAS: HS1283-2_3061PAAXX-HS1283-2_305Y8AAXX-HS1283-2_42ENEAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Breast Stem Cells, Donor RM035 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.4171
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BSC MRE 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Stem Cells MRE-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 96.86
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 28

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

extract_protocol: library construction protocol: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Breast

tag: histological type

value: Progenitor enriched cell

tag: is tumor

value: No

value: primary cell

value: breast progenitor enriched cell


description:
design description: MRE-Seq analysis of breast luminal epithelial cell from RM035 (HS1281) using Illumina Genome Analyzer II
library name: HS1281
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: N/A ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-400 bp
****************
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: GSM493620_Breast-Luminal-Epithelial-Cells-Individual-2.mre-seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast_Luminal_Epithelial_Cells_Individual_2.MRE-Seq.Level2.3
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells, Individual 2, MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in Breast Luminal Epithelial Cells, Individual 2, 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.1886
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM493620_UCSF-UBC.Breast_Luminal_Epithelial_Cells.MRE-Seq.RM035.bed
ANALYSIS ALIAS: HS1281-2_305Y8AAXX-HS1281-2_42THTAAXX-HS1281-2_3061PAAXX-HS1281-2_42EMFAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Breast Luminal Epithelial Cells, Donor RM035 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.4200
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 97.14
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 32

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

ANALYSIS FILE NAME: GSM493620_UCSF-UBC.Breast_Luminal_Epithelial_Cells.MRE-Seq.RM035.wig
ANALYSIS ALIAS: HS1281-2_305Y8AAXX-HS1281-2_42THTAAXX-HS1281-2_3061PAAXX-HS1281-2_42EMFAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM035 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.4172
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BLEC MRE 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Luminal Epithelial Cells MRE-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 97.14
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 32

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

value: Luminal epithelial cell

value: breast luminal epithelial cell


description:
design description: MRE-Seq analysis of breast luminal epithelial cell from RM037 (HS1155) using Illumina Genome Analyzer II
library name: HS1155
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-400 bp
****************
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: GSM493617_Breast_Luminal_Epithelial_Cells_Individual_1.mre-seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast_Luminal_Epithelial_Cells_Individual_1.MRE-Seq.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells, Individual 1, MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in Breast Luminal Epithelial Cells, Individual 1, 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.1876
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM493617_UCSF-UBC.Breast_Luminal_Epithelial_Cells.MRE-Seq.RM037.bed
ANALYSIS ALIAS: HS1155-1_313MYAAXX-HS1155-1_305Y8AAXX-HS1155-1_3061PAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Breast Luminal Epithelial Cells, Donor RM037 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.4204
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 95.59
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM493617_UCSF-UBC.Breast_Luminal_Epithelial_Cells.MRE-Seq.RM037.wig
ANALYSIS ALIAS: HS1155-1_313MYAAXX-HS1155-1_305Y8AAXX-HS1155-1_3061PAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM037 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.4176
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BLEC MRE 37
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Luminal Epithelial Cells MRE-Seq Donor RM037 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 95.59
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 14

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


description:
design description: MRE-Seq analysis of breast myoepithelial cell from RM035 (HS1282) using Illumina Genome Analyzer IIx
library name: HS1282
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: N/A ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-400 bp
****************
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: GSM493624_Breast_Myoepithelial_Cells_Individual_2.mre-seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast_Myoepithelial_Cells_Individual_2.MRE-Seq.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells, Individual 2, MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in Breast Myoepithelial Cells, Individual 2, 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.1879
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM493624_UCSF-UBC.Breast_Myoepithelial_Cells.MRE-Seq.RM035.bed
ANALYSIS ALIAS: HS1282-2_42EMFAAXX-HS1282-2_42THTAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Breast Myoepithelial Cells, Donor RM035 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.4211
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 95.83
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 21

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

ANALYSIS FILE NAME: GSM493624_UCSF-UBC.Breast_Myoepithelial_Cells.MRE-Seq.RM035.wig
ANALYSIS ALIAS: HS1282-2_42EMFAAXX-HS1282-2_42THTAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Breast Myoepithelial Cells, Donor RM035 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.4183
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC MRE 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells MRE-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 95.83
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 21

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

value: Myoepithelial cell

value: breast myoepithelial cell


title: CMV delta2b in rdr1/2/6 mutant of Arabidopsis thaliana

value: rdr1/2/6 mutant

value: leaves

value: FNY

value: 14 days after inoculation


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in IMR90 Cells; renlab.H3K4me3.IMR90-01.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL221
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1731
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121

****************
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: GSM469970_UCSD.IMR90.H3K4me3.UCSD_30WPBAAXX_6.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K4me3.Level1.1
ANALYSIS TITLE: Mapping of IMR90 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1794
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM469970_UCSD.IMR90.H3K4me3.UCSD_301FBAAXX_2.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K4me3.Level1.2
ANALYSIS TITLE: Mapping of IMR90 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1796
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM469970_UCSD.IMR90.H3K4me3.wig
ANALYSIS ALIAS: UCSD.IMR90.H3K4me3.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me3 in the IMR90 cell line 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.1797
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM469970_UCSD.IMR90.H3K4me3.LL221.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the IMR90 Cell Line, Library LL221 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.4408
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.909
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.8482
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.9124
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM469970_UCSD.IMR90.H3K4me3.LL221.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL221 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.4457
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 2
BROWSER_TRACK_NAME: IMR90 H3K4me3 21
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me3 Library LL221 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.909
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.8482
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.9124
POISSON_PERCENTILE: 100

