title: MLA1 expressing plants challenged with Bgh K1 isolate at 24hpi, replicate 2

description:
B12_K1_24hpi_2
PolyA-enriched RNA

value: leaves

value: Blumeria graminis f. sp. hordei isolate K1


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 18hpi, replicate 1

status: Public on Nov 22 2012

type: SRA

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

description:
pps_K1_18hpi_1
PolyA-enriched RNA

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Sequenced reads were mapped to the TAIR10 whole genome using tophat v1.3.2 with parameters -p 12 -a 10 -g 5 --library-type fr-unstranded -G TAIR10_GFF3_genes.gff
Read counts per gene per sample were obtained using the bedTools suite v2.13.2 (function coverageBed).
Genome_build: TAIR10
Supplementary_files_format_and_content: CompleteCountTable_At.txt: Tab-delimited text file including raw read counts per gene for each sample. This file is linked to the Series record as a supplementary file.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Bgh K1-infected pps leaves, 18hpi

growth_protocol: Growth of plants and pathogens was performed as described in V. Lipka, et al., Science 310, 1180 (2005) (PMID 16293760).

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). RNA-seq libraries were prepared from an input of 4 ug total RNA according to recommendations of the supplier (TruSeq RNA sample preparation v2 guide, Illumina). Libraries were quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq 2000. Library construction and sequencing were performed by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de).

treatment_protocol: Inoculation of the pathogens was perfomed as described in V. Lipka, et al., Science 310, 1180 (2005) (PMID 16293760).

tag: plant strain

value: Columbia-0 pen2-1 pad4-1 sag101-2 mutant

tag: tissue

tag: fungal isolate

tag: virulence

value: virulent

tag: time

tag: virulence_time (as used for model)


title: TF2B_ChIPSeq

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description:
Chromatin IP against TF2B, followed by high-througput sequencing
TF2B

library_source: genomic

data_processing:
Basecalls performed using Bustard from the Illumina Genome Analyzer II
Alignment : The sequenced tags were mapped onto the unmasked genome build hg18 using the fetchGWI software and allowing 1000 repeats on the genome. The tags mapping more than once onto the genome were then attributed a weight corresponding to the number of times the tag was sequenced divided by the number of genomic matches . The files with these weighted repeated tags as well as the unique tags were then used for peak detection
Peak detection : peaks were determined with the sissrs software (www.rajajothi.com/sissrs/). Peaks mapping in satellite and micro-satellite repeats and peaks mapping in 18 and 28S rRNA sequences, were eliminated from the analysis. This first analysis resulted in the identification of peaks.
For the SNAP subunits, we divided the genome into 200 nucleotide bins, counted tags obtained for each of the four SNAPc subunits analyzed, and and retained only bins displaying an enrichment for at least two of the SNAPc subunits. Bins were considered positive only if the tag number in bin reached at least the minimum tag count determined by sissrs for enriched regions with a 0.001 false discovery rate as the one used in sissrs set at the default parameters. Only the genomic regions containing POLR2B and GTF2B, or POLR3D and BRF2, sissrs peaks as well as a bin positive for two SNAPc subunits within 100 nucleotides of the polymerase sissrs peak were retained.
The obtained genomic loci were then quantified using the protocol described in PMID:20413673.
Genome_build: hg18
Supplementary_files_format_and_content: The Processed files include the weighted tags counts per nucleotide calculated in a window of minus 150 to plus 150 nucleotides around each SNAPc gene. For the polymerase III and polymerase II (RPC4 and RPB2) files, tags were neither centered nor extended. For the transcription factors (all other files), tags were extended to the insert length given by the bioanalyzer (minus the adapters length), and tags count per nucleotide was calculated on the whole insert length. In both cases, the nucleotide position score is the sum of the tags scores at that position, where the score for each tag is given by the ratio between the number of times the tag has been sequenced and the number of times the tag matches on the genome. For RPB2, the additional file called “RPB2_perfect_matches_on_SNAPc_genes.bedGraph” contains only the tags with one unique and perfect match on the genome.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The chromatin immunoprecipitations (ChIPs) were performed with exponentially growing IMR90HTert or HeLa cells. IMR90HTert cells are diploid fibroblast-like cells established from fetal female lung tissue and transfected with the gene coding for human Telomerase reverse Transcriptase. HeLa cells were grown as spinners in a flask.

extract_protocol: At least 10 ng was used to prepare sequencing libraries with the Illumina ChIP-Seq Sample Preparation Kit according to the protocol supplied with the reagents. Aliquots of the sequencing libraries were then loaded into Genome Analyzer flow cells and sequenced with the Genome Analyzer or Genome Analyzer II (Illumina) using the 36 Cycle Sequencing Kit v2 (Catalog number FC-204-2036). As controls, aliquots of the input DNA (collected after the crosslinking and sonication steps) were also subjected to ultra high throughput sequencing.

treatment_protocol: Both IMR90HTert and HeLa cells were cross-linked for seven minutes in 1% formaldehyde.  Following cell and nuclear lysis as described, extracted chromatin was sonicated to an average size of 200-600 base pairs and used for immunoprecipitations.  The sonicated chromatin was mixed with various antibodies and incubated on a rotating wheel overnight at 4˚C.  Immunoprecipitated material was recovered by addition of 10 ul of protein A agarose beads (pre-blocked with 10ug/ml of BSA and salmon sperm DNA) and incubation for 1 h at room temperature on a rotating wheel.  The beads were then washed with dialysis and wash buffer [PMID 17140114]

tag: cell line

tag: cell type

value: diploid fibroblast-like cells

tag: tissue origin

value: fetal female lung

tag: transfected with

value: human Telomerase reverse Transcriptase gene

tag: chip antibody

value: polyclonal rabbit antibody CS369 #10, 11

tag: chip antibody reference

value: Hu, P., Wu, S., and Hernandez, N. (2003) Mol. Cell 12, 699-709


title: RPB2_ChIPSeq

description:
Chromatin IP against RPB2, followed by high-througput sequencing
RPB2_1 and RPB2_2
The 'RPB2_perfect_matches_on_SNAPc_genes.bedGraph' file contains only the reads with unique and perfect matches on the genome whereas the 'RPB2_on_SNAPc_genes.bedGraph' file contains all the tags with up to 500 matches on the genome.

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 12hpi, replicate 3

description:
pps_K1_12hpi_3
PolyA-enriched RNA

source_name: Bgh K1-infected pps leaves, 12hpi


title: SNAP45_ChIPSeq_175-225

description:
MR90HTert stable cell line expressing the human SNAP45 fused to the Tobacco etch virus (TEV), the Flag epitope, and the biotin acceptor domain (BAD) growing DMEM, 10% FBS, and 0,1% of non essential amino acids, were cross-linked for 7 min by addition of 1% of Formaldehyde (Sigma, Cat. No. F-1635). Crosslinking was stopped by addition of glycine to a final concentration of 0.125 M, followed by 5-min incubation at room temperature. Fixed cells were washed twice with cold PBS and harvested in cold PBS containing protease inhibitors. Cells were pelleted by centrifugation, suspended in 1mL of Cell lysis buffer (5mM Pipes at pH 8.0, 0.5% NP40, 85mM KCl, 1mM DTT and protease inhibitors (sigma N° 8340)), and incubated for 10 min on ice. Cells were then pelleted by centrifugation, resuspended in 200 µL of Nuclear lysis buffer (50mM Tris-Cl pH 8.0, 10mM EDTA, 1% SDS, 1mM PMSF, 1mM DTT and protease inhibitors) and incubated for 30min at room temperature. Nuclear extraction was diluted 1:5 with salty buffer (250mM NaCl, 25mM Hepes pH 7.9, 2mM DTT, 0,5 mM PMSF). DNA was disrupted by sonication, yielding genomic DNA fragments  of a size of 200-600 bp. Crude chromatin was cleared by centrifugation at 16’000xg for 20 minutes. 500µl of cleared chromatin was next incubated overnight with 30µl of Dynabeads M280-streptavidin (Invitrogen N° 112.05D). Beads were then washed twice with SDS buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 10.5mM PMSF, 2% SDS) followed by two washes with IP wash buffer (100mM Tris at pH 8.0, 500mM LiCl, 1% NP-40, 1% deoxycholic acid), and two washes with TEV-buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 0.5mM PMSF).  Samples were then resuspended in 100µl TEV-buffer containing 1unit of TEV enzyme; incubated for 3 hours at room temperature. Beads were concentrate with a magnet and supernatant was collected as first elution. 100µl of TEV-buffer was added to beads and supernatant was pooled with the first elution, then 2µl of DNase-free RNase-A (10mg/ml) was added and samples were decrosslinked by an overnight incubation at 65 °C. Proteinase K and 5X Proteinase K buffer (50mM Tris at pH 7.5, 25mM EDTA, 1.25% SDS) were then added to the samples and incubate at 37°C for 2 hours. DNA from the samples was purified using Gene PCR cleanup columns (Sigma, NA-1020). Purified DNA was recovered in 50µl of elution buffer.  MR90HTert stable cell line expressing the human SNAP45 fused to the Tobacco etch virus (TEV), the Flag epitope, and the biotin acceptor domain (BAD) growing DMEM, 10% FBS, and 0,1% of non essential amino acids, were cross-linked for 7 min by addition of 1% of Formaldehyde (Sigma, Cat. No. F-1635). Crosslinking was stopped by addition of glycine to a final concentration of 0.125 M, followed by 5-min incubation at room temperature. Fixed cells were washed twice with cold PBS and harvested in cold PBS containing protease inhibitors. Cells were pelleted by centrifugation, suspended in 1mL of Cell lysis buffer (5mM Pipes at pH 8.0, 0.5% NP40, 85mM KCl, 1mM DTT and protease inhibitors (sigma N° 8340)), and incubated for 10 min on ice. Cells were then pelleted by centrifugation, resuspended in 200 µL of Nuclear lysis buffer (50mM Tris-Cl pH 8.0, 10mM EDTA, 1% SDS, 1mM PMSF, 1mM DTT and protease inhibitors) and incubated for 30min at room temperature. Nuclear extraction was diluted 1:5 with salty buffer (250mM NaCl, 25mM Hepes pH 7.9, 2mM DTT, 0,5 mM PMSF). DNA was disrupted by sonication, yielding genomic DNA fragments  of a size of 200-600 bp. Crude chromatin was cleared by centrifugation at 16’000xg for 20 minutes. 500µl of cleared chromatin was next incubated overnight with 30µl of Dynabeads M280-streptavidin (Invitrogen N° 112.05D). Beads were then washed twice with SDS buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 10.5mM PMSF, 2% SDS) followed by two washes with IP wash buffer (100mM Tris at pH 8.0, 500mM LiCl, 1% NP-40, 1% deoxycholic acid), and two washes with TEV-buffer (20mM Hepes pH 7.9, 200mM NaCl, 0.5mM EDTA, 10% glycerol 1mM DTT, 0.5mM PMSF).  Samples were then resuspended in 100µl TEV-buffer containing 1unit of TEV enzyme; incubated for 3 hours at room temperature. Beads were concentrate with a magnet and supernatant was collected as first elution. 100µl of TEV-buffer was added to beads and supernatant was pooled with the first elution, then 2µl of DNase-free RNase-A (10mg/ml) was added and samples were decrosslinked by an overnight incubation at 65 °C. Proteinase K and 5X Proteinase K buffer (50mM Tris at pH 7.5, 25mM EDTA, 1.25% SDS) were then added to the samples and incubate at 37°C for 2 hours. DNA from the samples was purified using Gene PCR cleanup columns (Sigma, NA-1020). Purified DNA was recovered in 50µl of elution buffer.
SNAP45_76_r41_l2_175-225
The processed data 'SNAP45_on_SNAPc_genes.bedGraph' available on Series records


title: MLA1 expressing plants challenged with Bgh K1 isolate at 12hpi, replicate 2

description:
B12_K1_12hpi_2
PolyA-enriched RNA

source_name: Bgh K1-infected B12 leaves, 12hpi

value: Columbia-0 pen2-1 pad4-1 sag101-2 mutant expressing MLA1-HA

value: avirulent


title: MLA1 expressing plants challenged with Bgh K1 isolate at 24hpi, replicate 1

description:
B12_K1_24hpi_1
PolyA-enriched RNA

source_name: Bgh K1-infected B12 leaves, 24hpi


title: MLA1 expressing plants challenged with Bgh K1 isolate at 12hpi, replicate 3

description:
B12_K1_12hpi_3
PolyA-enriched RNA


title: BRF2_ChIPSeq

description:
Chromatin IP against Brf2, followed by high-througput sequencing
BRF2_76_r12_l1

value: polyclonal rabbit antibody 940.505 #74

value: Rabbit anti-peptide antibody raised against anti-Brf2 peptides C-TYSRSTGENEQVSR-coNH2 (position 54-67) and C-IEQYLRTPQEVRDF-coNH2 (position 389-482):Faresse, N., et al. PLoS Genetics, submitted


title: RPC4_ChIPSeq_2

description:
Chromatin IP against RPC4, followed by high-througput sequencing
RPC4_36_r14_l1
The processed data 'RPC4_on_SNAPc_genes.bedGraph' available on Series records


title: MLA1 expressing plants challenged with Bgh K1 isolate at 12hpi, replicate 1

description:
B12_K1_12hpi_1
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh A6 isolate at 24hpi, replicate 1

description:
B12_A6_24hpi_1
PolyA-enriched RNA

source_name: Bgh A6-infected B12 leaves, 24hpi

value: Blumeria graminis f. sp. hordei isolate A6


title: MLA1 expressing plants challenged with Bgh A6 isolate at 12hpi, replicate 3

description:
B12_A6_12hpi_3
PolyA-enriched RNA

source_name: Bgh A6-infected B12 leaves, 12hpi


title: MLA1 expressing plants challenged with Bgh A6 isolate at 24hpi, replicate 2

description:
B12_A6_24hpi_2
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh A6 isolate at 24hpi, replicate 3

description:
B12_A6_24hpi_3
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh A6 isolate at 12hpi, replicate 2

description:
B12_A6_12hpi_2
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh A6 isolate at 12hpi, replicate 1

description:
B12_A6_12hpi_1
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh K1 isolate at 18hpi, replicate 1

description:
B12_K1_18hpi_1
PolyA-enriched RNA

source_name: Bgh K1-infected B12 leaves, 18hpi


title: MLA1 expressing plants challenged with Bgh K1 isolate at 18hpi, replicate 3

description:
B12_K1_18hpi_3
PolyA-enriched RNA


title: WT (Col-0)_sRNA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description: From the Ecker lab metadata: All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23C under a 16-hour light/8-hour dark cycle. Immature (unopened) flower buds were collected and frozen in liquid nitrogen. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Immediately following RNA precipitation, the flow through from the anion-exchange chromatography column was further precipitated in another 2.5 volumes of 100% ethanol (smRNA fraction). The smRNA fraction was further purified by a phenol-chloroform extraction and an additional ethanol precipitation. Small RNAs were resolved by electrophoresis of 2.5 mg of the smRNA fraction and 7.5 mg of total RNA on 15% polyacrylamide gels containing 7 M urea in TBE buffer (45 mM Tris-borate, pH 8.0, and 1.0 mM EDTA). A gel slice containing RNAs of 15 to 35 nucleotides (based on the 10 base pair ladder size standard (Invitrogen, Carlsbad, CA)) was excised and eluted in 0.3 M NaCl rotating at room temperature for 4 hours. The eluted RNAs were precipitated using ethanol and resuspended in diethyl pyrocarbonatetreated deionized water.

data_processing: Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances. The data were matched to the Arabidopsis genome (TAIR v9) as well as the transgenes described in Kanno et al. (2008). Of the 4,510,985 total reads from transgenic wild type and 2,327,100 from the ago6-4 mutant, 2,846,684 (wt) and 1,261,189 (ago6-4) reads matched the genome, excluding 362,400 (wt) and 207,909 (ago6-4) that matched tRNA, rRNA, snRNA or snoRNAs.

source_name: Mixed stage inflorescence tissue

growth_protocol: Seeds were germinated on soil and grown for approximately 5 weeks at 22-23°C under a light cycle of 8 hours dark, 16 hours light. Mixed stage floral inflorescences (inflorescence meristem and floral buds to stage 12) were harvested between 9 and 12 AM and stored in 50 ml Falcon tubes at -80°C.

extract_protocol: Total RNA was isolated from mixed stage inflorescence tissues of wild type Col-0, mutant rdr2 and mutant nrpd1 using TRIzol reagent (Invitrogen). Total RNA (200 ug) for each sample was used to construct the small RNA libraries as described previously (Lu et al., 2007) but with different adapters. The RNA oligos (Dharmacon) used for small RNA ligations were as follows: 5' RNA Adapter (5'OH-GUUCAGAGUUCUACAGUCCGACGAUC-OH 3’) and 3' RNA Adapter: (5'pUCGUAUGCCGUCUUCUGCUUGUidt 3’; p, phosphate; idT, inverted deoxythymidine). Libraries were sequenced using Illumina's sequencing-by-synthesis technology following the manufacturer's protocols at the Delaware Biotechnology Institute.

tag: genotype/variation

value: wild type Col-0 plant

tag: ecotype


title: nrpd1 rdr2_sRNA

description: sRNA library constructed from Arabidopsis nrpd1a-4 mutant inflorescence tissues including mix-stages of flowers and inflorescence stems. Materials was collected on 06/27/09 from 6-8-week-old plants grown under 16hr-day condition at 23 C

value: nrpd1a-4 mutant (PolIV mutant)


title: MLA1 expressing plants challenged with Bgh A6 isolate at 18hpi, replicate 3

description:
B12_A6_18hpi_3
PolyA-enriched RNA

source_name: Bgh A6-infected B12 leaves, 18hpi

value: leaves


title: MLA1 expressing plants challenged with Bgh A6 isolate at 18hpi, replicate 2

description:
B12_A6_18hpi_2
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh K1 isolate at 18hpi, replicate 2

description:
B12_K1_18hpi_2
PolyA-enriched RNA

value: Blumeria graminis f. sp. hordei isolate K1


title: MLA1 expressing plants challenged with Bgh A6 isolate at 6hpi, replicate 2

description:
B12_A6_6hpi_2
PolyA-enriched RNA

source_name: Bgh A6-infected B12 leaves, 6hpi


title: MLA1 expressing plants challenged with Bgh K1 isolate at 6hpi, replicate 1

description:
B12_K1_6hpi_1
PolyA-enriched RNA

source_name: Bgh K1-infected B12 leaves, 6hpi


title: MLA1 expressing plants challenged with Bgh K1 isolate at 6hpi, replicate 3