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

source_name: IMR90; renlab.H3K4me3.IMR90-01.01

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

value: IMR90 cells

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

tag: passage

tag: medium

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

value: Female

value: Histone H3K4me3

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam

value: unknown


description:
design description: H3K36me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS1347) using Illumina Genome Analyzer IIx
library name: HS1347
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 35.3 ug
SIZE_FRACTION: 80-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 395432
****************
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: GSM450268_UCSF-UBC.H1.H3K36me3.Run103374Lane6.bam
ANALYSIS ALIAS: UCSF-UBC.H3K36me3.Level1.2.1
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1758
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM450268_UCSF-UBC.H1.H3K36me3.Run104210Lane6.bam
ANALYSIS ALIAS: UCSF-UBC.H3K36me3.Level1.2.2
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1759
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM450268_UCSF-UBC.H1.H3K36me3.wig
ANALYSIS ALIAS: UCSF-UBC.H3K36me3.Level2.2.1
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in the H1 cell line 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.1760
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM450268_UCSF-UBC.H1.H3K36me3.H1EScd2-me3K36-B.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1347-1_42F2TAAXX-HS1347-1_305H8AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H1 Cell Line, Library H1EScd2-me3K36-B 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.4326
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.4111
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3604
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.991
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5974
POISSON_PERCENTILE: 74

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

ANALYSIS FILE NAME: GSM450268_UCSF-UBC.H1.H3K36me3.H1EScd2-me3K36-B.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1347-1_42F2TAAXX-HS1347-1_305H8AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd2-me3K36-B 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.4375
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 2
BROWSER_TRACK_NAME: H1 H3K36me3 B
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K36me3 Library H1EScd2-me3K36-B EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.4111
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3604
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.991
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5974
POISSON_PERCENTILE: 74

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

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: cell line

value: male

value: Embryo ICM

value: Embryonic stem cell

value: No


description:
design description: H3K9me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS1346) using Illumina Genome Analyzer IIx
library name: HS1346
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 35.3 ug
SIZE_FRACTION: 80-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab8898
CHIP_ANTIBODY_LOT: 492774
****************
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: GSM450266_UCSF-UBC.H3K9me3.Run103373Lane5.bam
ANALYSIS ALIAS: UCSF-UBC.H3K9me3.Level1.2.1
ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1762
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM450266_UCSF-UBC.H3K9me3.Run104209Lane5.bam
ANALYSIS ALIAS: UCSF-UBC.H3K9me3.Level1.2.2
ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1763
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM450266_UCSF-UBC.H3K9me3.bed.wig
ANALYSIS ALIAS: UCSF-UBC.H3K9me3.Level2.2.1
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9me3 in the H1 cell line 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.1764
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM450266_UCSF-UBC.H1.H3K9me3.H1EScd2-me3K9-B.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1346-1_42F2TAAXX-HS1346-1_305H8AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H1 Cell Line, Library H1EScd2-me3K9-B 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.4327
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.4165
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.3856
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.962
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5888
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM450266_UCSF-UBC.H1.H3K9me3.H1EScd2-me3K9-B.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1346-1_42F2TAAXX-HS1346-1_305H8AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd2-me3K9-B 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.4376
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 2
BROWSER_TRACK_NAME: H1 H3K9me3 B
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K9me3 Library H1EScd2-me3K9-B EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.4165
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.3856
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.962
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5888
POISSON_PERCENTILE: 100

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


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in IMR90 Cells; renlab.H3K27me3.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL223
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1667
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121

****************
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: GSM469968_UCSD.IMR90.H3K27me3.UCSD_30WNVAAXX_1.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K27me3.Level1.1
ANALYSIS TITLE: Mapping of IMR90 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1808
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM469968_UCSD.IMR90.H3K27me3.UCSD_42B3BAAXX_2.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K27me3.Level1.2
ANALYSIS TITLE: Mapping of IMR90 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1810
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM469968_UCSD.IMR90.H3K27me3.UCSD_301FBAAXX_4.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K27me3.Level1.3
ANALYSIS TITLE: Mapping of IMR90 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1812
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM469968_UCSD.IMR90.H3K27me3.UCSD_313BFAAXX_2.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K27me3.Level1.4
ANALYSIS TITLE: Mapping of IMR90 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the IMR90 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1814
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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

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

ANALYSIS FILE NAME: GSM469968_UCSD.IMR90.H3K27me3.wig
ANALYSIS ALIAS: UCSD.IMR90.H3K27me3.Level2.4
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K27me3 in the IMR90 cell line 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.1815
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM469968_UCSD.IMR90.H3K27me3.LL223.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the IMR90 Cell Line, Library LL223 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.4426
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 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.6623
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.386
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9888
IROC_PERCENTILE: 92
POISSON_SCORE: 0.6631
POISSON_PERCENTILE: 96

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

ANALYSIS FILE NAME: GSM469968_UCSD.IMR90.H3K27me3.LL223.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL223 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.4524
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 2
BROWSER_TRACK_NAME: IMR90 H3K27me3 23
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K27me3 Library LL223 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.6623
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.386
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9888
IROC_PERCENTILE: 92
POISSON_SCORE: 0.6631
POISSON_PERCENTILE: 96

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

value: IMR90 cells

value: genomic DNA

value: ATCC

value: Histone H3K27me3

value: Upstate