description:
B12_K1_6hpi_3
PolyA-enriched RNA


title: MLA1 expressing plants challenged with Bgh A6 isolate at 6hpi, replicate 3

description:
B12_A6_6hpi_3
PolyA-enriched RNA


title: 2',3'-cyclic phosphate-terminated RNA, Ski2Δ +DTT Technical Rep 2

status: Public on Nov 21 2012

city: San Francisco

first: Philipp

last: Kimmig

state: CA

address: Genentech Hall N316, 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: 2',3'-cyclic phosphate-terminated RNA

data_processing:
Basecalls performed using CASAVA version 1.4
The resulting sequences were aligned using the following method: the linker sequences at the 3’ends were removed prior to alignment.
The SOAP2.20 was used to align the sequence reads (allowing no more than 2 total mismatches)
Reads after linker removal were aligned against a library of S. pombe rRNA and tRNA sequences. Reads with any alignment against rRNA and tRNA were eliminated from further analysis.
the none-rRNA and none-tRNA reads were aligned against the S. pombe genomic sequences.
reads with no alignment against S. pombe genomics sequences were re-aligned against the library of pombe processed protein-coding transcripts.
Genome_build: Recent genome build (09/05/2011) from the PomBase
Supplementary_files_format_and_content: wig

organism: Schizosaccharomyces pombe

source_name: Ski2Δ +DTT

growth_protocol: Cells were cultured in YE5S media (rich media). Samples were taken from mid-log growing cells.

extract_protocol: Total RNA was extracted from cells using hot phenol method. PolyA+ mRNA were enriched by two sequential rounds of oligo-dT (Invitrogen) selection. rRNA depletion was performed by depletion of ll RNA smaller than 200nt (mirVana miRNA Purification Kit (Ambion) followed by two rounds of subtractive hybridization using Ribominus EukaryoteKit for RNA-seq (Invitrogen). To sequence 2',3'-cyclic phosphate cleavage products tRNA ligase was used to selectively ligate an RNA linker to all 2',3'-cyclic phosphates in total RNA. Deep-sequencing libraries were constructed as described in Ingolia et al, 2011. To capture 2',3'cyclic-phosphate 3' ends the libraries were constructed according to Schutz et al., 2010.

treatment_protocol: Samples were taken after treatment with 2mM DTT for 1 hour.

tag: stress

value: stress (+DTT)


title: MLA1 expressing plants challenged with Bgh A6 isolate at 6hpi, replicate 1

description:
B12_A6_6hpi_1
PolyA-enriched RNA

tag: plant strain

value: virulent


title: 2',3'-cyclic phosphate-terminated RNA Ire1Δ/Ski2Δ +DTT Technical Rep1

description: 2',3'-cyclic phosphate-terminated RNA

source_name: Ire1Δ/Ski2Δ +DTT


title: mRNA enriched, ire1Δ +DTT (rRNA depleted)

description:
total RNA (rRNA depleted)
mRNA enriched from total RNA by removing ribosomal RNA

source_name: Ire1Δ -DTT


title: mRNA enriched, WT +DTT Rep 2 (rRNA depleted)

source_name: WT +DTT

value: WT


title: RPC4_ChIPSeq_1

description:
Chromatin IP against RPC4, followed by high-througput sequencing
RPC4_36_r13_l5
The processed data 'RPC4_on_SNAPc_genes.bedGraph' available on Series records

value: diploid fibroblast-like cells

value: fetal female lung


title: 2',3'-cyclic phosphate-terminated RNA Ire1Δ/Ski2Δ +DTT Technical Rep2

description: 2',3'-cyclic phosphate-terminated RNA


title: MLA1 expressing plants challenged with Bgh K1 isolate at 6hpi, replicate 2

description:
B12_K1_6hpi_2
PolyA-enriched RNA

tag: tissue


title: MLA1 expressing plants challenged with Bgh A6 isolate at 18hpi, replicate 1

description:
B12_A6_18hpi_1
PolyA-enriched RNA

tag: fungal isolate


title: 2',3'-cyclic phosphate-terminated RNA, Ski2Δ +DTT Technical Rep 1

description: 2',3'-cyclic phosphate-terminated RNA


title: polyA+ enriched mRNA, Ire1Δ +DTT Rep 2

description: polyA+ RNA

molecule: polyA RNA


title: mRNA enriched, WT -DTT Rep 2 (rRNA depleted)

source_name: WT -DTT

value: control (-DTT)


title: polyA+ enriched mRNA, WT +DTT Rep 2

description: polyA+ RNA


title: polyA+ enriched mRNA, WT -DTT Rep 2

description: polyA +RNA


title: polyA+ enriched mRNA, WT +DTT Rep 1

description: polyA+ RNA


title: polyA+ enriched mRNA, Ire1Δ +DTT Rep 1

description: polyA+ RNA


title: polyA+ enriched mRNA, WT -DTT Rep 1

description: polyA+ RNA


title: EurFemale-R2

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

institute: University of Munich

data_processing:
Standard Illumina pipeline using Bustard for basecalling
Illumina sequence reads were mapped to the reference D. melanogaster transcriptome (FlyBase release 5.43) using Stampy (version 1.0.17) and setting --substitutionrate=0.01
Expression was quantified on a “per gene” basis. For this, if a sequence read mapped to one or more transcripts of the same gene, it was counted as one “hit” for that gene and all subsequent analyses were performed at the gene level. For calculations of RPKM, the length of the longest transcript of each gene was used
Genome_build: dmel_r5.43
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: All flies were maintained on standard cornmeal-molasses medium at 22° with a 14 h light:10 h dark cycle

extract_protocol:
Total RNA extraction and DNase I digestion were performed using the MasterPure RNA Purification Kit (Epicentre)
Poly-A mRNA was purified and fragmented by sonication. First strand single end cDNA was synthesized using random primers. Eight tagged libraries were generated, pooled and run on two lanes of a HiSeq 2000 sequencer (Illumina) to generate single reads of 50 bases

treatment_protocol: Adult flies aged 2–4 days were anesthetized on ice and brains were dissected in 1xPBS (phosphate buffered saline) and stored in RNAlater (Qiagen) to prevent RNA degradation

tag: Sex

value: female

tag: population

value: Europe (The Netherlands)

tag: age

value: 2-4 days


title: EurMale-R1

value: male


title: EurMale-R2


title: rdr2_sRNA

description: Biological replicate of small RNA library constructed from rdr2 mutant (in Col-0 background). Library was constructed by Stacey Simon and sequenced at DBI.

value: rdr2 mutant


title: EurFemale-R1


title: AfrMale-R1

value: Africa (Zimbabwe)


title: AfrFemale-R1


title: AfrFemale-R2


title: AfrMale-R2


title: mRNA enriched, WT -DTT Rep 1 (rRNA depleted)


title: mRNA enriched, WT +DTT Rep 1 (rRNA depleted)


title: FAIRE

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

data_processing:
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/) on 1/15/10.
Reads were aligned to mm9 or an in silico constructed version of the Cast genome using Bowtie.
SNP-containing reads were extracted using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BED files were generated from mm9 alignments, and reported read ends reflect average fragment size of corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.

organism: Mus musculus

source_name: F1 C/B trophoblast stem cells

growth_protocol: TSCs were grown under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006). To eliminate feeder cell contamination of TSC RNA and chromatin preparations, TSC cultures grown on sub-lethally irradiated feeders were trypsinized and pre-plated for 40 minutes before transferring to new plates. TSC cultures were then split an additional 2x or 4x before harvesting cells for chromatin and RNA, respectively.

extract_protocol: Strand-specific RNA-Seq libraries were prepared according to (Ingolia NT, et al. Science. 2009; PMID 19213877). ChIP-Seq libraries were prepared according to Illumina instructions. FAIRE-Seq libraries were prepared according to (Giresi PG, Lieb JD. Methods. 2009; PMID 19303047). DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).

value: F1 C/B trophoblast stem cells

tag: data type

value: FAIRE-Seq

tag: parent of origin

value: CAST/EiJ mother X C57BL/6J father

tag: tsc passage number

tag: total obtained reads


title: H4K20me1

tag: antibody

value: H4K20me1 (Active Motif 39175)

tag: cell type

value: ChIP-Seq


title: SP1

value: SP1 (Santa Cruz sc-17824)


title: H3K4me2

value: H3K4me2 (Millipore 07-030)


title: Total H3

value: Total H3 (Abcam ab1791)


title: H3K27ac

value: H3K27ac (Abcam 4729)


title: H3K36me3

value: H3K36me3 (Abcam ab9050)


title: CTCF

value: CTCF (Pugacheva et. al. 2005 Hum Mol Genet 14, 953-965)


title: H3K27me3

value: H3K27me3 (Abcam ab6002)


title: H3K4me1

value: H3K4me1 (Abcam ab8895)


title: Pol II

value: Pol II (Santa Cruz sc-899)


title: DNase

data_processing:
DNase-Seq reads were trimmed prior to all analyses to include only the first 20 bases; the remainder were linker derived (see Song L, et al. Genome Res. 2011; PMID 21750106).
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/) on 1/15/10.
Reads were aligned to mm9 or an in silico constructed version of the Cast genome using Bowtie.
SNP-containing reads were extracted using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BED files were generated from mm9 alignments, and reported read ends reflect average fragment size of corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.

value: DNase-Seq


title: B/C RNA

source_name: F1 B/C trophoblast stem cells

value: F1 B/C trophoblast stem cells

value: strand-specific RNA-Seq

value: C57BL/6J mother X CAST/EiJ father


title: WT rep4

status: Public on Nov 20 2012

city: La Jolla

first: Kun

last: Zhang

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Reads were aligned to the mouse reference genome (mm9) using SOAP2. Libraries processed with the Sigma Imprint kit contain a mixture of fully converted reads and poorly converted reads.
A post-mapping filtering was performed on libraries produced using Sigma Imprint kit to remove unconverted reads based on the criterion that cytosine in the non-CpG context is present at <1.2% in the raw sequencing reads, which ensured a bisulfite conversion rate of >98% in the filtered reads, as estimated by the percentage of un-methylated cytosines on the mitochondrial chromosome (chrM).  Libraries processed with the Zymo lightning kit were fully converted, such that the post-mapping filtering was not necessary.
Data from the two batches of libraries were pooled since global analysis on the two batches yielded consistent results. The global methylation distribution plot was generated using the average methylation levels of CpGs in 10kb non-overlapping bins along the genome.
DMRs (differentially methylated regions) between genotypes were identified by comparing the fraction of methylated cytosines in a sliding window that contains at least six CpG sites based on chi-square test. Repetitive regions were masked prior to DMR calling. Adjacent candidate DMRs (<250bp apart) were joined, and the flanking non-informative CpG sites were further trimmed. We required that there are at least 20 methylated or unmethylated cytosine observations for each sample in a DMR, and the mean methylation difference is at least 0.2. False discovery rate (FDR) was empirically estimated to be ~10%, by applying the same procedure on randomly permutated data sets in which the methylation level of each CpG site was randomly assigned to a different CpG site in the genome while maintaining the global distribution of CpG methylation in each sample.
Identified DMRs were correlated with Tet1 binding sites defined in ESCs 17 by requiring >1bp overlapping using BEDtools (http://code.google.com/p/bedtools/). FDR (false discovery rate) was then tested by 100 permutations of randomly placed DMRs along the genomes. DMRs were assigned to potential target genes and functional characterized by GREAT (http://great.stanford.edu/public/html/splash.php). For visualization, locally smoothed methylation levels were calculated by the Bsseq package with parameter of ns = 40, h = 2000 to obtain high confidence methylation levels for each genotypes
Genome_build: mm9
Supplementary_files_format_and_content: BED formated (tab-delimited) text files include chromosome position and methylation fraction value for each CpG in each sample.

source_name: Primordial germ cells

extract_protocol: gDNA was isolated by Wizard kit (Promega) when > 5,000 cells were available, whereas samples with <5,000 cells were directly lysed in a hypotonic lysis buffer (10mM Tris-HCl pH 7.5; 10mM NaCl; 3mM MgCl2) with 1% NP40 and 0.2 Au/ml protease (Qiagen).  Resultant DNA were fragmented and attached with a 5’ methylated adaptor by Tn5 transposon based tagmentation. A 3’ methylated adaptor was added during gap-filling and ligation.  Tagged DNA fragments were bisulfite converted by Imprint kit (Sigma) or Lightning kit (Zymo), followed by PCR amplification with Illumina adaptors. Barcoded libraries were pooled and sequenced with Illumina Hiseq 2000 instrument.

tag: strain

value: Primordial germ cells

value: embryonic 13.5 day

tag: genotype

value: wild type

tag: input cell number

tag: sequencing info

value: Run 3, multiplexed, Indx79

tag: bisulfite conversion protocol

value: EZ-DNA methylation lightning (Zymo-Research)


title: WT rep3_2

value: Run 3, multiplexed, Indx78


title: C/B RNA

value: F1 C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father


title: Tet1-/- rep4

value: Run 3, multiplexed, Indx80


title: Tet1-/- rep2

value: Run 3, multiplexed, Indx77


title: WT rep1_2

value: Run 2, multiplexed, Indx75

value: Imprint (Sigma-Aldrich)


title: Tet1-/- rep5

value: Run 3, multiplexed, Indx81


title: Tet1-/- rep3

value: Run 2, multiplexed, Indx80


title: Tet1-/- rep1

value: Run 2, multiplexed, Indx79


title: TBP

value: TBP (Abcam ab818)

value: ChIP-Seq


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D1-2-33

city: Vancouver

first: Christopher

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample33_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59

source_name: PBMCs from CF patient 1

extract_protocol: Total RNA was isolated from CF PBMCs using the RNeasy Kit (Qiagen).  500 ng of total RNA was used for library preparation, according to Illumina TruSeq RNA sample preparation guide (Illumina catalogue number FC-122-1002).  Briefly, mRNA was purified using poly-dT beads, then fist strand cDNA and second strand cDNA was  synthesized.  This was followed by end repair, addition of an “A” overhang, and finally ligation of the adapters and unique barcodes, as per the manufacturer’s instructions.  As a final step, DNA enrichment was carried out via a 15-cycle qRT-PCR .  Following quantification, 8 pM of dsDNA was used for cluster generation on a CBOT instrument (Illumina).  RNA sequencing was done on a GAIIx instrument (Illumina), performed as a single read run with 51  amplification cycles.

treatment_protocol: PBMCs were seeded at 2x106 cells/ml in standard tissue-culture treated plates (BD) in R10 media, and were stimulated with flagellin (fliC 250 ng/ml), with or without IDR-1018 (20 μM), then lysed at 4 hr post-treatment for RNA isolation

value: Peripheral blood mononuclear cells

tag: treatment

value: Flagelline at 0.25 ug/ml for 4 hours


title: Untreated PBMC-CF patient D-5

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample13_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59

source_name: PBMCs from CF patient 5

value: Untreated


title: H3K27me3, B/C

value: H3K27me3, B/C (Abcam ab6002)

value: F1 B/C trophoblast stem cells

value: C57BL/6J mother X CAST/EiJ father


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D1-2-27

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample27_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: Treated with 0.25 ug/ml of Flageline and 20 ug/ml of 1018 for 4 hours. PBMC-CF patient D-4

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample12_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59

source_name: PBMCs from CF patient 4

value: Flagelline at 0.25 ug/ml for 4 hours and 20 ug/ml of IDR-1018


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D-5

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample14_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: H3K27me3, C/B #2

value: F1 C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D-4

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample11_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: Untreated PBMC-CF patient D-2

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample4_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59

source_name: PBMCs from CF patient 2


title: Treated with 0.25 ug/ml of Flageline and 20 ug/ml of 1018 for 4 hours. PBMC-CF patient D-2

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample6_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: Untreated PBMC-CF patient D-4

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample10_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: Treated with 0.25 ug/ml of Flageline and 20 ug/ml of 1018 for 4 hours. PBMC-CF patient D-3

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample9_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59

source_name: PBMCs from CF patient 3


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D-3

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample8_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D-2

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample5_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: Treated with 0.25 ug/ml of Flageline and 20 ug/ml of 1018 for 4 hours. PBMC-CF patient D1-2

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample3_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: Untreated PBMC-CF patient D-3

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample7_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: WT rep2

tag: tissue

value: Primordial germ cells

value: embryonic 13.5 day

value: wild type

value: Run 1


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D1-2-32

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample32_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: TSKM-iPS

status: Public on Nov 17 2012

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute Of Biological Sciences, Beijing (NIBS)

data_processing: genome build: mm9/ncbi37

source_name: tet1 sox2 klf4 and c-Myc inducted iPS cells

growth_protocol: R1 ES cells and iPS cells were cultured on mitomycin C treated MEFs in ES medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 15% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF. The O/TSKM 2nd induction cells were derived from O/TSKM iPS mice and cultured with Feeder Medium for 3 passages. On passages 4 the culture were changed to ES Medium with doxycycline for 3 days.

extract_protocol:
In brief, the sonicated genomic DNA was treated using NEBNext master Mix to repair the ends of DNA fragments and ligate the paired-end sequencing specific adaptors (Illumina), the DNA product was then immunoprecipitated and purified. Here we used 500ng ligation product for each IP reaction. Fragments were amplified with 14–16 cycles using adaptor specific primers (Illumina). The final product (300-500bp) was gel-purified (Qiagen) before cluster generation and sequencing.
library strategy: hMeDIP-seq

value: iPS cells

tag: stage or passages

tag: hmedip


title: Untreated PBMC-CF patient D1-2

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample1_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59


title: TSKM 2nd 2#-3D

source_name: OSKM-iPS mouse derived fibroblast cells

value: fibroblast cells

value: p4 supply with doxycycline for 4 days


title: INPUT_DNA

city: Dublin

first: Adrian

middle: P.

last: Bracken

state: Dublin

address: Trinity College, Dublin

department: Genetics

country: Ireland

institute: Trinity College, Dublin

data_processing:
Low quality reads were removed with the BASh command grep -A 3 '^@.*:N:' <input_file> | egrep -v '^-$'”
Reads were aligned using Bowtie on the Galaxy server: “bowtie -q -p 8 -S --phred33-quals /galaxy/data/mm8/mm8full/bowtie_index/mm8full”
Peaks were called on Galaxy using MACS with MFOLD parameter 20 and p-value 10^{-5}
Genome_build: mm8

source_name: Embryonic stem cells

growth_protocol: E14 ES cells were maintained on gelatinized tissue cultures plates, in standard ES media containing LIF

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 150-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Pluripotent ES cells

tag: cell line

value: ES cell line E14

tag: chip antibody


title: PHF19_ChIP_seq

value: custom produced rabbit polyclonal PHF19


title: c-Myc ChIP-Seq at 48hrs Mock Induction

status: Public on Nov 16 2012

city: Philadelphia

first: Kenneth

middle: S.

last: Zaret

state: PA

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

description: DNA immunoprecipitated by c-Myc (R&D # AF3696)

data_processing:
Base-calling: Illumina software version 1.70
Alignment: ELAND, default parameters
Filtering: non-unique aligned sequence tags were discarded down to a single tag
Peak-calling: MACS, MFOLD = 16 using input as background
Filtering: peak sets were filtered to control the FDR at 0.5%
Multiple Transcription Factor Binding Regions (MTFBRs) were called using the algorithm described in the methods
Enrichment: bigWig files for each O, S, K, and M mark were created in the following way. Aligned, unique tags were binned in 25 bp intervals. Each interval count was normalized by RPKM (a measurement of the number of billions of bases sequenced per lane) and a normalized input count for the same interval was subtracted. The resulting interval enrichment scores were written to a bedGraph file, which was turned into a bigWig using the bedGraphToBigWig program from UCSC Genome Browser's online utilities package.
Genome_build: hg18
Supplementary_files_format_and_content: Tag-Aligned Files: BED6 files containing six tab-delimited columns: chromosome, start, stop, tag ID, null, strand (post-filtering for non-unique reads)
Supplementary_files_format_and_content: Peak Files: BED6 files containing six tab-delimited columns: chromosome, start, stop, null, null, strand (contains final, FDR-filtered peak sets only)
Supplementary_files_format_and_content: BigWig Files: 25 bp binned aligned, unique tags (binary data), per-lane normalized and input subtracted
Supplementary_files_format_and_content: DBRs: BED6 files containing the loci of the OSKM differentially-bound regions between 48 hrs reprogrammed fibroblasts and ES cells. A Series-specific BED file containing large, megabase-scale loci where no TFs bind.

source_name: BJ_c-Myc ChIP-Seq_48hr_mockinduction

growth_protocol: The human foreskin fibroblast cell line (BJ) were obtained from the American Type Culture Collection (ATCC # CRL-2522) at passage 6 and cultured in the ATCC-formulated Eagle's Minimum Essential supplemented with 10% FBS at 37ºC and CO2.

extract_protocol: Chromatin was obtained from BJ cells infected with OSKM plus rtTA2M2 lentiviruses and induced with dox for 48hrs. Chromatin fragments associated with Oct4, Sox2, Klf4, or c-Myc were prepared from eight pooled replicate populations of 107 OSKM-infected cells, as described previously in (Boyer et al., 2005), using 10 µg of specific antibodies raised against Oct4 (abcam # ab19857), Sox2 (R&D # AF2018), Klf4 (R&D # AF3640), and c-Myc (R&D # AF3696). DNA libraries were constructed from ~ 20 ng of DNA obtained from each ChIP of Oct4, Sox2, Klf4 and c-Myc expressed for 48 hr in OSKM-infected fibroblasts and from non-immunoenriched genomic DNA (input DNA) of OSKM infected fibroblasts using the Illumina library kit (illumina # 11257047). The DNA libraries were assessed using on Agilent Technologies 2100 Bioanalyzer and found to be in the 150-300 bp size range.

treatment_protocol: Lentiviral production and titration is described in the Supplemental Experimental Procedures. BJ cells at passage 10 were infected with lentiviruses encoding for dox-inducible Oct4, Sox2, Klf4, and c-Myc, along with lentiviruses expressing rtTA2M2 in the presence of 4.5 µg/ml polybrene. The expression of the OSKM factors was induced by treating the infected BJ cells with 1µg/ml dox for 48 hours. Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. BJ cells (MOCK, not-infected) were treated with 1µg/ml dox for 48 hours.

value: BJ

value: foreskin fibroblast cell

tag: genotype/variation

value: MOCK, not-infected

tag: time point

value: 48hrs mock induction with 1µg/ml dox

value: c-Myc

tag: chip antibody vendor

value: R&D

tag: chip antibody cat. #


title: Treated with Flageline at 0.25 ug/ml for 4 hours-PBMC-CF patient D1-2

data_processing:
Data processing was carried out in house, using CASAVA (Illumina) to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to genome using TOPHAT (http://tophat.cbcb.umd.edu/), and then mapped to genes using the Bioconductor package GenomeRanges.
Genome Build:
sample2_accepted_counts.txt: Genome Reference Consortium release GRCh37.rel59

value: Peripheral blood mononuclear cells

value: Flagelline at 0.25 ug/ml for 4 hours


title: OT-iPS

source_name: oct4 tet1 inducted iPS cells


title: R1

source_name: R1 ES cells

value: ES cells


title: Th2_WCE

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

country: United Kingdom

institute: University of Liverpool

description:
WCE Th2 cells (input control)
Th2_WCE.bed: alignment (bed format)
Th2_WCE_06.peaks.bed: MACS peaks (pvalue cut-off <= 1e-6)
Th2_WCE_Th1_back.bw: bigwig

data_processing: Image analysis and base calling were performed using the solexa pipeline. Reads were aligned to the human genome build hg18 using Eland. Only reads with zero to two mismatches were aligned. Uniquely aligned reads passing quality threshold were retained. When multiple reads matched to same position only a single read was considered for further analysis. Aligned sequences were extended by 150bp . Counts were background corrected and normalized to reads per million. Bigwig files were generated using 10bp windows. Peaks were called using MACS algorithm (http://liulab.dfci.harvard.edu/MACS/).

source_name: Th2 cells

growth_protocol: Naive human CD4+ T-cells (CD4+CD45RA+CD45RO-HLADR-CD62L+) were isolated from healthy donors by negative immunomagnetic selection (Miltenyi Biotec) and activated for 72 hours by plate bound anti-CD3 and anti-CD28 antibodies (2 ug/ml, BD Pharmingen). Cells were then cultured for 10 days with rhIL-2 (NCI, 100 U/ml) in the presence of rhIL-12 (10 ng/ml, R&D Systems) and anti-IL-4 (10 ug/ml, BD Pharmingen) for Th1 polarisation or rhIL-4 (10 ng/ml, R&D Systems) and anti-IFN-g (10 ug/ml, BD Pharmingen) for Th2 polarisation.

extract_protocol: ChIPs were performed according to Jenner lab protocol (see Jenner et al., PNAS 2009 or Kanhere et al., Mol Cell 2010). Libraries were constructed from half of the ChIP DNA sample or 200ng of input sample using the standard Illumina protocol and reagents, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. Libraries were quantified using by Qubit and Agilent bioanalyzer.

tag: cell number


title: Th1_GATA3

description:
Chromatin IP against GATA-3 in Th1 cells
Th1_GATA3.bed: alignment (bed format)
Th1_GATA3_06_peaks.bed: MACS peaks (pvalue cut-off <= 1e-6)
Th1_GATA3.bw: bigwig

source_name: Th1 cells

value: GATA-3; Antibody vendor:Santa Cruz; Antibody catalog number:sc-22206; Antibody lot number:F1306

tag: cell type


title: OSKM 2nd 1#-3D

source_name: TSKM-iPS mouse derived fibroblast cells

value: p4 supply with doxycycline for 3 days

tag: strain


title: Th1_Tbet

description:
Chromatin IP against T-bet in Th1 cells
Th1_Tbet.bed: alignment (bed format)
Th1_Tbet_06_peaks.bed: MACS peaks (pvalue cut-off <= 1e-6)
Th1_Tbet.bw: bigwig

value: T-bet; Antibody vendor:Lab produced (Szabo et al., Nature 2000).


title: Th1_WCE

description:
WCE Th1 cells (input control)
Th1_WCE.bed: alignment (bed format)


title: Th2_GATA3

description:
Chromatin IP against GATA-3 in Th2 cells
Th2_GATA3.bed: alignment (bed format)
Th2_GATA3_06_peaks.bed: MACS peaks (pvalue cut-off <= 1e-6)
Th1_GATA3.bw: bigwig


title: DNA Input ChIP-Seq at 48hrs Post-Induction

description: DNA without immunoprecipitation

data_processing:
Base-calling: Illumina software version 1.70
Alignment: ELAND, default parameters
Filtering: non-unique aligned sequence tags were discarded down to a single tag
Peak-calling: MACS, MFOLD = 16 using input as background
Filtering: peak sets were filtered to control the FDR at 0.5%
Multiple Transcription Factor Binding Regions (MTFBRs) were called using the algorithm described in the methods
Enrichment: bigWig files for each O, S, K, and M mark were created in the following way. Aligned, unique tags were binned in 25 bp intervals. Each interval count was normalized by RPKM (a measurement of the number of billions of bases sequenced per lane) and a normalized input count for the same interval was subtracted. The resulting interval enrichment scores were written to a bedGraph file, which was turned into a bigWig using the bedGraphToBigWig program from UCSC Genome Browser's online utilities package.
Genome_build: hg18
Supplementary_files_format_and_content:  Tag-Aligned Files: BED6 files containing six tab-delimited columns: chromosome, start, stop, tag ID, null, strand (post-filtering for non-unique reads)
Supplementary_files_format_and_content:  Peak Files: BED6 files containing six tab-delimited columns: chromosome, start, stop, null, null, strand (contains final, FDR-filtered peak sets only)
Supplementary_files_format_and_content:  BigWig Files: 25 bp binned aligned, unique tags (binary data), per-lane normalized and input subtracted
Supplementary_files_format_and_content:  DBRs: BED6 files containing the loci of the OSKM differentially-bound regions between 48 hrs reprogrammed fibroblasts and ES cells. A Series-specific BED file containing large, megabase-scale loci where no TFs bind.

source_name: BJ_DNA Input_control_48hr_postinduction

growth_protocol: The human foreskin fibroblast cell line (BJ) were obtained from the American Type Culture Collection (ATCC # CRL-2522) at passage 6 and cultured in the ATCC-formulated Eagle's Minimum Essential supplemented with 10% FBS at 37C and CO2.

extract_protocol: Chromatin was obtained from BJ cells infected with OSKM plus rtTA2M2 lentiviruses and induced with dox for 48hrs. Chromatin fragments associated with Oct4, Sox2, Klf4, or c-Myc were prepared from eight pooled replicate populations of 10e7 OSKM-infected cells, as described previously in (Boyer et al., 2005), using 10 µg of specific antibodies raised against Oct4 (abcam # ab19857), Sox2 (R&D # AF2018), Klf4 (R&D # AF3640), and c-Myc (R&D # AF3696). DNA libraries were constructed from ~ 20 ng of DNA obtained from each ChIP of Oct4, Sox2, Klf4 and c-Myc expressed for 48 hr in OSKM-infected fibroblasts and from non-immunoenriched genomic DNA (input DNA) of OSKM infected fibroblasts using the Illumina library kit (illumina # 11257047). The DNA libraries were assessed using on Agilent Technologies 2100 Bioanalyzer and found to be in the 150-300 bp size range.

value: infected with lentiviruses encoding for dox-inducible Oct4, Sox2, Klf4, and c-Myc, along with lentiviruses expressing rtTA2M2

value: 48hrs post-induction with with 1µg/ml dox


title: c-Myc ChIP-Seq at 48hrs Post-Induction

source_name: BJ_c-Myc ChIP-Seq_48hr_postinduction


title: Oct4 ChIP-Seq at 48hrs Mock Induction

description: DNA immunoprecipitated by Oct4 (abcam # ab19857)

source_name: BJ_Oct4 ChIP-Seq_48hr_mockinduction

value: abcam


title: HepG2 exposed to BaP for 24h, biological rep 2

city: Maastricht

first: Stan

last: Gaj

state: Limburg

address: Universiteitssingel 50

department: Department of Toxicogenomics

country: Netherlands

institute: Maastricht University

data_processing: RNA-seq reads were mapped to the EnsEMBL v58 cDNA sequences using bowtie v0.12.7 (Turro et al., 2011). On top of this alignment for uniquely mappable reads, RSEM v1.1.7 has been used to assign the ambiguous reads to different transcript isoforms using an expectation-maximization algorithm for estimation of each gene’s isoform distribution (Langmead et al., 2009). After the alignment step, RSEM provides read quantification at the individual transcript and gene level. Both lists were separately imported into R for further statistical analysis using the Bioconductor package edgeR (Robinson and Oshlack, 2010). Differentially expressed (DE) genes/transcripts were identified using the following criteria: (i) absolute fold-change ≥ 1.5, (ii) q-value (False Discovery Rate (FDR)) ≤ 0.05, and (iii) average read count in at least one experimental group ≥ 10.

source_name: hepatocellular carcinoma cell line

growth_protocol: HepG2 cells were maintained as a monolayer culture in 95% humidity, atmosphere with 5% of CO2 and 37 ºC. HepG2 cells were passaged at pre-confluent densities with the use of a trypsin-EDTA solution. Cells were cultured and passaged in a Minimal Essential Medium (MEM) with 10% of Foetal Bovine serum, 1% penicillin/streptomycin, 1% sodium-pyruvate and 1% non-essential amino acids.

extract_protocol: Poly-A RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) following the manufacturer's instructions and treated for 30 min at 37°C with TURBO™ DNase (Ambion) (0,2 units per 1 μg of RNA). First and second strand synthesis followed the manufacturer’s protocol. About 500 ng of double-stranded cDNA was fragmented by sonication with a UTR200 (Hielscher Ultrasonics GmbH, Germany). DNA was parcelled in 2% high resolution agarose gel and 230 – 270 bp fragments were cut. Library amplification consisted of two steps: (i) Real time PCR was done on StepOne™ Real-Time PCR system with SYBR® Green core reagents (Applied Biosystems) according to the manufacturer's instructions. (ii) Large scale PCR was performed on PTS-100™ Programmable Thermal Controller (MJ Research Inc.) with 2xPhusion® HF master mix (NEB) and primers for amplification of the mate-paired library (“PE_PCR primer 1.0" & "PE_PCR primer 2.0”, Illumina).

treatment_protocol: When the cells were 80% confluent, the medium was replaced with fresh medium containing either 2 µM BaP or the vehicle control (0.5% DMSO) during 12 and 24 hours in two independent experiments (biological replicates).

tag: time

tag: compound

value: Benzo[A]Pyrene

tag: vehicle

value: DMSO


title: HepG2 exposed to DMSO for 12h, biological rep 1


title: HepG2 exposed to DMSO for 12h, biological rep 2


title: HepG2 exposed to DMSO for 24h, biological rep 2


title: HepG2 exposed to BaP for 24h, biological rep 1


title: HepG2 exposed to BaP for 12h, biological rep 1

data_processing:
RNA-seq reads were mapped to the EnsEMBL v58 cDNA sequences using bowtie v0.12.7 (Turro et al., 2011). On top of this alignment for uniquely mappable reads, RSEM v1.1.7 has been used to assign the ambiguous reads to different transcript isoforms using an expectation-maximization algorithm for estimation of each gene’s isoform distribution (Langmead et al., 2009). After the alignment step, RSEM provides read quantification at the individual transcript and gene level.
Both lists were separately imported into R for further statistical analysis using the Bioconductor package edgeR (Robinson and Oshlack, 2010). Differentially expressed (DE) genes/transcripts were identified using the following criteria: (i) absolute fold-change ≥ 1.5, (ii) q-value (False Discovery Rate (FDR)) ≤ 0.05, and (iii) average read count in at least one experimental group ≥ 10.


title: HepG2 exposed to DMSO for 24h, biological rep 1


title: HepG2 exposed to BaP for 12h, biological rep 2


title: endogenous_FOXO3_background

status: Public on Nov 15 2012

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DLD1VIII1hIgGn28.txt: hg19

growth_protocol: DLD1 colon carcinoma cell line and DL23 clone containing pcDNA3-HA-FOXO33-ER or pcDNA3-ER-DBD-NLS were grown on RPMI-1640 medium with 10% FCS and standard supplements.

extract_protocol: Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD/AB sequencer to produce 50-bp long reads.

treatment_protocol: 4-hydroxy-tamoxifen (4OHT) was Sigma, was dissolved in ethanol and added to cells at a final concentration of 1uM. Cells were treated with LY 294002 at a concentration of 10 µM.

value: DLD1 cell line

value: rabbit IgG

value: Santa Cruz


title: endogenous_FOXO3_ChIP_seq

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DLD1VIII1haFOXO3n29.txt: hg19

value: aFOXO3 (H144)


title: stem bases_after cutting

city: Nanning

first: Haiwang

last: He

state: Guangxi

address: 100, Daxue Road

department: College of Agronomy

institute: Guangxi University

description: mRNA of  the stem bases

data_processing:
Basecalls performed using RTA version 1.9.
Raw reads of DGE libraries were filtered to generate clean tags by removing the 3’ adaptor sequence, empty reads, low quality tags, tags which were too long or too short, and tags with 1 copy number only.
For gene expression analysis, the number of expressed tags was calculated and then normalized to TPM.
Supplementary_files_format_and_content: The .txt file reports: Tag, CopyNumber, TPM(Transcript Per Million).

organism: Chromolaena odorata

source_name: stem bases_after cutting

growth_protocol: C. odorata shoots were obtained from College of Agronomy, Guangxi University, China, and divided into 5 cm segments with a single bud for each cutting. The cuttings were then planted in sand about 26° Celsius, with relative humidity between 50% and 70%. The stem bases of the cuttings (0.5 cm) were collected for transcriptome sequencing from different stages: 0, 3 and 7 days after cutting. Samples from the first stage and the mix sample of last two stages were used for DGE analysis. All materials were immediately frozem in liquid nitrogen and stored at -80° Celsius until further processing.

extract_protocol:
the stem bases of cutting were immediately frozem in liquid nitrogen and stored at -80° Celsius until further processing.Total RNA was isolated using the Trizol reagent (Invitrogen).
Briefly, 6 µg total RNA was extracted for mRNA purification using Oligo (dT) magnetic beads, and then first and second-strand cDNA was synthesized by using Oligo(dT) as primer. The 5’ ends of tags can be generated by endonuclease NlaIII, which recognizes and cuts off the CATG sites. Fragments of cDNA with 3’ ends were purified through magnetic bead precipitation, and Illumina adapter 1 was added to the 5’ ends. The junction of Illumina adaptor 1 and the CATG site was the recognition site for MmeI. This cuts 17bp downstream from the CATG site, and produces tags with adaptor 1. After removing 3’ fragments with magnetic bead precipitation, Illumina adaptor 2 was ligated to the 3’ ends of tags, acquiring 21bp tags with different adaptors at both ends to form a tag library. After 15 cycles of linear PCR amplification, 105bp fragments were purified by 6% TBE PAGE Gel electrophoresis. Fragments were then denatured and single-chain molecules were fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grew into a single-molecule cluster sequencing template through Situ amplification. Then four types of nucleotides labeled by color were added, and sequencing by synthesis was performed.

tag: developmental stage

value: the mix of 3 and 7days after cutting


title: DBD_ChIP_seq

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
F104OHT12haERn34.txt: hg19

value: DL23 cell line with pcDNA3-ER-DBD-NLS

value: ERα Antibody (MC-20)


title: Sox2 ChIP-Seq at 48hrs Post-Induction

description: DNA immunoprecipitated by Sox2 (R&D # AF2018)

source_name: BJ_Sox2 ChIP-Seq_48hr_postinduction

value: BJ

value: foreskin fibroblast cell

value: R&D


title: Oct4 ChIP-Seq at 48hrs Post-Induction

source_name: BJ_Oct4 ChIP-Seq_48hr_postinduction


title: Klf4 ChIP-Seq at 48hrs Post-Induction

description: DNA immunoprecipitated by Klf4 (R&D # AF3640)

source_name: BJ_Klf4 ChIP-Seq_48hr_postinduction


title: stem bases_before cutting

description: mRNA of  the stem bases

source_name: stem bases_before cutting

value: 0 day after cutting


title: RNAPII_4hours_DBD

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
F104OHT4hRNAPIIn43.txt: hg19

value: anti RBP1 (PB-7C2) antibody

value: Euromedex


title: RNAPII_4hours_DLD23_rep2

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DL234OHT4hRNAPIIn38.txt: hg19

value: DL23 cell line with pcDNA3-HA-FOXO33-ER


title: RNAPII_4hours_VIII_DLD23_rep1

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DL23VIII4hRNAPIIn40.txt: hg19


title: Fs1h_LS_Kc_ChIPseq

city: Atlanta

first: Wendy

middle: A

last: Kellner

state: GA

address: 1510 Clifton Road

department: Biology

institute: Emory University

description:
Antibody to both isoforms of Fs(1)h was a gift from Der-Hwa Huang described in Chang et al. 2007.
Chromatin IP against Fs(1)h-LS.

data_processing:
Alignment: Sequence reads were obtained and mapped to the D. melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Wiggle files were generated and peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples.
Genome_build: DM3
Supplementary_files_format_and_content: Fs1h_L_Kc_ChIPseq experiment has two processed file types: Fs1h_L_Kc.wig is the wiggle file produced from MACS in 10bp bins across the genome and Fs1h_L_Kc.bed is the peak file produced from MACS.
Supplementary_files_format_and_content: Fs1h_LS_Kc_ChIPseq experiment has two processed file types: Fs1h_LS_Kc.wig is the wiggle file produced from MACS in 10bp bins across the genome and Fs1h_LS_Kc.bed is the peak file produced from MACS.

source_name: Female late embryo-derived cell line, ChIP of both isoforms of Fs(1)h

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments. Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC. Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC. After washing and eluting from beads, the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair ('End-It DNA End Repair Kit' - Epicentre Cat# ER0720) and addition of 'A' base to 3' ends (Klenow 3'-5' exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

value: female late embryo-derived cell line

value: rabbit polyclonal antibody to both isoforms of Fs(1)h


title: shvec.H3K36me2_ChIPSeq

first: Meng

last: Zhao

address: 1518 Clifton Rd, #369

department: BIOS

description: Sample 2

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the hg18 genome assembly using bowtie with up to 3 mismatches
peaks were called using HPeak version 2.2R with the following setting: 25 bp window, 1e-3 significant level, fragment length 120-220 bp
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files were generated using HPeak ver. 2.2R, which provided peak loci, height, width, summit location and log(p-value)

source_name: MDA-MB-231 breast cancer cells

growth_protocol: Cells were grown in RPMI 1640 containing 10% FBS and selection antibiotics

extract_protocol:
ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode)
ChIP-Seq libraries were prepared using standard Illumina protocol. ChIP-enriched DNA samples (10-20 ng) were converted to blunt-ended fragments using a combination of T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3' to 5' exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina PE1.0/PE2.0 primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified using the Bioanalyzer 2100 (Agilent) and each sample was sequenced in a single lane on the Illumina Genome Analyzer II (40 nucleotide read length).

value: breast cancer cells

value: vector control

value: Anti-Histone H3 (di methyl K36) antibody

value: abcam


title: RNAPII_0hours_DLD23_rep3

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DL23ntRNAPIIn48.txt: hg19


title: Input_Kc_ChIPseq

description: ChIP input of sonicated DNA.

source_name: Female late embryo-derived cell line, input


title: RNAPII_0hours_DBD

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
F10ntRNAPIIn42.txt: hg19


title: RNAPII_4hours_DLD23_rep3

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DL234OHT4hRNAPIIn39.txt: hg19


title: RNAPII_ChIP-seq_0hours_DL23

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
POL2_00H_D23.aligned.txt: hg19

source_name: DL23 cell line with pcDNA3-HA-FOXO33-ER

value: DL23 clone containing pcDNA3-HA-FOXO33-ER

value: 0 hours

value: anti RBP1 (PB-7C2) antibody (Euromedex)


title: RNAPII_ChIP-seq_24hours_DL23

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
POL2_24H_D23.aligned.txt: hg19

value: 24 hours


title: RNAPII_ChIP-seq_4hours_DLD1

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
POL2_04H_D1.aligned.txt: hg19

source_name: DLD1 cell line

value: DLD1 colon carcinoma cell line

value: 4 hours


title: RNAPII_ChIP-seq_24hours_DLD1

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
POL2_24H_D1.aligned.txt: hg19


title: Fs1h_L_Kc_ChIPseq

description:
Antibody specific to the Fs(1)h long isoform was generated in our lab.
Chromatin IP against Fs(1)h-L.

source_name: Female late embryo-derived cell line, ChIP of Fs(1)h long isoform

value: rabbit polyclonal antibody specific to Fs(1)h long isoform


title: Background_DLD1

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
D1_aER.aligned.txt: hg19

value: ER antibody, Santa Cruz (MC-20)


title: FOXO3_ChIP-seq_DL23

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
D23_aER.aligned.txt: hg19


title: RNAPII_ChIP-seq_0hours_DLD1

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
POL2_00H_D1.aligned.txt: hg19


title: WCE P493-6 T=0HR

status: Public on Nov 14 2012

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: WCE P493-6 T=0HR (low c-Myc expression)

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: B-cell lymphoma

growth_protocol: RPMI 1640 + FBS.    Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 0 hours.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: c-Myc expression released for 0 hours.

tag: antibody catalog number

value: None WCE

tag: c-myc level

value: low


title: RNAPII_P493-6_No_Tet_ChipSeq

description: Chromatin IP against RNAPII in P493-6 without tetracycline treatment (No Tet)

growth_protocol: RPMI 1640 + 10% FBS + 1% Glutamax. No Pen/Strep. No tetracycline (these cells are untreated and express high levels of c-Myc)

treatment_protocol: No treatment.

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

value: steady state


title: WCE P493-6 T=1HR

description: WCE P493-6 T=1HR (moderate c-Myc expression)

growth_protocol: RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 1 hour.

treatment_protocol: c-Myc expression released for 1 hour.

value: intermediate


title: col-0 ribo-seq

city: Los Angeles

first: Fan

last: Li

address: 675 Charles E Young Drive South

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Basecalls performed with Bustard 1.13.48.
3' adapter sequences were trimmed using cutadapt (version 0.9.5 with parameters -e 0.06 -O 6 -m 14), and reads were subsequently aligned to the TAIR9 genome using bowtie (version 0.12.7 with parameters -n 1 -e 160 -l 25 -y -k 100 -B 1 –nomaqround).
Structure ‘hotspots’ and 'coldspots' were identified using a modified version of the CSAR software package (Muino et al., 2011). Specifically, structure scores were calculated for each base position in the genome and regions with significantly higher or lower than background at an FDR of 5% were called as ‘hotspots’ and ‘coldspots’, respectively. The background distribution was calculated by randomly shuffling dsRNA and ssRNA reads and then computing structure scores as described (Muino et al., 2011).
Genome_build: TAIR9
Supplementary_files_format_and_content: BED file: column 5 is [maximum absolute peak score]@@[location of peak score].
Supplementary_files_format_and_content: RPKM file is tab-delimited plain text format. Columns are TAIR ID, clone count, and RPKM.

source_name: immature flower bud clusters

extract_protocol:
The ssRNA-seq library was constructed as previously described (Li et al., 2012).
Ribo-seq libraries were made using ribosome-associated mRNAs from unopened flower buds that were isolated by differential centrifugation according to Mustroph et al. (Mustroph et al., 2009) with the following modifications.  The ribosomes and associated mRNAs pelleted by centrifugation through a sucrose cushion were resuspended in 0.2 M Tris pH 8.0, 0.2 M KCl, 0.035 M MgCl2, 50 ug/ml chloramphenicol, and 50 ug/ml cycloheximide.  Forty micrograms of resuspended RNA was centrifuged over a 15-60% sucrose gradient (0.04 M Tris, pH 8.0, 0.02 M KCl, 0.02 MgCl2, 5 ug/ml chloramphenicol, and 5 ug/ml cycloheximide).  Following centrifugation, 50 ul fractions of the gradient were isolated and the OD260 of each was measured.  The monosomal and polysomal fractions were pooled, and the RNA was isolated using the Qiagen miRNeasy Mini Kit. Eight micrograms of isolated RNA were depleted of ribosomal RNA using the RiboMinus Plant Kit (Life Technologies, Carlsbad, CA), fragmented using RNA Fragmentation Reagents (Ambion, Austin, TX), treated with T4 PNK (NEB, Boston, MA), and used for library preparation using the Illumina TruSeq smRNA-seq library preparation kit and accompanying protocols (Illumina, San Diego, CA).

tag: tissue

value: immature flower bud clusters


title: col-0 ssRNA-seq

description: Treated with dsRNase (RNase ONE)


title: WCE P493-6 T=24HR

description: WCE P493-6 T=24HR (high c-Myc expression)

growth_protocol: RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 24 hours.

treatment_protocol: c-Myc expression released for 24 hours.

value: very high


title: shEZH2_H3K36me2_ChIPSeq

description: Sample 1

value: breast cancer cells

value: stable EZH2 knockdown

value: Anti-Histone H3 (di methyl K36) antibody

value: abcam


title: WCE P493-6 No Tet

description: WCE P493-6 No Tet (constitutive, high c-Myc expression)

treatment_protocol: No treatment


title: RNAPII_ChIP-seq_4hours_DL23

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
POL2_04H_D23.aligned.txt: hg19

value: DL23 clone containing pcDNA3-HA-FOXO33-ER

value: anti RBP1 (PB-7C2) antibody (Euromedex)


title: H3K27ac_P493-6_No_Tet_ChipSeq

description: Chromatin IP against H3K27ac in P493-6 without tetracycline treatment (No Tet)

value: Abcam AB4729


title: Med1_P493-6_No_Tet_ChipSeq

description: Chromatin IP against Med1 in P493-6 without tetracycline treatment (No Tet)

value: Bethyl A300-793A


title: Max_P493-6_No_Tet_ChipSeq

description: Chromatin IP against Max in P493-6 without tetracycline treatment (No Tet)

value: Max

value: Santa Cruz SC-197


title: c-Myc_P493-6_No_Tet_ChipSeq

description: Chromatin IP against c-Myc in P493-6 without tetracycline treatment (No Tet)

value: c-Myc

value: Santa Cruz SC-764


title: Brd4 P493-6 T=24 hour_ChipSeq

description: Chromatin IP against Brd4 in P493-6 T=24 hours

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 24 hours.

value: Bethyl A301-985A


title: Brd4 P493-6 T=1 hour_ChipSeq

description: Chromatin IP against Brd4 in P493-6 T=1 hour

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 1 hour.


title: Brd4 P493-6 T=0_ChipSeq

description: Chromatin IP against Brd4 in P493-6 T=0

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 0 hours.

value: low


title: Digital Genomic Footprinting assay of flow sorted CD8+ Cells; DGF.DS17203

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17203
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1036373_UW.CD8_Primary_Cells.Digital_Genomic_Footprinting.RO_01679.DGF.DS17203.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17203.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD8 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on CD8 Primary Cells, Donor RO 01679, Library DGF.DS17203 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.15146
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 108,504,515
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5825
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5869
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5589
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1036373_UW.CD8_Primary_Cells.Digital_Genomic_Footprinting.RO_01679.DGF.DS17203.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17203.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  CD8 Primary Cells, Donor RO 01679, Library DGF.DS17203 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.15157
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD8 DGF 79 03
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells Digital Genomic Footprinting Donor RO 01679 Library DGF.DS17203 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 108,504,515
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5825
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5869
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5589
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD8+ Cells,year 21; DGF.DS17203

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD8 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 21

value: Male

value: Caucasian

value: Digital Genomic Footprinting

value: Qiagen minElut


title: TAF5-H9wt-rep2

status: Public on Nov 19 2012

type: genomic

city: Worcester

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description:
ChIP-chip for TAF5 vs No Antibody in wild-type H9 cells
platform design id: 100718_HG18_Refseq_Prom_ChIP

hyb_protocol: The labeled experimental and control ChIP DNA (20 pmol of each label) was precipitated with 0.1 volume 5M NaOAc and 2 volume ethanol, and hybridized using Nimblegen Hybridization kit according to recommended protocol. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed using Nimblegen wash kit reagents and protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Agilent High Resolution C Scanner (G2505-60502) at 5µ resolution

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 ChIP data extraction.

source_name: TAF5 ChIP DNA from H9 wt cells

label_protocol: 500 ng of purified ChIP or control (No Antibody) DNA were blunted by using the End-IT kit (Epicenter) and adapters (annealed oligos oJW102: 5’-GCGGTGACCCGGGAGATCTGAATTC and oJW103: 5’-GAATTCCAGATC) ligated to the fragment ends using the Fast-Link DNA ligation kit (Epicenter).  Ligated fragments were then amplified by pcr for 15 rounds with a primer directed against the adapter, gel-purified to a size range of 400-600 bp, and then amplified a second time for 30 rounds using either Cy5-dCTP (ChIP experiment) or Cy3-dCTP (Control chIP).  Amplified products were purified on Qiaquick columns to remove unincorporated label, and quantitated on a Nanodrop.

extract_protocol: 5x10E7 cells were rinsed with PBS, scraped, and pelleted in a 50 mL conical tube.  The cells were then fixed with 1.5 mM EGS in 90% PBS/10% DMSO for 30 minutes, then also with  1% formaldehyde for an additional 10 minutes at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50 mM HEPES pH8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na-Deoxycholate, 1 mM EDTA, 1 mM PMSF plus protease inhibitor cocktail) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 18 30-second pulses using a Misonix 3000 sonicator on power level 6 with 90 seconds rests between pulses while sample is immersed in icewater. The lysate was then centrifuged to remove cell debris, and the chromatin was quantified using BCA assay. The chromatin (500 µg) was pre-cleared with 25 µl protein G agarose beads (pre-absorbed with BSA) for 4 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein G agarose beads (80 µl) overnight at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; twice with lysis  buffer, once with high-salt lysis buffer (lysis buffer adjusted to 1 M NaCl) three times in LiCl buffer (250 mM LiCl, 50 mM HEPES pH8.0, 0.5% Na deoxycholate, 0.5% NP40) and once in TEN (50 mM Tris pH8.0, 10 mM EDTA, 50 mM NaCl). The protein-DNA complexes were eluted from the beads in 200 µl elution buffer (1% SDS, 100 mM NaHCO3) at 68C for 15 min followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

value: wild-type pluripotent H9 embryonic stem cell line

tag: chip antibody

value: TAF5, Sigma-Aldrich HPA006474

source_name: No Antibody control ChIP DNA from H9 wt cells

value: None, No Antibody control


title: POL2-H9wt-rep1

description:
ChIP-chip for RNA Pol2 vs No Antibody in wild-type H9 cells
platform design id: 090618_HG18_Refseq_Prom_ChIP

source_name: RNA Polymerase II ChIP DNA from H9 wt cells

value: RNA Polymerase II (8WG16, Covance)


title: Digital Genomic Footprinting assay of flow sorted CD56+ Cells; DGF.DS17189

description:
sample_term_id: CL_0000623
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17189
EDACC Genboree Experiment Page:

EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5358
****************
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: GSM1036372_UW.CD56_Primary_Cells.Digital_Genomic_Footprinting.RO_01679.DGF.DS17189.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17189.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD56 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on CD56 Primary Cells, Donor RO 01679, Library DGF.DS17189 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.15152
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 86,445,209
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4091
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3996
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9867
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4251
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1036372_UW.CD56_Primary_Cells.Digital_Genomic_Footprinting.RO_01679.DGF.DS17189.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17189.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD56 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  CD56 Primary Cells, Donor RO 01679, Library DGF.DS17189 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.15163
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD56 DGF 79 89
BROWSER_TRACK_DESCRIPTION: UW CD56 Primary Cells Digital Genomic Footprinting Donor RO 01679 Library DGF.DS17189 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 86,445,209
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4091
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3996
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9867
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4251
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD56+ Cells, year 21; DGF.DS17189

value: CD56 Primary Cells


title: RNAPII_4hours_VIII_DLD23_rep2

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DL23VIII4hRNAPIIn49.txt: hg19

tag: cell line

value: DL23 cell line with pcDNA3-HA-FOXO33-ER

value: anti RBP1 (PB-7C2) antibody

tag: chip antibody vendor

value: Euromedex


title: Digital Genomic Footprinting assay of flow sorted CD3+ Cells; DGF.DS17198

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17198
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14569
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5322
****************
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: GSM1036259_UW.CD3_Primary_Cells.Digital_Genomic_Footprinting.RO_01679.DGF.DS17198.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17198.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on CD3 Primary Cells, Donor RO 01679, Library DGF.DS17198 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.15143
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 343,052,385
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.596
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5872
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5544
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1036259_UW.CD3_Primary_Cells.Digital_Genomic_Footprinting.RO_01679.DGF.DS17198.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS17198.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  CD3 Primary Cells, Donor RO 01679, Library DGF.DS17198 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.15154
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD3 DGF 79 98
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells Digital Genomic Footprinting Donor RO 01679 Library DGF.DS17198 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 343,052,385
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.596
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5872
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5544
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD3+ Cells,year 21; DGF.DS17198

value: CD3 Primary Cells